Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold235
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: 1667838
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 72548 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:818025 original size:51 final size:50
Alignment explanation
Indices: 817906--818090 Score: 158
Period size: 51 Copynumber: 3.7 Consensus size: 50
817896 AAAATGATGG
* * * ** * *
817906 TCACCTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATATG-
1 TCACATGTGTAGTACTATGTTCAGGCTACTATGCATACCGGATAG-TATGA
* *
817956 TCGCATGTGTATTACTATGTTCAGGCTACTATGCATACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTTCAGGCTACTATGCATACCGGATAG-TAT-GA
* * * ** * *
818007 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTTCAGGCTACTATGCATACCGGATAGT-ATGA
* *
818058 TCACATGTGTAGTACTATGTTTAGGCTAATATG
1 TCACATGTGTAGTACTATGTTCAGGCTACTATG
818091 TGAACCGGTA
Statistics
Matches: 107, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 39 0.36
51 66 0.62
52 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTTCAGGCTACTATGCATACCGGATAGTATGA
Found at i:818362 original size:37 final size:38
Alignment explanation
Indices: 818293--818365 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
818283 ATGTGTGGAA
* * **
818293 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
*
818331 TTGAATTAAATAGTGA-TTGAAATTGAAAAAGTGAA
1 TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAA
818366 ATTATGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 16 0.53
38 14 0.47
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (38 bp):
TTGAATTAAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:823134 original size:42 final size:43
Alignment explanation
Indices: 823025--823151 Score: 152
Period size: 44 Copynumber: 3.0 Consensus size: 43
823015 TCTGATATCT
* *
823025 GATTTCGTGTAAGACCAC-GTCTGGGACATTGGAATCAATTTGA
1 GATTTCGTGTAAGACC-CTGTCTGGGACATTGGCATCAATATGA
* *
823068 GATTTACATGTAAGACCATGTCTGGGACATTGGCATCATATAT-A
1 GATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATCA-ATATGA
* *
823112 -ATTTCGTGTAAGACCCTATCTGGGACAGTGGCATCAATAT
1 GATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCAATAT
823152 TTGATAACAT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.05
42 28 0.38
43 9 0.12
44 29 0.40
45 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
GATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCAATATGA
Found at i:834284 original size:6 final size:6
Alignment explanation
Indices: 834273--834333 Score: 68
Period size: 6 Copynumber: 9.7 Consensus size: 6
834263 ATAAGTCTAA
* * *
834273 AAAAAT AAAAAT AAAGCAACT ACAAAC AAAAAT AAAGAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAA--AA-T AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
834324 AAAAAT AAAA
1 AAAAAT AAAA
834334 GAAATAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
6 39 0.85
7 2 0.04
8 2 0.04
9 3 0.07
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:834396 original size:13 final size:12
Alignment explanation
Indices: 834368--834410 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
834358 AAATTAAATG
* *
834368 TAATTGTAAGAA
1 TAATAGTAAAAA
834380 TAATAGTAAAAAA
1 TAATAGT-AAAAA
*
834393 TAATACTAAAAA
1 TAATAGTAAAAA
834405 TAATAG
1 TAATAG
834411 AAATAACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.28
Consensus pattern (12 bp):
TAATAGTAAAAA
Found at i:836588 original size:23 final size:23
Alignment explanation
Indices: 836561--836607 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
836551 ACTAGAGGAA
836561 AGCAAAACAA-CAAGATTAAGATC
1 AGCAAAA-AATCAAGATTAAGATC
836584 AGCAAAAAATCAAGATTAAGATC
1 AGCAAAAAATCAAGATTAAGATC
836607 A
1 A
836608 ATGAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.57, C:0.15, G:0.13, T:0.15
Consensus pattern (23 bp):
AGCAAAAAATCAAGATTAAGATC
Found at i:838036 original size:339 final size:340
Alignment explanation
Indices: 837299--838315 Score: 1910
Period size: 339 Copynumber: 3.0 Consensus size: 340
837289 GCCTTGACTA
* *
837299 TTTAATGTTTAGGGTTATTTTCATTCCAATTATCAGCTTCTCAACTATTTGCTTTTAGTACACTG
1 TTTAATGTTTAGGGTTATTTTCATTCCAATTATCAGCATCTCAACTATTTGCTTTTAGTAAACTG
837364 GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
66 GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
*
837429 TATTTATAACTCGATTAAGTTTCAATTCAAGCATGGATACACTTTTCACTTTCATGATTCAGTTA
131 TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
*
837494 AAAAGTTTTCATGCAACGTAAAAAAAGAATATATCATAGTGGCATATGCTCTCTCTTCTTACAAG
196 AAAAGTTTTCATGCAACGTAAAAAAAGAATATATCATAGTGGGATATGCTCTCTCTTCTTACAAG
*
837559 ACTCCATGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGATC
261 ACTCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGATC
*
837624 GACAATGATTTACTG
326 GACAATGATTTAATG
* *
837639 TTTAATGTTTAGGGTTATTTTCATTCCAATTACCAGCATCTCAACTATTTTCTTTTAGTAAACTG
1 TTTAATGTTTAGGGTTATTTTCATTCCAATTATCAGCATCTCAACTATTTGCTTTTAGTAAACTG
837704 GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
66 GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
837769 TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
131 TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
*
837834 AAAAGTTTTCATGCAACGTAAAAAAA-AAAATATCATAGTGGGATATGCTCTCTCTTCTTACAAG
196 AAAAGTTTTCATGCAACGTAAAAAAAGAATATATCATAGTGGGATATGCTCTCTCTTCTTACAAG
837898 ACTCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGATC
261 ACTCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGATC
837963 GACAATGATTTAATG
326 GACAATGATTTAATG
*
837978 TTTAATGTTTAGGTTTATTTTCATTCCAATTATCAGCATCTCAACTATTTGCTTTTAGTAAACTG
1 TTTAATGTTTAGGGTTATTTTCATTCCAATTATCAGCATCTCAACTATTTGCTTTTAGTAAACTG
*
838043 GTGATTAATAAAATTGTTGCATCCTGTTTTACTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
66 GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
838108 TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
131 TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
838173 AAAAGTTTTCATGCAACGTAAAAAGAAGAATATATCATAGTGGGATATGCTCTCTCTTCTTACAA
196 AAAAGTTTTCATGCAACGTAAAAA-AAGAATATATCATAGTGGGATATGCTCTCTCTTCTTACAA
*
838238 GACCCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGAT
260 GACTCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGAT
838303 CGACAATGATTTA
325 CGACAATGATTTA
838316 CTGTATAAGT
Statistics
Matches: 660, Mismatches: 15, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
339 329 0.50
340 218 0.33
341 113 0.17
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (340 bp):
TTTAATGTTTAGGGTTATTTTCATTCCAATTATCAGCATCTCAACTATTTGCTTTTAGTAAACTG
GTGATTAATAAAATTGTTGCATCCTGTTTTTCTAACCTTTAAGCTCAAGGCTGTGAATTTTCTTA
TATTTATAACTCGATTAAGTTTCAATTCATGCATGGATACACTTTTCACTTTCATGATTCAGTTA
AAAAGTTTTCATGCAACGTAAAAAAAGAATATATCATAGTGGGATATGCTCTCTCTTCTTACAAG
ACTCCACGTCAAGTTTTGCAACCAAATGATATAAAATTAATAGAAATTTCTTGGAAAGATTGATC
GACAATGATTTAATG
Found at i:842354 original size:89 final size:89
Alignment explanation
Indices: 842203--842382 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
842193 TTGTCTGCTT
842203 TTGGCTTGTTTTTCACTCCTGTCACTCCCAAATGTTCTCCTAAGTATATAAACATGAATTTAAAG
1 TTGGCTTGTTTTTCACTCCTGTCACTCCCAAATGTTCTCCTAAGTATATAAACATGAATTTAAAG
842268 CATTAGAAGCATCAAATTCACTAA
66 CATTAGAAGCATCAAATTCACTAA
*
842292 TTGGCTTGTTTTTCACTCCTTTCACTCCCAAATGTTCTCCTAAGTATATAAACATGAATTTAAAG
1 TTGGCTTGTTTTTCACTCCTGTCACTCCCAAATGTTCTCCTAAGTATATAAACATGAATTTAAAG
842357 CATTAGAAGCATCAAATTCACTAA
66 CATTAGAAGCATCAAATTCACTAA
842381 TT
1 TT
842383 TACATAATTA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (89 bp):
TTGGCTTGTTTTTCACTCCTGTCACTCCCAAATGTTCTCCTAAGTATATAAACATGAATTTAAAG
CATTAGAAGCATCAAATTCACTAA
Found at i:843990 original size:6 final size:6
Alignment explanation
Indices: 843982--844042 Score: 83
Period size: 6 Copynumber: 10.5 Consensus size: 6
843972 AACTAAAACA
*
843982 AAAATA AAAAT- AAAGAT- AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAA-ATG AAAATG AAAATG AAAATG AAAATG AAAATG
844029 AAAATG AAAA-G AAA
1 AAAATG AAAATG AAA
844043 TAAAATCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
5 9 0.17
6 44 0.83
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:844093 original size:12 final size:12
Alignment explanation
Indices: 844076--844119 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
844066 AAATTAAAGG
*
844076 TAATAGTAAGAA
1 TAATAGTAAAAA
844088 TAATAGTAAAAAAA
1 TAATAGT--AAAAA
*
844102 TAATACTAAAAA
1 TAATAGTAAAAA
844114 TAATAG
1 TAATAG
844120 AAATAGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 17 0.63
14 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (12 bp):
TAATAGTAAAAA
Found at i:844105 original size:14 final size:15
Alignment explanation
Indices: 844086--844118 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
844076 TAATAGTAAG
*
844086 AATAATAGTAAAAA-
1 AATAATACTAAAAAT
844100 AATAATACTAAAAAT
1 AATAATACTAAAAAT
844115 AATA
1 AATA
844119 GAAATAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACTAAAAAT
Found at i:844229 original size:15 final size:15
Alignment explanation
Indices: 844209--844257 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 15
844199 ATCAGTAAAA
844209 ATAAAAATAAATAAT
1 ATAAAAATAAATAAT
844224 ATAAAAAT-AATAAT
1 ATAAAAATAAATAAT
* *
844238 A-ATAAAGAAATAA-
1 ATAAAAATAAATAAT
844251 ATAAAAA
1 ATAAAAA
844258 AGAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.17
14 16 0.55
15 8 0.28
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAATAAT
Found at i:844235 original size:14 final size:14
Alignment explanation
Indices: 844209--844257 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
844199 ATCAGTAAAA
844209 ATAAAAATAAATAAT
1 ATAAAAAT-AATAAT
844224 ATAAAAATAATAAT
1 ATAAAAATAATAAT
*
844238 AATAAAGA-AATAA-
1 -ATAAAAATAATAAT
844251 ATAAAAA
1 ATAAAAA
844258 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 6 0.19
14 11 0.35
15 14 0.45
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
ATAAAAATAATAAT
Found at i:844240 original size:17 final size:16
Alignment explanation
Indices: 844209--844251 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
844199 ATCAGTAAAA
844209 ATAAAAAT-AAATAAT
