Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold169
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2015121
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 45543 characters in sequence are not A, C, G, or T
File 8 of 14
Found at i:1137763 original size:23 final size:22
Alignment explanation
Indices: 1137727--1137770 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1137717 AATTAAAATT
1137727 ATTTTAAATTTTAAATTATTTA
1 ATTTTAAATTTTAAATTATTTA
*
1137749 ATTTTAAATTATTAACTTATTT
1 ATTTTAAATT-TTAAATTATTT
1137771 TATCAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTAAATTTTAAATTATTTA
Found at i:1137795 original size:15 final size:15
Alignment explanation
Indices: 1137714--1137805 Score: 61
Period size: 15 Copynumber: 6.3 Consensus size: 15
1137704 TTCAGATAAT
*
1137714 TTAAATTAAAATTATT
1 TTAAATT-AAATTATA
1137730 TTAAATTTTAAATTAT-
1 TTAAA--TTAAATTATA
*
1137746 TTAATTTTAAA-T-TA
1 TTAA-ATTAAATTATA
* *
1137760 TTAACTT--ATTTTA
1 TTAAATTAAATTATA
*
1137773 TCAAATTAAATTATA
1 TTAAATTAAATTATA
1137788 TTAAATTAAATTA-A
1 TTAAATTAAATTATA
1137802 TTAA
1 TTAA
1137806 TATTTTTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 10 0.16
14 10 0.16
15 22 0.35
16 9 0.15
17 7 0.11
18 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAATTAAATTATA
Found at i:1138340 original size:2 final size:2
Alignment explanation
Indices: 1138333--1138364 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1138323 GAACTTACAA
1138333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1138365 TGAAGTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1138512 original size:20 final size:21
Alignment explanation
Indices: 1138487--1138531 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1138477 TTAAATATAA
*
1138487 ATATTTTTAA-TTTTTTTAAT
1 ATATTTTAAATTTTTTTTAAT
1138507 ATA-TTTAAATTTTTTTTAAT
1 ATATTTTAAATTTTTTTTAAT
1138527 A-ATTT
1 ATATTT
1138532 ATATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTTAAATTTTTTTTAAT
Found at i:1138513 original size:18 final size:18
Alignment explanation
Indices: 1138486--1138537 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
1138476 ATTAAATATA
*
1138486 AATATTTTTAATTTTTTT
1 AATATATTTAATTTTTTT
1138504 AATATATTTAAATTTTTTTT
1 AATATATTT-AA-TTTTTTT
1138524 AATA-ATTTATATTT
1 AATATATTTA-ATTT
1138538 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 12 0.40
19 7 0.23
20 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATATATTTAATTTTTTT
Found at i:1138519 original size:19 final size:19
Alignment explanation
Indices: 1138486--1138537 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1138476 ATTAAATATA
*
1138486 AATAT-TTTTAATTTTTTT
1 AATATATTTAAATTTTTTT
1138504 AATATATTTAAATTTTTTTT
1 AATATATTTAAA-TTTTTTT
*
1138524 AATA-ATTTATATTT
1 AATATATTTAAATTT
1138538 AAAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.27
19 11 0.37
20 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATATATTTAAATTTTTTT
Found at i:1138768 original size:37 final size:37
Alignment explanation
Indices: 1138687--1138787 Score: 100
Period size: 37 Copynumber: 2.7 Consensus size: 37
1138677 GGAAAAGTTA
* *
1138687 TAAATGTATTTAATATAAATATATTTTAATTTTAATTT
1 TAAATATATTTAA-ATAAATATATTTTAATTTTAATTC
* *
1138725 TTAATATATTTAAATAATTATATTTT-ATATTT-ATATC
1 TAAATATATTTAAATAAATATATTTTAAT-TTTAAT-TC
1138762 TAAATATATATTAAATATAA-ATATTT
1 TAAATATAT-TTAAATA-AATATATTT
1138788 AAAAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
36 4 0.08
37 24 0.45
38 24 0.45
39 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (37 bp):
TAAATATATTTAAATAAATATATTTTAATTTTAATTC
Found at i:1139494 original size:12 final size:12
Alignment explanation
Indices: 1139461--1139494 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1139451 AACATAATAC
1139461 TTTATAAATTTT
1 TTTATAAATTTT
1139473 TTTA-AAATTTT
1 TTTATAAATTTT
*
1139484 TTTATATATTT
1 TTTATAAATTT
1139495 AAAAGACCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATAAATTTT
Found at i:1143295 original size:6 final size:6
Alignment explanation
Indices: 1143286--1143315 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1143276 TATTAATTTT
*
1143286 TAAAAA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA
1143316 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAATA
Found at i:1143709 original size:19 final size:19
Alignment explanation
Indices: 1143666--1143719 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 19
1143656 TATATCATTT
*
1143666 TCAT-TTTAAAAATTT-TA
1 TCATATTTAATAATTTATA
* *
1143683 ACACATTTAATAATTTATA
1 TCATATTTAATAATTTATA
1143702 TCATATTT-AT-ATTTATA
1 TCATATTTAATAATTTATA
1143719 T
1 T
1143720 TTATATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (19 bp):
TCATATTTAATAATTTATA
Found at i:1143715 original size:6 final size:6
Alignment explanation
Indices: 1143695--1143734 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1143685 ACATTTAATA
*
1143695 ATTTAT A-TCAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
1143735 CACGGTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (6 bp):
ATTTAT
Found at i:1144768 original size:15 final size:16
Alignment explanation
Indices: 1144745--1144782 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1144735 TACTTCCATC
*
1144745 AATAAATTAT-TTAAA
1 AATATATTATATTAAA
1144760 AATATATTATATTAAA
1 AATATATTATATTAAA
*
1144776 TATATAT
1 AATATAT
1144783 CTTAATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATATTATATTAAA
Found at i:1145795 original size:17 final size:18
Alignment explanation
Indices: 1145747--1145817 Score: 65
Period size: 22 Copynumber: 3.8 Consensus size: 18
1145737 TCACGGTTCG
*
1145747 TTTTTTATAAAATGAATAA
1 TTTTTTAAAAAAT-AATAA
*
1145766 TTTTTT-AAGAATAA-AA
1 TTTTTTAAAAAATAATAA
1145782 TTTTTTAAAAAATACATATA
1 TTTTTTAAAAAATA-ATA-A
1145802 TTATTTTTAAAAAATA
1 -T-TTTTTAAAAAATA
1145818 TAAATATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 8 0.19
17 8 0.19
18 5 0.12
19 7 0.16
20 1 0.02
21 1 0.02
22 13 0.30
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTTTTAAAAAATAATAA
Found at i:1145834 original size:24 final size:22
Alignment explanation
Indices: 1145783--1145824 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1145773 AGAATAAAAT
*
1145783 TTTTTAAAAAATACATATATTA
1 TTTTTAAAAAATACAAATATTA
*
1145805 TTTTTAAAAAATATAAATAT
1 TTTTTAAAAAATACAAATAT
1145825 CTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTAAAAAATACAAATATTA
Found at i:1146342 original size:9 final size:8
Alignment explanation
Indices: 1146311--1146353 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
1146301 TTGTATTAAT
*
1146311 TTTTTATT
1 TTTTTATA
1146319 TTTTTA-A
1 TTTTTATA
*
1146326 TATTTATA
1 TTTTTATA
1146334 TTTTATATA
1 TTTT-TATA
1146343 TTTTTATA
1 TTTTTATA
1146351 TTT
1 TTT
1146354 GAATATAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 5 0.17
8 17 0.57
9 8 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTATA
Found at i:1146348 original size:17 final size:16
Alignment explanation
Indices: 1146311--1146353 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
1146301 TTGTATTAAT
*
1146311 TTTTTAT-TTTTTTAA
1 TTTTTATATTTTATAA
*
1146326 TATTTATATTTTATATA
1 TTTTTATATTTTATA-A
1146343 TTTTTATATTT
1 TTTTTATATTT
1146354 GAATATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 6 0.26
16 6 0.26
17 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATATTTTATAA
Found at i:1146546 original size:25 final size:25
Alignment explanation
Indices: 1146518--1146566 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1146508 ATCTATAAAA
*
1146518 TATAATT-TTAAATTATTTTAATATT
1 TATAATTAATAAATT-TTTTAATATT
*
1146543 TATAATTAATATATTTTTTAATAT
1 TATAATTAATAAATTTTTTAATAT
1146567 AAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATAATTAATAAATTTTTTAATATT
Found at i:1146626 original size:25 final size:24
Alignment explanation
Indices: 1146598--1146661 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
1146588 ATATTATGAT
1146598 ATTTATATTTTTATTAAATATATAA
1 ATTTATATTTTTATTAAATAT-TAA
*
1146623 ATTTA-ATTTTTA--AAAAATTAA
1 ATTTATATTTTTATTAAATATTAA
*
1146644 A--TATATTTATATTAAATA
1 ATTTATATTTTTATTAAATA
1146662 CATGAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 4 0.12
22 9 0.27
24 7 0.21
25 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTATATTTTTATTAAATATTAA
Found at i:1152498 original size:27 final size:27
Alignment explanation
Indices: 1152467--1152567 Score: 93
Period size: 24 Copynumber: 3.9 Consensus size: 27
1152457 AAAAACCACC
* *
1152467 CTTTTTATCTGTAAAAAATGGTGATTT
1 CTTTTTATTTGTAAAAAATGGTGAGTT
*
1152494 CTTTTTTATTTGTAAAAAATAGT-AGTT
1 C-TTTTTATTTGTAAAAAATGGTGAGTT
* *
1152521 CTTTTTTTTTGTCAAAAATGGTG-G--
1 CTTTTTATTTGTAAAAAATGGTGAGTT
* * *
