Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 117 of 132
Found at i:35569660 original size:21 final size:22
Alignment explanation
Indices: 35569636--35569688 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
35569626 TTTTAATAAT
35569636 TTTTTTCTA-AAATTTTAAATA
1 TTTTTTCTATAAATTTTAAATA
* *
35569657 -TTTTTGTATATATTTTAAATA
1 TTTTTTCTATAAATTTTAAATA
35569678 -TTTTTCTATAA
1 TTTTTTCTATAA
35569689 TCTTTTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTTCTATAAATTTTAAATA
Found at i:35569898 original size:10 final size:10
Alignment explanation
Indices: 35569846--35569898 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
35569836 ATATGTTTAT
35569846 ATTTTATAAT-
1 ATTTT-TAATA
35569856 ATTTTTAGATA
1 ATTTTTA-ATA
35569867 A-TTTTAATA
1 ATTTTTAATA
35569876 ATTTTCT-ATA
1 ATTTT-TAATA
35569886 ATTTTTAATA
1 ATTTTTAATA
35569896 ATT
1 ATT
35569899 ATATATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 7 0.18
10 29 0.76
11 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:35569905 original size:20 final size:19
Alignment explanation
Indices: 35569864--35569905 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
35569854 ATATTTTTAG
* *
35569864 ATAATTTTAATAATTTTCT
1 ATAATTTTAATAATTATAT
35569883 ATAATTTTTAATAATTATAT
1 ATAA-TTTTAATAATTATAT
35569903 ATA
1 ATA
35569906 TTTATTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATAATTTTAATAATTATAT
Found at i:35569908 original size:29 final size:30
Alignment explanation
Indices: 35569843--35569908 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
35569833 TCTATATGTT
*
35569843 TATATTTTATAATATTTTTAGATAATTTTA
1 TATATTTTATAATATTTTTAGATAATTATA
*
35569873 -ATAATTTTCT-ATAATTTTTA-ATAATTATA
1 TAT-ATTTTATAAT-ATTTTTAGATAATTATA
35569902 TATATTT
1 TATATTT
35569909 ATTGATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (30 bp):
TATATTTTATAATATTTTTAGATAATTATA
Found at i:35570944 original size:6 final size:6
Alignment explanation
Indices: 35570933--35570962 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35570923 AACCTGGGAA
35570933 GATGCC GATGCC GATGCC GATGCC GATGCC
1 GATGCC GATGCC GATGCC GATGCC GATGCC
35570963 TGAGGCTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (6 bp):
GATGCC
Found at i:35572457 original size:6 final size:6
Alignment explanation
Indices: 35572410--35572458 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
35572400 AAGAAGAAAA
* * *
35572410 GGGAAA GGGAAA GGGAAA GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG
35572458 G
1 G
35572459 AGAAAGATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:35572457 original size:12 final size:12
Alignment explanation
Indices: 35572410--35572464 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
35572400 AAGAAGAAAA
*
35572410 GGGAAAGGGAAA
1 GGGAAAGGGAAG
35572422 GGGAAAGGGAAG
1 GGGAAAGGGAAG
*
35572434 GGGAAGGGGAAG
1 GGGAAAGGGAAG
*
35572446 GGGAAGGGGAAG
1 GGGAAAGGGAAG
*
35572458 GAGAAAG
1 GGGAAAG
35572465 ATAAGGTTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (12 bp):
GGGAAAGGGAAG
Found at i:35572457 original size:18 final size:18
Alignment explanation
Indices: 35572407--35572464 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
35572397 AAGAAGAAGA
* *
35572407 AAAGGGAAAGGGAAAGGG
1 AAAGGGAAGGGGAAGGGG
35572425 AAAGGGAAGGGGAAGGGG
1 AAAGGGAAGGGGAAGGGG
* *
35572443 AAGGGGAAGGGGAAGGAG
1 AAAGGGAAGGGGAAGGGG
35572461 AAAG
1 AAAG
35572465 ATAAGGTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
AAAGGGAAGGGGAAGGGG
Found at i:35575910 original size:26 final size:27
Alignment explanation
Indices: 35575881--35575951 Score: 101
Period size: 25 Copynumber: 2.7 Consensus size: 27
35575871 AGCGATTGCA
35575881 AAATTTTTTTTTTTGAAAAGTA-TTTT
1 AAATTTTTTTTTTTGAAAAGTATTTTT
35575907 AAA-TTTTTTTTTTGAAAAAGTATTTTT
1 AAATTTTTTTTTTTG-AAAAGTATTTTT