1 ATAAAAATAAAATAAT
844224 ATAAAAATAATAATAAT
1 ATAAAAATAA-AATAAT
844241 A-AAGAAATAAA
1 ATAA-AAATAAA
844252 TAAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.32
16 4 0.16
17 13 0.52
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAAAAATAAAATAAT
Found at i:846848 original size:21 final size:23
Alignment explanation
Indices: 846811--846858 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
846801 TAAAAATCTT
846811 TTAATTTTATATGTTTTAT-AAG
1 TTAATTTTATATGTTTTATAAAG
846833 TTAA-TTTATTAT-TTTTATAAAG
1 TTAATTTTA-TATGTTTTATAAAG
846855 TTAA
1 TTAA
846859 AAGGTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TTAATTTTATATGTTTTATAAAG
Found at i:849753 original size:22 final size:22
Alignment explanation
Indices: 849701--849774 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
849691 CAGCAAAAAT
* *
849701 GCCAGTAACCAGAATGGCTA-AGA
1 GCCA-TAAACAGAATAGCTATA-A
* * *
849724 GCCGTAAATAGGATAGCTATAA
1 GCCATAAACAGAATAGCTATAA
* *
849746 GCTATAAACAGAATGGCTATAA
1 GCCATAAACAGAATAGCTATAA
849768 GCCATAA
1 GCCATAA
849775 GTACAGTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (22 bp):
GCCATAAACAGAATAGCTATAA
Found at i:849821 original size:32 final size:32
Alignment explanation
Indices: 849766--849965 Score: 190
Period size: 32 Copynumber: 6.3 Consensus size: 32
849756 GAATGGCTAT
* * * * *
849766 AAGCCATAAGT-ACAGTAAAATGATTGCCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
849797 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
849829 CAA-CCATCAATAATAGTAGTATGATCAGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
849861 AAGCAATTAGTAGTAGTAATATGATCAGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
849893 CAA-CCATCAGTAATGGTAATATGATCGGCACA
1 -AAGCCATCAGTAATAGTAATATGATCGGCACA
* * * *
849925 CAGCCACCAATAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
*
849957 AATCCATCA
1 AAGCCATCA
849966 ATAGCATCGC
Statistics
Matches: 138, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
31 13 0.09
32 121 0.88
33 4 0.03
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:849886 original size:64 final size:64
Alignment explanation
Indices: 849793--849968 Score: 228
Period size: 64 Copynumber: 2.8 Consensus size: 64
849783 AAATGATTGC
*
849793 CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAGTAGTATGATCAG
1 CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAGTAATATGATCAG
* * * * * *
849857 CACAAAGCAATTAGTAGTAGTAATATGATCAGCACACAACCATCAGTAATGGTAATATGATCGG
1 CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAGTAATATGATCAG
* * * * *
849921 CACACAGCCACCAATAATGGTAATATGATCGGCACA-AATCCATCAATA
1 CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAA-CCATCAATA
849969 GCATCGCAGC
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 2 0.02
64 93 0.98
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (64 bp):
CACAAAGCCATCAGTAGTAGTAATATGATCGGCACACAACCATCAATAATAGTAATATGATCAG
Found at i:850198 original size:24 final size:24
Alignment explanation
Indices: 850139--850249 Score: 107
Period size: 24 Copynumber: 4.6 Consensus size: 24
850129 GCCCTACACG
** *
850139 AAATCAGTCATACAAATCAAAGAC
1 AAATCAGTCATTTAAATCACAGAC
850163 AAATCAGTCATTTAAATCACAGAC
1 AAATCAGTCATTTAAATCACAGAC
* *
850187 AAATCAGTCATTTACATCTC-GAAC
1 AAATCAGTCATTTAAATCACAG-AC
* * * *
850211 AAATCATTCATTTACATCATAGGC
1 AAATCAGTCATTTAAATCACAGAC
* *
850235 AAAACAATCATTTAA
1 AAATCAGTCATTTAA
850250 CCTCGAGGGC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 71 0.97
25 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATCAGTCATTTAAATCACAGAC
Found at i:853474 original size:11 final size:11
Alignment explanation
Indices: 853458--853482 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
853448 ACATTCTGGA
853458 TGTATCGCATT
1 TGTATCGCATT
853469 TGTATCGCATT
1 TGTATCGCATT
853480 TGT
1 TGT
853483 TCGTTTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (11 bp):
TGTATCGCATT
Found at i:858902 original size:17 final size:18
Alignment explanation
Indices: 858880--858913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
858870 TGAAATATCA
858880 TTAAAAA-AATGTAAATT
1 TTAAAAATAATGTAAATT
*
858897 TTAAAAATAATTTAAAT
1 TTAAAAATAATGTAAAT
858914 GTTTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAAAATAATGTAAATT
Found at i:861547 original size:7 final size:7
Alignment explanation
Indices: 861506--861530 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
861496 TTGAGTAACT
861506 ATTTTCA
1 ATTTTCA
861513 ATTTTCA
1 ATTTTCA
861520 ATTTTCA
1 ATTTTCA
861527 ATTT
1 ATTT
861531 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTCA
Found at i:865961 original size:28 final size:28
Alignment explanation
Indices: 865930--866000 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
865920 GACTTATCCT
*
865930 AATACAGTATCAATGTGGGCTTTAGCCC
1 AATACAGTATCAATGTGGGCCTTAGCCC
* *
865958 AATACAGAATCAGTGTGGGCCTTAGCCC
1 AATACAGTATCAATGTGGGCCTTAGCCC
* *
865986 GATACAGTAACAATG
1 AATACAGTATCAATG
866001 CAGTGCAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (28 bp):
AATACAGTATCAATGTGGGCCTTAGCCC
Found at i:866135 original size:26 final size:26
Alignment explanation
Indices: 866119--866183 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
866109 GCAAAGTTGT
866119 CAGTAATAGTATAGTAGTAAAGCTGC
1 CAGTAATAGTATAGTAGTAAAGCTGC
* *
866145 CAGTAATAGTATCGCAGTAAAGCTGC
1 CAGTAATAGTATAGTAGTAAAGCTGC
866171 CAGTAATAGTATA
1 CAGTAATAGTATA
866184 TGTGGGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (26 bp):
CAGTAATAGTATAGTAGTAAAGCTGC
Found at i:866466 original size:27 final size:27
Alignment explanation
Indices: 866405--866468 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
866395 TCATCTCCGA
**
866405 AGGGTATAACAGTCATTTTACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATG
*
866432 AGGGTATTTCAGTTATTTTACCCTATG
1 AGGGTATTTCAGTCATTTTACCCTATG
*
866459 GGGGTATTTC
1 AGGGTATTTC
866469 GATCATTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTTTACCCTATG
Found at i:866481 original size:27 final size:27
Alignment explanation
Indices: 866405--866484 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 27
866395 TCATCTCCGA
** **
866405 AGGGTATAACAGTCATTTTACCCTATG
1 AGGGTATTTCAGTCATTCGACCCTATG
* **
866432 AGGGTATTTCAGTTATTTTACCCTATG
1 AGGGTATTTCAGTCATTCGACCCTATG
*
866459 GGGGTATTTC-GATCATTCGACCCTAT
1 AGGGTATTTCAG-TCATTCGACCCTAT
866485 TTTTGGGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTCGACCCTATG
Found at i:885100 original size:6 final size:6
Alignment explanation
Indices: 885089--885113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
885079 GAAACGATGT
885089 AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA A
885114 TGGTTTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:886292 original size:30 final size:30
Alignment explanation
Indices: 886230--886293 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
886220 CCTACAAGGG
* * **
886230 ACACGGTTATGTCGCATGGCTATGTGTTAC
1 ACACGGCTATGTCGCATGGCCATGTGCCAC
* *
886260 ACACGGCTATGTCGCGTGGCCGTGTGCCAC
1 ACACGGCTATGTCGCATGGCCATGTGCCAC
886290 ACAC
1 ACAC
886294 AATTGAGACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (30 bp):
ACACGGCTATGTCGCATGGCCATGTGCCAC
Found at i:887307 original size:19 final size:19
Alignment explanation
Indices: 887283--887322 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
887273 TTTTCTTAAA
887283 ACGATAAACCATTTCCTTT
1 ACGATAAACCATTTCCTTT
887302 ACGATAAACCATTTCCTTT
1 ACGATAAACCATTTCCTTT
887321 AC
1 AC
887323 TTACTTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.35
Consensus pattern (19 bp):
ACGATAAACCATTTCCTTT
Found at i:888059 original size:20 final size:20
Alignment explanation
Indices: 888034--888091 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
888024 GATGCATAAT
888034 AGGAGCACCAAAGTGCAATC
1 AGGAGCACCAAAGTGCAATC
* *
888054 AGGAGCACGAATA-TGCGATC
1 AGGAGCACCAA-AGTGCAATC
* *
888074 AGGGGCACTAAAGTGCAA
1 AGGAGCACCAAAGTGCAA
888092 ACAGAGGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (20 bp):
AGGAGCACCAAAGTGCAATC
Found at i:890825 original size:26 final size:29
Alignment explanation
Indices: 890772--890852 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
890762 AGTCAAAACT
890772 ATCCCTTTTCA-TATTTCGATGGTCGT-C
1 ATCCCTTTTCATTATTTCGATGGTCGTCC
890799 ATCCCTTTTCATTA-TT-GATGGTCGTCACC
1 ATCCCTTTTCATTATTTCGATGGTCGT--CC
* *
890828 ATCCCTTTTCATAATTT-TATGGTCG
1 ATCCCTTTTCATTATTTCGATGGTCG
890853 AAGCTATCCC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
26 9 0.19
27 13 0.28
28 2 0.04
29 14 0.30
30 9 0.19
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (29 bp):
ATCCCTTTTCATTATTTCGATGGTCGTCC
Found at i:890857 original size:116 final size:117
Alignment explanation
Indices: 890627--890899 Score: 379
Period size: 116 Copynumber: 2.3 Consensus size: 117
890617 GTGACCATCT
*
890627 TTTTCCATAATTCGATAGTCGAAGCTATCCCTTTTCATATTTTGATGGTCGTCACCATCCCTTTT
1 TTTT-CATAATTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCGT--CCATCCCTTTT
*
890692 CATAGTTGATGCTCATCACCATTCCTTTTCATAATTTGATAGCCAAAGCTATCCC
63 CATAGTTGATGCTCATCACCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCC
* * *
890747 TTTTCATAATTCAATAGTCAAAACTATCCCTTTTCATATTTCGATGGTCGT-CATCCCTTTTCAT
1 TTTTCATAATTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCCATCCCTTTTCA-
* * * * * *
890811 TA-TTGATGGTCGTCACCATCCCTTTTCATAATTTTATGGTCGAAGCTATCCC
65 TAGTTGATGCTCATCACCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCC
* *
890863 TTTTCATAACTCGATAGTCGAAGCTATTCCTTTTCAT
1 TTTTCATAATTCGATAGTCGAAGCTATCCCTTTTCAT
890900 TGGTTGATGA
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
116 87 0.64
117 2 0.01
119 43 0.32
120 4 0.03
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (117 bp):
TTTTCATAATTCGATAGTCGAAGCTATCCCTTTTCATATTTCGATGGTCGTCCATCCCTTTTCAT
AGTTGATGCTCATCACCATCCCTTTTCATAATTTGATAGCCAAAGCTATCCC
Found at i:890871 original size:30 final size:30
Alignment explanation
Indices: 890627--890899 Score: 188
Period size: 30 Copynumber: 9.2 Consensus size: 30
890617 GTGACCATCT
* *
890627 TTTTCCATAATTCGATAGTCGAAGCTATCCC