1152545 CTTATTATTTGTCAAAATTGGTG
1 CTTTTTATTTGTAAAAAATGGTG
1152568 CCTGATTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
24 20 0.32
26 19 0.30
27 5 0.08
28 19 0.30
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (27 bp):
CTTTTTATTTGTAAAAAATGGTGAGTT
Found at i:1152507 original size:28 final size:28
Alignment explanation
Indices: 1152468--1152543 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
1152458 AAAACCACCC
* *
1152468 TTTTTATCTGTAAAAAATGGTGATTTCT
1 TTTTTATTTGTAAAAAATGGTGAGTTCT
*
1152496 TTTTTATTTGTAAAAAATAGT-AGTTCT
1 TTTTTATTTGTAAAAAATGGTGAGTTCT
*
1152523 TTTTT-TTTGTCAAAAATGGTG
1 TTTTTATTTGTAAAAAATGGTG
1152544 GCTTATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.31
27 10 0.24
28 19 0.45
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTTTATTTGTAAAAAATGGTGAGTTCT
Found at i:1153364 original size:19 final size:19
Alignment explanation
Indices: 1153340--1153407 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1153330 AATTCAACGA
1153340 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1153359 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1153374 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1153391 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1153408 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1153378 original size:32 final size:32
Alignment explanation
Indices: 1153342--1153404 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1153332 TTCAACGATT
*
1153342 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1153374 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1153405 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1153379 original size:13 final size:13
Alignment explanation
Indices: 1153361--1153385 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1153351 ACATAAGTTT
1153361 TGTATCGATACAA
1 TGTATCGATACAA
1153374 TGTATCGATACA
1 TGTATCGATACA
1153386 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1153465 original size:13 final size:13
Alignment explanation
Indices: 1153447--1153472 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1153437 CATTTTTCTG
1153447 TGTATCGATACAT
1 TGTATCGATACAT
1153460 TGTATCGATACAT
1 TGTATCGATACAT
1153473 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1153469 original size:33 final size:33
Alignment explanation
Indices: 1153427--1153493 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1153417 GCCAAGGAAA
***
1153427 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1153460 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1153493 T
1 T
1153494 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1156008 original size:28 final size:27
Alignment explanation
Indices: 1155941--1156013 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1155931 CTTCACAATC
* *
1155941 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1155968 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1155996 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1156014 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1156058 original size:51 final size:51
Alignment explanation
Indices: 1155996--1156166 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1155986 TTATTTCTGA
* * *
1155996 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
1156047 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1156100 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1156152 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1156167 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1156185 original size:28 final size:28
Alignment explanation
Indices: 1156149--1156230 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
1156139 ATTTTTCACA
*
1156149 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1156177 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1156205 --CGAGGGAACACTCCAACCTTGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1156231 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 40 0.89
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1160556 original size:20 final size:18
Alignment explanation
Indices: 1160520--1160555 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1160510 AGTATATTCA
*
1160520 ATATTTTATAAGATTTTC
1 ATATTTTAAAAGATTTTC
1160538 ATATATTTAAAAGATTTT
1 ATAT-TTTAAAAGATTTT
1160556 TGAAAGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTTTAAAAGATTTTC
Found at i:1164046 original size:29 final size:29
Alignment explanation
Indices: 1164010--1164071 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
1164000 ATTCTTATTT
*
1164010 GTTTTTCTTTAAAAATTCAAGTTCGATTC
1 GTTTTTCTTTAAAAATTCAAATTCGATTC
*
1164039 GTTTTTCTTTTAAAATTCAAATTCGATTC
1 GTTTTTCTTTAAAAATTCAAATTCGATTC
1164068 GTTT
1 GTTT
1164072 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.52
Consensus pattern (29 bp):
GTTTTTCTTTAAAAATTCAAATTCGATTC
Found at i:1165280 original size:12 final size:13
Alignment explanation
Indices: 1165263--1165295 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1165253 TCAAATTATA
1165263 TTAAATTTAAA-C
1 TTAAATTTAAATC
*
1165275 TTAAATTTAAATT
1 TTAAATTTAAATC
1165288 TTAAATTT
1 TTAAATTT
1165296 TTTTGGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATTTAAATC
Found at i:1168418 original size:18 final size:19
Alignment explanation
Indices: 1168372--1168421 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
1168362 ATATTTTATT
1168372 TAATTTTAATTATAAAAATA
1 TAATTTTAA-TATAAAAATA
*
1168392 TAATATTAATAT-AAAATA
1 TAATTTTAATATAAAAATA
1168410 -AATTTTTAATAT
1 TAA-TTTTAATAT
1168422 TTTATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 14 0.52
19 3 0.11
20 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAATTTTAATATAAAAATA
Found at i:1168467 original size:6 final size:6
Alignment explanation
Indices: 1168456--1168484 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1168446 TAGATTTATT
1168456 AAATTA AAATTA AAATTA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATTA AAATT
1168485 TTAAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:1168598 original size:19 final size:18
Alignment explanation
Indices: 1168576--1168628 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1168566 TATTTATTTT
1168576 TATATATAAATATATATAA
1 TATATATAAATATATA-AA
*
1168595 TATATATAAAAATATAAA
1 TATATATAAATATATAAA
* *
1168613 AATAT-TATATATATAA
1 TATATATAAATATATAA
1168629 TTAAACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 15 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATATATAAATATATAAA
Found at i:1168600 original size:21 final size:21
Alignment explanation
Indices: 1168575--1168633 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1168565 ATATTTATTT
*
1168575 TTATATATAAATATATATAATA
1 TTATATATAAATATA-AAAATA
*
1168597 -TATATAAAAATATAAAAATA
1 TTATATATAAATATAAAAATA
1168617 TTATATATATAAT-TAAA
1 TTATATATA-AATATAAA
1168634 CAAATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.16
21 24 0.75
22 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTATATATAAATATAAAAATA
Found at i:1168609 original size:27 final size:25
Alignment explanation
Indices: 1168579--1168628 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
1168569 TTATTTTTAT
1168579 ATATAAATATATATAATATATATAAAA
1 ATATAAA-A-ATATAATATATATAAAA
*
1168606 ATATAAAAATATTATATATATAA
1 ATATAAAAATATAATATATATAA
1168629 TTAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
26 1 0.05
27 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAAAAATATAATATATATAAAA
Found at i:1181416 original size:18 final size:16
Alignment explanation
Indices: 1181372--1181405 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1181362 TTCGGCCTGG
1181372 ATTAAAATAATTTTGA
1 ATTAAAATAATTTTGA
1181388 ATTAAAATAATTTTGA
1 ATTAAAATAATTTTGA
1181404 AT
1 AT
1181406 GTTAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTAAAATAATTTTGA
Found at i:1184170 original size:26 final size:26
Alignment explanation
Indices: 1184120--1184170 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1184110 TTTTTATATT
*
1184120 TTTATAATTAAATTAAAATTAAAATA
1 TTTATAATTAAAATAAAATTAAAATA
* * *
1184146 TTTATTATTAAAATAATATTTAAAT
1 TTTATAATTAAAATAAAATTAAAAT
1184171 CGAATTGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTATAATTAAAATAAAATTAAAATA
Found at i:1186533 original size:9 final size:9
Alignment explanation
Indices: 1186504--1186547 Score: 61
Period size: 9 Copynumber: 4.6 Consensus size: 9
1186494 GTGTACACTT
1186504 ATTAATTCTA
1 ATTAATT-TA
1186514 ATTGAAATTTA
1 ATT--AATTTA
1186525 ATTAATTTA
1 ATTAATTTA
1186534 ATTAATTTA
1 ATTAATTTA
1186543 ATTAA
1 ATTAA
1186548 AGTTAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 20 0.62
10 3 0.09
11 5 0.16
12 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (9 bp):
