Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 1 of 75
Found at i:1171 original size:24 final size:24
Alignment explanation
Indices: 1144--1195 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1134 AAATTTAGGG
*
1144 TTTAGAAATTAGAAATAAAG-GCAA
1 TTTAGAAATTAAAAATAAAGAG-AA
**
1168 TTTAGGTATTAAAAATAAAGAGAA
1 TTTAGAAATTAAAAATAAAGAGAA
1192 TTTA
1 TTTA
1196 AATAATTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (24 bp):
TTTAGAAATTAAAAATAAAGAGAA
Found at i:4194 original size:39 final size:39
Alignment explanation
Indices: 4140--4250 Score: 186
Period size: 39 Copynumber: 2.8 Consensus size: 39
4130 TATAAGATTT
*
4140 TGAAACTAATAGTTACTGTTTGATGAGGATTGAAATTAA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
*
4179 TGAAATTAATAGTTACTGTTTGATAAGGATTGAAATTAA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
* *
4218 TGAAATTATTAGTTACTGTTGGATGAGGATTGA
1 TGAAATTAATAGTTACTGTTTGATGAGGATTGA
4251 GAGTTTAAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 67 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (39 bp):
TGAAATTAATAGTTACTGTTTGATGAGGATTGAAATTAA
Found at i:9160 original size:33 final size:33
Alignment explanation
Indices: 9105--9170 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
9095 CACAGAGAGT
* *
9105 TACACATCAATTACGATTATAGTCCTCATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
* * *
9138 TACACATCAATTTCCATAATAGTCTTTATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
9171 GTAGCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (33 bp):
TACACATCAATTACCATAATAGTCCTCATCAAA
Found at i:9593 original size:107 final size:107
Alignment explanation
Indices: 9398--9601 Score: 365
Period size: 107 Copynumber: 1.9 Consensus size: 107
9388 GAAATAGTAA
9398 ACTGACATGACATAATATATGTAGTATTATGTTCGCCACATAAGATCTTGAAATTAATAATAACT
1 ACTGACATGACATAATATATGTAGTATTATGTTCGCCACATAAGATCTTGAAATTAATAATAACT
9463 GTTTCATGAGGATCGAAAATTTAAAGTGCATAAAGTAGGGAG
66 GTTTCATGAGGATCGAAAATTTAAAGTGCATAAAGTAGGGAG
* *
9505 ACTGACATGACATAATATATGTAGTATTATGTTCGCCGCATAAGATCTTGAAATTAATAATTACT
1 ACTGACATGACATAATATATGTAGTATTATGTTCGCCACATAAGATCTTGAAATTAATAATAACT
*
9570 GTTTCATGAGGA-CTGAAAGTTTAAAGTGCATA
66 GTTTCATGAGGATC-GAAAATTTAAAGTGCATA
9602 TGGTACGGAG
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 1 0.01
107 92 0.99
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (107 bp):
ACTGACATGACATAATATATGTAGTATTATGTTCGCCACATAAGATCTTGAAATTAATAATAACT
GTTTCATGAGGATCGAAAATTTAAAGTGCATAAAGTAGGGAG
Found at i:11910 original size:33 final size:33
Alignment explanation
Indices: 11873--11937 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
11863 TTTAGGCTAC
* *
11873 TTTGATAAAGACTATT-ATTGTACTTGATGTGTA
1 TTTGATAAAGACT-TTAATCGTAATTGATGTGTA
* *
11906 TTTGATGAGGACTTTAATCGTAATTGATGTGT
1 TTTGATAAAGACTTTAATCGTAATTGATGTGT
11938 CTCCAACCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTGATAAAGACTTTAATCGTAATTGATGTGTA
Found at i:14970 original size:33 final size:33
Alignment explanation
Indices: 14915--14980 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
14905 CACAGAGAGT
* *
14915 TACACATCAATTACGATTATAGTCCTCATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
* * *
14948 TACACATCAATTTCCATAATAGTCTTTATCAAA
1 TACACATCAATTACCATAATAGTCCTCATCAAA
14981 GTAGCCTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (33 bp):
TACACATCAATTACCATAATAGTCCTCATCAAA
Found at i:16993 original size:2 final size:2
Alignment explanation
Indices: 16986--17011 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16976 GAGCTTCATA
16986 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
17012 GAATTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17848 original size:16 final size:16
Alignment explanation
Indices: 17824--17856 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17814 GCCCGAATAT
17824 AATAAATATTTTTAAA
1 AATAAATATTTTTAAA
*
17840 AATATATATTTTTAAA
1 AATAAATATTTTTAAA
17856 A
1 A
17857 TACTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATATTTTTAAA
Found at i:18003 original size:158 final size:159
Alignment explanation
Indices: 17765--18082 Score: 629
Period size: 158 Copynumber: 2.0 Consensus size: 159
17755 GCCCATTTAG
17765 AAAACGGGCCGGGACTCGGGCACCACTTTTTTGGCCCCGGCCCGGCCTGGCCCGAATATAATAAA
1 AAAACGGGCCGGGACTCGGGCACCACTTTTTTGGCCCCGGCCCGGCCTGGCCCGAATATAATAAA
17830 TATTTTTAAAAATATATATTTTTAAAATACTTTTTTTATCTTTAAAATATTTTTTAAAATTTTCT
66 TATTTTTAAAAATATATATTTTTAAAATACTTTTTTTATCTTTAAAATATTTTTTAAAATTTTCT
17895 AAAAAAATTTTTGATGTTTATTAAAAAAA
131 AAAAAAATTTTTGATGTTTATTAAAAAAA
17924 AAAACGGGCC-GGACTCGGGCACCACTTTTTTGGCCCCGGCCCGGCCTGGCCCGAATATAATAAA
1 AAAACGGGCCGGGACTCGGGCACCACTTTTTTGGCCCCGGCCCGGCCTGGCCCGAATATAATAAA
17988 TATTTTTAAAAATATATATTTTTAAAATACTTTTTTTATCTTTAAAATATTTTTTAAAATTTTCT
66 TATTTTTAAAAATATATATTTTTAAAATACTTTTTTTATCTTTAAAATATTTTTTAAAATTTTCT
18053 AAAAAAATTTTTGATGTTTATTAAAAAAA
131 AAAAAAATTTTTGATGTTTATTAAAAAAA
18082 A
1 A
18083 GGGGCCGAGC
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 149 0.94
159 10 0.06
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (159 bp):
AAAACGGGCCGGGACTCGGGCACCACTTTTTTGGCCCCGGCCCGGCCTGGCCCGAATATAATAAA
TATTTTTAAAAATATATATTTTTAAAATACTTTTTTTATCTTTAAAATATTTTTTAAAATTTTCT
AAAAAAATTTTTGATGTTTATTAAAAAAA
Found at i:18006 original size:16 final size:16
Alignment explanation
Indices: 17982--18014 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17972 GCCCGAATAT
17982 AATAAATATTTTTAAA
1 AATAAATATTTTTAAA
*
17998 AATATATATTTTTAAA
1 AATAAATATTTTTAAA
18014 A
1 A
18015 TACTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATAAATATTTTTAAA
Found at i:20535 original size:31 final size:31
Alignment explanation
Indices: 20497--20621 Score: 119
Period size: 31 Copynumber: 4.1 Consensus size: 31
20487 CTTTGCCAAG
*
20497 TGTGTATTTTCAGAACAGGAAAACACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
** ** *
20528 TGTGTATTTAGAGAA-A-GACAACATTGAAG
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
*
20557 TGGTGTATTTTCAGAACAGGACAATACCGAAA
1 T-GTGTATTTTCAGAACAGGACAACACCGAAA
** * * *
20589 TGCATATTTTCAAAACAAGACAATACCGAAA
1 TGTGTATTTTCAGAACAGGACAACACCGAAA
20620 TG
1 TG
20622 CGTAGGACAA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
29 10 0.13
30 13 0.17
31 42 0.56
32 10 0.13
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (31 bp):
TGTGTATTTTCAGAACAGGACAACACCGAAA
Found at i:20685 original size:29 final size:29
Alignment explanation
Indices: 20648--20752 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
20638 AGTGTGTATT
* * *
20648 TTCATAACAAGACAGCACTGAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
* *
20677 TTCAGAACAAGACAACA-TCAAAGTGTGTATT
1 TTCAGAACAAGACAACACT-AAA--GTGCATA
* *
20708 TTCAGAACAGGACAACACCAAAGTGCATA
1 TTCAGAACAAGACAACACTAAAGTGCATA
*
20737 TTCAGAACAAGGCAAC
1 TTCAGAACAAGACAAC
20753 GCTGAAATGC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 36 0.59
31 24 0.39
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (29 bp):
TTCAGAACAAGACAACACTAAAGTGCATA
Found at i:20732 original size:60 final size:60
Alignment explanation
Indices: 20627--20752 Score: 180
Period size: 60 Copynumber: 2.1 Consensus size: 60
20617 AAATGCGTAG
* * * **
20627 GACAACACCGAAGTGTGTATTTTCATAACAAGACAGCACTGAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
* *
20687 GACAACATCAAAGTGTGTATTTTCAGAACAGGACAACACCAAAGTGCATATTCAGAACAA
1 GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
*
20747 GGCAAC
1 GACAAC
20753 GCTGAAATGC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (60 bp):
GACAACACCAAAGTGTGTATTTTCAGAACAAGACAACACCAAAGTGCATATTCAGAACAA
Found at i:20849 original size:29 final size:29
Alignment explanation
Indices: 20625--20850 Score: 86
Period size: 29 Copynumber: 7.6 Consensus size: 29
20615 CGAAATGCGT
* * *
20625 AGGACAACACCGAAGTGTGTATTTTCATAAC
1 AGGACAACACTGAAGTGCGTA--TTCAGAAC
* * *
20656 AAGACAGCACTGAAGTGCATATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* * *
20685 AAGACAACA-TCAAAGTGTGTATTTTCAGAAC
1 AGGACAACACT-GAAGTGCGTA--TTCAGAAC
** *
20716 AGGACAACACCAAAGTGCATATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* *
20745 AAGG-CAACGCTGAAATGCGCGCGTATTTTCAGAAC
1 -AGGACAACACTG-AA---GTGCGTA--TTCAGAAC
* * * * ***
20780 AGGAC-AGATTAAAGTGTGTATTTTTAA-
1 AGGACAACACTGAAGTGCGTATTCAGAAC
* * *
20807 A--ATAGCACCGAAGTGCGTATTCAGAAC
1 AGGACAACACTGAAGTGCGTATTCAGAAC
20834 AGGACAACACTGAAGTG
1 AGGACAACACTGAAGTG
20851 TTTATTTTTA
Statistics
Matches: 138, Mismatches: 41, Indels: 34
0.65 0.19 0.16
Matches are distributed among these distances:
25 1 0.01
26 13 0.09
27 2 0.01
28 5 0.04
29 46 0.33
30 10 0.07
31 40 0.29
33 7 0.05
34 5 0.04
35 9 0.07
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (29 bp):
AGGACAACACTGAAGTGCGTATTCAGAAC
Found at i:20901 original size:29 final size:29
Alignment explanation
Indices: 20823--20902 Score: 79
Period size: 31 Copynumber: 2.7 Consensus size: 29
20813 ACCGAAGTGC
* * * *
20823 GTATTCAGAACAGGACAACACTGAAGTGT
1 GTATTTAGAACAAGACAACACTAAAGAGT
* * *
20852 TTATTTTTAGAATAAGGCAACACTAAAGAGT
1 GTA--TTTAGAACAAGACAACACTAAAGAGT
20883 GTATTTAGAACAAGACAACA
1 GTATTTAGAACAAGACAACA
20903 TCAAAGTGCA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
29 17 0.44
31 22 0.56
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (29 bp):
GTATTTAGAACAAGACAACACTAAAGAGT
Found at i:22793 original size:23 final size:23
Alignment explanation
Indices: 22767--22812 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22757 TCGCTCTCGT
22767 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
22790 TGTCAGTCATTGTCTCTTAACCC
1 TGTCAGTCATTGTCTCTTAACCC
22813 ATGCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.39
Consensus pattern (23 bp):
TGTCAGTCATTGTCTCTTAACCC
Found at i:25277 original size:131 final size:136
Alignment explanation
Indices: 25018--25279 Score: 336
Period size: 136 Copynumber: 1.9 Consensus size: 136
25008 TAAATATGGA
* * * * * *
25018 TTTGAATTTTTAAAACGATATTTTTGATAGAGGTACCCATATAAATCTCGAATATAGACAGTAAA
1 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATA-CCAAATAAATCTCGAACATAGACAGTAAA