1 TTTT-CATAATTTGATGGTCGAAGCTATCCC
* * *
890658 TTTTCATATTTTGATGGTCGTCA-CCATCCC
1 TTTTCATAATTTGATGGTCG-AAGCTATCCC
* * * *
890688 TTTTCAT-AGTTGATGCTC-ATCA-CCATTCC
1 TTTTCATAATTTGATGGTCGA--AGCTATCCC
* * *
890717 TTTTCATAATTTGATAGCCAAAGCTATCCC
1 TTTTCATAATTTGATGGTCGAAGCTATCCC
** * * *
890747 TTTTCATAATTCAATAGTCAAAACTATCCC
1 TTTTCATAATTTGATGGTCGAAGCTATCCC
*
890777 TTTTCAT-ATTTCGATGGTCG--TC-ATCCC
1 TTTTCATAATTT-GATGGTCGAAGCTATCCC
* * *
890804 TTTTCATTA-TTGATGGTCGTCA-CCATCCC
1 TTTTCATAATTTGATGGTCG-AAGCTATCCC
*
890833 TTTTCATAATTTTATGGTCGAAGCTATCCC
1 TTTTCATAATTTGATGGTCGAAGCTATCCC
* * * *
890863 TTTTCATAACTCGATAGTCGAAGCTATTCC
1 TTTTCATAATTTGATGGTCGAAGCTATCCC
890893 TTTTCAT
1 TTTTCAT
890900 TGGTTGATGA
Statistics
Matches: 194, Mismatches: 34, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
26 8 0.04
27 14 0.07
28 3 0.02
29 40 0.21
30 123 0.63
31 6 0.03
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTTCATAATTTGATGGTCGAAGCTATCCC
Found at i:899091 original size:25 final size:25
Alignment explanation
Indices: 899062--899133 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 25
899052 TCCTGTACAT
*
899062 GTATGCTCACACGAGCTGTGAATC-
1 GTATGCTTACACGAGCTGTGAATCA
* *
899086 GATATGCTTACATGAGCTGTAAATCA
1 G-TATGCTTACACGAGCTGTGAATCA
899112 GTATGCTTACACGAGCTGTGAA
1 GTATGCTTACACGAGCTGTGAA
899134 AATGGGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (25 bp):
GTATGCTTACACGAGCTGTGAATCA
Found at i:912178 original size:12 final size:11
Alignment explanation
Indices: 912161--912201 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
912151 CTGTATATAA
* *
912161 TTTTTTTTCAA
1 TTTTTTTTGAT
912172 TTTTTTTTGATT
1 TTTTTTTTGA-T
912184 TTTTTTTTGAT
1 TTTTTTTTGAT
912195 TTTTTTT
1 TTTTTTT
912202 ATGAACCTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.10, C:0.02, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAT
Found at i:913611 original size:20 final size:19
Alignment explanation
Indices: 913547--913611 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
913537 TATAAACACA
913547 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGCTG
* *
913567 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAGCT-G
*
913588 -ATGAGGTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
913607 AATGA
1 AATGA
913612 ACTTGAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 5 0.14
20 30 0.83
21 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.29, T:0.25
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:922199 original size:20 final size:20
Alignment explanation
Indices: 922164--922212 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
922154 ATCATGGTCT
*
922164 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
922183 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
922203 TTGCTTACTT
1 TTGCTTACTT
922213 AAATAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:923381 original size:10 final size:11
Alignment explanation
Indices: 923358--923382 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
923348 CAAGGACTTC
923358 AAAAACATTAA
1 AAAAACATTAA
923369 AAAAACATTAA
1 AAAAACATTAA
923380 AAA
1 AAA
923383 CGAGGATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAACATTAA
Found at i:925012 original size:13 final size:13
Alignment explanation
Indices: 924994--925018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
924984 CCCAATGGGT
924994 AATTGAACTTTAA
1 AATTGAACTTTAA
925007 AATTGAACTTTA
1 AATTGAACTTTA
925019 GATCGAAAAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AATTGAACTTTAA
Found at i:930440 original size:19 final size:20
Alignment explanation
Indices: 930400--930444 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
930390 ATTAATATCC
930400 AAAT-AAGTAAAATAAAATA
1 AAATAAAGTAAAATAAAATA
930419 AAATAAAGT-AAA-AAAATAA
1 AAATAAAGTAAAATAAAAT-A
930438 AAATAAA
1 AAATAAA
930445 AATTGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (20 bp):
AAATAAAGTAAAATAAAATA
Found at i:935092 original size:11 final size:11
Alignment explanation
Indices: 935076--935108 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
935066 GGATCATACT
935076 CATAATAAATA
1 CATAATAAATA
*
935087 CATAATTAATA
1 CATAATAAATA
935098 CATAA-AAATA
1 CATAATAAATA
935108 C
1 C
935109 GTTATTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (11 bp):
CATAATAAATA
Found at i:939104 original size:64 final size:64
Alignment explanation
Indices: 939018--939138 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
939008 ACATGGGCGA
*
939018 TCCACACGGCCGTGTGAAATTGGGAATTAGGCTTTTTGGGTGATTTTTGGTGCCACATAGATGG
1 TCCACACGGCCATGTGAAATTGGGAATTAGGCTTTTTGGGTGATTTTTGGTGCCACATAGATGG
* *
939082 TCCACACGGTCATGTGAAATTGGGAATTAGGCTTTTTTGGTGATTTTTGGTGCCACA
1 TCCACACGGCCATGTGAAATTGGGAATTAGGCTTTTTGGGTGATTTTTGGTGCCACA
939139 CAGCCATGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.35
Consensus pattern (64 bp):
TCCACACGGCCATGTGAAATTGGGAATTAGGCTTTTTGGGTGATTTTTGGTGCCACATAGATGG
Found at i:939419 original size:21 final size:21
Alignment explanation
Indices: 939365--939421 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
939355 CATGGGTTTC
*
939365 TCACATGGAAGTGTGTGGCCT
1 TCACATGGACGTGTGTGGCCT
* *
939386 CCACACAGG-CGTGTGTGGCCT
1 TCACA-TGGACGTGTGTGGCCT
939407 TCACATGGACGTGTG
1 TCACATGGACGTGTG
939422 GACCCCCACA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
TCACATGGACGTGTGTGGCCT
Found at i:953402 original size:21 final size:21
Alignment explanation
Indices: 953361--953407 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
953351 GACTGAGCCC
* *
953361 TAAATCGGGAAAATGAGTCAA
1 TAAAACGGGAAAATGACTCAA
*
953382 TAAAACGGGAAAATGTCTCAA
1 TAAAACGGGAAAATGACTCAA
*
953403 CAAAA
1 TAAAA
953408 AAATGAGTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (21 bp):
TAAAACGGGAAAATGACTCAA
Found at i:954251 original size:6 final size:6
Alignment explanation
Indices: 954242--954311 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
954232 TAAGTCTAAG
*
954242 AAAATA AAAATAA AACAACTA AAAACA AAACATA AAAATAAA AAAATA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAA-ATA AAAAT--A AAAATA
* * *
954290 AAACTA AAACTA AAAAGA AAAA
1 AAAATA AAAATA AAAATA AAAA
954312 CAAATAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 31 0.58
7 10 0.19
8 11 0.21
9 1 0.02
ACGTcount: A:0.79, C:0.09, G:0.01, T:0.11
Consensus pattern (6 bp):
AAAATA
Found at i:954278 original size:28 final size:29
Alignment explanation
Indices: 954245--954320 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
954235 GTCTAAGAAA
*
954245 ATAAAAATAAAACAACTAAAAAC-AAAAC
1 ATAAAAATAAAACAAATAAAAACTAAAAC
954273 ATAAAAATAAAA-AAAT-AAAACTAAAAC
1 ATAAAAATAAAACAAATAAAAACTAAAAC
*
954300 -TAAAAAGAAAAACAAATAAAA
1 ATAAAAA-TAAAACAAATAAAA
954321 TCAATGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 11 0.26
27 12 0.29
28 16 0.38
29 3 0.07
ACGTcount: A:0.78, C:0.09, G:0.01, T:0.12
Consensus pattern (29 bp):
ATAAAAATAAAACAAATAAAAACTAAAAC
Found at i:954285 original size:20 final size:20
Alignment explanation
Indices: 954262--954305 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
954252 TAAAACAACT
954262 AAAAACAAAACATAAAAATAA
1 AAAAACAAAAC-TAAAAATAA
* *
954283 AAAAATAAAACTAAAACTAA
1 AAAAACAAAACTAAAAATAA
954303 AAA
1 AAA
954306 GAAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAACAAAACTAAAAATAA
Found at i:954321 original size:33 final size:33
Alignment explanation
Indices: 954258--954321 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 33
954248 AAAATAAAAC
* *
954258 AACTAAAAACAAAACATAAAAATAAAAAAATAA
1 AACTAAAAACAAAACAGAAAAACAAAAAAATAA
954291 AACT-AAAACTAAAA-AGAAAAACAAATAAAAT
1 AACTAAAAAC-AAAACAGAAAAACAAA-AAAAT
954322 CAATGATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (33 bp):
AACTAAAAACAAAACAGAAAAACAAAAAAATAA
Found at i:954335 original size:3 final size:3
Alignment explanation
Indices: 954314--954386 Score: 87
Period size: 3 Copynumber: 24.7 Consensus size: 3
954304 AAGAAAAACA
*
954314 AAT AA- AAT CAAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** *
954359 AAT AAT AAT AGC AA- AAC AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
954387 CATAGTGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:954576 original size:370 final size:372
Alignment explanation
Indices: 954012--954756 Score: 1458
Period size: 370 Copynumber: 2.0 Consensus size: 372
954002 ACAAACAAAT
954012 ATAATCATAGTGTAAGCAGAATATCATAAGAGATGGAGAAAACTGAAACTGCCCTGAATATCGGA
1 ATAATCATAGTGTAAGCAGAATATCATAAGAGATGGAGAAAACTGAAACTGCCCTGAATATCGGA
954077 TGAAATTGCCGGAATAGTGAAAAACGTAATTGTAGGCAAATCTAAATGTAGTGCATGATTCTGAG
66 TGAAATTGCCGGAATAGTGAAAAACGTAATTGTAGGCAAATCTAAATGTAGTGCATGATTCTGAG
954142 CACACTAATAAGAAAATAAATACAAATAAGAAAGGATATTAAGAAACTACCATAAAAATAAAAAT
131 CACACTAATAAGAAAATAAATACAAATAAGAAAGGATATTAAGAAACTACCATAAAAATAAAAAT
954207 ATAGTTCAAAAGATAATAAATGAAATAAGTCTAAGAAAATAAAAATAAAACAACTAAAAACAAAA
196 ATAGTTCAAAAGATAATAAATGAAATAAGTCTAAGAAAATAAAAATAAAACAACTAAAAACAAAA
954272 CATAAAAATAAAAAAATAAAACTAAAACTAAAAAGAAAAACAAATAAAATCAATGATAATAATAA
261 CATAAAAATAAAAAAATAAAACTAAAACTAAAAAGAAAAACAAATAAAATCAATGATAATAATAA
*
954337 TAATAATAATAATAATAATAATAATAATAATAGCAAAAC-AATAATA
326 TAATAATAATAATAATAATAATAATAATAACAGCAAAACAAATAATA
954383 ATAA-CATAGTGTAAGCAGAATATCATAAGAGATGGAGAAAACTGAAACTGCCCTGAATATCGGA
1 ATAATCATAGTGTAAGCAGAATATCATAAGAGATGGAGAAAACTGAAACTGCCCTGAATATCGGA
954447 TGAAATTGCCGGAATAGTGAAAAACGTAATTGTAGGCAAATCTAAATGTAGTGCATGATTCTGAG
66 TGAAATTGCCGGAATAGTGAAAAACGTAATTGTAGGCAAATCTAAATGTAGTGCATGATTCTGAG
954512 CACACTAATAAGAAAATAAATACAAATAAGAAAGGATATTAAGAAACTACCATAAAAATAAAAAT
131 CACACTAATAAGAAAATAAATACAAATAAGAAAGGATATTAAGAAACTACCATAAAAATAAAAAT
954577 ATAGTTCAAAAGATAATAAATGAAATAAGTCTAAGAAAATAAAAATAAAACAACTAAAAACAAAA
196 ATAGTTCAAAAGATAATAAATGAAATAAGTCTAAGAAAATAAAAATAAAACAACTAAAAACAAAA
954642 CATAAAAATAAAAAAATAAAACTAAAACTAAAAAGAAAAACAAATAAAATCAATGATAATAATAA
261 CATAAAAATAAAAAAATAAAACTAAAACTAAAAAGAAAAACAAATAAAATCAATGATAATAATAA
*
954707 TAATAATAATAATAATAATAATAATAATAACAGTAAAACAAATAATA
326 TAATAATAATAATAATAATAATAATAATAACAGCAAAACAAATAATA
954754 ATA
1 ATA
954757 GTAATGAAAA
Statistics