**
35575934 AAATTTTTTGATTTGAAA
1 AAATTTTTTTTTTTGAAA
35575952 TTGGAGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.28
26 10 0.25
27 10 0.25
28 9 0.22
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (27 bp):
AAATTTTTTTTTTTGAAAAGTATTTTT
Found at i:35575933 original size:27 final size:26
Alignment explanation
Indices: 35575885--35575951 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
35575875 ATTGCAAAAT
35575885 TTTTTTTTTTG-AAAAGTATTTTAAA
1 TTTTTTTTTTGAAAAAGTATTTTAAA
35575910 TTTTTTTTTTGAAAAAGTATTTTTAAA
1 TTTTTTTTTTGAAAAAGTA-TTTTAAA
*
35575937 TTTTTTGATTTGAAA
1 TTTTTT-TTTTGAAA
35575952 TTGGAGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
25 11 0.29
26 7 0.18
27 13 0.34
28 7 0.18
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (26 bp):
TTTTTTTTTTGAAAAAGTATTTTAAA
Found at i:35577199 original size:23 final size:23
Alignment explanation
Indices: 35577171--35577218 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
35577161 GATTTTGAAT
*
35577171 AAAAAATACTAAAAGAAATTTAAAC
1 AAAAAA-A-TAAAAGAAATTAAAAC
35577196 AAAAAAATAAAAGAAATTAAAAC
1 AAAAAAATAAAAGAAATTAAAAC
35577219 CTCTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 1 0.05
25 6 0.27
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (23 bp):
AAAAAAATAAAAGAAATTAAAAC
Found at i:35577883 original size:30 final size:30
Alignment explanation
Indices: 35577818--35578053 Score: 176
Period size: 30 Copynumber: 7.8 Consensus size: 30
35577808 TTTTGACCCT
* * *
35577818 TAAACTTATCTAAAATTACA-TTTAACCCC
1 TAAACTTTTCCAAAATTACATTTTAGCCCC
35577847 -AAACTTTTCCAAAATTACATTTTAGCCCC
1 TAAACTTTTCCAAAATTACATTTTAGCCCC
* * * *
35577876 TAAACTTTTCCATAATTACATTTTAACTCA
1 TAAACTTTTCCAAAATTACATTTTAGCCCC
* *
35577906 TGAACTTTTCCAAAGTTACATTTT-GACCCC
1 TAAACTTTTCCAAAATTACATTTTAG-CCCC
* * *
35577936 AAAACTTTTCCAAAATTATATTTTTA--CCT
1 TAAACTTTTCCAAAATTACA-TTTTAGCCCC
* ** ** * *
35577965 TAAAATTTTTGAAAAAAAATCATTTTTTGACCC
1 T-AAACTTTTCCAAAATTA-CA-TTTTAGCCCC
* *
35577998 TAAACTTTTCCAAAATTACATTTTTATCCCT
1 TAAACTTTTCCAAAATTACA-TTTTAGCCCC
*
35578029 TAAACTTTTCCCAAAATTACGTTTT
1 TAAACTTTT-CCAAAATTACATTTT
35578054 GACCCTGTAT
Statistics
Matches: 160, Mismatches: 37, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
28 17 0.11
29 10 0.06
30 76 0.47
31 32 0.20
32 22 0.14
33 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (30 bp):
TAAACTTTTCCAAAATTACATTTTAGCCCC
Found at i:35583500 original size:23 final size:23
Alignment explanation
Indices: 35583470--35583584 Score: 203
Period size: 23 Copynumber: 5.0 Consensus size: 23
35583460 GCTATTTGTT
*
35583470 ATTAGCACTGTGTGTGCTCTCTA
1 ATTAGCACTGTGTGTGCTCTCTG
35583493 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
35583516 ATTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
*
35583539 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
*
35583562 TTTAGCACTGTGTGTGCTCTCTG
1 ATTAGCACTGTGTGTGCTCTCTG
35583585 TTGCCCAGCA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.41
Consensus pattern (23 bp):
ATTAGCACTGTGTGTGCTCTCTG
Found at i:35583585 original size:23 final size:23
Alignment explanation
Indices: 35583439--35583586 Score: 190
Period size: 23 Copynumber: 6.3 Consensus size: 23
35583429 ACTAGCGCGT
*
35583439 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGTTTAGCACTGTGT-GTGC
* *
35583462 TATTTGTTATTAGCACTGTGTGTGC
1 TCTCTG-T-TTAGCACTGTGTGTGC
**
35583487 TCTCTAATTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
*
35583510 TCTCTGATTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
* *
35583533 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
35583556 TCTCTGTTTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTGTGTGTGC
35583579 TCTCTGTT
1 TCTCTGTT
35583587 GCCCAGCACT
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
23 93 0.84
24 1 0.01
25 14 0.13