** * *
25083 ACGGATATGAAATAAATAAATAAATAAGTGAAGTTTGAGAAATGATGCCGAGAACTTGTCTATAT
65 ACGGATATGAAAT-AATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATAT
25148 ATAAGTGG
129 ATAAGTGG
* * *
25156 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATA-CAAATAATTTTTGAACATAGACAGTAAAA
1 TTTGAATTTTTAAAACGATATTCTTAAGAGAGATACCAAATAAATCTCGAACATAGACAGTAAAA
* *
25220 CGGATATGAAAT-A-AAA-AAA-AGGTGAAGTAAGAGAAATGATGATGAGAACTTGCCTATATA
66 CGGATATGAAATAATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATATA
25280 AGTGCAATCG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
131 35 0.32
132 3 0.03
133 3 0.03
134 1 0.01
136 36 0.33
138 31 0.28
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (136 bp):
TTTGAATTTTTAAAACGATATTCTTAAGAGAGATACCAAATAAATCTCGAACATAGACAGTAAAA
CGGATATGAAATAATAAATAAATAAGTGAAGTAAGAGAAATGATGACGAGAACTTGCCTATATAT
AAGTGG
Found at i:26804 original size:20 final size:20
Alignment explanation
Indices: 26776--26822 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
26766 CAAAACTATG
26776 AAAAAATATTAATAATTATA
1 AAAAAATATTAATAATTATA
* *
26796 AACAAATATTAATAATTTTA
1 AAAAAATATTAATAATTATA
26816 AAAAAAT
1 AAAAAAT
26823 TCTTACACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAATATTAATAATTATA
Found at i:33967 original size:2 final size:2
Alignment explanation
Indices: 33960--33998 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33950 GAATTTACAA
33960 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
33999 ACAATGCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:34199 original size:30 final size:30
Alignment explanation
Indices: 34143--34218 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
34133 ATTTCTTATG
*
34143 CCAATATCTCGATACTCATATATTTGACTT-T
1 CCAATAT-TTGATAC-CATATATTTGACTTGT
*
34174 CCAATATTTGATACCAATATCTTTGACTTGT
1 CCAATATTTGATACC-ATATATTTGACTTGT
*
34205 -CATTATTTGATACC
1 CCAATATTTGATACC
34219 CATTGTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 1 0.03
30 31 0.77
31 8 0.20
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (30 bp):
CCAATATTTGATACCATATATTTGACTTGT
Found at i:34689 original size:7 final size:7
Alignment explanation
Indices: 34674--34704 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
34664 TCTTTTGTAA
*
34674 TTTTCTT
1 TTTTATT
34681 TTTTATT
1 TTTTATT
34688 TTTTATT
1 TTTTATT
34695 TTTTATT
1 TTTTATT
34702 TTT
1 TTT
34705 GGCGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:34690 original size:13 final size:13
Alignment explanation
Indices: 34662--34704 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
34652 AAAAAGGGAC
* *
34662 TTTCTTTTGTAAT
1 TTTCTTTTTTATT
34675 TTTCTTTTTTATTT
1 TTTCTTTTTTA-TT
*
34689 TTTATTTTTTATT
1 TTTCTTTTTTATT
34702 TTT
1 TTT
34705 GGCGATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTATT
Found at i:41464 original size:30 final size:30
Alignment explanation
Indices: 41380--41464 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
41370 CCAATATCTC
* *
41380 GATACCCATATCTTTAACTTTCCAGTATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
41410 GATACCCATATCTTTGACTTTCCATTATTT
1 GATACCCATATCTTTGACTTTCCATTATTT
*
41440 GATACTCATATCTTTGACTTTCCAT
1 GATACCCATATCTTTGACTTTCCAT
41465 AAATATGGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.45
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCCATTATTT
Found at i:45840 original size:3 final size:3
Alignment explanation
Indices: 45832--45898 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
45822 AAATGAGCGG
45832 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45880 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
45899 CTCAATTCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:47255 original size:223 final size:224
Alignment explanation
Indices: 46856--47303 Score: 889
Period size: 223 Copynumber: 2.0 Consensus size: 224
46846 TTTTATACTT
46856 TTATCTTTTATTCGTTTTCGGTACTAATTTACTTTTTTTTTTTCAGAAGTTTGCTTCGTATTTGA
1 TTATCTTTTATTCGTTTTCGGTACTAATTTACTTTTTTTTTTTCAGAAGTTTGCTTCGTATTTGA
46921 GCAAATTTAAGGTATTTATTCCTATGTTTCCCTAACTAGTTTTCTTAAAAAAACATCTCGAATTG
66 GCAAATTTAAGGTATTTATTCCTATGTTTCCCTAACTAGTTTTCTTAAAAAAACATCTCGAATTG
46986 TTTAAATTTTTTTATGGTTATATTTTAGCTTTATATTTTAATTATTATTTTTGAATTTTAGGAAA
131 TTTAAATTTTTTTATGGTTATATTTTAGCTTTATATTTTAATTATTATTTTTGAATTTTAGGAAA
47051 TGAAAATATTAGAAAAATCCCTTCGTTTA
196 TGAAAATATTAGAAAAATCCCTTCGTTTA
47080 TTATCTTTTA-TCGTTTTCGGTACTAATTTACTTTTTTTTTTTCAGAAGTTTGCTTCGTATTTGA
1 TTATCTTTTATTCGTTTTCGGTACTAATTTACTTTTTTTTTTTCAGAAGTTTGCTTCGTATTTGA
47144 GCAAATTTAAGGTATTTATTCCTATGTTTCCCTAACTAGTTTTCTTAAAAAAACATCTCGAATTG
66 GCAAATTTAAGGTATTTATTCCTATGTTTCCCTAACTAGTTTTCTTAAAAAAACATCTCGAATTG
47209 TTTAAATTTTTTTATGGTTATATTTTAGCTTTATATTTTAATTATTATTTTTGAATTTTAGGAAA
131 TTTAAATTTTTTTATGGTTATATTTTAGCTTTATATTTTAATTATTATTTTTGAATTTTAGGAAA
47274 TGAAAATATTAGAAAAATCCCTTCGTTTA
196 TGAAAATATTAGAAAAATCCCTTCGTTTA
47303 T
1 T
47304 ATTTGAACTT
Statistics
Matches: 224, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
223 214 0.96
224 10 0.04
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (224 bp):
TTATCTTTTATTCGTTTTCGGTACTAATTTACTTTTTTTTTTTCAGAAGTTTGCTTCGTATTTGA
GCAAATTTAAGGTATTTATTCCTATGTTTCCCTAACTAGTTTTCTTAAAAAAACATCTCGAATTG
TTTAAATTTTTTTATGGTTATATTTTAGCTTTATATTTTAATTATTATTTTTGAATTTTAGGAAA
TGAAAATATTAGAAAAATCCCTTCGTTTA
Found at i:48326 original size:43 final size:43
Alignment explanation
Indices: 48279--48499 Score: 311
Period size: 43 Copynumber: 5.1 Consensus size: 43
48269 AAAGGGTACT
* *
48279 TTTAGCGGCGTTTGTGATAAAAGCGCCACTAGAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
48322 TTTAGCAGCATTTGTGATAAAAGCGCTGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
* * *
48365 TTTAACGGCTTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
*
48408 TTTAGCGGCGTTTGTGGGT-AAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
*
48451 TTTAGCGGCGTTTGTGGAT-AAAGCACCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGGTCATGTTC
*
48494 TATAGC
1 TTTAGC
48500 AGTGTTTTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
43 158 0.99
44 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGTTC
Found at i:52711 original size:17 final size:17
Alignment explanation
Indices: 52689--52734 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
52679 CTAAGTTTAG
52689 AAATAATTGTAAATACT
1 AAATAATTGTAAATACT
* * *
52706 AAATAATTG-GATTATT
1 AAATAATTGTAAATACT
52722 AAATAATTGTAAA
1 AAATAATTGTAAA
52735 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (17 bp):
AAATAATTGTAAATACT
Found at i:52857 original size:16 final size:16
Alignment explanation
Indices: 52838--52868 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52828 TAGAAAAAAT
52838 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
52854 TTTCAAATTTATATG
1 TTTCAAATATATATG
52869 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:54467 original size:22 final size:22
Alignment explanation
Indices: 54440--54500 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
54430 TAACGAATTA
54440 ATTATAAATTATTTTATTTGAT
1 ATTATAAATTATTTTATTTGAT
* *
54462 TTTATATA-TATGTTTATTT-AT
1 ATTATAAATTAT-TTTATTTGAT
*
54483 ATT-T-AATTATTTTGTTTG
1 ATTATAAATTATTTTATTTG
54501 CTAACGTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 7 0.23
22 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
ATTATAAATTATTTTATTTGAT
Found at i:55453 original size:21 final size:24
Alignment explanation
Indices: 55424--55470 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 24
55414 TATATTGTTG
55424 ATTACTTAAATT-TAAATT-TATT
1 ATTACTTAAATTATAAATTATATT
55446 ATTA-TTAAATTAATAAATTATATT
1 ATTACTTAAATT-ATAAATTATATT
55470 A
1 A
55471 ATAATTTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.32
22 4 0.18
23 6 0.27
24 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTACTTAAATTATAAATTATATT
Found at i:64194 original size:14 final size:15
Alignment explanation
Indices: 64171--64207 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
64161 TTATCAACAA
*
64171 TATTTT-AATATTAT
1 TATTTTAAATAATAT
64185 T-TTTTAAATAATAT
1 TATTTTAAATAATAT
64199 TATTTTAAA
1 TATTTTAAA
64208 ACAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTTAAATAATAT
Found at i:79176 original size:17 final size:16
Alignment explanation
Indices: 79154--79186 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
79144 TAATTAAATT
79154 ATTATAAATTTATAAAA
1 ATTATAAA-TTATAAAA
79171 ATTATAAATTATAAAA
1 ATTATAAATTATAAAA
79187 TCCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATAAATTATAAAA
Found at i:82573 original size:2 final size:2
Alignment explanation
Indices: 82566--82594 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82556 NNNNNNNNNN
82566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
82595 GATCTAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:85479 original size:42 final size:43
Alignment explanation
Indices: 85319--85495 Score: 214
Period size: 43 Copynumber: 4.1 Consensus size: 43
85309 GAAAAAAGTA
* * * *
85319 CCGCTATAGAACATGACATTTAGCGGCGC-TTTACCCTCAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACG
** * ** *
85362 CCGCTAAAGGTCATGATCTTTAGCGTTGCTTTTATCACAAACT
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
85405 CCGCTAAAGAACATGACCTTTAGCGGCACTTTTATCACAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
85448 CCGCTAAAG-ACATGACCTTTAGCGACGCTTTTATCACAAACG
1 CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
85490 CTGCTA
1 CCGCTA
85496 TAAGTACCGT
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 36 0.32
43 73 0.65
44 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (43 bp):
CCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
Found at i:88990 original size:31 final size:31
Alignment explanation
Indices: 88952--89020 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
88942 TAAAAAAAAA
** *
88952 TAGTGACTTAAATAAAAACTTTTGAATAGTT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
*
88983 TAGTGACTTAAATGAAAACTTTCAAATAATT
1 TAGTGACTTAAATAAAAACTTTCAAATAATT
89014 TAGTGAC
1 TAGTGAC
89021 CAAATTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAACTTTCAAATAATT
Found at i:101740 original size:16 final size:16
Alignment explanation
Indices: 101721--101759 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
101711 AGTTTTTATT
101721 AATTTAGTAGTATATA
1 AATTTAGTAGTATATA
* **
101737 AATTTATTTTTATATA
1 AATTTAGTAGTATATA
101753 AATTTAG
1 AATTTAG
101760 AATTAACATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
AATTTAGTAGTATATA
Found at i:102848 original size:13 final size:14
Alignment explanation
Indices: 102824--102856 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
102814 CTCTCTCAAC
102824 AAAAATTACAAAAA
1 AAAAATTACAAAAA
*
102838 AAAAATT-CAAAAT
1 AAAAATTACAAAAA
102851 AAAAAT
1 AAAAAT
102857 ATTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATTACAAAAA
Found at i:107393 original size:21 final size:21
Alignment explanation
Indices: 107369--107418 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
107359 TTCTGCTCTG
107369 CTCTGCTTCCCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAAC
**
107390 CTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAAC
107411 CTCTGCTT
1 CTCTGCTT
107419 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.48, G:0.16, T:0.32
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAAC
Found at i:109039 original size:46 final size:45
Alignment explanation
Indices: 108986--109124 Score: 188
Period size: 46 Copynumber: 3.0 Consensus size: 45
108976 ACGTTGTTAT
*
108986 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTAC-GAAATACCATACCTACTTTTCAC
* * **
109032 AACTCAGTACGGTTTTCTTTATTGAAATACCATACCTACTTTTTGC
1 AACTCAGTATGGTTTTCTTTA-CGAAATACCATACCTACTTTTCAC
* *
109078 AACTCAGTATGGTTTTCTTTATCGAAATATCGTACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTA-CGAAATACCATACCTACTTTTCAC
109124 A
1 A
109125 CTTTGCCATG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTTACGAAATACCATACCTACTTTTCAC
Found at i:119677 original size:28 final size:27
Alignment explanation
Indices: 119638--119691 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
119628 GAAGAAGAAA
*
119638 TTTAAAATATTTTTAAAT-TAAAAATAC
1 TTTAAAACA-TTTTAAATATAAAAATAC
*
119665 TTTATAAACATTTTAAATATGAAAATA
1 TTTA-AAACATTTTAAATATAAAAATA
119692 AACTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
TTTAAAACATTTTAAATATAAAAATAC
Found at i:120067 original size:21 final size:23
Alignment explanation
Indices: 120028--120072 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
120018 AATAAAATAT
* *
120028 AAGTATAAATAATATAATT-AAG
1 AAGTATAAATAACAAAATTCAAG
120050 AAGT-TAAATAACAAAATTCAAG
1 AAGTATAAATAACAAAATTCAAG
120072 A
1 A
120073 GGGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (23 bp):
AAGTATAAATAACAAAATTCAAG
Found at i:120468 original size:22 final size:23
Alignment explanation
Indices: 120434--120477 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
120424 TTAACAATTT
* *
120434 TTTAAGTTAAATT-TTTTTAAAC
1 TTTAACTTAAATTAATTTTAAAC
*
120456 TTTAACTTCAATTAATTTTAAA
1 TTTAACTTAAATTAATTTTAAA
120478 TATTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAACTTAAATTAATTTTAAAC
Found at i:124987 original size:39 final size:39
Alignment explanation
Indices: 124938--125016 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
124928 TGATTCTTTG
124938 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
1 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
124977 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
1 TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
125016 T
1 T
125017 ATCTTTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.10, C:0.33, G:0.08, T:0.49
Consensus pattern (39 bp):
TTGTTATCTTTTCCCTTCCCTCCCAGTATTCATCCTGTT
Found at i:125858 original size:83 final size:83
Alignment explanation
Indices: 125719--125968 Score: 482
Period size: 83 Copynumber: 3.0 Consensus size: 83
125709 AATGTCATTC
*
125719 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCGATCCTCATTGCAACCATAAAT
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
125784 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
125802 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
125867 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
*
125885 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
125950 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
125968 T
1 T
125969 TTCCCTTTTC
Statistics
Matches: 165, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 165 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (83 bp):
TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
GATGATTTAGAGAACATG
Found at i:131750 original size:43 final size:44
Alignment explanation
Indices: 131676--131781 Score: 101
Period size: 43 Copynumber: 2.5 Consensus size: 44
131666 TCGAAAGTGT
* * *
131676 ATGGCACTAAGTGTGCGAATTCAAGATAGCTTTAGTTGAAT-AA
1 ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
* * * * **
131719 ATGGCACTAAGTGTGCGGCACT-GAGAGAGCTTCGGTTTAATGTG
1 ATGGCACTAAGTGTGC-GAACTCAAGAGAGCTTCAGTTGAATGAA
131763 ATGGCACTAAGTGTG-GAAC
1 ATGGCACTAAGTGTGCGAAC
131782 ATCGTTATAG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
42 3 0.06
43 30 0.59
44 18 0.35
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (44 bp):
ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
Found at i:132007 original size:19 final size:19
Alignment explanation
Indices: 131962--132008 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
131952 AGGTTTGATG
131962 GAATAT-ATATATATAAAT
1 GAATATGATATATATAAAT
*
131980 GAGTAATGAT-TATATGAAAT
1 GAAT-ATGATATATAT-AAAT
132000 GAATATGAT
1 GAATATGAT
132009 GATCCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (19 bp):
GAATATGATATATATAAAT
Found at i:134423 original size:40 final size:40
Alignment explanation
Indices: 134379--134510 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
134369 CTATGTTTAT
* * *
134379 CACTTAGTGAGAGAATTGAGATAACTTCAGCTATTTATGG
1 CACTTAGTGTGAGAATTGAGATAGCTTCGGCTATTTATGG
* *
134419 CACTTAGTGTGCG-ATTGGGAATAGCTTCGGCTATATT-TGG
1 CACTTAGTGTGAGAATTGAG-ATAGCTTCGGCTAT-TTATGG
* * * *
134459 CACTTAGTGTGTGAGACTGAGATAGCTTCGGCTATGTAAGG
1 CACTTAGTGTGAGA-ATTGAGATAGCTTCGGCTATTTATGG
134500 CACTTAGTGTG
1 CACTTAGTGTG
134511 CGAGATTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
39 5 0.06
40 39 0.51
41 29 0.38
42 4 0.05
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
CACTTAGTGTGAGAATTGAGATAGCTTCGGCTATTTATGG
Found at i:134493 original size:41 final size:40
Alignment explanation
Indices: 134395--134515 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 40
134385 GTGAGAGAAT
* * * *
134395 TGAGATAACTTCAGCTATTTATGGCACTTA--GTGTGCGAT
1 TGAGATAGCTTCGGCTATTT-TGGCACTTAGTGTGTGAGAC
*
134434 TGGGAATAGCTTCGGCTATATTTGGCACTTAGTGTGTGAGAC
1 TGAG-ATAGCTTCGGCTAT-TTTGGCACTTAGTGTGTGAGAC
** *
134476 TGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGA
1 TGAGATAGCTTCGGCTAT-TTTGGCACTTAGTGTGTGAGA
134516 TTATAATGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.04
40 21 0.31
41 34 0.50
42 10 0.15
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (40 bp):
TGAGATAGCTTCGGCTATTTTGGCACTTAGTGTGTGAGAC
Found at i:140138 original size:29 final size:28
Alignment explanation
Indices: 140106--140166 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
140096 AAAAGCCCTC
140106 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
140135 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
140163 TTTT
1 TTTT
140167 CTGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:140423 original size:22 final size:22
Alignment explanation
Indices: 140397--140447 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
140387 CTCTCTAATC
*
140397 CTCTCAATTTCGTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
140419 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
140441 CTCTCAA
1 CTCTCAA
140448 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.39
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:142345 original size:24 final size:24
Alignment explanation
Indices: 142312--142367 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
142302 ATGCAGAACC
*
142312 GGAAGAACCACAACCACCACTGGA
1 GGAAGAACCACAACCACCACTAGA
* *
142336 GGAAGGACCACAATCACCACTAGA
1 GGAAGAACCACAACCACCACTAGA
142360 GGAAGAAC
1 GGAAGAAC
142368 AACCGCCGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.29, G:0.23, T:0.05
Consensus pattern (24 bp):
GGAAGAACCACAACCACCACTAGA
Found at i:142598 original size:28 final size:28
Alignment explanation
Indices: 142558--143099 Score: 805
Period size: 28 Copynumber: 18.9 Consensus size: 28
142548 ATTATTTGAT
142558 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
142586 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
142614 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
142642 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
142670 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142698 ACCTAAATTAACTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142726 ACCTAAATTAATTGAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142754 ACCTAAATTAACTAAAAACCCTAACATAACCCTA
1 ACCTAAATTAATTAAAAACCCT-A-AT----CTA
*
142788 ACCTAAATTAACTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142816 ACCTAAATTAATTAAAAACCATAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
* * *
142844 ACCTAAATTAACTAAAACCCCTAAACCTA
1 ACCTAAATTAATTAAAAACCCT-AATCTA
*
142873 ACCTAAATTAATTAAAAACCCTAACCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142901 ACCTAAATTAACTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142929 ACCTAAATTAACTAAAAACCCTAACCTAACCCTA
1 ACCTAAATTAATTAAAAACCCTAA--T----CTA
*
142963 ACCTAAATTAACTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
142991 ACCTAAATTAATTAAAAACCATAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
* * *
143019 ACCTAAATTAACTAAAACCCCTAAACCTA
1 ACCTAAATTAATTAAAAACCCT-AATCTA
143048 ACCTAAATTAATTAAAAACCCTAATCTA
1 ACCTAAATTAATTAAAAACCCTAATCTA
*
143076 ACCTAAATTAACTAAAAACCCTAA
1 ACCTAAATTAATTAAAAACCCTAA
143100 NNNNNNNNNN
Statistics
Matches: 475, Mismatches: 25, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
28 365 0.77
29 51 0.11