ATTAATTTA
Found at i:1186534 original size:5 final size:5
Alignment explanation
Indices: 1186505--1186564 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
1186495 TGTACACTTA
* *
1186505 TTAAT TCTAAT TGAAAT TTAA- TTAAT TTAA- TTAAT TTAAT TAAAGT
1 TTAAT T-TAAT T-TAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAA-T
*
1186551 TAAAT TTAAT TTAA
1 TTAAT TTAAT TTAA
1186565 CTTAGTAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
4 8 0.17
5 24 0.52
6 14 0.30
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (5 bp):
TTAAT
Found at i:1186540 original size:30 final size:30
Alignment explanation
Indices: 1186504--1186564 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
1186494 GTGTACACTT
*
1186504 ATTAATTCTAATTGAAA-TTTAA-TTAATTTA
1 ATTAATT-TAATT-AAAGTTAAATTTAATTTA
1186534 ATTAATTTAATTAAAGTTAAATTTAATTTA
1 ATTAATTTAATTAAAGTTAAATTTAATTTA
1186564 A
1 A
1186565 CTTAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 3 0.11
29 9 0.32
30 16 0.57
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (30 bp):
ATTAATTTAATTAAAGTTAAATTTAATTTA
Found at i:1187062 original size:16 final size:16
Alignment explanation
Indices: 1187018--1187064 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1187008 TGATTAAAAA
* * *
1187018 TTAAAATAATATGAAC
1 TTAAAATAATTTAAAT
1187034 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAT
*
1187050 TTAAAATAGTTTAAA
1 TTAAAATAATTTAAA
1187065 AAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:1187069 original size:25 final size:26
Alignment explanation
Indices: 1187034--1187082 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1187024 TAATATGAAC
*
1187034 TTAAAATAATTTAA-ATTTAAAATAGT
1 TTAAAATAA-TTAATATTAAAAATAGT
1187060 TTAAAA-AATTAATATTAAAAATA
1 TTAAAATAATTAATATTAAAAATA
1187083 ATAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TTAAAATAATTAATATTAAAAATAGT
Found at i:1192026 original size:20 final size:20
Alignment explanation
Indices: 1191989--1192026 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1191979 GATTAAACTT
* *
1191989 CCCAAAAGCTTAACACTGTC
1 CCCAAAAGCATAAAACTGTC
1192009 CCCAAAAGCATAAAACTG
1 CCCAAAAGCATAAAACTG
1192027 CTGATACTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.32, G:0.11, T:0.16
Consensus pattern (20 bp):
CCCAAAAGCATAAAACTGTC
Found at i:1196246 original size:3 final size:3
Alignment explanation
Indices: 1196238--1196267 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1196228 GTATTTATGG
1196238 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1196268 TCGATAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1196372 original size:16 final size:15
Alignment explanation
Indices: 1196322--1196366 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
1196312 TAAATTAAAT
1196322 TAATTTATTTTGAAGTAA
1 TAATTT-TTTT-AA-TAA
1196340 -AATTTTTTTAATAA
1 TAATTTTTTTAATAA
1196354 TAATTTTTTTAAT
1 TAATTTTTTTAAT
1196367 TTATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.12
15 14 0.54
16 4 0.15
17 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (15 bp):
TAATTTTTTTAATAA
Found at i:1196428 original size:20 final size:20
Alignment explanation
Indices: 1196403--1196444 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1196393 TTTAAAAATA
*
1196403 AATATAAAATTATTTTAATT
1 AATATAAAATTATTATAATT
**
1196423 AATATATTATTATTATAATT
1 AATATAAAATTATTATAATT
1196443 AA
1 AA
1196445 AGCAATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATATAAAATTATTATAATT
Found at i:1196650 original size:2 final size:2
Alignment explanation
Indices: 1196643--1196678 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1196633 TTTCGTTTAC
1196643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1196679 TATTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196890 original size:25 final size:24
Alignment explanation
Indices: 1196829--1196883 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1196819 TATAATTCAA
*
1196829 ATTAATATATAAATTTAATTTTAAAT
1 ATTAATATA-AAA-ATAATTTTAAAT
*
1196855 ATTAATATAAAAATAATTATTTAAT
1 ATTAATATAAAAATAATT-TTAAAT
1196880 ATTA
1 ATTA
1196884 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 12 0.46
26 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAATATAAAAATAATTTTAAAT
Found at i:1197276 original size:16 final size:17
Alignment explanation
Indices: 1197247--1197279 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1197237 TTAAATTTTA
1197247 TTTATAAATAATTATTT
1 TTTATAAATAATTATTT
*
1197264 TTTATTAAT-ATTATTT
1 TTTATAAATAATTATTT
1197280 AAAAGATAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATAAATAATTATTT
Found at i:1197515 original size:22 final size:21
Alignment explanation
Indices: 1197489--1197548 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1197479 TTGATTTAAA
1197489 TTAATTTAATTAAAATTAA-TAT
1 TTAATTTAATTAAAA--AATTAT
1197511 TTAA--TAATTAAAAAATTAT
1 TTAATTTAATTAAAAAATTAT
*
1197530 TTAAATTTAATTATAAAAT
1 TT-AATTTAATTAAAAAAT
1197549 ATATAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 11 0.33
22 15 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATTTAATTAAAAAATTAT
Found at i:1197532 original size:19 final size:19
Alignment explanation
Indices: 1197495--1197533 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1197485 TAAATTAATT
1197495 TAATTAAAATTAATATTTAA
1 TAATTAAAA-TAATATTTAA
1197515 TAATTAAAA-AATTATTTAA
1 TAATTAAAATAA-TATTTAA
1197534 ATTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 7 0.39
20 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATTAAAATAATATTTAA
Found at i:1197565 original size:21 final size:22
Alignment explanation
Indices: 1197515--1197567 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1197505 TAATATTTAA
* *
1197515 TAATTAAAAAATTATTTAAATT
1 TAATTATAAAATTATATAAATT
1197537 TAATTATAAAA-TATATAAATAT
1 TAATTATAAAATTATATAAAT-T
1197559 TAA-TATAAA
1 TAATTATAAA
1197568 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATTATAAAATTATATAAATT
Found at i:1197910 original size:23 final size:25
Alignment explanation
Indices: 1197875--1197942 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 25
1197865 TAAATTTTTT
1197875 TATTAAAT-TTATTTATAAAAAT-A
1 TATTAAATATTATTTATAAAAATAA
1197898 TA-TAAATATTA-TTATAAAAATAA
1 TATTAAATATTATTTATAAAAATAA
* *
1197921 TATTTAATATTTTTTA-AAAAAT
1 TATTAAATATTATTTATAAAAAT
1197943 TATTATTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 13 0.33
25 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTAAATATTATTTATAAAAATAA
Found at i:1197946 original size:22 final size:21
Alignment explanation
Indices: 1197877--1197942 Score: 53
Period size: 24 Copynumber: 2.9 Consensus size: 21
1197867 AATTTTTTTA
1197877 TTAA-ATTTATTTATAAAAATAT
1 TTAATATTT-TTTA-AAAAATAT
* *
1197899 ATAAATATTATTATAAAAATAATAT
1 -TTAATATT-TT-TTAAAA-AATAT
1197924 TTAATATTTTTTAAAAAAT
1 TTAATATTTTTTAAAAAAT
1197943 TATTATTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
21 3 0.09
22 5 0.14
23 5 0.14
24 14 0.40
25 8 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATATTTTTTAAAAAATAT
Found at i:1198568 original size:10 final size:10
Alignment explanation
Indices: 1198555--1198601 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1198545 AAATTTTAAC
1198555 AAATATTTAT
1 AAATATTTAT
*
1198565 AAATATTTTT
1 AAATATTTAT
1198575 AAA-ATTTTAAT
1 AAATA-TTT-AT
*
1198586 ATATATTTAT
1 AAATATTTAT
1198596 AAATAT
1 AAATAT
1198602 AATATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 1 0.03
10 22 0.73
11 6 0.20
12 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
AAATATTTAT
Found at i:1198579 original size:21 final size:21
Alignment explanation
Indices: 1198537--1198598 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1198527 TTATTTTTTT
* *
1198537 TATTT-TAAAAATTTTAACAAA
1 TATTTATAAATATTTTTA-AAA
1198558 TATTTATAAATATTTTTAAAA
1 TATTTATAAATATTTTTAAAA
* *
1198579 T-TTTAATATATATTTATAAA
1 TATTT-ATAAATATTTTTAAA
1198599 TATAATATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.09
21 22 0.63
22 10 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTATAAATATTTTTAAAA
Found at i:1198579 original size:31 final size:31
Alignment explanation
Indices: 1198537--1198601 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1198527 TTATTTTTTT
1198537 TATTTTAAAAATTTTAACAAATATTTATAAA
1 TATTTTAAAAATTTTAACAAATATTTATAAA
* * *
1198568 TATTTTTAAAATTTTAATATATATTTATAAA
1 TATTTTAAAAATTTTAACAAATATTTATAAA
1198599 TAT
1 TAT
1198602 AATATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (31 bp):
TATTTTAAAAATTTTAACAAATATTTATAAA
Found at i:1198593 original size:12 final size:15
Alignment explanation
Indices: 1198583--1198613 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1198573 TTAAAATTTT
1198583 AATAT-ATATTTATA
1 AATATAATATTTATA