26 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (23 bp):
TCTCTGTTTAGCACTGTGTGTGC
Found at i:35592520 original size:209 final size:208
Alignment explanation
Indices: 35592015--35592735 Score: 879
Period size: 209 Copynumber: 3.4 Consensus size: 208
35592005 CATAGGGAAA
* * * * * *
35592015 AGTGAAACTTTC-AAACCCCATCTTCTTGATTAAATACAGAGAAGTGGGTCAAATCAATAAAGCA
1 AGTGAAAC-TTCGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCG
* * ** * * *
35592079 ATTATCTTCTTGACAAGATACGGAGAAGTGAACCAAATCCGTCTTCCTAATGAGATACAGAGAAG
65 ATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
*
35592144 TGGATTGAAACAATGAGACGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAA
130 TGGATTAAAACAATGAG-CGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAA
* *
35592209 GTGAAGCTCAATGTG
194 GCGAAGCTCAATGCG
* ** * * *
35592224 AGTGAAACTTCGAACCCCTATCTTCCTGATGAGATATTGAGAAGTGGGTTAAAGTAATAAAGCGG
1 AGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
* * * * * *
35592289 TCGTCTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGGTGAGATACAAAGAAGC
66 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGT
* * *
35592354 GGATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACAAAAAAGTAGACCAAATCGATGAA
131 GGATTAAAACAA-TGA-GCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAA
35592419 GCGAAGCTCAATGCG
194 GCGAAGCTCAATGCG
* *
35592434 AGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACTGAG-AGTGGGTCAAAACAATAAAGCGA
1 AGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
* * *
35592498 TCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCATATTCCTGATGAGATACAGAGAAGT
66 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGT
* * * * *
35592563 AGATCACAATAATGAAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAATGAA
131 GGATTAAAACAATG-AGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATC-GATGAA
* *
35592628 GCAAAGATCAATGCG
194 GCGAAGCTCAATGCG
* * *** * * * *
35592643 AGTGAAGCTTCAAACCTTTATATTCCTAATGAGATACAGAGAAGTGGGTCGAAGCAATAAAGCGG
1 AGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
** *
35592708 TCATCTTATTGATGAGATATAGAGAAGT
66 TCATCTTCCTGATGAGATACAGAGAAGT
35592736 AGACTAAGAT
Statistics
Matches: 435, Mismatches: 71, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
208 44 0.10
209 247 0.57
210 143 0.33
211 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (208 bp):
AGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGA
TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGT
GGATTAAAACAATGAGCGATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGC
GAAGCTCAATGCG
Found at i:35592598 original size:85 final size:84
Alignment explanation
Indices: 35592451--35592620 Score: 250
Period size: 85 Copynumber: 2.0 Consensus size: 84
35592441 CTTCGAACCC
* * * *
35592451 CCATCTTCCTGATGAGATACTGAGAGTGGGTCAAAACAATAAAGCGATCATCTTCCTAATGAGAT
1 CCATATTCCTGATGAGATACAGAGAGTAGATCAAAACAATAAAGCGATCATCTTCCTAATGAGAT
*
35592516 ACAGAGAAGTGGACCAAAT
66 ACAGAGAAGTAGACCAAAT
* * * *
35592535 CCATATTCCTGATGAGATACAGAGAAGTAGATCACAATAATGAAGCGATCATCTTCCTGATGAGA
1 CCATATTCCTGATGAGATACAGAG-AGTAGATCAAAACAATAAAGCGATCATCTTCCTAATGAGA
35592600 TACAGAGAAGTAGACCAAAT
65 TACAGAGAAGTAGACCAAAT
35592620 C
1 C
35592621 AAATGAAGCA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
84 22 0.29
85 54 0.71
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (84 bp):
CCATATTCCTGATGAGATACAGAGAGTAGATCAAAACAATAAAGCGATCATCTTCCTAATGAGAT
ACAGAGAAGTAGACCAAAT
Found at i:35594538 original size:57 final size:58
Alignment explanation
Indices: 35594461--35594587 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 58
35594451 AATAAATCAT
* * * * * *
35594461 ATTTTGACTCCTAAACTTCTTCAAAATTACATTATGACCC-AAACTTTTCCAAAATTAC
1 ATTTTAAC-CCTAAACTTCTTCAAAATCAAATTATAACCCTAAAATTTCCCAAAATTAC
* * *