30 3 0.01
32 3 0.01
33 1 0.00
34 52 0.11
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (28 bp):
ACCTAAATTAATTAAAAACCCTAATCTA
Found at i:142942 original size:175 final size:175
Alignment explanation
Indices: 142558--143099 Score: 927
Period size: 175 Copynumber: 3.1 Consensus size: 175
142548 ATTATTTGAT
* *
142558 ACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCT-A-AT----CTAACC
1 ACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACATAACCCTAACC
* * *
142617 TAAATTAATTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAAT
66 TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
* * *
142682 TAAAAACCCT-AATCTAACCTAAATTAACTAAAAACCCTAATCTA
131 TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTA
* *
142726 ACCTAAATTAATTGAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACATAACCCTAACC
1 ACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACATAACCCTAACC
142791 TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
66 TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
*
142856 TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAACCTA
131 TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTA
*
142901 ACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCTAACC
1 ACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACATAACCCTAACC
142966 TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
66 TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
143031 TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTA
131 TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTA
143076 ACCTAAATTAACTAAAAACCCTAA
1 ACCTAAATTAACTAAAAACCCTAA
143100 NNNNNNNNNN
Statistics
Matches: 354, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
168 48 0.14
169 1 0.00
170 2 0.01
174 77 0.22
175 226 0.64
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (175 bp):
ACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACATAACCCTAACC
TAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCATAATCTAACCTAAATTAAC
TAAAACCCCTAAACCTAACCTAAATTAATTAAAAACCCTAATCTA
Found at i:145536 original size:100 final size:100
Alignment explanation
Indices: 145363--145567 Score: 401
Period size: 100 Copynumber: 2.0 Consensus size: 100
145353 TTTTTATTCG
145363 GATTTGTGATCTCGAAACCACTATTCCGATTAGGGTCAAAACCGGGTTGTTACAACAATCAAGGC
1 GATTTGTGATCTCGAAACCACTATTCCGATTAGGGTCAAAACCGGGTTGTTACAACAATCAAGGC
145428 ACAAAACGGCGCCGTTTTTACTCCCTGTAAAAACT
66 ACAAAACGGCGCCGTTTTTACTCCCTGTAAAAACT
145463 GATTTGTGATCTCGAAACCACTATTCCGATTAGGGTCAAAACCGGGTTGTTACAACAATCAAGGC
1 GATTTGTGATCTCGAAACCACTATTCCGATTAGGGTCAAAACCGGGTTGTTACAACAATCAAGGC
145528 ACAAAACGGCGCCGTTTTTACTCCCTGTAAAAACT
66 ACAAAACGGCGCCGTTTTTACTCCCTGTAAAAACT
*
145563 AATTT
1 GATTT
145568 TTTTTAAACT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 104 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (100 bp):
GATTTGTGATCTCGAAACCACTATTCCGATTAGGGTCAAAACCGGGTTGTTACAACAATCAAGGC
ACAAAACGGCGCCGTTTTTACTCCCTGTAAAAACT
Found at i:147715 original size:51 final size:51
Alignment explanation
Indices: 147605--147833 Score: 171
Period size: 51 Copynumber: 4.5 Consensus size: 51
147595 TATCGATGAA
** * * * * *
147605 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAG-TAATG-G
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCT-TTGAG
* *
147655 TCACATGTGTAGTACTAAGTGAAGGCTATTATGTGTACCAAGAAGCTTTGAG
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* ** * * * * * **
147707 CATGTGTGTAGTACTGTGTGAATGCTACCACGTGT-CTC-GGTAAACTACG-G
1 CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTAC-CAAG-AAGCTTTGAG
* *
147757 TTACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
1 -CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* *
147809 CACGAGTGTAGTACTGAGTGAAGGC
1 CACGTGTGTAGTACTAAGTGAAGGC
147834 GTGAGCCGTA
Statistics
Matches: 133, Mismatches: 37, Indels: 16
0.72 0.20 0.09
Matches are distributed among these distances:
50 3 0.02
51 125 0.94
52 5 0.04
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:147740 original size:102 final size:102
Alignment explanation
Indices: 147605--147833 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 102
147595 TATCGATGAA
* * *
147605 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGAT-AAGTAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACT-ACGGTCACATGTGTAGTA
*
147669 CTAAGTGAAGGCTATTATGTGTACCAAGAAGCTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * * * *
147707 CATGTGTGTAGTACTGTGTGAATGCTACCACGTGTCTCGGTAAACTACGGTTACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACTACGGTCACATGTGTAGTAC
147772 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* *
147809 CACGAGTGTAGTACTGAGTGAAGGC
1 CACGTGTGTAGTACTGTGTGAAGGC
147834 GTGAGCCGTA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 110 0.97
103 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACCACGTGTATCGATAAACTACGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:155840 original size:18 final size:18
Alignment explanation
Indices: 155783--155829 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
155773 AGAACTATTT
155783 ATGGTCAAAATAGAAATG
1 ATGGTCAAAATAGAAATG
155801 ATGGTCAAAATAGAAATG
1 ATGGTCAAAATAGAAATG
155819 ATGGTCAAAAT
1 ATGGTCAAAAT
155830 TGGAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.23
Consensus pattern (18 bp):
ATGGTCAAAATAGAAATG
Found at i:155887 original size:45 final size:45
Alignment explanation
Indices: 155804--155895 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
155794 AGAAATGATG
* *
155804 GTCAAAATAGAAATGATGGTCAAAATTGGAATAATGGCATGCAAA
1 GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
* ** **
155849 GTCAAAATAGAAATGGTAGTCAAAATTGGGGTGCTGGCATACAAA
1 GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
155894 GT
1 GT
155896 GAGAAATTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (45 bp):
GTCAAAATAGAAATGATAGTCAAAATTGGAATAATGGCATACAAA
Found at i:156712 original size:18 final size:18
Alignment explanation
Indices: 156677--156712 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
156667 CCTACTGTTG
*
156677 ACGGGAGATAATGGTGAC
1 ACGGGAGATAATGCTGAC
*
156695 ACGGGAGATATTGCTGAC
1 ACGGGAGATAATGCTGAC
156713 GGGCCGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.36, T:0.19
Consensus pattern (18 bp):
ACGGGAGATAATGCTGAC
Found at i:168682 original size:27 final size:28
Alignment explanation
Indices: 168627--168688 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
168617 TTTTTTGGGT
***
168627 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAATAGGATA
168655 ATATTTTGGTAAATAAAAAAA-AGGATA
1 ATATTTTGGTAAATAAAAAAATAGGATA
*
168682 ACATTTT
1 ATATTTT
168689 AGTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAATAGGATA
Found at i:172612 original size:21 final size:19
Alignment explanation
Indices: 172586--172624 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
172576 TTTCTTTCAA
172586 TTCCTTATATACTATTATTCC
1 TTCCTTATAT--TATTATTCC
*
172607 TTCCTTCTATTATTATTC
1 TTCCTTATATTATTATTC
172625 TTCAGCTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTCCTTATATTATTATTCC
Found at i:175426 original size:15 final size:16
Alignment explanation
Indices: 175408--175445 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
175398 TTATTCAATC
*
175408 TTATTTTATAT-TTTT
1 TTATTTTATATCATTT
175423 TTATTTT-TATCATTT
1 TTATTTTATATCATTT
175438 TTATTTTA
1 TTATTTTA
175446 GTCAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATATCATTT
Found at i:178277 original size:17 final size:17
Alignment explanation
Indices: 178244--178281 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
178234 TAACCTACCT
178244 AATATATCACATCTATA
1 AATATATCACATCTATA
*
178261 AATA-ATCATATCATATA
1 AATATATCACATC-TATA
178278 AATA
1 AATA
178282 CATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATATCACATCTATA
Found at i:187011 original size:88 final size:87
Alignment explanation
Indices: 186782--187157 Score: 259
Period size: 90 Copynumber: 4.3 Consensus size: 87
186772 AAAATGTCAA
* * * * *
186782 CATCGTAGATAAAACAAACCAAAACAATCCA-ACTAT-TGATAATAAACCAAACATGAAAGATGT
1 CATCATAGAAAAAACAAACCAAAACAA-CCAGAATATGT-ATAATAAAACAAACATGAAAGATGC
* *
186845 CGAT-AAAAGAAA-TTTACTCA-A-
64 CGATAAAAAAAAACATTA-TCACAT
** * * *** * * * **
186866 CATCATAGCTAAAACAAACTAAAACCATTTGAACATGAACAATAAAACTGACATGAAAGATGCCG
1 CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
186931 ATAAAAGAAAAACATTATCA-AT
66 ATAAAA-AAAAACATTATCACAT
* * * *
186953 GGCATCCTA-AAAAAACAAACCAAAGCAACTC-GAATATAG-ATAATAAAACAAATATGAAAAAT
1 --CATCATAGAAAAAACAAACCAAAACAAC-CAGAATAT-GTATAATAAAACAAACATGAAAGAT
* *
187015 GCCGATGAGAAAAAACTATTATCAGCAT
62 GCCGATAAAAAAAAAC-ATTATCA-CAT
* * *
187043 CATCATATGGAAAAACAAACCAAAACAACCAGAATATGTGTAGTAAAACAAACATGAAAGATGCC
1 CATCATA-GAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCC
* * *
187108 GACAAAACAAAAACACTATCTGCAT
65 GATAAAA-AAAAACATTATC-ACAT
**
187133 CATCATAGGTAAAACAAACTCAAAA
1 CATCATAGAAAAAACAAAC-CAAAA
187158 AAGAAAAAAA
Statistics
Matches: 226, Mismatches: 46, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
84 50 0.22
85 3 0.01
86 8 0.04
87 9 0.04
88 58 0.26
89 20 0.09
90 72 0.32
91 6 0.03
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (87 bp):
CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
ATAAAAAAAAACATTATCACAT
Found at i:200978 original size:24 final size:24
Alignment explanation
Indices: 200946--200994 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
200936 CATACAATAA
200946 AAGTGTTGCGACTCAAAAGAGTAG
1 AAGTGTTGCGACTCAAAAGAGTAG
200970 AAGTGTTGCGACTCAAAAGAGTAG
1 AAGTGTTGCGACTCAAAAGAGTAG
200994 A
1 A
200995 GGAATACATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (24 bp):
AAGTGTTGCGACTCAAAAGAGTAG
Found at i:201111 original size:21 final size:23
Alignment explanation
Indices: 201069--201115 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
201059 TTTATAGTAG
* *
201069 TAAACTTATATATATTTATTTAT
1 TAAAATTATATATATATATTTAT
201092 TAAAATTATATATA-AT-TTTAT
1 TAAAATTATATATATATATTTAT
201113 TAA
1 TAA
201116 CAACTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAAATTATATATATATATTTAT
Found at i:201654 original size:21 final size:21
Alignment explanation
Indices: 201630--201692 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
201620 ATGGGACAGT
201630 TGACATGGCTAGTTAACTAGC
1 TGACATGGCTAGTTAACTAGC
* * *
201651 TGACGTGGCTAATTAACTACC
1 TGACATGGCTAGTTAACTAGC
* * * *
201672 TGATATGACCAGCTAACTAGC
1 TGACATGGCTAGTTAACTAGC
201693 CATGATGGAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (21 bp):
TGACATGGCTAGTTAACTAGC
Found at i:203775 original size:7 final size:7
Alignment explanation
Indices: 203763--203793 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
203753 ATTCTAACCT
203763 TTTAGGG
1 TTTAGGG
203770 TTTAGGG
1 TTTAGGG
203777 TTTAGGG
1 TTTAGGG
203784 TTTAGGG
1 TTTAGGG
203791 TTT
1 TTT
203794 CTCGATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:204605 original size:13 final size:14
Alignment explanation
Indices: 204570--204615 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
204560 ACATGTTAGT
204570 AAAAT-AATTAATA
1 AAAATAAATTAATA
*
204583 AAAATGAATTAA-A
1 AAAATAAATTAATA
* *
204596 ATAATAAATTAAGA
1 AAAATAAATTAATA
204610 AAAATA
1 AAAATA
204616 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAATAAATTAATA
Found at i:205628 original size:21 final size:21
Alignment explanation
Indices: 205580--205628 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
205570 TAATCAGTAT
*
205580 ACGACACA-TAGGTGCCTGAA
1 ACGACACACGAGGTGCCTGAA
*
205600 ACGACACACGAGGTGCCTGAT
1 ACGACACACGAGGTGCCTGAA
*
205621 ACGGCACA
1 ACGACACA
205629 TAAAGTGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.33, C:0.29, G:0.27, T:0.12
Consensus pattern (21 bp):
ACGACACACGAGGTGCCTGAA
Found at i:205636 original size:21 final size:21
Alignment explanation
Indices: 205612--205669 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
205602 GACACACGAG
205612 GTGCCTGATACGGCACATAAA
1 GTGCCTGATACGGCACATAAA
* *
205633 GTGCCTGAGATAAGACACATAAA
1 GTGCCT--GATACGGCACATAAA
205656 GTGCCTGAT-CGGCA
1 GTGCCTGATACGGCA
205670 AAGCCGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 3 0.10
21 9 0.29
23 19 0.61
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (21 bp):
GTGCCTGATACGGCACATAAA
Found at i:206681 original size:16 final size:16
Alignment explanation
Indices: 206660--206690 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
206650 ACTTTATTTC
206660 TATAATAATAATATAT
1 TATAATAATAATATAT
*
206676 TATAATAATCATATA
1 TATAATAATAATATA
206691 ATAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAATAATAATATAT
Found at i:206830 original size:5 final size:5
Alignment explanation
Indices: 206820--206851 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
206810 GTCATCTATT
206820 TAATA TAATA TAATA TAATA TAATA T-ATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAA
206852 ATCATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:208099 original size:17 final size:18
Alignment explanation
Indices: 208068--208101 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
208058 AAATTCATAA
208068 ATCAAAATTATAAAAATG
1 ATCAAAATTATAAAAATG
*
208086 ATCAAATTTA-AAAAAT
1 ATCAAAATTATAAAAAT
208102 AACCTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (18 bp):
ATCAAAATTATAAAAATG
Found at i:216231 original size:29 final size:29
Alignment explanation
Indices: 216177--216232 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
216167 AATAGGGCCT
** *
216177 GGTGCCGCCTGACAATGTCCCTCCACCTG
1 GGTGCCGCCAAACAATGTCCCCCCACCTG
216206 GGTGCCGCCAAACAA-GTCTCCCCCACC
1 GGTGCCGCCAAACAATGTC-CCCCCACC
216233 CCTCCAACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (29 bp):
GGTGCCGCCAAACAATGTCCCCCCACCTG
Found at i:217160 original size:13 final size:13
Alignment explanation
Indices: 217142--217166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217132 AATTCTTTAT
217142 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
217155 TGCTTTTGAGAA
1 TGCTTTTGAGAA
217167 ATTTCAGTGT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:219546 original size:41 final size:41
Alignment explanation
Indices: 219501--219585 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
219491 GCTTCAAGGC
*
219501 CAAAGAACCAGCAAAGGGCAGAGGGTAGGGAAATTGAAAAT
1 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
*
219542 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAATTTGAAAAT
1 CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
219583 CAA
1 CAA
219586 TCCCAGACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.09
Consensus pattern (41 bp):
CAAAGAACCAGCAAAGGGCAGAGGGCAGGGAAATTGAAAAT
Found at i:219692 original size:23 final size:23
Alignment explanation
Indices: 219661--219707 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
219651 AGGGCAGAGA
219661 AACAAAGAACCAGCAAAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
* *
219684 AACACAGAACCAGCAGAGGGCAG
1 AACAAAGAACCAGCAAAGGGCAG
219707 A
1 A
219708 GATGAGGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.28, T:0.00
Consensus pattern (23 bp):
AACAAAGAACCAGCAAAGGGCAG
Found at i:221296 original size:21 final size:21
Alignment explanation
Indices: 221270--221314 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
221260 GTGGGACAAT
*
221270 TGACGTGGCTAGCTAACTAGC
1 TGACGTGGCCAGCTAACTAGC
*
221291 TGACGTGGCCAGTTAACTAGC
1 TGACGTGGCCAGCTAACTAGC
221312 TGA
1 TGA
221315 TATGATCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (21 bp):
TGACGTGGCCAGCTAACTAGC
Found at i:222251 original size:75 final size:76
Alignment explanation
Indices: 222128--222304 Score: 248
Period size: 75 Copynumber: 2.3 Consensus size: 76
222118 TGATTCCCCC
* * * * *
222128 AAGGGTTTGCTAAGTGCTGATTCCCCGAATCGTTGGTGGTTGTTAAGTGCTGATCCCACCGTATA
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
*
222193 TT-AAATGTGA
66 TTAAAATGTAA
* * *
222203 AAGGGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
222268 TTAAAATGTAA
66 TTAAAATGTAA
*
222279 AAGGGGGTTGCTAAGTACTGATTCCC
1 AA-GGGGTTGCTAAGTGCTGATTCCC
222305 CCAAAGGGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 59 0.66
76 9 0.10
77 22 0.24
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (76 bp):
AAGGGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATA
TTAAAATGTAA
Found at i:222329 original size:104 final size:103
Alignment explanation
Indices: 222206--222408 Score: 325
Period size: 104 Copynumber: 2.0 Consensus size: 103
222196 AATGTGAAAG
*
222206 GGGTTGCTAAGTGCTGATTCCCAGATTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
1 GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
222271 AAATGTAAAAGGGGGTTGCTAAGTACTGATTCCCCCAAA
66 AAATGTAAAA-GGGGTTGCTAAGTACTGATTCCCCCAAA
* * * *
222310 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTTTT
1 GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
* * *
222375 GAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AAATGTAAAAGGGGTTGCTAAGTACTGATTCCCC
222409 GAATCACTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
103 23 0.25
104 68 0.75
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (103 bp):
GGGTTGCTAAGTGCTGATTCCCAGAATCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTTA
AAATGTAAAAGGGGTTGCTAAGTACTGATTCCCCCAAA
Found at i:222353 original size:33 final size:34
Alignment explanation
Indices: 222311--222444 Score: 128
Period size: 33 Copynumber: 3.7 Consensus size: 34
222301 TCCCCCAAAG
222311 GGTTGCTAAGTGCTGATTCC-CCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
* * *
222344 GGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCG-A---AT-CAT-TG---GT
*
222387 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
*
222420 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
222445 TAACGGATAA
Statistics
Matches: 82, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
33 40 0.49
34 7 0.09
35 1 0.01
36 2 0.02
37 1 0.01
38 2 0.02
39 2 0.02
40 2 0.02
41 1 0.01
42 3 0.04
43 21 0.26
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGGT
Found at i:222430 original size:180 final size:179
Alignment explanation
Indices: 222098--222443 Score: 570
Period size: 179 Copynumber: 1.9 Consensus size: 179
222088 ACATTGAATA
* *
222098 AAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCGTTG
1 AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCATTG
*
222163 GTGGTTGTTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
66 GTGGTTGCTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
* *
222228 AGATTCATTGGTGGTTGCTAAGTGCT-AATTCCACCGTATCTTAAAATGT
131 AGAATCACTGGTGGTTGCTAAGTGCTGAA-TCCACCGTATCTTAAAATGT
222277 AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAAGGG-TTGCTAAGTGCTGATTCCCCGAATCATT
1 AAAAGGGGGTTGCTAAGTACTGATTCCCCC-AAGGGTTTGCTAAGTGCTGATTCCCCGAATCATT
* * *
222341 GGTGGTTGCTAAGTGCTGATTCCACCGTATTTTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTC
65 GGTGGTTGCTAAGTGCTGATCCCACCGTA-TATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTC
*
222406 CCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
129 CCAGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
222444 ATAACGGATA
Statistics
Matches: 155, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
179 83 0.54
180 70 0.45
181 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (179 bp):
AAAAGGGGGTTGCTAAGTACTGATTCCCCCAAGGGTTTGCTAAGTGCTGATTCCCCGAATCATTG
GTGGTTGCTAAGTGCTGATCCCACCGTATATTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCC
AGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTTAAAATGT
Found at i:224300 original size:9 final size:9
Alignment explanation
Indices: 224282--224341 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
224272 CACTCTAGAA
224282 TTTTTC-TC
1 TTTTTCTTC
224290 TTTTTCTTC
1 TTTTTCTTC
224299 TTTTTCTTC
1 TTTTTCTTC
**
224308 TCCTTC-TC
1 TTTTTCTTC
*
224316 TTCTTCTT-
1 TTTTTCTTC
224324 TTTCTTCTTC
1 TTT-TTCTTC
224334 TTTTTCTT
1 TTTTTCTT
224342 TTACTAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 15 0.34
9 26 0.59
10 3 0.07
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:224308 original size:3 final size:3
Alignment explanation
Indices: 224288--224341 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