Matches: 371, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
370 357 0.96
371 14 0.04
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (372 bp):
ATAATCATAGTGTAAGCAGAATATCATAAGAGATGGAGAAAACTGAAACTGCCCTGAATATCGGA
TGAAATTGCCGGAATAGTGAAAAACGTAATTGTAGGCAAATCTAAATGTAGTGCATGATTCTGAG
CACACTAATAAGAAAATAAATACAAATAAGAAAGGATATTAAGAAACTACCATAAAAATAAAAAT
ATAGTTCAAAAGATAATAAATGAAATAAGTCTAAGAAAATAAAAATAAAACAACTAAAAACAAAA
CATAAAAATAAAAAAATAAAACTAAAACTAAAAAGAAAAACAAATAAAATCAATGATAATAATAA
TAATAATAATAATAATAATAATAATAATAACAGCAAAACAAATAATA
Found at i:954621 original size:6 final size:6
Alignment explanation
Indices: 954612--954681 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
954602 TAAGTCTAAG
*
954612 AAAATA AAAATAA AACAACTA AAAACA AAACATA AAAATAAA AAAATA
1 AAAATA AAAAT-A AA-AA-TA AAAATA AAA-ATA AAAAT--A AAAATA
* * *
954660 AAACTA AAACTA AAAAGA AAAA
1 AAAATA AAAATA AAAATA AAAA
954682 CAAATAAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 31 0.58
7 10 0.19
8 11 0.21
9 1 0.02
ACGTcount: A:0.79, C:0.09, G:0.01, T:0.11
Consensus pattern (6 bp):
AAAATA
Found at i:954648 original size:28 final size:29
Alignment explanation
Indices: 954615--954690 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
954605 GTCTAAGAAA
*
954615 ATAAAAATAAAACAACTAAAAAC-AAAAC
1 ATAAAAATAAAACAAATAAAAACTAAAAC
954643 ATAAAAATAAAA-AAAT-AAAACTAAAAC
1 ATAAAAATAAAACAAATAAAAACTAAAAC
*
954670 -TAAAAAGAAAAACAAATAAAA
1 ATAAAAA-TAAAACAAATAAAA
954691 TCAATGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 11 0.26
27 12 0.29
28 16 0.38
29 3 0.07
ACGTcount: A:0.78, C:0.09, G:0.01, T:0.12
Consensus pattern (29 bp):
ATAAAAATAAAACAAATAAAAACTAAAAC
Found at i:954655 original size:20 final size:20
Alignment explanation
Indices: 954632--954675 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
954622 TAAAACAACT
954632 AAAAACAAAACATAAAAATAA
1 AAAAACAAAAC-TAAAAATAA
* *
954653 AAAAATAAAACTAAAACTAA
1 AAAAACAAAACTAAAAATAA
954673 AAA
1 AAA
954676 GAAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.80, C:0.09, G:0.00, T:0.11
Consensus pattern (20 bp):
AAAAACAAAACTAAAAATAA
Found at i:954691 original size:33 final size:33
Alignment explanation
Indices: 954628--954691 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 33
954618 AAAATAAAAC
* *
954628 AACTAAAAACAAAACATAAAAATAAAAAAATAA
1 AACTAAAAACAAAACAGAAAAACAAAAAAATAA
954661 AACT-AAAACTAAAA-AGAAAAACAAATAAAAT
1 AACTAAAAAC-AAAACAGAAAAACAAA-AAAAT
954692 CAATGATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.12
Consensus pattern (33 bp):
AACTAAAAACAAAACAGAAAAACAAAAAAATAA
Found at i:954705 original size:3 final size:3
Alignment explanation
Indices: 954684--954775 Score: 91
Period size: 3 Copynumber: 30.7 Consensus size: 3
954674 AAGAAAAACA
*
954684 AAT AA- AAT CAAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
954729 AAT AAT AAC AGT AA- AACA AAT AAT AAT AGT AAT GAA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT
954774 AA
1 AA
954776 AAATGACAAC
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.08
3 61 0.82
4 7 0.09
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:954780 original size:18 final size:18
Alignment explanation
Indices: 954746--954781 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
954736 ACAGTAAAAC
**
954746 AAATAATAATAGTAATGA
1 AAATAATAATAAAAATGA
954764 AAATAATAATAAAAATGA
1 AAATAATAATAAAAATGA
954782 CAACTAAAAA
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:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (18 bp):
AAATAATAATAAAAATGA
Found at i:954924 original size:5 final size:5
Alignment explanation
Indices: 954904--954940 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
954894 AACAGATCAG
954904 TAAAA TAAAA -ATAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA
954941 GACTAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:954924 original size:15 final size:15
Alignment explanation
Indices: 954863--954940 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 15
954853 CACTAAAAGT
954863 AAATAAATGAATAATAAA
1 AAATAAAT-AA-AAT-AA
954881 AAATAAATAAGAA-AA
1 AAATAAATAA-AATAA
* * *
954896 CAGATCAGTAAAATAA
1 -AAATAAATAAAATAA
954912 AAATAAATAAAAT-A
1 AAATAAATAAAATAA
954926 AAATAAAATAAAATA
1 AAAT-AAATAAAATA
954941 GACTAAAGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
14 5 0.10
15 23 0.47
16 9 0.18
17 4 0.08
18 8 0.16
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (15 bp):
AAATAAATAAAATAA
Found at i:968381 original size:23 final size:24
Alignment explanation
Indices: 968335--968382 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
968325 ATAAACTTAG
* *
968335 GACATATTTAAAAGGCTCAGATTAT
1 GACATATTT-AAAGACTCAAATTAT
968360 GACATATTT-AAGACTCAAATTAT
1 GACATATTTAAAGACTCAAATTAT
968383 TGATGTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
GACATATTTAAAGACTCAAATTAT
Found at i:971651 original size:20 final size:20
Alignment explanation
Indices: 971625--971723 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 20
971615 TTATGCATAA
*
971625 CAGAGGCACCAAAGTGTAGAT
1 CAGAGGCACCAAAGTGCA-AT
* *
971646 -AGAGGCACGAATGTGCAAT
1 CAGAGGCACCAAAGTGCAAT
* *
971665 CAGAGGCACCGAAGTGCAAA
1 CAGAGGCACCAAAGTGCAAT
** **
971685 CAGAGGCATGAATTTGCAAT
1 CAGAGGCACCAAAGTGCAAT
971705 CAGAGGCACCAAAGTGCAA
1 CAGAGGCACCAAAGTGCAA
971724 ACCCTATTGG
Statistics
Matches: 60, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
19 2 0.03
20 58 0.97
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.13
Consensus pattern (20 bp):
CAGAGGCACCAAAGTGCAAT
Found at i:971669 original size:40 final size:40
Alignment explanation
Indices: 971625--971725 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
971615 TTATGCATAA
* * *
971625 CAGAGGCACCAAAGTGTAGATAGAGGCACGAATGTGCAAT
1 CAGAGGCACCAAAGTGCAAACAGAGGCACGAATGTGCAAT
* * *
971665 CAGAGGCACCGAAGTGCAAACAGAGGCATGAATTTGCAAT
1 CAGAGGCACCAAAGTGCAAACAGAGGCACGAATGTGCAAT
971705 CAGAGGCACCAAAGTGCAAAC
1 CAGAGGCACCAAAGTGCAAAC
971726 CCTATTGGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.13
Consensus pattern (40 bp):
CAGAGGCACCAAAGTGCAAACAGAGGCACGAATGTGCAAT
Found at i:972398 original size:16 final size:15
Alignment explanation
Indices: 972362--972400 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
972352 AAAATATTTC
972362 TATTTAA-AATTTAA
1 TATTTAACAATTTAA
972376 TATTTTAACAATTTAA
1 TA-TTTAACAATTTAA
972392 TCATTTAAC
1 T-ATTTAAC
972401 TAAAGACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 5 0.23
16 14 0.64
17 1 0.05
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTAACAATTTAA
Found at i:986323 original size:26 final size:26
Alignment explanation
Indices: 986284--986402 Score: 130
Period size: 26 Copynumber: 4.5 Consensus size: 26
986274 CGATATCTGG
986284 ACCGAAATACCCCCGTAGGGTAGAAT
1 ACCGAAATACCCCCGTAGGGTAGAAT
*
986310 ACTGAAATACCCCCGTAGGGTAGAAT
1 ACCGAAATACCCCCGTAGGGTAGAAT
* * *
986336 ACCGAAATACCCCCATATGGTAAAAT
1 ACCGAAATACCCCCGTAGGGTAGAAT
* * * * *
986362 GATCGTAATACCCCTGTAAGGTAAAAT
1 -ACCGAAATACCCCCGTAGGGTAGAAT
*
986389 GACCGTAATACCCC
1 -ACCGAAATACCCC
986403 TGTAACATAA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 47 0.58
27 34 0.42
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (26 bp):
ACCGAAATACCCCCGTAGGGTAGAAT
Found at i:986371 original size:27 final size:27
Alignment explanation
Indices: 986283--986819 Score: 559
Period size: 27 Copynumber: 20.1 Consensus size: 27
986273 TCGATATCTG
* * *
986283 GACCGAAATACCCCCGTAGGGTAGAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * * *
986310 -ACTGAAATACCCCCGTAGGGTAGAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* ** *
986336 -ACCGAAATACCCCCATATGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* *
986362 GATCGTAATACCCCTGTAAGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
***
986389 GACCGTAATACCCCTGTAACATAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * * *
986416 GACCGTAATGCCTCTATAGGGTAAAAC
1 GACCGTAATACCCCTGTAGGGTAAAAT
* *
986443 GACTGTAATA-CCCTGTAAGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * *
986469 GATCGTAATGCCCCTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * *
986496 GACCGTAATGCGCCTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
986523 GACCGTAACACCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* *
986550 GACCGTAATACCCTTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* *
986577 GACCGTAATACCCTTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
986604 GACCGTAA-GCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
986630 GACTGTAATACCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * * *
986657 GATCGTAATGCCCCTATAAGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
*
986684 GACCGTAATGCCCCTGTAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* * *
986711 GACCGTAATGCCCTTATAGGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
** * *
986738 GTTCGTGATACCCCTGTAAGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
* *
986765 GACCGTAATGCCCCTGTAAGGTAAAAT
1 GACCGTAATACCCCTGTAGGGTAAAAT
986792 GACCG-AA-ACGCCCTGGT-GGGT-AAAT
1 GACCGTAATAC-CCCT-GTAGGGTAAAAT
986817 GAC
1 GAC
986820 TATTTTTCCC
Statistics
Matches: 437, Mismatches: 68, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
25 8 0.02
26 97 0.22
27 332 0.76
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (27 bp):
GACCGTAATACCCCTGTAGGGTAAAAT
Found at i:986475 original size:107 final size:106
Alignment explanation
Indices: 986283--986796 Score: 532
Period size: 107 Copynumber: 4.8 Consensus size: 106
986273 TCGATATCTG
* * * * * * * * * *
986283 GACCGAAATACCCCCGTAGGGTAGAAT-ACTGAAATACCCCCGTAGGGTAGAAT-ACCGAAATAC
1 GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATA-
* * * * *
986346 CCCCATATGGTAAAATGATCGTAATACCCCTGTAAGGTAAAAT
65 -CCCTTAAGGTAAAATGACCGTAATACCCCTATAGGGTAAAAT
* *** * * * *
986389 GACCGTAATACCCCTGTAACATAAAATGACCGTAATGCCTCTATAGGGTAAAACGACTGTAATAC
1 GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATAC
* *
986454 CCTGTAAGGTAAAATGATCGTAATGCCCCTATAGGGTAAAAT
66 CCT-TAAGGTAAAATGACCGTAATACCCCTATAGGGTAAAAT
* * * *