35594519 ATTTTAACCCTAAACTTCTTGAAAATCAAATTTTAACCCTAAAATTTCCCAAAATTGC
1 ATTTTAACCCTAAACTTCTTCAAAATCAAATTATAACCCTAAAATTTCCCAAAATTAC
*
35594577 ATTTTTACCCT
1 ATTTTAACCCT
35594588 TTAAACTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 26 0.45
58 32 0.55
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (58 bp):
ATTTTAACCCTAAACTTCTTCAAAATCAAATTATAACCCTAAAATTTCCCAAAATTAC
Found at i:35594543 original size:29 final size:29
Alignment explanation
Indices: 35594461--35594613 Score: 116
Period size: 29 Copynumber: 5.2 Consensus size: 29
35594451 AATAAATCAT
*
35594461 ATTTTGACTCCTAAACTTCTTCAAAATTAC
1 ATTTTAAC-CCTAAACTTCTTCAAAATTAC
* *
35594491 ATTATGACCC-AAACTT-TTCCAAAATTAC
1 ATTTTAACCCTAAACTTCTT-CAAAATTAC
* * *
35594519 ATTTTAACCCTAAACTTCTTGAAAATCAA
1 ATTTTAACCCTAAACTTCTTCAAAATTAC
* * *
35594548 ATTTTAACCCTAAAATT-TCCCAAAATTGC
1 ATTTTAACCCTAAACTTCT-TCAAAATTAC
*
35594577 ATTTTTACCCTTTAAACTT-TTCCCAAAATTAC
1 ATTTTAACCC--TAAACTTCTT--CAAAATTAC
*
35594609 GTTTT
1 ATTTT
35594614 GACCTCGTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.02
28 24 0.24
29 44 0.45
30 9 0.09
31 7 0.07
32 12 0.12
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (29 bp):
ATTTTAACCCTAAACTTCTTCAAAATTAC
Found at i:35598819 original size:17 final size:17
Alignment explanation
Indices: 35598797--35598835 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35598787 CTCCACCTTG
* * *
35598797 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
35598814 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
35598831 ACAAG
1 ACAAG
35598836 TTCTTCCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:35615417 original size:31 final size:31
Alignment explanation
Indices: 35615379--35615460 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
35615369 GTGGAGATGG
*
35615379 GTAAGTTTACAATTTGGTCATTCAACTATTA
1 GTAAGTTTATAATTTGGTCATTCAACTATTA
** * *
35615410 GTAAGTTTATAACACT-GCCATTCAATTATTA
1 GTAAGTTTATAA-TTTGGTCATTCAACTATTA
*
35615441 GTAAATTTATAATTTGGTCA
1 GTAAGTTTATAATTTGGTCA
35615461 CTTTTCAGCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (31 bp):
GTAAGTTTATAATTTGGTCATTCAACTATTA
Found at i:35616179 original size:29 final size:31
Alignment explanation
Indices: 35616113--35616179 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
35616103 TTTGGATCAT
* * *
35616113 GATTATAATTGATCAATTTATAAAGTATATG
1 GATTAAAATTGATCAAATTATAAAGTATAGG
* *
35616144 AATTAAAATTGATCAAATTA-ATA-TATAGG
1 GATTAAAATTGATCAAATTATAAAGTATAGG
35616173 GATTAAA
1 GATTAAA
35616180 TCTATAACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 11 0.37
30 2 0.07
31 17 0.57
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (31 bp):
GATTAAAATTGATCAAATTATAAAGTATAGG
Found at i:35617130 original size:16 final size:16
Alignment explanation
Indices: 35617109--35617140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35617099 CAGTTGGTTC
35617109 AAATATCAGAGCTCAA
1 AAATATCAGAGCTCAA
35617125 AAATATCAGAGCTCAA
1 AAATATCAGAGCTCAA
35617141 TTGCAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (16 bp):
AAATATCAGAGCTCAA
Found at i:35624120 original size:2 final size:2
Alignment explanation
Indices: 35624108--35624140 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
35624098 CAGGTTTGTT
*
35624108 TA TA TA CA 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 TA TA T
35624141 GCACTTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35630932 original size:12 final size:12
Alignment explanation
Indices: 35630918--35630980 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
35630908 CCAAACAATC
*
35630918 AAAATAACAACC
1 AAAATAACAACA
* *
35630930 AAAACAGCAACA
1 AAAATAACAACA
35630942 AAAATAACAACA
1 AAAATAACAACA
*
35630954 AAAATAACAGCA
1 AAAATAACAACA
* *
35630966 AAAACAACACCA
1 AAAATAACAACA
35630978 AAA
1 AAA
35630981 CAGTAAAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.70, C:0.22, G:0.03, T:0.05