224278 AGAATTTTTC
* * * *
224288 TCT TTT TCT TCT TTT TCT TCT CCT TC- TCT TCT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
224335 TTT TCT T
1 TCT TCT T
224342 TTACTAACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:224331 original size:12 final size:12
Alignment explanation
Indices: 224293--224341 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
224283 TTTTCTCTTT
224293 TTCTTCTTTTTC
1 TTCTTCTTTTTC
* *
224305 TTC-TCCTTCTC
1 TTCTTCTTTTTC
224316 TTCTTCTTTTTC
1 TTCTTCTTTTTC
224328 TTCTTCTTTTTC
1 TTCTTCTTTTTC
224340 TT
1 TT
224342 TTACTAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 9 0.28
12 23 0.72
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:235178 original size:2 final size:2
Alignment explanation
Indices: 235168--235208 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
235158 AAATATATAT
* *
235168 AC AC CC AC AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
235209 AAAGAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:241959 original size:12 final size:12
Alignment explanation
Indices: 241944--241968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
241934 TAATCGAGTC
241944 TAATTACGAGCT
1 TAATTACGAGCT
241956 TAATTACGAGCT
1 TAATTACGAGCT
241968 T
1 T
241969 TCGAGCTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TAATTACGAGCT
Found at i:250532 original size:18 final size:18
Alignment explanation
Indices: 250509--250543 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
250499 ATATTAGTAG
250509 TATATATTTATATATGTA
1 TATATATTTATATATGTA
250527 TATATATTTATATATGT
1 TATATATTTATATATGT
250544 TAATGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (18 bp):
TATATATTTATATATGTA
Found at i:251943 original size:16 final size:16
Alignment explanation
Indices: 251910--251947 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
251900 ATTTAAGAAA
* *
251910 TAATA-ATTTTTATGT
1 TAATATATTATTATAT
251925 TAATATATTATTATAT
1 TAATATATTATTATAT
251941 TAATATA
1 TAATATA
251948 ATAAACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TAATATATTATTATAT
Found at i:254541 original size:16 final size:16
Alignment explanation
Indices: 254520--254550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
254510 TCAACAAGCA
*
254520 ATCGAATAGAAAAAAG
1 ATCGAATACAAAAAAG
254536 ATCGAATACAAAAAA
1 ATCGAATACAAAAAA
254551 AAATTAAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.13, T:0.13
Consensus pattern (16 bp):
ATCGAATACAAAAAAG
Found at i:257307 original size:255 final size:255
Alignment explanation
Indices: 256856--257627 Score: 1517
Period size: 255 Copynumber: 3.0 Consensus size: 255
256846 CTCCTAACTC
256856 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
1 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
256921 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
66 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
256986 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
131 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
257051 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
196 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
257111 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
1 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
257176 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
66 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
257241 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
131 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
257306 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
196 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
257366 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
1 AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
*
257431 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACCAGCTTCTTCAATATTCACCTTCTATGA
66 AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
* *
257496 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTATCTCTAATAGTTTCCTAGCAATGCTATCTAAA
131 ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
257561 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
196 TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
257621 AAGTGCT
1 AAGTGCT
257628 TTCCCTTCTT
Statistics
Matches: 514, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 514 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (255 bp):
AAGTGCTGCAGACACCAAGTTTATTCTTAAGAAACTCAAAAACGACTTACATGAAAAATTTAGTA
AAAATATTCGTCATCTGATCTCTGATTTGCAATAAACTAGCTTCTTCAATATTCACCTTCTATGA
ATTCCTTATTGACTAGTGTAGCTTCAAGAGTTACCTCTAATAGTTTCCTAGCAATGCCATCTAAA
TCAAACTTCCATAATTCAAAATCATCACAAGCTGCTCCAGAAAAGTCATGAGAGTGGTCA
Found at i:261833 original size:303 final size:304
Alignment explanation
Indices: 261275--261881 Score: 1207
Period size: 303 Copynumber: 2.0 Consensus size: 304
261265 ATTCAATATC
261275 TAAACATATTAATTTTAAATTCTTTTGTTTAAAAATTATATAAAAAATAAAAAAAATGTAATAAC
1 TAAACATATTAATTTTAAATTCTTTTGTTTAAAAATTATATAAAAAATAAAAAAAATGTAATAAC
261340 AATCCTTTAATAAAATATAGATATACTTTTCATTTTAATTTTAAAAATATAATTTATTTTTTATC
66 AATCCTTTAATAAAATATAGATATACTTTTCATTTTAATTTTAAAAATATAATTTATTTTTTATC
261405 ATGTTGTATTGAGAGCTATATCATGTGGATGTTGACAATTGGCCTATTTAGGCCAACTTCAAATA
131 ATGTTGTATTGAGAGCTATATCATGTGGATGTTGACAATTGGCCTATTTAGGCCAACTTCAAATA
261470 TAAAATTTTAACCTTTGACTAATTAGATGGTAAAATATTTTGAAGAGTTATGTTCTCTGAGTACG
196 TAAAATTTTAACCTTTGACTAATTAGATGGTAAAATATTTTGAAGAGTTATGTTCTCTGAGTACG
261535 GTTTATCTTTTGTCTGAAAATAGTAACTTCCTGTCGTGTAAAAA
261 GTTTATCTTTTGTCTGAAAATAGTAACTTCCTGTCGTGTAAAAA
261579 TAAACATATT-ATTTTAAATTCTTTTGTTTAAAAATTATATAAAAAATAAAAAAAATGTAATAAC
1 TAAACATATTAATTTTAAATTCTTTTGTTTAAAAATTATATAAAAAATAAAAAAAATGTAATAAC
261643 AATCCTTTAATAAAATATAGATATACTTTTCATTTTAATTTTAAAAATATAATTTATTTTTTATC
66 AATCCTTTAATAAAATATAGATATACTTTTCATTTTAATTTTAAAAATATAATTTATTTTTTATC
261708 ATGTTGTATTGAGAGCTATATCATGTGGATGTTGACAATTGGCCTATTTAGGCCAACTTCAAATA
131 ATGTTGTATTGAGAGCTATATCATGTGGATGTTGACAATTGGCCTATTTAGGCCAACTTCAAATA
261773 TAAAATTTTAACCTTTGACTAATTAGATGGTAAAATATTTTGAAGAGTTATGTTCTCTGAGTACG
196 TAAAATTTTAACCTTTGACTAATTAGATGGTAAAATATTTTGAAGAGTTATGTTCTCTGAGTACG
261838 GTTTATCTTTTGTCTGAAAATAGTAACTTCCTGTCGTGTAAAAA
261 GTTTATCTTTTGTCTGAAAATAGTAACTTCCTGTCGTGTAAAAA
261882 AAAAGTGCAC
Statistics
Matches: 303, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
303 293 0.97
304 10 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.41
Consensus pattern (304 bp):
TAAACATATTAATTTTAAATTCTTTTGTTTAAAAATTATATAAAAAATAAAAAAAATGTAATAAC
AATCCTTTAATAAAATATAGATATACTTTTCATTTTAATTTTAAAAATATAATTTATTTTTTATC
ATGTTGTATTGAGAGCTATATCATGTGGATGTTGACAATTGGCCTATTTAGGCCAACTTCAAATA
TAAAATTTTAACCTTTGACTAATTAGATGGTAAAATATTTTGAAGAGTTATGTTCTCTGAGTACG
GTTTATCTTTTGTCTGAAAATAGTAACTTCCTGTCGTGTAAAAA
Found at i:287839 original size:22 final size:24
Alignment explanation
Indices: 287814--287858 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
287804 ATATGGCAAG
287814 GAATTAAG-TAGAAAAG-AAGTAT
1 GAATTAAGTTAGAAAAGTAAGTAT
287836 GAATTAAGTTAGAAAAGTAAGTA
1 GAATTAAGTTAGAAAAGTAAGTA
287859 AACTTAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24
Consensus pattern (24 bp):
GAATTAAGTTAGAAAAGTAAGTAT
Found at i:290894 original size:12 final size:12
Alignment explanation
Indices: 290877--290921 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
290867 AACTAATCCT
290877 CTCTCAAATTTC
1 CTCTCAAATTTC
*
290889 CTCTC-AATTTG
1 CTCTCAAATTTC
290900 CTCTCAAA-TTC
1 CTCTCAAATTTC
290911 CT-TCCAAATTT
1 CTCT-CAAATTT
290922 TTGTGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 18 0.64
12 9 0.32
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:290982 original size:51 final size:51
Alignment explanation
Indices: 290890--290989 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
290880 TCAAATTTCC
* * *
290890 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTTTGTGAAATCCATATTTAA
1 TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
* * *
290941 TCTCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTCAAATCCCTATTT
1 TCTCAATTTGCTCTCAAATTCCTTC-CAAATTTCTCTCAAATCCATATTT
290990 TTTAATTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 40 0.95
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAAATTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:292319 original size:128 final size:126
Alignment explanation
Indices: 292033--292472 Score: 539
Period size: 128 Copynumber: 3.5 Consensus size: 126
292023 CCCAAACATG
* * * *
292033 CTACTATAGCAAAAGCGCGTCCACGAGGGCACGATTTCATAAATTCTTCTCA-AATAGCATCCTA
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
* * * * * * *
292097 CTAGAA--GTGTTTTTATACTATTTACTCAGAATCGTCAACTCAAAATTATTTTTTCAAGAC
65 CTTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * *
292157 CTATTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTA
*
292221 CTTGAAGCGTTTTTTTAAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGAC
65 CTTGAAGCGTTTTTTT-ATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* *
292285 CTACTGTAGTGAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTATTCTCATAAAGCATCCTAC
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
* * *
292350 TTGAAGCG-TTTTTTATACTGTTTGCTCATAAACGTCAACTCGAAATTATTTTTCTAGGAC
66 TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* ** * * * * * * *
292410 CTACCGTAGTAAAAGCATGTACACGTGGGCGCGACTTCAGAAATCCATCTGATAAAGCATCCT
1 CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
292473 GCTTTGATTT
Statistics
Matches: 277, Mismatches: 34, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
124 64 0.23
125 59 0.21
126 41 0.15
127 39 0.14
128 72 0.26
129 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (126 bp):
CTACTGTAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAC
TTGAAGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:293696 original size:18 final size:18
Alignment explanation
Indices: 293661--293698 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
293651 TTAAAAGATA
*
293661 TATTATTTTTTTTAATTT
1 TATTATTTTTATTAATTT
293679 TATTATTTTATATT-ATTT
1 TATTATTTT-TATTAATTT
293697 TA
1 TA