986496 GACCGTAATGCGCCTATAGGGTAAAATGACCGTAACACCCCTGTAGGGTAAAATGACCGTAATAC
1 GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATAC
*
986561 CCTTATAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAAT
66 CCTTA-A-GGTAAAATGACCGTAATACCCCTATAGGGTAAAAT
*
986604 GACCGTAA-GCCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGGGTAAAATGA-TCGTAATG
1 GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACT-GTAAT-
* * *
986667 CCCCTATAAGGTAAAATGACCGTAATGCCCCTGTAGGGTAAAAT
64 ACCCT-TAAGGTAAAATGACCGTAATACCCCTATAGGGTAAAAT
* * ** * * * *
986711 GACCGTAATGCCCTTATAGGGTAAAATGTTCGTGATACCCCTGTAAGGTAAAATGACCGTAATGC
1 GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAAT-A
986776 CCCTGTAAGGTAAAATGACCG
65 CCCT-TAAGGTAAAATGACCG
986797 AAACGCCCTG
Statistics
Matches: 344, Mismatches: 54, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
106 26 0.08
107 197 0.57
108 119 0.35
109 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (106 bp):
GACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATAC
CCTTAAGGTAAAATGACCGTAATACCCCTATAGGGTAAAAT
Found at i:986727 original size:161 final size:161
Alignment explanation
Indices: 986293--986794 Score: 616
Period size: 161 Copynumber: 3.1 Consensus size: 161
986283 GACCGAAATA
* * * * * * * * * *
986293 CCCCCGTAGGGTAGAAT-ACTGAAATACCCCCGTAGGGTAGAAT-ACCGAAATACCCCCATATGG
1 CCCCTGTAAGGTAAAATGACTGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAAGG
* * * * ***
986356 TAAAATGATCGTAATACCCCTGTAAGGTAAAATGACCGTAATACCCCTGTAACATAAAATGACCG
66 TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGACCG
* * * *
986421 TAAT-GCCTCTATAGGGTAAAACGACTGTAAT
131 TAATACCCT-TATAGGGTAAAATGACCGTAAG
* * * * *
986452 ACCCTGTAAGGTAAAATGA-TCGTAATGCCCCTATAGGGTAAAATGACCGTAATGCGCCTATAGG
1 CCCCTGTAAGGTAAAATGACT-GTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAAG
*
986516 GTAAAATGACCGTAACACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGACC
65 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGACC
986581 GTAATACCCTTATAGGGTAAAATGACCGTAAG
130 GTAATACCCTTATAGGGTAAAATGACCGTAAG
* *
986613 CCCCTGTAGGGTAAAATGACTGTAATACCCCTGTAGGGTAAAATGATCGTAATGCCCCTATAAGG
1 CCCCTGTAAGGTAAAATGACTGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAAGG
* * **
986678 TAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACCGTAATGCCCTTATAGGGTAAAATGTTCG
66 TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGACCG
* * * *
986743 TGATACCCCTGTAAGGTAAAATGACCGTAATG
131 TAATACCCTTATAGGGTAAAATGACCGTAA-G
986775 CCCCTGTAAGGTAAAATGAC
1 CCCCTGTAAGGTAAAATGAC
986795 CGAAACGCCC
Statistics
Matches: 294, Mismatches: 43, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
159 14 0.05
160 19 0.06
161 237 0.81
162 24 0.08
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (161 bp):
CCCCTGTAAGGTAAAATGACTGTAATACCCCTGTAGGGTAAAATGACCGTAATGCCCCTATAAGG
TAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCGTAATACCCTTATAGGGTAAAATGACCG
TAATACCCTTATAGGGTAAAATGACCGTAAG
Found at i:987003 original size:27 final size:27
Alignment explanation
Indices: 986961--987025 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
986951 ATGGAGGAAG
986961 TACT-TTACTGGTGGCTCT-GCCACA-A
1 TACTATTACTGGTGGCT-TGGCCACATA
986986 TCACTATTACTGGTGGCTTGGCCACATA
1 T-ACTATTACTGGTGGCTTGGCCACATA
987014 TACTATTACTGG
1 TACTATTACTGG
987026 CAGCCTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.11
27 29 0.81
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.34
Consensus pattern (27 bp):
TACTATTACTGGTGGCTTGGCCACATA
Found at i:987309 original size:32 final size:32
Alignment explanation
Indices: 987069--987335 Score: 218
Period size: 32 Copynumber: 8.4 Consensus size: 32
987059 GCTGCGATGC
* * *
987069 TACTGATGGCTTTGTGCCGATCGTAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * *
987101 TACTGATGGCTTTGTGCTGATCATAATACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* *
987133 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
** * *
987165 TACCAATGGCTGTGTACCGATCAT-TTAACTGT
1 TACTGATGGCTTTGTGCCGATCATATT-ACTGT
* ** **
987197 TACTAATGG-TTGTGTGCCGATCATACCACTAC
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
* * *
987229 TACTGATGGGTTTATGCCGATCATGTTACTGT
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
* * **
987261 TACTGATGG-TTGTGTGTCGATCATATCACTAC
1 TACTGATGGCTT-TGTGCCGATCATATTACTGT
* * * *
987293 TACTGATGGCTTTGTGTCAATCACATTACT-A
1 TACTGATGGCTTTGTGCCGATCATATTACTGT
*
987324 TACTTATGGCTT
1 TACTGATGGCTT
987336 GTAGTCATTC
Statistics
Matches: 194, Mismatches: 35, Indels: 13
0.80 0.14 0.05
Matches are distributed among these distances:
31 16 0.08
32 174 0.90
33 4 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTGT
Found at i:991648 original size:44 final size:44
Alignment explanation
Indices: 991586--991684 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
991576 TTTCGAAGGG
*
991586 TACAC-GGCTATTTGGCTTGGCCATGTGACCCAAGTCATTGAGT
1 TACACAGGCAATTTGGCTTGGCCATGTGACCCAAGTCATTGAGT
991629 TACACAGGCAATTTGGCTTGGCCATGTGACCCAAGTCATTGAGT
1 TACACAGGCAATTTGGCTTGGCCATGTGACCCAAGTCATTGAGT
*
991673 TACACAGACAAT
1 TACACAGGCAAT
991685 GACCTGTCTC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
43 5 0.09
44 48 0.91
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (44 bp):
TACACAGGCAATTTGGCTTGGCCATGTGACCCAAGTCATTGAGT
Found at i:997200 original size:27 final size:27
Alignment explanation
Indices: 997162--997216 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
997152 TGCACGTAAG
997162 TGATTTTGTAAGAATCTACATGTATCA
1 TGATTTTGTAAGAATCTACATGTATCA
997189 TGATTTTGTAAGAATCTACATGTATCA
1 TGATTTTGTAAGAATCTACATGTATCA
997216 T
1 T
997217 TTCTCGATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (27 bp):
TGATTTTGTAAGAATCTACATGTATCA
Found at i:1031083 original size:17 final size:18
Alignment explanation
Indices: 1031051--1031085 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1031041 GAAAACCAAA
*
1031051 AACTTTATGATATCATTG
1 AACTTAATGATATCATTG
1031069 AACTTAATG-TATCATTG
1 AACTTAATGATATCATTG
1031086 CCTTGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
AACTTAATGATATCATTG
Found at i:1031978 original size:9 final size:9
Alignment explanation
Indices: 1031964--1031989 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1031954 TTTTTATTAA
1031964 TATTTTATT
1 TATTTTATT
1031973 TATTTTATT
1 TATTTTATT
1031982 TATTTTAT
1 TATTTTAT
1031990 AATAGATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTTATT
Found at i:1032634 original size:17 final size:17
Alignment explanation
Indices: 1032612--1032648 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1032602 TCTATTTAGC
1032612 CAAGAGAGGTAAGTACT
1 CAAGAGAGGTAAGTACT
*
1032629 CAAGAGAGGTAAGTATT
1 CAAGAGAGGTAAGTACT
1032646 CAA
1 CAA
1032649 AAATGTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.27, T:0.19
Consensus pattern (17 bp):
CAAGAGAGGTAAGTACT
Found at i:1039059 original size:14 final size:14
Alignment explanation
Indices: 1039040--1039079 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1039030 TCAACACTCA
1039040 ATTTTTTAATATTT
1 ATTTTTTAATATTT
*
1039054 ATTTTTTAACATTT
1 ATTTTTTAATATTT
*
1039068 AGTTTTTCAATA
1 A-TTTTTTAATA
1039080 ATTACTGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (14 bp):
ATTTTTTAATATTT
Found at i:1039203 original size:22 final size:19
Alignment explanation
Indices: 1039170--1039209 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 19
1039160 AAAGCAAAGC
1039170 TGGGGAGTAATAATGAAATT
1 TGGGGAGTAATAA-GAAATT
1039190 TGGGGAGTGGAATAAGAAAT
1 TGGGGAGT--AATAAGAAAT
1039210 AAAGAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (19 bp):
TGGGGAGTAATAAGAAATT
Found at i:1048647 original size:27 final size:26
Alignment explanation
Indices: 1048578--1048649 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
1048568 TTTTTCACAC
*
1048578 TCAAGTCTTTGTTTCAAAATTATAAA
1 TCAAGTCTTTGTTTCAAAATCATAAA
1048604 TCCAAGT-TTTGGTTTCAAAATCATAACA
1 T-CAAGTCTTT-GTTTCAAAATCATAA-A
* *
1048632 TCAACTCTTTGATTCAAA
1 TCAAGTCTTTGTTTCAAA
1048650 TTGAACTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 30 0.77
28 5 0.13
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (26 bp):
TCAAGTCTTTGTTTCAAAATCATAAA
Found at i:1048941 original size:20 final size:20
Alignment explanation
Indices: 1048916--1048953 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1048906 AGTTTAAATT
*
1048916 TTTTTAACTCAATTGAAACA
1 TTTTTAAATCAATTGAAACA
1048936 TTTTTAAATCAATTGAAA
1 TTTTTAAATCAATTGAAA
1048954 AACTACTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTTAAATCAATTGAAACA
Found at i:1050099 original size:19 final size:18
Alignment explanation
Indices: 1050075--1050111 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1050065 TCATCCTAAG
*
1050075 TTTTATTTAGTAAATAAAT
1 TTTTATTTAATAAA-AAAT
1050094 TTTTATTTAATAAAAAAT
1 TTTTATTTAATAAAAAAT
1050112 CTTGCTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTTATTTAATAAAAAAT
Found at i:1051139 original size:14 final size:14
Alignment explanation
Indices: 1051120--1051169 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1051110 TTTTGGGTTT
1051120 GGGTTTGGGGTTCA
1 GGGTTTGGGGTTCA
*
1051134 GGGTTTGGGATTCA
1 GGGTTTGGGGTTCA
* *
1051148 AGG-TTGAAGGTT-A
1 GGGTTTG-GGGTTCA
1051161 GGGTTTGGG
1 GGGTTTGGG
1051170 TTAGAGTTCG
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
13 7 0.25
14 21 0.75
ACGTcount: A:0.14, C:0.04, G:0.48, T:0.34
Consensus pattern (14 bp):
GGGTTTGGGGTTCA
Found at i:1051173 original size:12 final size:12
Alignment explanation
Indices: 1051111--1051189 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
1051101 AATGTTCAAT
*
1051111 TTTGGGTTTGGG
1 TTTGGGTTAGGG
1051123 TTTGGGGTTCAGGG
1 TTT-GGGTT-AGGG
*
1051137 TTTGGGATTCAAGG
1 TTTGGG-TT-AGGG
1051151 -TTGAAGGTTAGGG
1 TTTG--GGTTAGGG
*
1051164 TTTGGGTTAGAG
1 TTTGGGTTAGGG
* *
1051176 TTCGGGTTCGGG
1 TTTGGGTTAGGG
1051188 TT
1 TT
1051190 CGGGCTTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
12 21 0.39
13 14 0.26
14 17 0.31
15 2 0.04
ACGTcount: A:0.11, C:0.05, G:0.44, T:0.39
Consensus pattern (12 bp):
TTTGGGTTAGGG
Found at i:1051190 original size:12 final size:12