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:35630946 original size:24 final size:23
Alignment explanation
Indices: 35630918--35631005 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 23
35630908 CCAAACAATC
*
35630918 AAAATAACAACCAAAACAGCAACA
1 AAAACAAC-ACCAAAACAGCAACA
* * * * *
35630942 AAAATAACAACAAAAATAACAGCA
1 AAAACAAC-ACCAAAACAGCAACA
* *
35630966 AAAACAACACCAAAACAGTAAAA
1 AAAACAACACCAAAACAGCAACA
35630989 AAAACAACACCAAAACA
1 AAAACAACACCAAAACA
35631006 ACAGTATAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
23 26 0.49
24 27 0.51
ACGTcount: A:0.69, C:0.23, G:0.03, T:0.05
Consensus pattern (23 bp):
AAAACAACACCAAAACAGCAACA
Found at i:35630988 original size:20 final size:21
Alignment explanation
Indices: 35630959--35631005 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
35630949 CAACAAAAAT
35630959 AACAGC-AAAAACAACACCAA
1 AACAGCAAAAAACAACACCAA
*
35630979 AACAGTAAAAAAAACAACACCAA
1 AACAG--CAAAAAACAACACCAA
35631002 AACA
1 AACA
35631006 ACAGTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
23 18 0.78
ACGTcount: A:0.68, C:0.26, G:0.04, T:0.02
Consensus pattern (21 bp):
AACAGCAAAAAACAACACCAA
Found at i:35631003 original size:12 final size:12
Alignment explanation
Indices: 35630918--35631008 Score: 69
Period size: 12 Copynumber: 7.8 Consensus size: 12
35630908 CCAAACAATC
* *
35630918 AAAATAACAACC
1 AAAACAACAACA
*
35630930 AAAACAGCAACA
1 AAAACAACAACA
*
35630942 AAAATAACAACA
1 AAAACAACAACA
* *
35630954 AAAATAACAGCA
1 AAAACAACAACA
*
35630966 AAAACAAC-ACC
1 AAAACAACAACA
** *
35630977 AAAACAGTAAAA
1 AAAACAACAACA
*
35630989 AAAACAAC-ACC
1 AAAACAACAACA
35631000 AAAACAACA
1 AAAACAACA
35631009 GTATAATTTT
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
11 16 0.27
12 44 0.73
ACGTcount: A:0.69, C:0.23, G:0.03, T:0.04
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:35635089 original size:44 final size:44
Alignment explanation
Indices: 35635041--35635127 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
35635031 GTAAACTACA
*
35635041 AAAATAGTCACTTATGTATGGTTTAGATTACATTTCAGTCATTC
1 AAAATAGTCACTTACGTATGGTTTAGATTACATTTCAGTCATTC
*
35635085 AAAATAGTCACTTACGTATGGTTTATATTACATTTCAGTCATT
1 AAAATAGTCACTTACGTATGGTTTAGATTACATTTCAGTCATT
35635128 GAACTTTAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (44 bp):
AAAATAGTCACTTACGTATGGTTTAGATTACATTTCAGTCATTC
Found at i:35642545 original size:25 final size:24
Alignment explanation
Indices: 35642517--35642573 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
35642507 AATTCTCAAT
* *
35642517 AATTATTTTTGGTGTAGTGGTAATG
1 AATTATTTTTGGTGCA-AGGTAATG
35642542 AATT-TTTTTGGTGCAAGGTAATG
1 AATTATTTTTGGTGCAAGGTAATG
35642565 AATTTATTT
1 AA-TTATTT
35642574 GGTAAATGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 9 0.32
24 12 0.43
25 7 0.25
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (24 bp):
AATTATTTTTGGTGCAAGGTAATG
Found at i:35642561 original size:23 final size:24
Alignment explanation
Indices: 35642517--35642576 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
35642507 AATTCTCAAT
* *
35642517 AATTATTTTTGGTGTAGTGGTAATG
1 AATT-TTTTTGGTGCAGAGGTAATG
35642542 AATTTTTTTGGTGCA-AGGTAATG
1 AATTTTTTTGGTGCAGAGGTAATG
*
35642565 AATTTATTTGGT
1 AATTTTTTTGGT
35642577 AAATGCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 18 0.56
24 10 0.31
25 4 0.12
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (24 bp):
AATTTTTTTGGTGCAGAGGTAATG
Found at i:35647602 original size:21 final size:22
Alignment explanation
Indices: 35647566--35647606 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35647556 ACCATGAAAA
*
35647566 AAAATTTATTAAAATAAAATTT
1 AAAATTTATAAAAATAAAATTT
35647588 AAAATTT-TAAAAATAAAAT
1 AAAATTTATAAAAATAAAAT