293699 ATACATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTATTTTTATTAATTT
Found at i:299739 original size:10 final size:10
Alignment explanation
Indices: 299724--299845 Score: 79
Period size: 10 Copynumber: 11.6 Consensus size: 10
299714 AAGAAGAAGG
299724 AAAGAAAGAA
1 AAAGAAAGAA
299734 AAAGAAAGAA
1 AAAGAAAGAA
*
299744 AAGGAAAGGAGA
1 AAAGAAA-GA-A
299756 GGAAAGAAAGAA
1 --AAAGAAAGAA
*
299768 AAAG-AAGGA
1 AAAGAAAGAA
*
299777 AAGGAGAAGAAA
1 AAAGA-AAG-AA
299789 AAAGAAAGAA
1 AAAGAAAGAA
*
299799 AAAGAAGGAA
1 AAAGAAAGAA
*
299809 AGAA-AAGGAA
1 A-AAGAAAGAA
* *
299819 AGGAGAAGGAA
1 A-AAGAAAGAA
299830 AAA-AAAGAA
1 AAAGAAAGAA
299839 AGAAGAA
1 A-AAGAA
299846 GAAGAAGAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
9 13 0.14
10 44 0.48
11 19 0.21
12 7 0.08
13 2 0.02
14 6 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:299760 original size:34 final size:34
Alignment explanation
Indices: 299721--299877 Score: 141
Period size: 34 Copynumber: 4.7 Consensus size: 34
299711 AAGAAGAAGA
299721 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
*
299755 AGGAAAGAAAGAAAAAG-AAGGAAAGGAGAA-GA-
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGA-AAGGAG
* * * *
299787 A-AAAAGAAAGAAAAAG-AAGGAAAGAAAAGGAA
1 AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
*
299819 AGGAGAAGGAAA-AAAAAGAAAGAAGAA-G-AAGAAG
1 AGGA-AA-GAAAGAAAAAGAAAGAA-AAGGAAAGGAG
* *
299853 AGGGAATGAAGGAAAAAGAAAGAAA
1 A-GGAAAGAAAGAAAAAGAAAGAAA
299878 GAAAAGGTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
30 2 0.02
31 25 0.24
32 2 0.02
33 16 0.16
34 45 0.44
35 11 0.11
36 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (34 bp):
AGGAAAGAAAGAAAAAGAAAGAAAAGGAAAGGAG
Found at i:299812 original size:69 final size:67
Alignment explanation
Indices: 299711--299884 Score: 210
Period size: 69 Copynumber: 2.6 Consensus size: 67
299701 AGGAGAGGGA
*
299711 AAGAAGAAGAAGGAAAGAAAGAA-AAAGAAAGAAAAGGAAAGGAG-AGGAAAGAAAGAA-AAAGA
1 AAGAAGAAGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAAGGAGAAGGAAA-AAA-AAGAAAGA
299773 AGGAAAG
63 A-G-AAG
* * *
299780 GAGAAGAAAAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
1 AAGAAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
299845 AG
66 AG
* * *
299847 AAGAAGAGGGAATGAAGGAAAAAGAAAGAAAGAAAAGG
1 AAGAAGA-AGAAAGAAAGAAAAAGAAAGAAAGAAAAGG
299885 TAATTTTTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
67 9 0.10
68 30 0.33
69 46 0.51
70 6 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (67 bp):
AAGAAGAAGAAAGAAAGAAAAAGAAAGAAAGAAAAGGAAAGGAGAAGGAAAAAAAAGAAAGAAGA
AG
Found at i:299831 original size:31 final size:31
Alignment explanation
Indices: 299709--299846 Score: 120
Period size: 31 Copynumber: 4.8 Consensus size: 31
299699 GAAGGAGAGG
*
299709 GAAAGAAGAAGAAGGAAA-GA-AA-GAAAAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
299737 GAAAG---AA-AAGGAAAGGAG-AGG--AAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
*
299761 GAAAGAAAAAGAAGGAAAGGAGAAGAAAAAA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
* *
299792 GAAAGAAAAAGAAGGAAA-GAAAAGGAAAGGA
1 GAAAGAAAAAGAAGGAAAGGAGAAGGAAA-AA
* * *
299823 GAAGGAAAAA-AAAGAAAGAAGAAG
1 GAAAGAAAAAGAAGGAAAGGAGAAG
299847 AAGAAGAGGG
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
24 15 0.17
25 5 0.06
26 1 0.01
27 2 0.02
28 16 0.18
29 2 0.02
30 14 0.16
31 35 0.39
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (31 bp):
GAAAGAAAAAGAAGGAAAGGAGAAGGAAAAA
Found at i:300401 original size:159 final size:160
Alignment explanation
Indices: 300236--300808 Score: 666
Period size: 159 Copynumber: 3.6 Consensus size: 160
300226 AAATTAATAA
* * * * * * * *
300236 ATTTCAAACATAATGTACTAAAATCATGTAAAATAATAAAATTAGAAATTATGATA-TTTT-TTG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
300299 AAAGTAAAAACATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATT
66 AAAGTAAAAA-ATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATT
300364 TTTTAAAAATTCAAAAATAATTAATACAAAT
130 TTTTAAAAATTCAAAAATAATTAATACAAAT
300395 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
* * * ** * ** * * *
300460 AAAGTAATAAAATTC-AAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTA
66 AAAGTAA-AAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAG--TGTTTT--ACTA
* * * *
300524 AGTTAATTTAAAAA-ACACACAA-AATTAAT---AA-
126 AATT-TTTTAAAAATTCA-AAAATAATTAATACAAAT
* * * * * * *
300555 ATTTCAAACATAATGCACTGAAATAATGTAAAATTATAAAATTAGAAATTATTATA-TTTT-TTG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
300618 AAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATT
66 AAAGT-AAAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATT
*
300683 TTTTAAAAATTCAGAAATAATTAATACAAAT
130 TTTTAAAAATTCAAAAATAATTAATACAAAT
300714 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
1 ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
* * *
300779 AAAGTAATAAAATTC-AAGAAAATAATACGA
66 AAAGTAA-AAAATGCGGAGAAAAAAATACGA
300809 GCAAAAGGCA
Statistics
Matches: 338, Mismatches: 56, Indels: 39
0.78 0.13 0.09
Matches are distributed among these distances:
154 10 0.03
155 16 0.05
157 5 0.01
158 16 0.05
159 129 0.38
160 98 0.29
161 29 0.09
162 8 0.02
164 16 0.05
165 11 0.03
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.30
Consensus pattern (160 bp):
ATTTCAAACAAAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTG
AAAGTAAAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGTAAGAGTGTTTTACTAAATTT
TTTAAAAATTCAAAAATAATTAATACAAAT
Found at i:300579 original size:160 final size:154
Alignment explanation
Indices: 300209--300906 Score: 677
Period size: 160 Copynumber: 4.4 Consensus size: 154
300199 AAAAATGATA
* * * * *
300209 TATTTAAAACACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATCATGTAAAATAATA
1 TATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAAGA
* * * * * *
300274 AAATTAGAAATTATGATATTTTTTGAAAGTAA-AAACATGCGGAGAAAAAAATACGAATAAATGG
66 AAATAAGAAAATATTATATTTTTTGAAAGTAATAAA-ATGCGAAGAAAAAAATACGAACAAAAGG
** *
300338 CCGAAGTAAGAGTGTTTTACTAAAT
130 CAAAAATAAGAGTGTTTTACTAAAT
* * * * *
300363 TTTTTAAAAATTCA-AAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAA
1 TATTTAAAAA-ACACACAA-AATTAAT---AA-ATTTCAAACATAATGTACTGAAATAATGTAAA
* * *
300427 ATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAAAATTC-AAGAAAATAATACGAG
60 ATAAGAAAATAAGAAAATATTATA-TTTT-TTGAAAGTAATAAAATGCGAAGAAAAAAATACGAA
* * *
300491 CAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGT
123 CAAAAGGCAAAAATAAGAG--TGTTTT--ACTAAAT
* * *
300527 TAATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTAT
1 T-ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAAG
* * * * * *
300592 AAAATTAGAAATTATTATATTTTTTGAAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGG
65 AAAATAAGAAAATATTATATTTTTTGAAAGTAATAAAATGCGAAGAAAAAAATACGAACAAAAGG
** *
300657 CCGAAGTAAGAGTGTTTTACTAAAT
130 CAAAAATAAGAGTGTTTTACTAAAT
* * * * *
300682 TTTTTAAAAATTCAGA-AATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAA
1 TATTTAAAAA-ACACACAA-AATTAAT---AA-ATTTCAAACATAATGTACTGAAATAATGTAAA
* * *
300746 ATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAAAATTC-AAGAAAATAATACGAG
60 ATAAGAAAATAAGAAAATATTATA-TTTT-TTGAAAGTAATAAAATGCGAAGAAAAAAATACGAA
* * *
300810 CAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGT
123 CAAAAGGCAAAAATAAGAG--TGTTTT--ACTAAAT
*
300846 TAATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAA
1 T-ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAA
300907 GTTTCCTAAT
Statistics
Matches: 437, Mismatches: 77, Indels: 54
0.77 0.14 0.10
Matches are distributed among these distances:
154 20 0.05
155 26 0.06
157 5 0.01
158 20 0.05
159 127 0.29
160 139 0.32
161 33 0.08
162 13 0.03
164 33 0.08
165 21 0.05
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (154 bp):
TATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAAGA
AAATAAGAAAATATTATATTTTTTGAAAGTAATAAAATGCGAAGAAAAAAATACGAACAAAAGGC
AAAAATAAGAGTGTTTTACTAAAT
Found at i:300703 original size:319 final size:319
Alignment explanation
Indices: 300210--300906 Score: 1313
Period size: 319 Copynumber: 2.2 Consensus size: 319
300200 AAAATGATAT
* * * * *
300210 ATTTAAAACACACACTAAATTAATAAATTTCAAACATAATGTACTAAAATCATGTAAAATAATAA
1 ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATAATAA
*
300275 AATTAGAAATTATGATATTTTTTGAAAGTAAAAACATGCGGAGAAAAAAATACGAATAAATGGCC
66 AATTAGAAATTATGATATTTTTTGAAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGGCC
300340 GAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
131 GAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
300405 AAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAA
196 AAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAA
300470 AATTCAAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTA
261 AATTCAAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTA
*
300529 ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATTATAA
1 ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATAATAA
*
300594 AATTAGAAATTATTATATTTTTTGAAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGGCC
66 AATTAGAAATTATGATATTTTTTGAAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGGCC
*
300659 GAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACA
131 GAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
300724 AAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAA
196 AAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAA
300789 AATTCAAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTA
261 AATTCAAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTA
300848 ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAA
1 ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAA
300907 GTTTCCTAAT
Statistics
Matches: 369, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
319 369 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (319 bp):
ATTTAAAAAACACACAAAATTAATAAATTTCAAACATAATGCACTGAAATAATGTAAAATAATAA
AATTAGAAATTATGATATTTTTTGAAAGTAAAAAAATGCGGAGAAAAAAATACGAATAAATGGCC
GAAGTAAGAGTGTTTTACTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACA
AAATGTACTGAAATAATATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAA
AATTCAAGAAAATAATACGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTA
Found at i:301094 original size:236 final size:234
Alignment explanation
Indices: 300676--301140 Score: 786
Period size: 236 Copynumber: 2.0 Consensus size: 234
300666 GAGTGTTTTA
*
300676 CTAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAAT
1 CTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAAT
*
300741 ATAAAATAAGAAAATAAGAAAATATTATATTTTTATTGAAAGTAATAAAATTCAAGAAAATAATA
66 ATAAAATAAGAAAATAAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCAAGAAAATAATA
*
300806 CGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAGTTAATTTAAAAAACACACAAAATTAA
131 CGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAATTAATTT-AAAAA-ACACAAAATTAA
300871 TAAATTTCAAACATAATGCACTGAAATAATGTAAAAGTTTC
194 TAAATTTCAAACATAATGCACTGAAATAATGTAAAAGTTTC
* *
300912 CTAATTTTTTTAAAAATTTAAAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAAT
1 CTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAAT
* * ***
300977 ATAAAATAATAAAATACGAAAATAATATATTTTTATTGAAAGTAATAAAATTTGGGAAAATAATA
66 ATAAAATAAGAAAATAAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCAAGAAAATAATA
* ** *
301042 CGAGCAAAGGGCAGGAATAATGGTTTTTTTTACACTAAATTAATTTAAAAAACACAAAATTAATA
131 CGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACAAAATTAATA
301107 AATTTCAAACATAATGCACTGAAATAATGTAAAA
196 AATTTCAAACATAATGCACTGAAATAATGTAAAA
301141 TTATAAAATA
Statistics
Matches: 215, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
234 48 0.22
235 5 0.02
236 162 0.75
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (234 bp):
CTAAATTTTTTAAAAATTCAAAAATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAAT
ATAAAATAAGAAAATAAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCAAGAAAATAATA
CGAGCAAAAGGCAAAAATAAGGGTTTTTTTTACACTAAATTAATTTAAAAAACACAAAATTAATA
AATTTCAAACATAATGCACTGAAATAATGTAAAAGTTTC
Found at i:305546 original size:25 final size:26
Alignment explanation
Indices: 305504--305552 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
305494 CTAAACCCTA
305504 AAAACTAATAATAATAAT-ACTAACT
1 AAAACTAATAATAATAATAACTAACT
* **
305529 AAAACTATTAATCTTAATAACTAA
1 AAAACTAATAATAATAATAACTAA
305553 ACAACAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (26 bp):
AAAACTAATAATAATAATAACTAACT
Found at i:305660 original size:10 final size:10
Alignment explanation
Indices: 305632--305668 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
305622 AAATACCTTT
305632 TTTTTCTCTTC
1 TTTTTCTC-TC
*
305643 TCTTTCTCTC
1 TTTTTCTCTC
305653 TTTTTCTCTC
1 TTTTTCTCTC
305663 TTTTTC
1 TTTTTC
305669 CGACAGCACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:305780 original size:27 final size:27
Alignment explanation
Indices: 305742--305836 Score: 102
Period size: 27 Copynumber: 3.5 Consensus size: 27
305732 TAACACAAGT
* * *
305742 GGTGCTGCCTATGGGAAAGGTACCTTC
1 GGTGCCGCCTATGGGAAAGGCACCATC
305769 GGTGCCGCCTATGGGAAAGGCACCATC
1 GGTGCCGCCTATGGGAAAGGCACCATC
* ** * *
305796 GGTGCCGCCTCTGACAGAGGCA-CAAC
1 GGTGCCGCCTATGGGAAAGGCACCATC
305822 TGGTGCCGCCTATGG
1 -GGTGCCGCCTATGG
305837 CACCCCCTCC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 3 0.05
27 54 0.95
ACGTcount: A:0.19, C:0.28, G:0.34, T:0.19
Consensus pattern (27 bp):
GGTGCCGCCTATGGGAAAGGCACCATC
Found at i:306454 original size:16 final size:16
Alignment explanation
Indices: 306433--306489 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
306423 TTTGGTTCGC
*
306433 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
306449 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
306465 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
306481 TGTAATGGA
1 TGTAATGGA
306490 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:317038 original size:43 final size:43
Alignment explanation
Indices: 316991--317088 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
316981 TATGTGAAAG
* * *
316991 AACGCAGCTAAAGAACATGATCTTTAGCGGCATTTTACCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
*
317034 AACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACA
1 AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
317077 AACGCCGCTAAA
1 AACGCCGCTAAA
317089 AGTATGGTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTACCCACA
Found at i:318870 original size:7 final size:7
Alignment explanation
Indices: 318860--319014 Score: 91
Period size: 7 Copynumber: 21.7 Consensus size: 7
318850 TCATAAAACA
318860 TAAACCC
1 TAAACCC
318867 TAAACCCC
1 TAAA-CCC
*
318875 TAACCCC
1 TAAACCC
318882 TAAACTCC
1 TAAAC-CC
*
318890 TAAACCT
1 TAAACCC
318897 TAAACCC
1 TAAACCC
*
318904 -CAACCC
1 TAAACCC
*
318910 TTAAACCG
1 -TAAACCC
*
318918 TAAACCG
1 TAAACCC
*
318925 TAAACCA
1 TAAACCC
*
318932 TAAACCA
1 TAAACCC
*
318939 TAAACCA
1 TAAACCC
*
318946 TAAACCA
1 TAAACCC
*
318953 TAATCCC
1 TAAACCC
* *
318960 AAAACCT
1 TAAACCC
*
318967 TAAA--A
1 TAAACCC
318972 TAGTAACTCC
1 TA--AAC-CC
*
318982 TAAACCA
1 TAAACCC
*
318989 TATACCC
1 TAAACCC
*
318996 TAAACCA
1 TAAACCC
319003 TAAACCC
1 TAAACCC
319010 TAAAC
1 TAAAC
319015 TATAATGATA
Statistics
Matches: 117, Mismatches: 22, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
5 2 0.02
6 5 0.04
7 88 0.75
8 20 0.17
10 2 0.02
ACGTcount: A:0.45, C:0.35, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:318877 original size:8 final size:8
Alignment explanation
Indices: 318860--318916 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
318850 TCATAAAACA
318860 TAAA-CCC
1 TAAACCCC
318867 TAAACCCC
1 TAAACCCC
318875 T-AACCCC
1 TAAACCCC
*
318882 TAAACTCC
1 TAAACCCC
*
318890 TAAA-CCT
1 TAAACCCC
318897 TAAACCCC
1 TAAACCCC
*
318905 --AACCCT
1 TAAACCCC
318911 TAAACC
1 TAAACC
318917 GTAAACCGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.12
7 16 0.40
8 19 0.47
ACGTcount: A:0.39, C:0.44, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAACCCC
Found at i:318884 original size:15 final size:15
Alignment explanation
Indices: 318864--318916 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
318854 AAAACATAAA
318864 CCCTAAACCCCTAAC
1 CCCTAAACCCCTAAC
* *
318879 CCCTAAACTCCTAAA
1 CCCTAAACCCCTAAC
*
318894 CCTTAAACCCC-AAC
1 CCCTAAACCCCTAAC
*
318908 CCTTAAACC
1 CCCTAAACC
318917 GTAAACCGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 11 0.33
15 22 0.67
ACGTcount: A:0.36, C:0.47, G:0.00, T:0.17
Consensus pattern (15 bp):
CCCTAAACCCCTAAC
Found at i:319474 original size:22 final size:21
Alignment explanation
Indices: 319429--319482 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
319419 TACCTTTATT
* *
319429 TTTAATTAAAAATAAATTAAAA
1 TTTAATT-AATATAAATAAAAA
319451 TTTAATTAATATAAATAAACAA
1 TTTAATTAATATAAATAAA-AA
*
319473 -TTAAATAATA
1 TTTAATTAATA
319483 AATAGTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAATTAATATAAATAAAAA
Found at i:319578 original size:41 final size:40
Alignment explanation
Indices: 319501--319690 Score: 247
Period size: 41 Copynumber: 4.7 Consensus size: 40
319491 ATAAAATGTT
* * **
319501 TTTTGAAAAACGCCTCTAAAG-GTCGAGCATTAGCGGCGC
1 TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
*
319540 TTTTACAAAAACGCCGCTAAATCCCCGAGCATTAGCGGCGC
1 TTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
* *
319581 TTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGTGGTGC
1 -TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
* *
319622 TTTTCCAAAAACGCCGCTAAAGCCCCGATCATTAGCGGTGC
1 TTTT-CAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
*
319663 TTTGTCAAAAACGTCGCTAAAGCCCCGA
1 TTT-TCAAAAACGCCGCTAAAGCCCCGA
319691 AAGCTAAGAA
Statistics
Matches: 135, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.03
40 18 0.13
41 108 0.80
42 5 0.04
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (40 bp):
TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTAGCGGCGC
Found at i:319850 original size:40 final size:40
Alignment explanation
Indices: 319758--319891 Score: 146
Period size: 40 Copynumber: 3.4 Consensus size: 40
319748 AAAATGAGCA
* * * *
319758 TTAGCGGCATTTTTGAAATAGCGTCGCTATTGCTTGATCT
1 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
319798 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
1 TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
* * * * *
319838 TTAGCGGTG-TTTTCTAAAAAGTGCCGCTAATT-CTCTATTT
1 TTAGCGGCGTTTTTC-AAATAGCGCCGCT-ATTGCTCGATCT
*
319878 TTAGCGACGTTTTT
1 TTAGCGGCGTTTTT
319892 GATCCAAACG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
39 5 0.06
40 68 0.85
41 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TTAGCGGCGTTTTTCAAATAGCGCCGCTATTGCTCGATCT
Found at i:320407 original size:32 final size:30
Alignment explanation
Indices: 320330--320408 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 30
320320 GAAATATGGG
* **
320330 TTTGGGATTTTTTTAATTTTAAAATACTTT
1 TTTGGTATTTTTTTAATTTTAAAATAAATT
** *
320360 TTTAATTTTTGTTTTAATTTTTAAAATAAATT
1 TTTGGTATTT-TTTTAA-TTTTAAAATAAATT
320392 TTTGGTATTTATTTTAA
1 TTTGGTATTT-TTTTAA
320409 AAAATGGGCC
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
30 6 0.16
31 6 0.16
32 25 0.68
ACGTcount: A:0.29, C:0.01, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTGGTATTTTTTTAATTTTAAAATAAATT
Found at i:329926 original size:27 final size:27
Alignment explanation
Indices: 329864--329926 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
329854 ACATTGTGCG
* *
329864 TCACATGGGCCGTATGTTCAACATTCA
1 TCACATGGGCCGCATATTCAACATTCA
329891 TCA-AGTGGGCCGCATATTCAACA-TCTA
1 TCACA-TGGGCCGCATATTCAACATTC-A
329918 TCACATGGG
1 TCACATGGG
329927 TCCAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.10
27 27 0.87
28 1 0.03
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (27 bp):
TCACATGGGCCGCATATTCAACATTCA
Found at i:351131 original size:24 final size:24
Alignment explanation
Indices: 351103--351154 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
351093 TTAGTAAGTC
* *
351103 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
351127 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
351151 AAAT
1 AAAT
351155 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.