Alignment explanation
Indices: 1051156--1051198 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1051146 CAAGGTTGAA
*
1051156 GGTTAGGGTTTG
1 GGTTAGGGTTCG
*
1051168 GGTTAGAGTTCG
1 GGTTAGGGTTCG
*
1051180 GGTTCGGGTTCG
1 GGTTAGGGTTCG
1051192 GGCTTAG
1 GG-TTAG
1051199 ATTAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.09, C:0.09, G:0.47, T:0.35
Consensus pattern (12 bp):
GGTTAGGGTTCG
Found at i:1051485 original size:21 final size:21
Alignment explanation
Indices: 1051461--1051513 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1051451 AAAACTTAAA
1051461 TTTTATTATTTATATT-AACTT
1 TTTTATTATTTAT-TTGAACTT
* * * *
1051482 TTTTATGAATCATTTGTACTT
1 TTTTATTATTTATTTGAACTT
1051503 TTTTATTATTT
1 TTTTATTATTT
1051514 TAATTTTATT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATTATTTATTTGAACTT
Found at i:1052292 original size:6 final size:6
Alignment explanation
Indices: 1052271--1052307 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1052261 AATTAAAAAA
1052271 ATTAA- ATTAA- ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
1052308 GATTAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:1060777 original size:69 final size:69
Alignment explanation
Indices: 1060690--1060883 Score: 174
Period size: 69 Copynumber: 2.8 Consensus size: 69
1060680 GAAGAGTTAT
* ** *
1060690 GACCTCCAACATAATTAGCGAGAGCAAATCTCCCAGCTATAAAATGAAGGTTCGCAGGCGAAGTG
1 GACCTCCAACATAATTAGCGAGAGCAAAACTCCCAGCTATAAAACCAAAGTTCGCAGGCGAAGTG
1060755 CCGG
66 CCGG
* * * * * * **
1060759 GACCTCTACCATAGTTAGCGAGAGCAAAACTCCTAGTTGTAAAACCAAAGTTCGCAGGCGAAGAA
1 GACCTCCAACATAATTAGCGAGAGCAAAACTCCCAGCTATAAAACCAAAGTTCGCAGGCGAAGTG
* *
1060824 CTGT
66 CCGG
* * * * * * * *
1060828 GACCTCCAGCACAGTTAGCAAGAGCAAAGCTCCAAGTTGTAAAACC-AAGATTCGCA
1 GACCTCCAACATAATTAGCGAGAGCAAAACTCCCAGCTATAAAACCAAAG-TTCGCA
1060884 TATAATTTTT
Statistics
Matches: 104, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
68 3 0.03
69 101 0.97
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (69 bp):
GACCTCCAACATAATTAGCGAGAGCAAAACTCCCAGCTATAAAACCAAAGTTCGCAGGCGAAGTG
CCGG
Found at i:1063941 original size:44 final size:44
Alignment explanation
Indices: 1063886--1063971 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
1063876 CCAAAAAATG
*
1063886 TTAGCACCAGGGATAAAGAATGTCAGTGCTTTCGGTCCAAAGAC
1 TTAGCACCAGGGATAAAGAATGTCAGTGCCTTCGGTCCAAAGAC
1063930 TTAGCACCAGGGATAAAGAATGTCAGTGCCTTCGGTCCAAAG
1 TTAGCACCAGGGATAAAGAATGTCAGTGCCTTCGGTCCAAAG
1063972 GCCAAGACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (44 bp):
TTAGCACCAGGGATAAAGAATGTCAGTGCCTTCGGTCCAAAGAC
Found at i:1065072 original size:6 final size:7
Alignment explanation
Indices: 1065042--1065071 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1065032 AATACTAATT
*
1065042 AAATTAA
1 AAATAAA
1065049 AAATAAA
1 AAATAAA
1065056 AAATAAA
1 AAATAAA
1065063 AAATAAA
1 AAATAAA
1065070 AA
1 AA
1065072 TTATTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:1065349 original size:18 final size:19
Alignment explanation
Indices: 1065328--1065367 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1065318 TTAAAAATCA
*
1065328 AAATAA-AATTATAGTAAT
1 AAATAATAATTAGAGTAAT
*
1065346 AAATAATAATTAGAGTATT
1 AAATAATAATTAGAGTAAT
1065365 AAA
1 AAA
1065368 GACTTTTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
AAATAATAATTAGAGTAAT
Found at i:1076649 original size:18 final size:17
Alignment explanation
Indices: 1076601--1076667 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 17
1076591 GTGAAGAAAC
1076601 AAACAAAATTAAAAACA-A
1 AAAC-AAATTAAAAA-ATA
*
1076619 GAAACAAAATAAAAAATA
1 -AAACAAATTAAAAAATA
1076637 AAACGAAATTAAAAAATA
1 AAAC-AAATTAAAAAATA
1076655 AAACAAATTAAAA
1 AAACAAATTAAAA
1076668 GCGAGCCTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
17 14 0.32
18 26 0.59
19 4 0.09
ACGTcount: A:0.76, C:0.07, G:0.03, T:0.13
Consensus pattern (17 bp):
AAACAAATTAAAAAATA
Found at i:1082147 original size:51 final size:51
Alignment explanation
Indices: 1082066--1082178 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
1082056 CGGATCATAT
1082066 TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCT-AAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTGAAA-CTACCAC
* *
1082117 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAACTACTAC
1 TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTGAAACTACCAC
1082168 TTATCACTTGT
1 TTATCACTTGT
1082179 TACTAATCAG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 56 0.95
52 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATAAGATAAGTGTAGCTGAAACTACCAC
Found at i:1083661 original size:44 final size:44
Alignment explanation
Indices: 1083613--1083711 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 44
1083603 TGTCCCAGAC
** * *
1083613 ATGGTCTTACATGGAAATCTCATATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACATCAAAATCTCAAATAGATGCCAATAGCCCAGCT
1083657 ATGGTCTTACA-CAAAATCTCAAATAGATGCCAATAGCCCAGCT
1 ATGGTCTTACATCAAAATCTCAAATAGATGCCAATAGCCCAGCT
1083700 ATGGTCTTACAT
1 ATGGTCTTACAT
1083712 ATAAACACTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 39 0.78
44 11 0.22
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (44 bp):
ATGGTCTTACATCAAAATCTCAAATAGATGCCAATAGCCCAGCT
Found at i:1083772 original size:33 final size:33
Alignment explanation
Indices: 1083679--1083873 Score: 113
Period size: 33 Copynumber: 5.7 Consensus size: 33
1083669 AAAATCTCAA
* *
1083679 ATAGATGCCAATAGCCCAGCTATGGTCTTACATATAA
1 ATAG-TGCC-ATAACCCAGCTATGGTCTTACAT-T-C
* * ** * *
1083716 ACACTGCCATAGTCCAACCATGGTCTTACATTC
1 ATAGTGCCATAACCCAGCTATGGTCTTACATTC
*
1083749 ATAGTGCCATAACCCAGTTATGGTCTTATCA-TC
1 ATAGTGCCATAACCCAGCTATGGTCTTA-CATTC
* * * * *
1083782 AGAATGCCATAGCTCAGCTATGGTCTTACATATAA
1 ATAGTGCCATAACCCAGCTATGGTCTTACAT-T-C
* * *** * * *
1083817 ACACTGCCATGGTCCAACCATGGTCTTACGTTC
1 ATAGTGCCATAACCCAGCTATGGTCTTACATTC
*
1083850 ATAGTGCCATAACCCAGTTATGGT
1 ATAGTGCCATAACCCAGCTATGGT
1083874 ATTATGCGGG
Statistics
Matches: 118, Mismatches: 36, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
32 2 0.02
33 62 0.53
34 5 0.04
35 43 0.36
36 4 0.03
37 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (33 bp):
ATAGTGCCATAACCCAGCTATGGTCTTACATTC
Found at i:1083864 original size:101 final size:102
Alignment explanation
Indices: 1083683--1083878 Score: 349
Period size: 101 Copynumber: 1.9 Consensus size: 102
1083673 TCTCAAATAG
1083683 ATGCCAATAGCCCAGCTATGGTCTTACATATAAACACTGCCATAGTCCAACCATGGTCTTACATT
1 ATGCCAATAGCCCAGCTATGGTCTTACATATAAACACTGCCATAGTCCAACCATGGTCTTACATT
*
1083748 CATAGTGCCATAACCCAGTTATGGTCTTATCATCAGA
66 CATAGTGCCATAACCCAGTTATGGTATTATCATCAGA
* * *
1083785 ATGCC-ATAGCTCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTT
1 ATGCCAATAGCCCAGCTATGGTCTTACATATAAACACTGCCATAGTCCAACCATGGTCTTACATT
1083849 CATAGTGCCATAACCCAGTTATGGTATTAT
66 CATAGTGCCATAACCCAGTTATGGTATTAT
1083879 GCGGGATCTC
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
101 85 0.94
102 5 0.06
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (102 bp):
ATGCCAATAGCCCAGCTATGGTCTTACATATAAACACTGCCATAGTCCAACCATGGTCTTACATT
CATAGTGCCATAACCCAGTTATGGTATTATCATCAGA
Found at i:1090724 original size:30 final size:30
Alignment explanation
Indices: 1090690--1090753 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1090680 GACACGGGAA
* *
1090690 TGTGTCTT-AGCCGTGTGAGGCACATGGCCC
1 TGTGT-TTCAGCCATGTGAGGCACACGGCCC
*
1090720 TGTGTTTCAGCCATGTGAGGCACACGGCCG
1 TGTGTTTCAGCCATGTGAGGCACACGGCCC
1090750 TGTG
1 TGTG
1090754 ACCCCTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.14, C:0.25, G:0.34, T:0.27
Consensus pattern (30 bp):
TGTGTTTCAGCCATGTGAGGCACACGGCCC
Found at i:1097148 original size:23 final size:22
Alignment explanation
Indices: 1097099--1097149 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1097089 AACTTAGCTA
1097099 ATTCATTACATAACATAATAGC
1 ATTCATTACATAACATAATAGC
*
1097121 TTTCATGTACATAACAT-ATAAGC
1 ATTCAT-TACATAACATAAT-AGC
1097144 ATTCAT
1 ATTCAT
1097150 ACTTTCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (22 bp):
ATTCATTACATAACATAATAGC
Found at i:1102275 original size:20 final size:20
Alignment explanation
Indices: 1102250--1102288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1102240 ATGCTAACAA
*
1102250 AGGCACTGAAGTACAAATCG
1 AGGCACCGAAGTACAAATCG
*
1102270 AGGCACCGAAGTGCAAATC
1 AGGCACCGAAGTACAAATC
1102289 CGTATAAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.26, T:0.13
Consensus pattern (20 bp):
AGGCACCGAAGTACAAATCG
Found at i:1107179 original size:50 final size:50
Alignment explanation
Indices: 1107062--1107353 Score: 289
Period size: 50 Copynumber: 5.7 Consensus size: 50
1107052 GAATATAACA
* * * ** * * * *
1107062 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * **
1107111 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* ** * *
1107161 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * *
1107211 TGCCAACGCCATGTCCCAGGCATCGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* *
1107261 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATTTGAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
1107317 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1107354 TCTCATCCTC
Statistics
Matches: 202, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
49 37 0.18
50 127 0.63
53 1 0.00
56 37 0.18
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:1107731 original size:30 final size:30
Alignment explanation
Indices: 1107697--1107754 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1107687 CCTCGACTCT
**
1107697 AACTTTGACAAAATTATGATTTTTCCCCTA
1 AACTTTGACAAAATTACAATTTTTCCCCTA
* *
1107727 AACTTTTACATAATTACAATTTTTCCCC
1 AACTTTGACAAAATTACAATTTTTCCCC
1107755 AAAGCTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTTCCCCTA
Found at i:1122531 original size:29 final size:30
Alignment explanation
Indices: 1122476--1122532 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1122466 ATCTATCCTA
* **
1122476 AAAAGAAAAGAGAAAACTTAATTTAAAATG
1 AAAAGAAAAGAGAAAACCTAACCTAAAATG
1122506 AAAAGAAAAGA-AAAACCTAACCTAAAA
1 AAAAGAAAAGAGAAAACCTAACCTAAAA