35647607 ACTTGGTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTTATAAAAATAAAATTT
Found at i:35650345 original size:27 final size:28
Alignment explanation
Indices: 35650295--35650348 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
35650285 TGAATATTAA
*
35650295 TTTATAATTTTTTGTAGGAGTCAAAATT
1 TTTATAATTTTTTATAGGAGTCAAAATT
35650323 TTTATAATTTTTTCATA-GA-TCAAAAT
1 TTTATAATTTTTT-ATAGGAGTCAAAAT
35650349 ATAAGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 7 0.29
28 15 0.62
29 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (28 bp):
TTTATAATTTTTTATAGGAGTCAAAATT
Found at i:35651430 original size:7 final size:7
Alignment explanation
Indices: 35651418--35651445 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35651408 CGATGATGAA
35651418 AATATTT
1 AATATTT
35651425 AATATTT
1 AATATTT
35651432 AATATTT
1 AATATTT
35651439 AATATTT
1 AATATTT
35651446 TAAATTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATATTT
Found at i:35663949 original size:7 final size:7
Alignment explanation
Indices: 35663937--35663977 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
35663927 TTTTTTTCTA
35663937 AAAAAAG
1 AAAAAAG
35663944 AAAAAAG
1 AAAAAAG
*
35663951 AAAAAGG
1 AAAAAAG
35663958 AAAAAAG
1 AAAAAAG
*
35663965 CAAAAAG
1 AAAAAAG
35663972 AAAAAA
1 AAAAAA
35663978 CTTCGCTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35663961 original size:21 final size:21
Alignment explanation
Indices: 35663937--35663976 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35663927 TTTTTTTCTA
35663937 AAAAAAGAAAAAAGAAAAAGG
1 AAAAAAGAAAAAAGAAAAAGG
*
35663958 AAAAAAGCAAAAAGAAAAA
1 AAAAAAGAAAAAAGAAAAA
35663977 ACTTCGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAAAAAGG
Found at i:35670968 original size:5 final size:5
Alignment explanation
Indices: 35670958--35670985 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35670948 CGTCATGCAT
35670958 GGGGA GGGGA GGGGA GGGGA GGGGA GGG
1 GGGGA GGGGA GGGGA GGGGA GGGGA GGG
35670986 AAAAAGCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (5 bp):
GGGGA
Found at i:35671146 original size:30 final size:30
Alignment explanation
Indices: 35671110--35671190 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 30
35671100 ATCATTTTAA
35671110 TAAATTATATTTTTATCATTTATAAAAGAT
1 TAAATTATATTTTTATCATTTATAAAAGAT
* * *
35671140 TAAATTAAATTTTTAT-ATTTTTAAGAGAT
1 TAAATTATATTTTTATCATTTATAAAAGAT
* *
35671169 TAAAATATAATTTTATC-TTTAT
1 TAAATTATATTTTTATCATTTAT
35671191 TAATTTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 28 0.65
30 15 0.35
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (30 bp):
TAAATTATATTTTTATCATTTATAAAAGAT
Found at i:35671704 original size:24 final size:25
Alignment explanation
Indices: 35671675--35671736 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
35671665 ATTAATCAGG
*
35671675 GTTTAACT-GGAAAATAATAGGAGA
1 GTTTAACTAGGAAAACAATAGGAGA
*
35671699 GTTTAATTAGGGAAAACAATAGGAGA
1 GTTTAACTA-GGAAAACAATAGGAGA
*
35671725 GTTTAATTAGGA
1 GTTTAACTAGGA
35671737 GAAGAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 7 0.21
25 3 0.09
26 24 0.71
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.27
Consensus pattern (25 bp):
GTTTAACTAGGAAAACAATAGGAGA
Found at i:35671714 original size:26 final size:26
Alignment explanation
Indices: 35671683--35671735 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
35671673 GGGTTTAACT
*
35671683 GGAAAATAATAGGAGAGTTTAATTAG
1 GGAAAACAATAGGAGAGTTTAATTAG
35671709 GGAAAACAATAGGAGAGTTTAATTAG
1 GGAAAACAATAGGAGAGTTTAATTAG
35671735 G
1 G
35671736 AGAAGAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.28, T:0.25
Consensus pattern (26 bp):
GGAAAACAATAGGAGAGTTTAATTAG
Found at i:35682210 original size:23 final size:21
Alignment explanation
Indices: 35682177--35682219 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