1198597 AATATAATATTTATA
1 AATATAATATTTATA
1198612 AA
1 AA
1198614 ATTAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATAATATTTATA
Found at i:1198738 original size:10 final size:10
Alignment explanation
Indices: 1198723--1198780 Score: 53
Period size: 10 Copynumber: 6.7 Consensus size: 10
1198713 AATAAATATT
1198723 ATTATAATTA
1 ATTATAATTA
1198733 ATTATAA-TA
1 ATTATAATTA
1198742 A--AT-ATT-
1 ATTATAATTA
1198748 ATTATAATTA
1 ATTATAATTA
1198758 ATTATAA-TA
1 ATTATAATTA
1198767 A--AT-ATTA
1 ATTATAATTA
1198774 ATTATAA
1 ATTATAA
1198781 ATATTAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
6 3 0.08
7 8 0.21
8 2 0.05
9 11 0.28
10 15 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTATAATTA
Found at i:1198744 original size:25 final size:25
Alignment explanation
Indices: 1198682--1198794 Score: 142
Period size: 25 Copynumber: 4.4 Consensus size: 25
1198672 TATATTTTTT
1198682 ATTA-AAT-AATATTTATTATAATTATA
1 ATTATAATAAATA-TTATTATAA-T-TA
*
1198708 AATATAATAAATATTATTATAATTA
1 ATTATAATAAATATTATTATAATTA
1198733 ATTATAATAAATATTATTATAATTA
1 ATTATAATAAATATTATTATAATTA
*
1198758 ATTATAATAAATATTAATTATAAAT-
1 ATTATAATAAATATT-ATTATAATTA
1198783 ATTAATAATAAA
1 ATT-ATAATAAA
1198795 AAAATTAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
25 44 0.55
26 20 0.25
27 12 0.15
28 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATAATAAATATTATTATAATTA
Found at i:1198775 original size:16 final size:16
Alignment explanation
Indices: 1198729--1198780 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
1198719 TATTATTATA
1198729 ATTAATTATAATAAAT
1 ATTAATTATAATAAAT
1198745 ATT-A-T-T-AT--A-
1 ATTAATTATAATAAAT
1198754 ATTAATTATAATAAAT
1 ATTAATTATAATAAAT
1198770 ATTAATTATAA
1 ATTAATTATAA
1198781 ATATTAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
9 3 0.10
10 2 0.07
11 1 0.03
12 3 0.10
13 3 0.10
14 1 0.03
15 2 0.07
16 14 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAATTATAATAAAT
Found at i:1198793 original size:13 final size:12
Alignment explanation
Indices: 1198710--1198794 Score: 89
Period size: 13 Copynumber: 6.8 Consensus size: 12
1198700 TAATTATAAA
1198710 TATAATAAATAT
1 TATAATAAATAT
* *
1198722 TATTATAATTAAT
1 TATAATAAAT-AT
1198735 TATAATAAATAT
1 TATAATAAATAT
* *
1198747 TATTATAATTAAT
1 TATAATAAAT-AT
1198760 TATAATAAATAT
1 TATAATAAATAT
*
1198772 TAATTATAAATAT
1 T-ATAATAAATAT
1198785 TAATAATAAA
1 T-ATAATAAA
1198795 AAAATTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
12 21 0.35
13 39 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATAATAAATAT
Found at i:1200561 original size:20 final size:20
Alignment explanation
Indices: 1200517--1200570 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1200507 TTTAACAATT
1200517 TGTATCGATACAGTAGGGTAA
1 TGTATCGATACA-TAGGGTAA
*
1200538 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATAGGGT-AA
*
1200558 TGTATTGATACAT
1 TGTATCGATACAT
1200571 GTCAAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 12 0.40
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAGGGTAA
Found at i:1201497 original size:161 final size:161
Alignment explanation
Indices: 1201232--1201554 Score: 542
Period size: 161 Copynumber: 2.0 Consensus size: 161
1201222 TTCAGCTTGA
* * *
1201232 TTACAACTTGTGAAAAAAGCTGAACAAGCTGGATTGCTTATTCAAACTAGCAAATTAGCTTAGTC
1 TTACAACTTCTGAAAAAAGCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGTC
*
1201297 AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTTTGTTTTTGTCATTATCATCATTT
66 AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATTT
**
1201362 TAGTCAACTCTTCATA-TTTCTATGCCCCTTT
131 TAGTCAACTCCCCATATTTTC-ATGCCCCTTT
*
1201393 TTACAACTTCTGAAAAAATG-TGAACAAGTTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGT
1 TTACAACTTCTGAAAAAA-GCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGT
1201457 CAACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATT
65 CAACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATT
*
1201522 TTAGTCAACTCCCCATGTTTTCATGCCCCTTT
130 TTAGTCAACTCCCCATATTTTCATGCCCCTTT
1201554 T
1 T
1201555 AAGACTTTCA
Statistics
Matches: 152, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
161 147 0.97
162 5 0.03
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (161 bp):
TTACAACTTCTGAAAAAAGCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGTC
AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATTT
TAGTCAACTCCCCATATTTTCATGCCCCTTT
Found at i:1206084 original size:20 final size:21
Alignment explanation
Indices: 1206061--1206106 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1206051 AAGATTAATG
1206061 TTAAATTAT-AAAAAAAATAA
1 TTAAATTATGAAAAAAAATAA
* * *
1206081 TTAAATTCTGAATAAAAGTAA
1 TTAAATTATGAAAAAAAATAA
1206102 TTAAA
1 TTAAA
1206107 AAAGAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAAATTATGAAAAAAAATAA
Found at i:1206821 original size:14 final size:14
Alignment explanation
Indices: 1206802--1206831 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1206792 TTTTACCTTC
1206802 ACTCATATTTACCT
1 ACTCATATTTACCT
*
1206816 ACTCATATTTATCT
1 ACTCATATTTACCT
1206830 AC
1 AC
1206832 ATCAAAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (14 bp):
ACTCATATTTACCT
Found at i:1210288 original size:52 final size:52
Alignment explanation
Indices: 1210203--1210327 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
1210193 ATATGAAAAG
* *
1210203 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1210255 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
1210307 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1210328 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1210340 original size:52 final size:50
Alignment explanation
Indices: 1210203--1210347 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
1210193 ATATGAAAAG
* *
1210203 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
1210255 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
1210307 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1210348 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1210354 original size:13 final size:13
Alignment explanation
Indices: 1210336--1210360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1210326 CAAAGATCAG
1210336 TGTATCGATACAA
1 TGTATCGATACAA
1210349 TGTATCGATACA
1 TGTATCGATACA
1210361 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1210442 original size:33 final size:33
Alignment explanation
Indices: 1210400--1210469 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1210390 GGCAGTAGCT
1210400 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1210433 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1210466 TACA
1 TACA
1210470 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1210443 original size:13 final size:13
Alignment explanation
Indices: 1210425--1210449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1210415 CAAAAAAATA
1210425 TGTATCGATACAT
1 TGTATCGATACAT
1210438 TGTATCGATACA
1 TGTATCGATACA
1210450 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1211316 original size:67 final size:68
Alignment explanation
Indices: 1211190--1211316 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
1211180 ATTGGGTTTT
* * * *
1211190 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
1211255 AGA
66 AGA
* * * * *
1211258 AAAG-TGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAATGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGA
1211317 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1211471 original size:49 final size:48
Alignment explanation
Indices: 1211319--1211981 Score: 736
Period size: 49 Copynumber: 13.9 Consensus size: 48
1211309 AATGATGAGA
* * *
1211319 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--G
* *
1211372 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1211416 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1211463 AAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 -AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1211508 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * *
1211555 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1211600 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1211647 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAA-AG
** * *
1211697 TGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--G
*
1211749 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1211793 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
**** * *
1211840 GTGGGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*** *
1211888 GTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * *
1211936 ATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1211982 GAAGGGTTGC
Statistics
Matches: 528, Mismatches: 54, Indels: 60
