dme-mir-4971- 12- and 20-way alignments

dme-mir-4971	chr2L:3463289-3463400 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 3463361-3463381
   star strand at position 3463306-3463328
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr2L:3463274-3463415 -	GGAAGGGCCAACTTCTCGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droSim1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_129:25371-25512 -	GGAAGGGCCAACTTCTCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droYak2	chr2L:3450843-3450984 -	GGAAGGGCCAACTTCTCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droEre2	scaffold_4929:3498112-3498253 -	GGAAGGGCCAACTTCACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG
droAna3	scaffold_12943:2497935-2498076 +	GGCAGAGCCAACTTCGGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CATAAAGAATCCTGCCGCTGGCGACAGACAGTCGGCCACTGACAACGCGCACTCGCTGTTCGAGGAAATAATGTCTGGCTCCGACG
dp4	chr4_group3:936699-936854 -	GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG
droPer1	super_1:2415168-2415323 -	GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG
droWil1	scaffold_180703:541137-541228 +	CGACCCGA----------------------------------ATG-----------------------------AGGATGCCTG-TCCTGGTGACAGTTTAACAGCCACTGAAACGGCTCATTCTTTGTTCGAGGATATTATGTCGGGCTCAGATG
droVir3	scaffold_12963:15952027-15952156 -	GATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT---------------CAATGCTGCCGCTGGCGACAGCC--TCGG-CGCTGACAAGGAGCATGCCATGTTTGAGTATTTCCTCAACGAAGATGACG
droMoj3	scaffold_6500:5396196-5396319 -	GATATGGAACGCAATGTGCTCAG--------AAAGTCGGCCGATATGCTTGTCAGCGCTGG---------------TAATGCTGCTGCTGGCGACGGCAGTATGGACGGTGACAAGGATGAGGCCATTTTGGAGCGTATCTTCTCGG---------
droGri2	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:3463274-3463415 -	NA	GGAAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droSim1	chr3R:4556078-4556201 -	2551	GCCAACTGGCAAGTCC---TCGCCAGT--------GGATGTC----ACCAGC-AACCAGTTGCCCAGC------CAG---GAGCC-----------------------GGTC-ATGTTGACCAC-T--GTGCCACAGCCC----------------------ACGCCGCCCAGGAGCAGCGCCTTCAG-G--------CCTGTGATA
droSec1	super_129:25371-25512 -	3501	GGAAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------AGTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droYak2	chrU:14964015-14964156 +	5553	GGAAGG-GCCAACTTC---TCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droEre2	scaffold_4929:3498112-3498253 -	4935	GGAAGG-GCCAACTTC---ACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droEug1	scf7180000409554:2625850-2625991 +	2493	GGAAGG-GCCAATTTC---TCGGCCCT--------CGACACAGTAGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAATTCTGCCGCT---GGCGATA--GATT------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCT-G--------GCTCGGATG
droBia1	scf7180000302261:1009341-1009482 -	5882	GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAACTCTGCCGCT---GGCGACA--GACT------CTCAGCCA--CTGACAACGCCC----------------------ACCTGCTGTTCGAGGAGATCATGTCC-G--------GCTCGGACG
droTak1	scf7180000415438:449917-450058 +	5419	GGAAGG-GCCAACTTC---TCGGCTTT--------GGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------GTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAGATAATGTCC-G--------GTTCGGATG
droEle1	scf7180000490728:125384-125525 -	3855	GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCC---GGCGACA--GATT------GTCAGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG
droRho1	scf7180000779523:136149-136290 -	13115	GGAATG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCC---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTTGAGGAGATCATGTCC-G--------GCTCGGATG
droFic1	scf7180000453924:1447325-1447466 -	391	GGCAGG-CCGAACTAC---TCGGCCCT--------CGACACGGTGGACGAACTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCT---GGCGACA--GACT------GTCCGCCA--CTGACAACGCCC----------------------ACTCGTTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG
droKik1	scf7180000302472:1777222-1777363 +	1613	GGAATG-GCCAACTTC---TCGGCCCT--------CGACACAGTGGACGAGCTTGTCAGTGGCGGATC------AAC---GAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droAna3	scaffold_12943:2497935-2498076 +	674	GGCAGA-GCCAACTTC---GGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CAT---AAAGAATCCTGCCGCT---GGCGACA--GACA------GTCGGCCA--CTGACAACGCGC----------------------ACTCGCTGTTCGAGGAAATAATGTCT-G--------GCTCCGACG
droBip1	scf7180000396728:833305-833449 -	5880	GGCAGA-GCCAACTTT---GGAGCCCT--------CGAAACAGTCGACGAGCTTGTCAGTGGCGGATC------GAT---TAAGAACCCTGCCGCC---GGCGACA--GGCTCCT---CTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAAATCATGTCT-G--------GCTCGGACG
dp4	chr4_group3:936699-936854 -	1448	GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG
droPer1	super_1:2415168-2415323 -	3812	GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG
droWil1	scaffold_189765:461-602 -	8580	GTAACG-ATAGACGGA---GATACCTT--------CGAGGTGGTGGACGAGTTCGTCTACCTCGGATC------CTT---GTTGATGGCTGACAAC---AA----------T------GTTAGTCG--GGAAATACGAAG----------------------GCGCATTATCAGCGGAAGTCGTGCCT-ACTATTGGCTCCAGAAGA
droVir3	scaffold_12963:15952027-15952160 -	4352	ATTAGATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT------------------CAATGCTGCCGCT---GGCGACA--GCC--------TCGG-CG--CTGACAAGGAGC----------------------ATGCCATGTTTGAGTATTTCCTCAAC-G--------AAGATGACG
droMoj3	scaffold_6473:12510219-12510341 +	1358	GGTTTG-----------------------------------------TGTGTGTGTGTGTGGTGGAAC------TTCAATGCGAACCTCTTGC--CACAATCGAGTGCAATT------AACTGCCA--TGATATATGGCCAATCCC----------------ATA---TGCAGACGGCGACCGAGTCGAA--------GTTCGGCTG
droGri2	scaffold_14853:4216060-4216150 -	607	---------------------------------------------------------------------------------------TCGACCGCT---GGCCACA--AATG------GCCGGACAGACAGACA-------GACAGACAGACAGACAGACAGACTCACTGACATAATTGATCATATC-----------GCTTATACG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGAAGGGCCAACTTCTCGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG

Size

Hit Count

Total Norm

droSim1

------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GGAAGGGCCAACTTCTCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCAGTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................TGTTCGAGGAGATCATGTCGGGCTCGGA..	28	1	1.00	1.00	0.00	0.00
............................................................................................................................TCTGTCCGAGGAGATCAT..............	18	1	1.00	0.00	1.00	0.00
................................GACACGGTTGATGAGATTG.........................................................................................................	19	1	1.00	0.00	0.00	1.00
....................CTG--------CGACACGGTTGATGAG.............................................................................................................	19	1	1.00	1.00	0.00	0.00
......................G--------CGACACGGTTGATGAGA............................................................................................................	18	1	1.00	0.00	0.00	1.00
.......................................TTGATGAxCTGGTCAGTGG..................................................................................................	18	1	1.00	0.00	1.00	0.00
..................................CACGGTTGATGAGATTGA........................................................................................................	18	1	1.00	0.00	0.00	1.00
........................................................................................................................................GATCATGTCGGGCTCGGAT.	19	1	1.00	0.00	1.00	0.00
.................................ACACGGTTGATGAGATTG.........................................................................................................	18	1	1.00	0.00	0.00	1.00
.................................ACACGGTTGATGAGCTTGTCAGTGGC.................................................................................................	26	1	1.00	1.00	0.00	0.00
...............................CGACACGGTTGATGAGATTGA........................................................................................................	21	1	1.00	0.00	0.00	1.00
....................................................CTGTGGCGGATC------CGGGAGC...............................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

GGAAGGGCCAACTTCTCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................................................................................GATCATGTCGGGCTCGGAT.	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................GGTGGATGAGCTTGTCAGTGG..................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
................................GACACGGTGGATGAGCTTGTCAGTGGC.................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GGAAGGGCCAACTTCACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGATCATCGGCCACTGACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................ATGCCCACTCGCTGTTCGAGGAG...................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................GATGAGCTTGTCAGTGGTGGAAA------......................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................GATGAGCTTGTCAGTGGTGGA..............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
..........................................ATGAGCTTGTCAGTGGTGGA..............................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
..........................................ATGAGCTTGTCAGTGGTGGATC------......................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................GATCATCGGCGACAGACA..........................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................ATGAGCTTGTCATTGGTGGAT.............................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................CCT--------GGACACGGTGGAGGA..............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................ATGAGCTTGTCAGTGGTGG...............................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

GGCAGAGCCAACTTCGGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CATAAAGAATCCTGCCGCTGGCGACAGACAGTCGGCCACTGACAACGCGCACTCGCTGTTCGAGGAAATAATGTCTGGCTCCGACG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................GAGCCCT--------TGAAACGGTCGACGAGCT...........................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
................GAGCCCG--------TGGAACGGTCG..................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................CGACAGACAGACGGACA................................................	17	1	1.00	0.00	0.00	1.00	0.00
..................................AATGGTTGACGAGCTT..........................................................................................................	16	2	0.50	0.00	0.00	0.50	0.00

dp4

GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........................................ATGAGCTGGTTAGGGGTG................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CAGATTGTCGGCCACTGAC...........................................	19	1	1.00	0.00	1.00	0.00	0.00

droPer1

GGAGTGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGATTGTCGGCCACTGACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................GAAATCATGTxGGGCTCTG...	18	1	2.00	2.00	0.00	0.00	0.00	0.00
..........................................................................................................................AGACTGTTCGAGGAGATCAT..............	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CGACCCGA----------------------------------ATG-----------------------------AGGATGCCTG-TCCTGGTGACAGTTTAACAGCCACTGAAACGGCTCATTCTTTGTTCGAGGATATTATGTCGGGCTCAGATG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......GA----------------------------------ATG-----------------------------AGGATGCCTG-TCCTGGT................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................CTCATTCTTTGTTCGAGGA....................	19	1	1.00	0.00	1.00	0.00	0.00
.....CGA----------------------------------ATG-----------------------------AGGATGCCTG-TCC....................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..TCCCGA----------------------------------ATG-----------------------------AGGATGCCTG-TCCT...................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................................GGCTCATTCTTTGTTCGAGGAT...................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................TTCGAGGATATTATGTCGGG........	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................CGAGGATATTATGTCGGGCTCAGAT.	25	1	1.00	0.00	0.00	0.00	1.00

droVir3

GATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT---------------CAATGCTGCCGCTGGCGACAGCC--TCGG-CGCTGACAAGGAGCATGCCATGTTTGAGTATTTCCTCAACGAAGATGACG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...................................................................................................................GGGGCATGCCxTGTTTGAG......................	18	1	5.00	1.00	3.00	0.00	1.00	0.00
.....CGATTCCGGTTCGTCCAC--------C............................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
...................................................................................................................GGGGCATGCCxTGTTTGAGT.....................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................GACATCC--TCGG-CGCTGTC...........................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................AGGAGCATGCCxTGTTTGAGTG....................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................T---------------CCATGCTGCTGCTGG.................................................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................................GACAAGGAGCATGACATCT...........................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................CC--TCGG-CGCTGACAAGGAGCA...................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
....................CAT--------CAAGTCTGCTGTTGA..............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

GATATGGAACGCAATGTGCTCAG--------AAAGTCGGCCGATATGCTTGTCAGCGCTGG---------------TAATGCTGCTGCTGGCGACGGCAGTATGGACGGTGACAAGGATGAGGCCATTTTGGAGCGTATCTTCTCGG---------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................................................CTGG---------------TCATTCTGCTGCTG..................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................AAGGATGAGGCCATTTTGGA.......................	20	1	1.00	1.00	0.00	0.00	0.00
GATATGGAACGCAATGTGCT........................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................AGTATGGACGGTGACAAGGATGAGGC................................	26	1	1.00	1.00	0.00	0.00	0.00

droGri2

------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image		None										None
UNAFold Image		None										None

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image