35682167 ATAATTATAA
35682177 TAAAAAATTATGGTTTATAATTT
1 TAAAAAATTAT--TTTATAATTT
*
35682200 TAAAAAGTTATTTTATAATT
1 TAAAAAATTATTTTATAATT
35682220 ATATCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAAAAATTATTTTATAATTT
Found at i:35687426 original size:59 final size:58
Alignment explanation
Indices: 35687304--35687427 Score: 135
Period size: 59 Copynumber: 2.1 Consensus size: 58
35687294 GTAATTGAGG
* * * * *
35687304 ATTAAATTGATAGAATTTGTAAATGTGAGGATTAAATGTGTTGAATTATTTGAATTAAG
1 ATTAAATTGATAAAATGTGTAAATGTGAGGACTAAATGTGTT-AATTATCTGAATTAAA
* *
35687363 ATTAACTTGATAAAATGTGTAAATATTGAGGACTAAATGTGTT-ATTATACT-AATTAGAA
1 ATTAAATTGATAAAATGTGTAAAT-GTGAGGACTAAATGTGTTAATTAT-CTGAATTA-AA
35687422 ATTAAA
1 ATTAAA
35687428 ATTAAAATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
58 10 0.19
59 28 0.52
60 16 0.30
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (58 bp):
ATTAAATTGATAAAATGTGTAAATGTGAGGACTAAATGTGTTAATTATCTGAATTAAA
Found at i:35688597 original size:16 final size:16
Alignment explanation
Indices: 35688578--35688610 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35688568 TGCATTTTAG
35688578 AACATATACATTTGAA
1 AACATATACATTTGAA
*
35688594 AACATATATATTTGAA
1 AACATATACATTTGAA
35688610 A
1 A
35688611 TTTCTTTCAA
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:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (16 bp):
AACATATACATTTGAA
Found at i:35692112 original size:30 final size:29
Alignment explanation
Indices: 35692069--35692472 Score: 202
Period size: 29 Copynumber: 13.8 Consensus size: 29
35692059 TCTAGTCCCT
*
35692069 AAACTTTCCAAAATTCTATTTTTAACCTC
1 AAACTTTCCAAAATTCCATTTTTAACCTC
*
35692098 AAAAC-TTCCAAAAATTACCA-TTTTAGGCCT-
1 -AAACTTTCC-AAAATT-CCATTTTTA-ACCTC
35692128 AAACTTTCCAAAATTCCATTTTTAACCTC
1 AAACTTTCCAAAATTCCATTTTTAACCTC
*
35692157 GAAA-TTTCCAAAAATTACCA-TTTT-ACCCC
1 -AAACTTTCC-AAAATT-CCATTTTTAACCTC
35692186 TAAACTTTCCAAAATTCCATTTTTAA-CTC
1 -AAACTTTCCAAAATTCCATTTTTAACCTC
* * *
35692215 -GA-TTTGACCTAAAATTACC-GTTTT-ACCCC
1 AAACTTT--CC-AAAATT-CCATTTTTAACCTC
* *
35692244 TAAACTTTCTAAAATTCCATTTTTAGCCTC
1 -AAACTTTCCAAAATTCCATTTTTAACCTC
* * *
35692274 -GA-TTTCACATAAATTACCA-TTTTATCCCC
1 AAACTTTC-CA-AAATT-CCATTTTTAACCTC
*
35692303 AAACTTTCCAAAATTCCA-TTTTAAGCTC
1 AAACTTTCCAAAATTCCATTTTTAACCTC
* * * * *
35692331 -GATTTTACCCAAAATTATCA-TTTTACCCTT
1 AAACTTT--CCAAAATT-CCATTTTTAACCTC
35692361 AAACTTTCCAAAATTCCATTTTTAACC-C
1 AAACTTTCCAAAATTCCATTTTTAACCTC
** *
35692389 TGA-TTTCACCCAAAATTACCA-TTTTACCCTC
1 AAACTTT---CCAAAATT-CCATTTTTAACCTC
* * *
35692420 GAACTTTCTAAAATTCTATTTTTAAACC-C
1 AAACTTTCCAAAATTCCATTTTT-AACCTC
* * *
35692449 AAATTTTCTCGAAATTACATTTTT
1 AAACTTTC-CAAAATTCCATTTTT
35692473 TCCTCGAGAG
Statistics
Matches: 286, Mismatches: 47, Indels: 82
0.69 0.11 0.20
Matches are distributed among these distances:
26 3 0.01
27 12 0.04
28 31 0.11
29 124 0.43
30 88 0.31
31 22 0.08
32 6 0.02
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (29 bp):
AAACTTTCCAAAATTCCATTTTTAACCTC
Found at i:35692244 original size:58 final size:58
Alignment explanation
Indices: 35692065--35692444 Score: 443
Period size: 59 Copynumber: 6.5 Consensus size: 58
35692055 GCTCTCTAGT
* * * *
35692065 CCCTAAACTTTCCAAAATTCTATTTTTAACCTCAAAACTT-CCAAAAATTACCATTTTAG
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTC--GATTTACCAAAAATTACCATTTTAC
*
35692124 GCCTAAACTTTCCAAAATTCCATTTTTAACCTCGAAATTT-CCAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCG--ATTTACCAAAAATTACCATTTTAC
* *
35692183 CCCTAAACTTTCCAAAATTCCATTTTTAA-CTCGATTTGACCTAAAATTACCGTTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTT-ACCAAAAATTACCATTTTAC
* * *
35692241 CCCTAAACTTTCTAAAATTCCATTTTTAGCCTCGATTT-CACATAAATTACCATTTTATC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTAC-CAAAAATTACCATTTTA-C
* * *