0.82 0.08 0.09
Matches are distributed among these distances:
43 159 0.30
48 89 0.17
49 198 0.38
50 3 0.01
52 74 0.14
53 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (48 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:1211508 original size:92 final size:92
Alignment explanation
Indices: 1211320--1211986 Score: 949
Period size: 92 Copynumber: 7.1 Consensus size: 92
1211310 ATGATGAGAA
* * *
1211320 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
1211385 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
1211416 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
1211481 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
** *
1211508 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
1211573 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
1211600 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1211665 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
1211692 AATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTG
1 -A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTG
1211757 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
57 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * **** *
1211793 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG-GTGGGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
**
1211857 TGATTCAAGGCCAGCTACGTTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
**
1211884 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAA
* *
1211949 TATGCTGATTCAGGGCCAGCTATATTGGGCTT
61 TATGCTGATTCAAGGCCAGCTATATTGGACTT
1211981 AGAAGG
1 A-AAGG
1211987 GTTGCCACCG
Statistics
Matches: 522, Mismatches: 33, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
91 37 0.07
92 222 0.43
93 4 0.01
95 84 0.16
96 49 0.09
97 36 0.07
98 46 0.09
100 1 0.00
101 43 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:1211785 original size:22 final size:22
Alignment explanation
Indices: 1211760--1211825 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
1211750 AAAGGTGCCA
1211760 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
*
1211782 ATAT--TGGACTTAAAGGTGCCA---
1 ATATGCT-GA-TTCAA-G-GCCAGCT
1211803 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
1211825 A
1 A
1211826 CGTTGGACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 10 0.30
22 11 0.33
23 2 0.06
24 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
ATATGCTGATTCAAGGCCAGCT
Found at i:1211818 original size:21 final size:21
Alignment explanation
Indices: 1211751--1211818 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1211741 AAAGATGGAA
1211751 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
1211772 AA-G-GCCAGCTATATTGGACTTA
1 AAGGTGCCA-ATATGCT-GA-TTC
1211794 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1211815 AAGG
1 AAGG
1211819 CCAGCTACGT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 10 0.29
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1212022 original size:32 final size:31
Alignment explanation
Indices: 1211974--1212047 Score: 123
Period size: 32 Copynumber: 2.4 Consensus size: 31
1211964 CCAGCTATAT
1211974 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
1212004 TGGGCTTTAGAGAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
1212036 TGGGCTTTAGAA
1 TGGGCTTTAGAA
1212048 AAGGTGAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
30 5 0.12
31 6 0.15
32 30 0.73
ACGTcount: A:0.18, C:0.16, G:0.36, T:0.30
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:1212115 original size:34 final size:34
Alignment explanation
Indices: 1212034--1212727 Score: 756
Period size: 34 Copynumber: 20.3 Consensus size: 34
1212024 CATCGACTTG
** * *
1212034 TGTGGGCTTTAGAAAAGGTGAAAGATGCCACGAAGT
1 TGTGGGCTTTA-AAAA-GAAAAAGGTGCCACGGAGT
* * *
1212070 TGTGGAC-TTAAAAAGAACAAGGTGCCACAGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1212103 TGTGGGCTTTAAAAAGGAAAAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAA-G----AAAAAG-GTGCCACGGAGT
* * *
1212143 TGTGGGC-TT-AGAAGGAAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
*
1212176 TGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
* *
1212209 CGTGGAC-TT-AAAAG-----GGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1212236 TGTGGGC-TTAGAAGGAAAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAG-AAA-AAGGTGCCACGGAGT
*
1212271 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGAAGT
1 TGTGGGCTTTAAAAA--GAAAAAG-GTGCCACGGAGT
*
1212308 TGTGGGTTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
1212342 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGT
*
1212379 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
*
1212414 TGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1212448 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * *
1212482 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGT
* *
1212516 TGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
*
1212550 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* * *
1212584 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAA-AAGAAAAAGGTGCCACGGAGT
* * *
1212618 TGTAGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1212652 TGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
* *
1212686 TGTGGGCTTT--AAAGGAAAAGGTGCCACGAAGT
1 TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
1212718 TGTGGGCTTT
1 TGTGGGCTTT
1212728 GAAGAAAAAA
Statistics
Matches: 573, Mismatches: 57, Indels: 60
0.83 0.08 0.09
Matches are distributed among these distances:
27 19 0.03
28 4 0.01
32 31 0.05
33 82 0.14
34 250 0.44
35 82 0.14
36 25 0.04
37 51 0.09
38 4 0.01
39 7 0.01
40 18 0.03
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGT
Found at i:1212229 original size:27 final size:27
Alignment explanation
Indices: 1212191--1212250 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1212181 GCTTTAAAGG
*
1212191 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
1212218 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
1212245 AGAAGG
1 AAAAGG
1212251 AAAAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:1212836 original size:125 final size:126
Alignment explanation
Indices: 1212505--1212917 Score: 356
Period size: 125 Copynumber: 3.2 Consensus size: 126
1212495 ATGAAAAAAG
* * * * * *
1212505 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
1 TGCCACTGAGTCGTGGACTTT--AAAGAAGAAGGTGCCACGGAGTCGTGGACTTT--AAAGGAAA
* * * * * * *
1212570 AGGTGCCACGGAGTTGTGGACTTAAAGATG-AAAAAAGTGCCACGGAGTTGTAGG-CTTTGAAAA
62 AGGTGCCACTGAGTCGTGGACTT--TGA-GCAAAAAA-CGCCACTGAGTCGT-GGACTTTGAGAA
1212633 GAAGAA
122 G-AGAA
* * * * *
1212639 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAA
1 --TGCCACTGAGTCGTGGACTTT--AAAGAAGAAGGTGCCACGGAGTCGTGGACTTTAAAGGAAA
* *
1212704 AGGTGCCAC-GAAGTTGTGGGCTTTGAAG-AAAAAACGCCACTGAGTCGTGGACTTTGAGACA-A
62 AGGTGCCACTG-AGTCGTGGACTTTG-AGCAAAAAACGCCACTGAGTCGTGGACTTTGAGA-AGA
1212766 -AA
124 GAA
*
1212768 TGCCACTGAGTCGTGGACTTTAAAGAA-AAGGATGCCACTGAGTCGTGGACTTTAAA-GAAAAGG
1 TGCCACTGAGTCGTGGACTTTAAAGAAGAAGG-TGCCACGGAGTCGTGGACTTTAAAGGAAAAGG
* * ** *
1212831 ATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
65 -TGCCACTGAGTCGTGGACTTTGAGCAAAAAACGCCACTGAGTCGTGGACTTTGAGAAGAGAA
*
1212894 TGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
1212918 AAAGGTATTT
Statistics
Matches: 246, Mismatches: 21, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
124 14 0.06
125 73 0.30
126 25 0.10
127 18 0.07
129 2 0.01
130 3 0.01
131 18 0.07
132 9 0.04
133 2 0.01
134 27 0.11
136 55 0.22
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (126 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAGAAGGTGCCACGGAGTCGTGGACTTTAAAGGAAAAGGT
GCCACTGAGTCGTGGACTTTGAGCAAAAAACGCCACTGAGTCGTGGACTTTGAGAAGAGAA
Found at i:1212870 original size:31 final size:30
Alignment explanation
Indices: 1212700--1212914 Score: 236
Period size: 31 Copynumber: 6.9 Consensus size: 30
1212690 GGCTTTAAAG
* * *
1212700 GAAAAGGTGCCAC-GAAGTTGTGGGCTTTGAA
1 GAAAAGATGCCACTG-AGTCGTGGACTTTG-A
* *
1212731 GAAAAAACGCCACTGAGTCGTGGACTTTGA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGA
*
1212761 GACAAA-ATGCCACTGAGTCGTGGACTTTAAA
1 GA-AAAGATGCCACTGAGTCGTGGACTTT-GA
*
1212792 GAAAAGGATGCCACTGAGTCGTGGACTTTAAA
1 GAAAA-GATGCCACTGAGTCGTGGACTTT-GA
1212824 GAAAAGGATGCCACTGAGTCGTGGACTTTGA
1 GAAAA-GATGCCACTGAGTCGTGGACTTTGA
* *
1212855 GCAGAGATTGCCACTGAGTCGTGGACTTTGA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGA
* *
1212886 GAAGAGATTGCCACTTAGTCGTGGACTTT
1 GAAAAGA-TGCCACTGAGTCGTGGACTTT
1212915 AAAAAAGGTA
Statistics
Matches: 166, Mismatches: 12, Indels: 12
0.87 0.06 0.06
Matches are distributed among these distances:
30 29 0.17
31 82 0.49
32 55 0.33