1122533 CTATGAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.14
Consensus pattern (30 bp):
AAAAGAAAAGAGAAAACCTAACCTAAAATG
Found at i:1132755 original size:20 final size:20
Alignment explanation
Indices: 1132727--1132766 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1132717 CCGCATCACC
1132727 ATTCAAGCTATGTTGGTTGT
1 ATTCAAGCTATGTTGGTTGT
*
1132747 ATTCTAGCTATGTTGGTTGT
1 ATTCAAGCTATGTTGGTTGT
1132767 CTTTTGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.25, T:0.47
Consensus pattern (20 bp):
ATTCAAGCTATGTTGGTTGT
Found at i:1133554 original size:31 final size:30
Alignment explanation
Indices: 1133514--1133576 Score: 108
Period size: 31 Copynumber: 2.1 Consensus size: 30
1133504 AACATAATTG
*
1133514 ATAAGTGCTAAGTAGTCATAGATTCTGATA
1 ATAAGTGCTAAGTAATCATAGATTCTGATA
1133544 ATAATGTGCTAAGTAATCATAGATTCTGATA
1 ATAA-GTGCTAAGTAATCATAGATTCTGATA
1133575 AT
1 AT
1133577 CCAATTCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (30 bp):
ATAAGTGCTAAGTAATCATAGATTCTGATA
Found at i:1136251 original size:22 final size:20
Alignment explanation
Indices: 1136225--1136305 Score: 94
Period size: 19 Copynumber: 4.0 Consensus size: 20
1136215 TAGATTAGAA
1136225 TTTTGTATGAATATTCTAACTT
1 TTTTGTATGAATATTCTAA--T
*
1136247 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTCTAAT
*
1136267 TTTT-TATGAATATTGTAA-
1 TTTTGTATGAATATTCTAAT
* *
1136285 TGTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTCTAAT
1136305 T
1 T
1136306 ATTTTATAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 3 0.05
19 28 0.51
20 6 0.11
22 18 0.33
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (20 bp):
TTTTGTATGAATATTCTAAT
Found at i:1136269 original size:21 final size:21
Alignment explanation
Indices: 1136225--1136656 Score: 338
Period size: 21 Copynumber: 20.2 Consensus size: 21
1136215 TAGATTAGAA
*
1136225 TTTTGTATGAATATTCTAACTT
1 TTTTGTATGAATATTGTAA-TT
1136247 TTTTGTATGAATATTGTAA-T
1 TTTTGTATGAATATTGTAATT
1136267 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
1136285 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
1136306 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
1136328 TATAGTTTTGGAT-TAGTAA--
1 TTTTG-TATGAATATTGTAATT
**
1136347 -TTTGTATGAATGCTGTAATT
1 TTTTGTATGAATATTGTAATT
1136367 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
1136388 TTTTGAATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
1136410 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
1136435 AGTTTTGTATGAATATTGTAATT
1 --TTTTGTATGAATATTGTAATT
1136458 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
1136479 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
1136501 TATAGTTTTGGAT-TAGTAA--
1 TTTTG-TATGAATATTGTAATT
**
1136520 -TTTGTATGAATGCTGTAATT
1 TTTTGTATGAATATTGTAATT
1136540 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
1136561 TTTTGAATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
1136583 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
1136608 AGTTTTGTATGAATATTGTAATT
1 --TTTTGTATGAATATTGTAATT
1136631 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
1136652 ATTTT
1 -TTTT
1136657 ATAATTAATT
Statistics
Matches: 333, Mismatches: 41, Indels: 72
0.75 0.09 0.16
Matches are distributed among these distances:
17 10 0.03
18 15 0.05
19 28 0.08
20 11 0.03
21 124 0.37
22 77 0.23
23 20 0.06
24 8 0.02
25 4 0.01
26 2 0.01
27 34 0.10
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:1136417 original size:91 final size:92
Alignment explanation
Indices: 1136338--1136628 Score: 241
Period size: 103 Copynumber: 3.0 Consensus size: 92
1136328 TATAGTTTTG
*
1136338 GATTAGTA-ATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT-TTTTGAATGAATA
1 GATTA-TAGATTTGTATGAATACTGTAATTTTTTGTATGAATATTGTAATTATTTTGAATGAATA
1136401 TTGTAATTTTTTTGTATGAATATTGTAA
65 TTGTAATTTTTTTGTATGAATATTGTAA
* * * * *
1136429 TATTATAGTTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAA-A
1 GATTATAGATTTGTATGAATACTGTAATTTTTTGTATGAATATTGTAATTATTTT-GAATGAATA
* * *
1136493 TTTGTATTTATAGTTTTGGATTAGTAAT-TTGTAT
65 -TTGTAATT-T--TTTTGTA-T-G-AATATTGTAA
* * * * *
1136527 GAATGCTGTA-ATTTTTTGTATGAATATTGTAATTTTTTGAATGAATATTGTAATTTTTTTGTAT
1 G-AT--TATAGA---TTTGTATGAATACTGTAATTTTTTGTATGAATATTGTAATTATTTTGAAT
1136591 GAATATTGTAATATTATAGTTTTGTATGAATATTGTAA
60 GAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAA
1136629 TTTTTTGTAT
Statistics
Matches: 160, Mismatches: 20, Indels: 29
0.77 0.10 0.14
Matches are distributed among these distances:
90 2 0.01
91 43 0.27
92 5 0.03
93 12 0.08
94 1 0.01
96 6 0.04
97 1 0.01
98 6 0.04
99 5 0.03
101 6 0.04
102 14 0.09
103 47 0.29
104 12 0.08
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (92 bp):
GATTATAGATTTGTATGAATACTGTAATTTTTTGTATGAATATTGTAATTATTTTGAATGAATAT
TGTAATTTTTTTGTATGAATATTGTAA
Found at i:1136453 original size:70 final size:64
Alignment explanation
Indices: 1136437--1136656 Score: 202
Period size: 70 Copynumber: 3.4 Consensus size: 64
1136427 AATATTATAG
* * *
1136437 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTATTTTATAATTAA-ATTTGT-AT
1 TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTGT-ATGAATA-TTGTAAT
1136500 T
64 T
* * * * * **
1136501 TATAGTTTTGGAT-TAGTAA---TTTGTATGAATGCTGTAA-TTTTTTGTATGAATATTGTAATT
1 TTTTG-TATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATT
*
1136561 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1 TTTTGTATGAATATTGTAA-TTTTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTG
1136626 TAATT
60 TAATT
1136631 TTTTGTATGAATATTGTAATTATTTT
1 TTTTGTATGAATATTGTAATT-TTTT
1136657 ATAATTAATT
Statistics
Matches: 122, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
59 12 0.10
60 18 0.15
61 16 0.13
64 22 0.18
65 6 0.05
66 1 0.01
67 1 0.01
68 1 0.01
69 2 0.02
70 43 0.35
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (64 bp):
TTTTGTATGAATATTGTAATTTTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATT
Found at i:1136576 original size:173 final size:173
Alignment explanation
Indices: 1136225--1136669 Score: 777
Period size: 173 Copynumber: 2.6 Consensus size: 173
1136215 TAGATTAGAA
* * *
1136225 TTTTGTATGAATATTCTAACTTTTTTGTATGAATATTG---TA--AT--TTTT-TATGAATATTG
1 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
*
1136282 TAA--TGTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGT
66 TAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGT
1136345 AATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT
131 AATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT
1136388 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1136453 TAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGT
66 TAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGT
1136518 AATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT
131 AATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT
1136561 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1 TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
1136626 TAATTTTTTGTATGAATATTGTAATTATTTTATAATT-AATTTGT
66 TAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGT
1136670 TAGTAATTTG
Statistics
Matches: 268, Mismatches: 4, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
163 35 0.13
166 2 0.01
168 2 0.01
170 4 0.01
171 14 0.05
172 7 0.03
173 204 0.76
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (173 bp):
TTTTGAATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG
TAATTTTTTGTATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTTTTGGATTAGT
AATTTGTATGAATGCTGTAATTTTTTGTATGAATATTGTAATT
Found at i:1136759 original size:30 final size:29
Alignment explanation
Indices: 1136718--1136784 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1136708 ACCAATAAAA
* *
1136718 GCCGTTTTTTTTCAAAATTTATCGAAATGG
1 GCCGATTTTTTT-AAAATTTACCGAAATGG
** *
1136748 GCCGATTTTTTTATTATTTACCGGAATGG
1 GCCGATTTTTTTAAAATTTACCGAAATGG
1136777 GCC-ATTTT
1 GCCGATTTT
1136785 CCGCGAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 5 0.16
29 16 0.50
30 11 0.34
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (29 bp):
GCCGATTTTTTTAAAATTTACCGAAATGG
Found at i:1137880 original size:15 final size:15
Alignment explanation
Indices: 1137839--1137880 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1137829 GTTAACTCAT
*
1137839 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
1137854 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
1137870 TTAAATTTTAT
1 TTAAATTTTAT
1137881 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:1139503 original size:6 final size:6
Alignment explanation
Indices: 1139492--1139520 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1139482 TCATGCACCA
1139492 GAGCCT GAGCCT GAGCCT GAGCCT GAGCC
1 GAGCCT GAGCCT GAGCCT GAGCCT GAGCC
1139521 AGAGACAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.14
Consensus pattern (6 bp):
GAGCCT
Found at i:1142719 original size:22 final size:23
Alignment explanation
Indices: 1142694--1142746 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
1142684 ATACCTTTTT
* *
1142694 TTTTTCTTCT-TTTCCTTCCTTC
1 TTTTTCTTCTGCTTCCTTCATTC
1142716 -TTTTCTTCTGCTTCCTTCATTC
1 TTTTTCTTCTGCTTCCTTCATTC
1142738 TTATTTCTT
1 TT-TTTCTT
1142747 TCATTTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 1 0.04
24 6 0.23
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTTCTTCTGCTTCCTTCATTC
Found at i:1144739 original size:17 final size:17
Alignment explanation
Indices: 1144719--1144762 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1144709 TTATTGAATT
1144719 GATTAATTAATTAAGTC
1 GATTAATTAATTAAGTC
* *
1144736 GATTAGTTAATTAAGTT
1 GATTAATTAATTAAGTC
1144753 GATTAATTAA
1 GATTAATTAA
1144763 CAAAAGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (17 bp):
GATTAATTAATTAAGTC
Found at i:1145387 original size:29 final size:29
Alignment explanation
Indices: 1145336--1145392 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1145326 ATTAAAATAT
*
1145336 TAATTAACATAAAATAACATAATTGAATG
1 TAATTAACATAAAATAACATAATGGAATG
* * * *
1145365 TAATTAACCTAAGATATCCTAATGGAAT
1 TAATTAACATAAAATAACATAATGGAAT