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (30 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGA
Found at i:1212900 original size:94 final size:94
Alignment explanation
Indices: 1212675--1212917 Score: 291
Period size: 94 Copynumber: 2.6 Consensus size: 94
1212665 AAGAAGAAGG
* * * * * * *
1212675 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGG-TGCCAC-GAAGTTGTGGGCTTTGAAGAAAA-A
1 TGCCACTGAGTCGTGGACTTTAAA-GAAAAGGATGCCACTG-AGTCGTGGACTTTAAAGAAAAGG
*
1212737 ACGCCACTGAGTCGTGGACTTTGAGACAAAA
64 ATGCCACTGAGTCGTGGACTTTGAGACAAAA
1212768 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
*
1212833 GCCACTGAGTCGTGGACTTTGAG-CAGAGAT
66 GCCACTGAGTCGTGGACTTTGAGACA-A-AA
* * *
1212863 TGCCACTGAGTCGTGGACTTT-GAGAAGA-GATTGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGGA-TGCCACTGAGTCGTGGACTTTAAA
1212918 AAAGGTATTT
Statistics
Matches: 132, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
92 7 0.05
93 49 0.37
94 54 0.41
95 22 0.17
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24
Consensus pattern (94 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGAT
GCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1214135 original size:7 final size:7
Alignment explanation
Indices: 1214121--1214161 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
1214111 TTTGCACTTT
1214121 TTTTTTG
1 TTTTTTG
*
1214128 TTTGTTG
1 TTTTTTG
1214135 TTTTTTG
1 TTTTTTG
1214142 -TTTTT-
1 TTTTTTG
1214147 TTTTTTG
1 TTTTTTG
1214154 TTTTTTG
1 TTTTTTG
1214161 T
1 T
1214162 GTTTACTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:1214140 original size:19 final size:19
Alignment explanation
Indices: 1214118--1214161 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1214108 GCCTTTGCAC
*
1214118 TTTTT-TTTTGTTTGTTGT
1 TTTTTGTTTTTTTTGTTGT
*
1214136 TTTTTGTTTTTTTTTTTGT
1 TTTTTGTTTTTTTTGTTGT
1214155 TTTTTGT
1 TTTTTGT
1214162 GTTTACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (19 bp):
TTTTTGTTTTTTTTGTTGT
Found at i:1214164 original size:9 final size:10
Alignment explanation
Indices: 1214128--1214165 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
1214118 TTTTTTTTTG
1214128 TTTGTTGTTT
1 TTTGTTGTTT
1214138 TTTGTT-TTT
1 TTTGTTGTTT
*
1214147 TTTTTTGTTT
1 TTTGTTGTTT
1214157 TTTG-TGTTT
1 TTTGTTGTTT
1214166 ACTTTTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTTGTTGTTT
Found at i:1214171 original size:19 final size:19
Alignment explanation
Indices: 1214132--1214172 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1214122 TTTTTGTTTG
* **
1214132 TTGTTTTTTGTTTTTTTTT
1 TTGTTTTTTGTGTTTACTT
1214151 TTGTTTTTTGTGTTTACTT
1 TTGTTTTTTGTGTTTACTT
1214170 TTG
1 TTG
1214173 ACTGTTCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.80
Consensus pattern (19 bp):
TTGTTTTTTGTGTTTACTT
Found at i:1214171 original size:26 final size:26
Alignment explanation
Indices: 1214118--1214171 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1214108 GCCTTTGCAC
* **
1214118 TTTTTTTTTGTTTGTTGTTTTTTGTT
1 TTTTTTTTTGTTTGTTGTGTTTACTT
*
1214144 TTTTTTTTTGTTTTTTGTGTTTACTT
1 TTTTTTTTTGTTTGTTGTGTTTACTT
1214170 TT
1 TT
1214172 GACTGTTCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.02, C:0.02, G:0.13, T:0.83
Consensus pattern (26 bp):
TTTTTTTTTGTTTGTTGTGTTTACTT
Found at i:1221158 original size:52 final size:54
Alignment explanation
Indices: 1221057--1221183 Score: 222
Period size: 52 Copynumber: 2.4 Consensus size: 54
1221047 ATATGAAAAG
* *
1221057 TTGCTTGCATGTATCGATACATTAATAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTAATAATAATGTATCGATACATCTGGGCAAAT
1221111 TTGCCTGCATGTATCGATACATT-ATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTAATAATAATGTATCGATACATCTGGGCAAAT
1221163 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1221184 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 45 0.63
53 4 0.06
54 22 0.31
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
TTGCCTGCATGTATCGATACATTAATAATAATGTATCGATACATCTGGGCAAAT
Found at i:1221196 original size:52 final size:51
Alignment explanation
Indices: 1221057--1221204 Score: 201
Period size: 52 Copynumber: 2.8 Consensus size: 51
1221047 ATATGAAAAG
*
1221057 TTGCTTGCATGTATCGATACATTAATAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AA-AATAGTGTATCGATACATCTGGGCAAAT
1221111 TTGCCTGCATGTATCGATACATTATAAA-A-TGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AAATAGTGTATCGATACATCTGGGCAAAT
*
1221163 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACAAAAAT-AGTGTATCGATACAT
1221205 GTATCGATAC
Statistics
Matches: 88, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
49 2 0.02
50 1 0.01
51 1 0.01
52 57 0.65
53 1 0.01
54 25 0.28
55 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACAAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1221209 original size:12 final size:12
Alignment explanation
Indices: 1221192--1221237 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
1221182 CAAAGATCAG
1221192 TGTATCGATACA
1 TGTATCGATACA
1221204 TGTATCGATACA
1 TGTATCGATACA
1221216 TG--T-GAGTA-A
1 TGTATCGA-TACA
1221225 TGTATCGATACA
1 TGTATCGATACA
1221237 T
1 T
1221238 TTTTTTTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 3 0.10
12 18 0.62
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:1221297 original size:33 final size:33
Alignment explanation
Indices: 1221255--1221324 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1221245 GGCAGTAGCT
*
1221255 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGAGACAAAAAAATATGTATCGA
* ***
1221288 TACATTGTATCGAGACAACATTTTATGTATCGA
1 TACATTGTATCGAGACAAAAAAATATGTATCGA
1221321 TACA
1 TACA
1221325 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (33 bp):
TACATTGTATCGAGACAAAAAAATATGTATCGA
Found at i:1222087 original size:14 final size:16
Alignment explanation
Indices: 1222058--1222089 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1222048 TTTTTATGTA
1222058 TAAAGAATATATTAAT
1 TAAAGAATATATTAAT
1222074 TAAA-AATA-ATTAAT
1 TAAAGAATATATTAAT
1222088 TA
1 TA
1222090 TGAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAAGAATATATTAAT
Found at i:1223188 original size:28 final size:28
Alignment explanation
Indices: 1223128--1223205 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
1223118 CAAATGTCAC
*
1223128 CCTTTGTATTTGT-CAATATGGTGGTTT
1 CCTTTGTATTTGTAAAATATGGTGGTTT
1223155 CCTTTGTATTTGTAAAATATGGTGGTTAT
1 CCTTTGTATTTGTAAAATATGGTGGTT-T
* *
1223184 -TTTTGTA--TGTAAAAAATGGTGG
1 CCTTTGTATTTGTAAAATATGGTGG
1223206 CTTGTTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.30
27 13 0.28
28 18 0.39
29 1 0.02
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.47
Consensus pattern (28 bp):
CCTTTGTATTTGTAAAATATGGTGGTTT
Found at i:1223222 original size:24 final size:24
Alignment explanation
Indices: 1223186--1223231 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1223176 GTGGTTATTT
1223186 TTGTATGTAAAAAAT-GGTGGCTTG
1 TTGTATGT-AAAAATCGGTGGCTTG
* *
1223210 TTGTTTGTCAAAATCGGTGGCT
1 TTGTATGTAAAAATCGGTGGCT
1223232 AATTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (24 bp):
TTGTATGTAAAAATCGGTGGCTTG
Found at i:1235187 original size:34 final size:32
Alignment explanation
Indices: 1235115--1235625 Score: 147
Period size: 34 Copynumber: 14.8 Consensus size: 32
1235105 AAAGGGAAAA
1235115 AAAAGAGTGCGCACGAGTTGTGGGCTTAGAAGG
1 AAAAGAGTGC-CACGAGTTGTGGGCTTAGAAGG
1235148 AAAAGAGTGCCACGTAG-TGTGGGGTCTTTA-AAGG
1 AAAAGAGTGCCACG-AGTTGT-GGG-C-TTAGAAGG
* * * * **
1235182 AAAAGAGTGCCACG-G-AGT--CCGTGGAACT
1 AAAAGAGTGCCACGAGTTGTGGGCTTAGAAGG
*
1235210 AAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAAGAGTGCCAC-GAGTTGTGGGCTTAGAAGG
*
1235243 -AAAGAAGGTGCCACGGGAGTTTGTGGGCTTTAAAAAGG
1 AAAAG-A-GTGCCAC--GAG-TTGTGGGC-TT-AGAAGG
* * *
1235281 AAAAAGAGTGCCACGAAGTTGTGCGGTTTTAAAAAAATG
1 -AAAAGAGTGCCACG-AGTTGTG-GG-CTT---AGAAGG
* * *
1235320 AAAAAAGGTGCCAACGGAGTTTGTGGGATTGTGAAAAGGGG
1 AAAAGA-GTGCC-AC-GAG-TTGTGGG-CT-T-AGAA--GG
* *
1235361 AAAAAGAGTGCACACGGAGTTGTTGGGCTTTAAAAGA
1 -AAAAGAGTGC-CAC-GAGTTG-TGGGC-TTAGAAGG
* * * *
1235398 AAAAGTGTGGTTCACAGATTTGTGGGCTTTA-ACAGA
1 AAAAGAGT-G-CCAC-GAGTTGTGGGC-TTAGA-AGG
* *
1235434 AAAAG-GTGCCACGGAGTTGTGGGCTTAAAAAG
1 AAAAGAGTGCCAC-GAGTTGTGGGCTTAGAAGG
* *
1235466 AAAA-AGTGCCACG-GTTGTGGACTTA-AGATG
1 AAAAGAGTGCCACGAGTTGTGGGCTTAGA-AGG
*
1235496 AAAA-AGTGACCACGGAGTTGGTGGGCTT-GAAAAG
1 AAAAGAGTG-CCAC-GAGTT-GTGGGCTTAG-AAGG
* *
1235530 AAGAAG-GTGCCAACGGAGTTGTGGGCTTTGAAAAG
1 AA-AAGAGTGCC-AC-GAGTTGTGGGCTTAG-AAGG
*
1235565 AAAA-AGGTGCCACGGAGTTGTGGACTTA-AAGATG
1 AAAAGA-GTGCCAC-GAGTTGTGGGCTTAGAAG--G
* *
1235599 AAAAAAGTGCCACGGAGTTGTAGGCTT
1 AAAAGAGTGCCAC-GAGTTGTGGGCTT
1235626 TGAAAAAGAA
Statistics
Matches: 381, Mismatches: 42, Indels: 109
0.72 0.08 0.20
Matches are distributed among these distances:
27 1 0.00
28 15 0.04
29 2 0.01
30 22 0.06
31 7 0.02
32 32 0.08
33 37 0.10
34 89 0.23
35 38 0.10
36 38 0.10
37 18 0.05
38 17 0.04
39 20 0.05
40 16 0.04
41 23 0.06
42 6 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (32 bp):
AAAAGAGTGCCACGAGTTGTGGGCTTAGAAGG
Found at i:1235272 original size:36 final size:36
Alignment explanation
Indices: 1235210--1235633 Score: 249
Period size: 34 Copynumber: 12.0 Consensus size: 36
1235200 CCGTGGAACT
* *
1235210 AAAAGGGTGCCAC-GGAGTTGTGGGC-TT-AGAAGG
1 AAAAAGGTGCCACGGGAGTTGTGGGCTTTAAAAAGG
1235243 AAAGAAGGTGCCACGGGAGTTTGTGGGCTTTAAAAAGG
1 AAA-AAGGTGCCACGGGAG-TTGTGGGCTTTAAAAAGG
* * *
1235281 AAAAAGAGTGCCAC-GAAGTTGTGCGGTTTTAAAAAAATGA
1 AAAAAG-GTGCCACGGGAGTTGTG-GGCTTT--AAAAA-GG
* *
1235321 AAAAAGGTGCCAAC-GGAGTTTGTGGGATTGTGAAAAGGGG
1 AAAAAGGTGCC-ACGGGAG-TTGTGGGCTT-T-AAAA-AGG
1235361 AAAAAGAGTGCACAC-GGAGTTGTTGGGCTTT-AAAA-G
1 AAAAAG-GTGC-CACGGGAGTTG-TGGGCTTTAAAAAGG
* * * *
1235397 AAAAAGTGTGGTTCAC-AGATTTGTGGGCTTT-AACA-G
1 AAAAAG-GT-G-CCACGGGAGTTGTGGGCTTTAAAAAGG
1235433 AAAAAGGTGCCAC-GGAGTTGTGGGC-TTAAAAA-G
1 AAAAAGGTGCCACGGGAGTTGTGGGCTTTAAAAAGG
* * *
1235466 AAAAA-GTGCCAC--G-GTTGTGGAC-TT-AAGATG
1 AAAAAGGTGCCACGGGAGTTGTGGGCTTTAAAAAGG
*
1235496 AAAAA-GTGACCAC-GGAGTTGGTGGGC-TTGAAAA-G
1 AAAAAGGTG-CCACGGGAGTT-GTGGGCTTTAAAAAGG
* *
1235530 AAGAAGGTGCCAAC-GGAGTTGTGGGCTTTGAAAA-G
1 AAAAAGGTGCC-ACGGGAGTTGTGGGCTTTAAAAAGG
* * *
1235565 AAAAAGGTGCCAC-GGAGTTGTGGAC-TTAAAGATG
1 AAAAAGGTGCCACGGGAGTTGTGGGCTTTAAAAAGG
* *
1235599 AAAAAAGTGCCAC-GGAGTTGTAGGCTTTGAAAAAG
1 AAAAAGGTGCCACGGGAGTTGTGGGCTTT-AAAAAG
1235634 AAGGGCCAGG
Statistics
Matches: 324, Mismatches: 35, Indels: 61
0.77 0.08 0.15
Matches are distributed among these distances:
29 3 0.01
30 19 0.06
31 5 0.02
32 10 0.03
33 33 0.10
34 66 0.20
35 40 0.12
36 44 0.14
37 22 0.07
38 18 0.06
39 10 0.03
40 31 0.10
41 22 0.07
42 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.33, T:0.21
Consensus pattern (36 bp):
AAAAAGGTGCCACGGGAGTTGTGGGCTTTAAAAAGG
Found at i:1235609 original size:69 final size:66
Alignment explanation
Indices: 1235210--1235706 Score: 336
Period size: 68 Copynumber: 7.1 Consensus size: 66
1235200 CCGTGGAACT
* * * *
1235210 AAAAGGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAGAAGGTGCCACGGGAGTTTGTGGGCTTTA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTA-AAAGAAA-AAAGTGCCAC-GGAG-TTGTGGGCTTTG
1235275 AAAAGG
62 AAAA-G
* *
1235281 AAAAAGAGTGCCACGAAGTTGTGCGGTTTTAAAAAAATGAAAAAAGGTGCCAACGGAGTTTGTGG
1 AAAAAG-GTGCCACGGAGTTGTG-GG-CTT---AAAA-GAAAAAA-GTGCC-ACGGAG-TTGTGG
*
1235346 GATTGTGAAAAGGGG
56 GCTT-TGAAAA---G
* * * *
1235361 AAAAAGAGTGCACACGGAGTTGTTGGGCTTTAAAAGAAAAAGTGTGGTTCACAGATTTGTGGGCT
1 AAAAAG-GTGC-CACGGAGTTG-TGGGC-TTAAAAGAAAAA-AGT-G-CCACGGAGTTGTGGGCT
*
1235426 TT-AACAG
59 TTGAAAAG
*
1235433 AAAAAGGTGCCACGGAGTTGTGGGCTTAAAA-AGAAAAAGTGCCAC-G-GTTGTGGAC-TT-AAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGA-AAAAAGTGCCACGGAGTTGTGGGCTTTGAA-
*
1235493 ATG
64 AAG
* *
1235496 AAAAA-GTGACCACGGAGTTGGTGGGCTTGAAAAGAAGAAGGTGCCAACGGAGTTGTGGGCTTTG
1 AAAAAGGTG-CCACGGAGTT-GTGGGCTT-AAAAGAAAAAAGTGCC-ACGGAGTTGTGGGCTTTG
1235560 AAAAG
62 AAAAG
* *
1235565 AAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTAGGCTTTGAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTAAA-A-GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAA
1235630 AA-
64 AAG
* * * * *
1235632 AGAAGGGCCAGGCCACGGAGTTGTGGGCTTGAAAAGAAGAAGGTG-C-C-GAGGTTGTGGGCTTT
1 AAAAAGG---TGCCACGGAGTTGTGGGCTT-AAAAGAAAAAAGTGCCACGGA-GTTGTGGGCTTT
1235694 --AAAG
61 GAAAAG
*
1235698 GAAAAGGTG
1 AAAAAGGTG
1235707 AGGGGGGGGG
Statistics
Matches: 348, Mismatches: 40, Indels: 84
0.74 0.08 0.18
Matches are distributed among these distances:
62 7 0.02
63 24 0.07
64 9 0.03
65 18 0.05
66 10 0.03
67 24 0.07
68 48 0.14
69 42 0.12
70 34 0.10
71 12 0.03
72 22 0.06
73 2 0.01
74 2 0.01
75 3 0.01
76 5 0.01
77 41 0.12
78 16 0.05
79 1 0.00
80 13 0.04
81 13 0.04
82 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.34, T:0.21
Consensus pattern (66 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAA
G
Found at i:1235845 original size:31 final size:31
Alignment explanation
Indices: 1235799--1235857 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1235789 AATCCACTGA
1235799 TCGTGGACGTTAAAGAAAAGGATTGCCACGAG
1 TCGTGGACGTTAAAGAAAAGGA-TGCCACGAG
* *
1235831 TCGTGGA-TTTAAAGAAAAGTATGCCAC
1 TCGTGGACGTTAAAGAAAAGGATGCCAC
1235858 TGAGGAGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 12 0.48
32 7 0.28
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (31 bp):
TCGTGGACGTTAAAGAAAAGGATGCCACGAG
Found at i:1237783 original size:21 final size:20
Alignment explanation
Indices: 1237745--1237783 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1237735 GACAAGGAGT
*
1237745 GGCAAAATGTGATGAGGAAA
1 GGCAAAATGTGATAAGGAAA
*
1237765 GGCAGAAATGTGGTAAGGA
1 GGCA-AAATGTGATAAGGA
1237784 CACAAGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.05, G:0.38, T:0.15
Consensus pattern (20 bp):
GGCAAAATGTGATAAGGAAA
Found at i:1244368 original size:15 final size:16
Alignment explanation
Indices: 1244338--1244385 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
1244328 ATAAATGCTT
1244338 TAAAATATTCTTTTATTA
1 TAAAAT-TT-TTTTATTA
*
1244356 TACAA-TTTTTTATT-
1 TAAAATTTTTTTATTA
1244370 TAAAATTTTTTTATTA
1 TAAAATTTTTTTATTA
1244386 AATCAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 16 0.62
16 2 0.08
18 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (16 bp):
TAAAATTTTTTTATTA
Found at i:1244633 original size:30 final size:25
Alignment explanation
Indices: 1244576--1244684 Score: 91
Period size: 27 Copynumber: 4.2 Consensus size: 25
1244566 TATTTTTTAT
1244576 TAAATAA-TATT-TATTATAATTATAAA
1 TAAATAATTATTATA-T-TAATTAT-AA
1244602 TAAA-AATATATTATAATTAATTATAA
1 TAAATAAT-TATTAT-ATTAATTATAA
1244628 TAAAT-ATTATTATATTAATTATAA
1 TAAATAATTATTATATTAATTATAA
* *
1244652 TAAATATAATTATAAATATTAATAATAA
1 T-AA-ATAATTAT-TATATTAATTATAA
*
1244680 AAAAT
1 TAAAT
1244685 TAAAATTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
24 12 0.17
25 10 0.14
26 16 0.23
27 18 0.25
28 14 0.20
29 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATAATTATTATATTAATTATAA
Found at i:1244659 original size:9 final size:9
Alignment explanation
Indices: 1244579--1244661 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 9
1244569 TTTTTATTAA
*
1244579 ATAATATTT
1 ATAATAATT
*
1244588 ATTATAATT
1 ATAATAATT
1244597 ATAAATAA--
1 AT-AATAATT
1244605 A-AATATATT
1 ATAATA-ATT
1244614 ATAATTAATT
1 ATAA-TAATT
1244624 ATAATAA--
1 ATAATAATT
*
1244631 AT-ATTATT
1 ATAATAATT
*
1244639 ATATTAATT
1 ATAATAATT
*
1244648 ATAATAAAT
1 ATAATAATT
1244657 ATAAT
1 ATAAT
1244662 TATAAATATT
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
6 7 0.12
7 3 0.05
8 3 0.05
9 29 0.51
10 13 0.23
11 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATAATAATT
Found at i:1244672 original size:24 final size:25
Alignment explanation
Indices: 1244592--1244694 Score: 115
Period size: 24 Copynumber: 4.2 Consensus size: 25
1244582 ATATTTATTA
*
1244592 TAATTATAAATAAAAATATATTATAAT
1 TAATTAT-AATAAATATA-ATTATAAT
*
1244619 TAATTATAATAAATATTATTAT-AT
1 TAATTATAATAAATATAATTATAAT
*
1244643 TAATTATAATAAATATAATTATAAA
1 TAATTATAATAAATATAATTATAAT
*
1244668 T-ATTAATAATAAA-A-AATTAAAAT
1 TAATT-ATAATAAATATAATTATAAT
1244691 TAAT
1 TAAT
1244695 AAATAACGAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.12
24 29 0.43
25 15 0.22
26 8 0.12
27 7 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATTATAATAAATATAATTATAAT
Found at i:1244984 original size:17 final size:17
Alignment explanation
Indices: 1244949--1244990 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1244939 TTAAAAAAAA
* * *
1244949 ATTAAATTTATATTTAT
1 ATTAAATATAAATTAAT
1244966 ATTAAATATAAATTAAT
1 ATTAAATATAAATTAAT
1244983 A-TAAATAT
1 ATTAAATAT
1244991 TTTAAAAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAAATATAAATTAAT
Found at i:1244990 original size:23 final size:22
Alignment explanation
Indices: 1244947--1244991 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1244937 TTTTAAAAAA
* **
1244947 AAATTAAATTTATATTTATATT
1 AAATTAAATTAATATAAATATT
1244969 AAATATAAATTAATATAAATATT
1 AAAT-TAAATTAATATAAATATT
1244992 TTAAAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATTAAATTAATATAAATATT
Found at i:1245266 original size:20 final size:20
Alignment explanation
Indices: 1245241--1245279 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1245231 TCTCTAGATA
1245241 AAATAAAAAATTAATTATAC
1 AAATAAAAAATTAATTATAC
**
1245261 AAATAAATTATTAATTATA
1 AAATAAAAAATTAATTATA
1245280 TCTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAAAAAATTAATTATAC
Found at i:1246420 original size:20 final size:20
Alignment explanation
Indices: 1246376--1246429 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1246366 TTTAACAATT
1246376 TGTATCGATACAGTAGGGTAA
1 TGTATCGATACA-TAGGGTAA
*
1246397 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATAGGGT-AA
*
1246417 TGTATTGATACAT
1 TGTATCGATACAT
1246430 GTCAAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 12 0.40
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAGGGTAA
Found at i:1247354 original size:161 final size:161
Alignment explanation
Indices: 1247089--1247411 Score: 542
Period size: 161 Copynumber: 2.0 Consensus size: 161
1247079 TTCAGCTTGA
* * *
1247089 TTACAACTTGTGAAAAAAGCTGAACAAGCTGGATTGCTTATTCAAACTAGCAAATTAGCTTAGTC
1 TTACAACTTCTGAAAAAAGCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGTC
*
1247154 AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTTTGTTTTTGTCATTATCATCATTT
66 AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATTT
**
1247219 TAGTCAACTCTTCATA-TTTCTATGCCCCTTT
131 TAGTCAACTCCCCATATTTTC-ATGCCCCTTT
*
1247250 TTACAACTTCTGAAAAAATG-TGAACAAGTTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGT
1 TTACAACTTCTGAAAAAA-GCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGT
1247314 CAACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATT
65 CAACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATT
*
1247379 TTAGTCAACTCCCCATGTTTTCATGCCCCTTT
130 TTAGTCAACTCCCCATATTTTCATGCCCCTTT
1247411 T
1 T
1247412 AAGACTTTCA
Statistics
Matches: 152, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
161 147 0.97
162 5 0.03
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (161 bp):
TTACAACTTCTGAAAAAAGCTGAACAAGCTGCATTGCTCATTCAAACTAGCAAATTAGCTTAGTC
AACTTTATTGGTATATTTGCCAAGCTTGCTACTTTCATTTTCTGTTTTTGTCATTATCATCATTT
TAGTCAACTCCCCATATTTTCATGCCCCTTT
Found at i:1251931 original size:20 final size:21
Alignment explanation
Indices: 1251908--1251953 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1251898 AAGATTAATG
1251908 TTAAATTAT-AAAAAAAATAA
1 TTAAATTATGAAAAAAAATAA
* * *
1251928 TTAAATTCTGAATAAAAGTAA
1 TTAAATTATGAAAAAAAATAA
1251949 TTAAA
1 TTAAA
1251954 AAAGAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TTAAATTATGAAAAAAAATAA
Found at i:1252667 original size:14 final size:14
Alignment explanation
Indices: 1252648--1252677 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1252638 TTTTACCTTC
1252648 ACTCATATTTACCT
1 ACTCATATTTACCT
*
1252662 ACTCATATTTATCT
1 ACTCATATTTACCT
1252676 AC
1 AC
1252678 ATCAAAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (14 bp):
ACTCATATTTACCT
Found at i:1256131 original size:52 final size:52
Alignment explanation
Indices: 1256046--1256170 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
1256036 ATATGAAAAG
* *
1256046 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1256098 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
1256150 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1256171 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1256183 original size:52 final size:50
Alignment explanation
Indices: 1256046--1256190 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
1256036 ATATGAAAAG
* *
1256046 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
1256098 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
1256150 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1256191 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1256197 original size:13 final size:13
Alignment explanation
Indices: 1256179--1256203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1256169 CAAAGATCAG
1256179 TGTATCGATACAA
1 TGTATCGATACAA
1256192 TGTATCGATACA
1 TGTATCGATACA
1256204 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1256286 original size:33 final size:33
Alignment explanation
Indices: 1256244--1256313 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1256234 GGCAGTAGCT
1256244 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1256277 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1256310 TACA
1 TACA
1256314 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1256287 original size:13 final size:13
Alignment explanation
Indices: 1256269--1256293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1256259 CAAAAAAATA
1256269 TGTATCGATACAT
1 TGTATCGATACAT
1256282 TGTATCGATACA
1 TGTATCGATACA
1256294 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1257160 original size:67 final size:68
Alignment explanation
Indices: 1257034--1257160 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
1257024 ATTGGGTTTT
* * * *
1257034 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
1257099 AGA
66 AGA
* * * * *
1257102 AAAG-TGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAATGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGA
1257161 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGACCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1257315 original size:49 final size:48
Alignment explanation
Indices: 1257163--1257825 Score: 736
Period size: 49 Copynumber: 13.9 Consensus size: 48
1257153 AATGATGAGA
* * *
1257163 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--G
* *
1257216 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1257260 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1257307 AAAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 -AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1257352 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * *
1257399 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1257444 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1257491 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAA-AG
** * *
1257541 TGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--G
*
1257593 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1257637 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
**** * *
1257684 GTGGGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*** *
1257732 GTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * *
1257780 ATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1257826 GAAGGGTTGC
Statistics
Matches: 528, Mismatches: 54, Indels: 60
0.82 0.08 0.09
Matches are distributed among these distances:
43 159 0.30
48 89 0.17
49 198 0.38
50 3 0.01
52 74 0.14
53 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (48 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:1257352 original size:92 final size:92
Alignment explanation
Indices: 1257164--1257830 Score: 949
Period size: 92 Copynumber: 7.1 Consensus size: 92
1257154 ATGATGAGAA
* * *
1257164 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
1257229 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
1257260 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
1257325 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
** *
1257352 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
1257417 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
1257444 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
1257509 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
1257536 AATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTG
1 -A-----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTG
1257601 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
57 CCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * **** *
1257637 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACGTTGGACTTAAAG-GTGGGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
**
1257701 TGATTCAAGGCCAGCTACGTTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
**
1257728 AAAGGTGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAA
1 -AA----AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAA
* *
1257793 TATGCTGATTCAGGGCCAGCTATATTGGGCTT
61 TATGCTGATTCAAGGCCAGCTATATTGGACTT
1257825 AGAAGG
1 A-AAGG
1257831 GTTGCCACCG
Statistics
Matches: 522, Mismatches: 33, Indels: 35
0.88 0.06 0.06
Matches are distributed among these distances:
91 37 0.07
92 222 0.43
93 4 0.01
95 84 0.16
96 49 0.09
97 36 0.07
98 46 0.09
100 1 0.00
101 43 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:1257629 original size:22 final size:22
Alignment explanation
Indices: 1257604--1257669 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
1257594 AAAGGTGCCA
1257604 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
*
1257626 ATAT--TGGACTTAAAGGTGCCA---
1 ATATGCT-GA-TTCAA-G-GCCAGCT
1257647 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
1257669 A
1 A
1257670 CGTTGGACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 10 0.30
22 11 0.33
23 2 0.06
24 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
ATATGCTGATTCAAGGCCAGCT
Done.