1145393 TTCCTATTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.32
Consensus pattern (29 bp):
TAATTAACATAAAATAACATAATGGAATG
Found at i:1148534 original size:18 final size:20
Alignment explanation
Indices: 1148506--1148547 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1148496 GCTCTCCAAT
1148506 TCTTCTCTCTCCAAAAATCC
1 TCTTCTCTCTCCAAAAATCC
1148526 TCTTCTCTCTCCAAAAATCC
1 TCTTCTCTCTCCAAAAATCC
1148546 TC
1 TC
1148548 CCCTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (20 bp):
TCTTCTCTCTCCAAAAATCC
Found at i:1148553 original size:20 final size:20
Alignment explanation
Indices: 1148510--1148555 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1148500 TCCAATTCTT
**
1148510 CTCTCTCCAAAAATCCTCTT
1 CTCTCTCCAAAAATCCTCCC
1148530 CTCTCTCCAAAAATCCTCCC
1 CTCTCTCCAAAAATCCTCCC
1148550 CTCTCT
1 CTCTCT
1148556 TTTCTTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.33
Consensus pattern (20 bp):
CTCTCTCCAAAAATCCTCCC
Found at i:1169954 original size:14 final size:15
Alignment explanation
Indices: 1169935--1169963 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1169925 CTCTTTCGTT
1169935 CTCTTTTCC-TCTTC
1 CTCTTTTCCTTCTTC
1169949 CTCTTTTCCTTCTTC
1 CTCTTTTCCTTCTTC
1169964 TTGCCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTCTTTTCCTTCTTC
Found at i:1175961 original size:16 final size:17
Alignment explanation
Indices: 1175934--1175967 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1175924 CAAGCAAAGC
1175934 AGCAACAGAGAAATAAT
1 AGCAACAGAGAAATAAT
1175951 AGCAA-AGAGAAATAAT
1 AGCAACAGAGAAATAAT
1175967 A
1 A
1175968 AACAATGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.62, C:0.09, G:0.18, T:0.12
Consensus pattern (17 bp):
AGCAACAGAGAAATAAT
Found at i:1181356 original size:44 final size:44
Alignment explanation
Indices: 1181291--1182336 Score: 474
Period size: 44 Copynumber: 23.0 Consensus size: 44
1181281 CATCATAGTG
* *
1181291 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * *
1181335 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-ACT
* * * * *
1181379 AAGTCTTATCTCCCTGAAGTTGCAGTGGACCAAACTGAAGATAGCG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CT
* *** * *
1181425 AATCTTATTTCCCTGAAGTTGCAGTGGAATGGATTGAATCTATAAATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--T--ACT
* * * * *
1181473 ACAGATCTTATCTCTCTGAAGTTGCAATAGAGCA-AATCATAGC-A--
1 --A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGCTACT
* * * * * *
1181517 AACCTTATCTCCCTGGAGTTGCAATGGAGTAGGTTGAAGTTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * *
1181560 AAGTCTTATCTCCCTAAAGTTACAGTGGAGCAGACTGAAGATAGCA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CT
* * * *
1181606 AATTTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTA-T
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * *
1181649 AAATTGCAAATTTTATCTCTCTGAAGTTGTAGTAGAGCAGA-T-CA--TATCG
1 -AA-T-C-----TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CT
* * * * * * ** *
1181698 AACCTTATCTCCTTGAAGTTGTAGTGGAACAGGTTAAAAATAAACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT--ACT
* *
1181744 AATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTAAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * * *
1181788 AACCTTATCTCTCTGAAGTTACAGTGGAGCAGGTTGAAGATACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
*
1181832 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * *
1181876 AATCCTATCT-CCTGGAAGTTGCAGTGGAGCGGATTAAAACGA-T
1 AATCTTATCTCCCT-GAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * * *
1181919 GAAT-TCTATAC-CTCTGAGGTTACAGTAGG-TCAGATTAAATCTACCAT
1 -AATCT-TAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAGCTA-C-T
* * * * *
1181966 AACAAGTCTTATCTCCTTGAGGTTGCAGTGGAATAGACTAAAGCTAT-AAGGTAGCA
1 ---AA-TCTTATCTCCCTGAAGTTGCAGTGG---AG-C---AGAT-TGAAGCTA-CT
* * * *
1182022 AATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * * * *
1182066 AATCTTATTTCCTTGAAGTTCCAATGGAACAGACTAAAGCTACAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-----T-GAAGCTACT
* * * *
1182117 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * *
1182161 AACCTTATATCCCTGAAGTTGCAGT-GAGGCAGGTTGAAGTTGC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTGAAGCTACT
* * * * * * *
1182204 AAGTCTTATCTCCCTAAATTTGTAGTGGAGCAGACTAAAGATAGCA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CT
* * *
1182250 AATCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
* * * * *
1182294 AATCTTATTTCTCTGAAGTTCCAGTAGAACAGATTGAAGCTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
1182337 AAGTTACAAG
Statistics
Matches: 759, Mismatches: 173, Indels: 140
0.71 0.16 0.13
Matches are distributed among these distances:
41 51 0.07
42 5 0.01
43 11 0.01
44 337 0.44
45 156 0.21
46 42 0.06
47 5 0.01
48 2 0.00
49 9 0.01
50 23 0.03
51 84 0.11
52 22 0.03
53 2 0.00
54 1 0.00
57 8 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
Found at i:1181537 original size:92 final size:91
Alignment explanation
Indices: 1181338--1181815 Score: 252
Period size: 92 Copynumber: 5.3 Consensus size: 91
1181328 AGCCACTAGT
* * * * * *
1181338 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAA-GAT-AA-CA-AG-TCTTATCTCCCTGAAG
1 CTTATCTCCCTGAAGTTGCAGTGGAATGGATTGAACTATAAATTACAGATCTTATCTCTCTGAAG
* * * * *
1181398 TTGCAGTGGACCAAACTGAAGATAGCGAAT
66 TTGCAGTAGAGCAAA-T---CATAGCAAAC
*
1181428 CTTATTTCCCTGAAGTTGCAGTGGAATGGATTGAATCTATAAATTACAGATCTTATCTCTCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAATGGATTGAA-CTATAAATTACAGATCTTATCTCTCTGAA
*
1181493 GTTGCAATAGAGCAAATCATAGCAAAC
65 GTTGCAGTAGAGCAAATCATAGCAAAC
* * * * * * *
1181520 CTTATCTCCCTGGAGTTGCAATGGAGTAGG-TTGAAGT-T--A-CA-AG-TCTTATCTCCCTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAAT-GGATTGAACTATAAATTACAGATCTTATCTCTCTGAA
* * ** *
1181578 GTTACAGTGGAGCAGACTGAAGATAGCAAAT
65 GTTGCAGTAGAGCA-A---ATCATAGCAAAC
* * * ** * * *
1181609 TTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTATAAATTGCAAATTTTATCTCTCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAATGGATTGAA-CTATAAATTACAGATCTTATCTCTCTGAA
* * * *
1181674 GTTGTAGTAGAGCAGATCATATCGAAC
65 GTTGCAGTAGAGCAAATCATAGCAAAC
* * * ** * *
1181701 CTTATCTCCTTGAAGTTGTAGTGGAACAGG-TT-AAAAATAAA--CCA-ATCTTATCTCCCTGAA
1 CTTATCTCCCTGAAGTTGCAGTGGAA-TGGATTGAACTATAAATTACAGATCTTATCTCTCTGAA
* * * *
1181761 GTTGCAGTGGAGCATATTAAAGCTACTAAC
65 GTTGCAGTAGAGCAAATCATAGC-A--AAC
* *
1181791 CTTATCTCTCTGAAGTTACAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
1181816 GCAGGTTGAA
Statistics
Matches: 291, Mismatches: 74, Indels: 46
0.71 0.18 0.11
Matches are distributed among these distances:
85 24 0.08
86 3 0.01
87 32 0.11
88 4 0.01
89 34 0.12
90 62 0.21
91 4 0.01
92 67 0.23
93 6 0.02
94 1 0.00
95 4 0.01
96 50 0.17
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (91 bp):
CTTATCTCCCTGAAGTTGCAGTGGAATGGATTGAACTATAAATTACAGATCTTATCTCTCTGAAG
TTGCAGTAGAGCAAATCATAGCAAAC
Found at i:1181599 original size:181 final size:182
Alignment explanation
Indices: 1181338--1181718 Score: 539
Period size: 181 Copynumber: 2.1 Consensus size: 182
1181328 AGCCACTAGT
* * *
1181338 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAACAAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAATGGAGTAGACTGAAGATAACAAGTCTTATCTCCCTAAAGTTACA
* * ** *
1181403 GTGGACCAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAATGGATTGAATCTAT
66 GTGGACCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTAT
*
1181468 AAATTACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAAATCATAGCAAAC
131 AAATTACAAATCTTATCTCTCTGAAGTTGCAATAGAGCAAATCATAGCAAAC
* ** *
1181520 CTTATCTCCCTGGAGTTGCAATGGAGTAGGTTGAAG-TTACAAGTCTTATCTCCCTAAAGTTACA
1 CTTATCTCCCTGAAGTTGCAATGGAGTAGACTGAAGATAACAAGTCTTATCTCCCTAAAGTTACA
* * *
1181584 GTGGAGCAGACTGAAGATAGCAAATTTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTAT
66 GTGGACCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTAT
* * * * * * *
1181649 AAATTGCAAATTTTATCTCTCTGAAGTTGTAGTAGAGCAGATCATATCGAAC
131 AAATTACAAATCTTATCTCTCTGAAGTTGCAATAGAGCAAATCATAGCAAAC
*
1181701 CTTATCTCCTTGAAGTTG
1 CTTATCTCCCTGAAGTTG
1181719 TAGTGGAACA
Statistics
Matches: 174, Mismatches: 25, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
181 142 0.82
182 32 0.18
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (182 bp):
CTTATCTCCCTGAAGTTGCAATGGAGTAGACTGAAGATAACAAGTCTTATCTCCCTAAAGTTACA
GTGGACCAAACTGAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGCGGAACAGATTGAAGCTAT
AAATTACAAATCTTATCTCTCTGAAGTTGCAATAGAGCAAATCATAGCAAAC
Found at i:1182032 original size:52 final size:50
Alignment explanation
Indices: 1181967--1182144 Score: 181
Period size: 52 Copynumber: 3.6 Consensus size: 50
1181957 ATCTACCATA
* * *
1181967 ACAAGTCTTATCTCCTTGAGGTTGCAGTGGAATAGACTAAAGCTATAAGGT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAATAGACTAAAGCTA-AAGCT
* * *
1182018 AGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGA-T-----TAAAGCT
1 A-CAAATCTTATCTCCTTGAAGTTGCAGTGGAATAGACTAAAGCTAAAGCT
* * * *
1182063 ACAAATCTTATTTCCTTGAAGTTCCAATGGAACAGACTAAAGCTACAAGCT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAATAGACTAAAGCTA-AAGCT
1182114 ACAAATCTTATCTTCC-TGAAGTTGCAGTGGA
1 ACAAATCTTATC-TCCTTGAAGTTGCAGTGGA
1182145 GCAGATTAAA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
44 28 0.27
45 6 0.06
46 2 0.02
50 2 0.02
51 31 0.30
52 33 0.32
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (50 bp):
ACAAATCTTATCTCCTTGAAGTTGCAGTGGAATAGACTAAAGCTAAAGCT
Found at i:1182134 original size:51 final size:51
Alignment explanation
Indices: 1182058--1182161 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
1182048 GAGTAGATTA
*
1182058 AAGCTACAAATCTTATTTCCTTGAAGTTCCAATGGAACAGACTAAAGCTAC
1 AAGCTACAAATCTTATTTCCTTGAAGTTCCAATGGAACAGACTAAAGCCAC
* * * *
1182109 AAGCTACAAATCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCCAC
1 AAGCTACAAATCTTAT-TTCCTTGAAGTTCCAATGGAACAGACTAAAGCCAC
1182160 AA
1 AA
1182162 ACCTTATATC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 43 0.91
52 4 0.09
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (51 bp):
AAGCTACAAATCTTATTTCCTTGAAGTTCCAATGGAACAGACTAAAGCCAC
Done.