35692300 CCC-AAACTTTCCAAAATTCCA-TTTTAAGCTCGATTTTACCCAAAATTATCATTTTAC
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTCGA-TTTACCAAAAATTACCATTTTAC
* *
35692357 CCTTAAACTTTCCAAAATTCCATTTTTAACC-CTGATTTCACCCAAAATTACCATTTTA-
1 CCCTAAACTTTCCAAAATTCCATTTTTAACCTC-GATTT-ACCAAAAATTACCATTTTAC
* * *
35692415 CCCTCGAACTTTCTAAAATTCTATTTTTAA
1 CCCT-AAACTTTCCAAAATTCCATTTTTAA
35692445 ACCCAAATTT
Statistics
Matches: 281, Mismatches: 26, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
56 4 0.01
57 14 0.05
58 121 0.43
59 142 0.51
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTACCAAAAATTACCATTTTAC
Found at i:35692345 original size:116 final size:114
Alignment explanation
Indices: 35692069--35692444 Score: 454
Period size: 116 Copynumber: 3.2 Consensus size: 114
35692059 TCTAGTCCCT
* * ** **
35692069 AAACTTTCCAAAATTCTATTTTTAACCTCAAAACTT-CCAAAAATTACCATTTTAGGCCTAAACT
1 AAACTTTCCAAAATTCCATTTTTAA-CTC-GATTTTACCAAAAATTACCATTTTACCCCTAAACT
35692133 TTCCAAAATTCCATTTTTAACCTCGAAATTTC-CAAAAATTACCATTTTACCCC
64 TTCCAAAATTCCATTTTTAACCTCG--ATTTCAC-AAAATTACCATTTTACCCC
* * *
35692186 TAAACTTTCCAAAATTCCATTTTTAACTCGATTTGACCTAAAATTACCGTTTTACCCCTAAACTT
1 -AAACTTTCCAAAATTCCATTTTTAACTCGATTTTACCAAAAATTACCATTTTACCCCTAAACTT
* *
35692251 TCTAAAATTCCATTTTTAGCCTCGATTTCACATAAATTACCATTTTATCCCC
65 TCCAAAATTCCATTTTTAACCTCGATTTCACA-AAATTACCATTTTA-CCCC
* * *
35692303 AAACTTTCCAAAATTCCA-TTTTAAGCTCGATTTTACCCAAAATTATCATTTTACCCTTAAACTT
1 AAACTTTCCAAAATTCCATTTTTAA-CTCGATTTTACCAAAAATTACCATTTTACCCCTAAACTT
35692367 TCCAAAATTCCATTTTTAACC-CTGATTTCACCCAAAATTACCATTTTACCCTC
65 TCCAAAATTCCATTTTTAACCTC-GATTTCA--CAAAATTACCATTTTACCC-C
* * *
35692420 GAACTTTCTAAAATTCTATTTTTAA
1 AAACTTTCCAAAATTCCATTTTTAA
35692445 ACCCAAATTT
Statistics
Matches: 227, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
115 13 0.06
116 98 0.43
117 84 0.37
118 32 0.14
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (114 bp):
AAACTTTCCAAAATTCCATTTTTAACTCGATTTTACCAAAAATTACCATTTTACCCCTAAACTTT
CCAAAATTCCATTTTTAACCTCGATTTCACAAAATTACCATTTTACCCC
Found at i:35704608 original size:201 final size:200
Alignment explanation
Indices: 35704235--35704854 Score: 832
Period size: 201 Copynumber: 3.1 Consensus size: 200
35704225 ACGGCGAGGT
* * * * * *
35704235 GGTCATCTTCTTGATGAGATACAGAGAATAATATCAATTCAATGCTCAACA-CAAGCCAATCTTC
1 GGTCATCTTCCTGATGAGATACAGAGAATAATACCAACTCAACGCTCAA-AGCGAGCAAATCTTC
* *
35704299 GTACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAACAATAAAATGGTTAGCTTCCTGAT
65 GTACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCTTGAT
* *
35704364 AAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAAGAGATCCAGAGAAGTGAATTAAAAACAA
130 AAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATT-AAAACAA
35704429 GTGATGC
194 GTGATGC
* * *
35704436 GGTTATCTTCCTGATGAGATACAGAGTAGAATACCAACTCAACGCTCAAAGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAATAATACCAACTCAACGCTCAAAGCGAGCAAATCTTCG
* * * * * *
35704501 TACCTAGCTTTCTGATGAGACACTGAGAAGCAGGTCAAAACAATAACATGGTTAGTTTCTTGATG
66 TACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCTTGATA
* * * * **
35704566 AGATACAGAGAAGTGAACCAAATTTGTCTGCCTGAGGAGATCCAGAGAAGCAAATTAAAACAACA
131 AGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGT
*
35704631 GAGGC
196 GATGC
* * * * * *
35704636 -ATCATGTTTCTGATGAGATATAGAGAATAATACCAACTCAACACTCAACGCGAGCAAATCTTCG
1 GGTCATCTTCCTGATGAGATACAGAGAATAATACCAACTCAACGCTCAAAGCGAGCAAATCTTCG
* * * * *
35704700 AACCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAAAGGTTAGCTTCTTGATA
66 TACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCTTGATA
* *
35704765 AGACACAGAGAAGTGGACCAAATTCGACTTCCTGAGGAGATCCAGAGAAGCGAATTAAAAC-AGA
131 AGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAG-
35704829 TGATTGC
195 TGA-TGC
35704836 GGTCATCTTCCTGATGAGA
1 GGTCATCTTCCTGATGAGA
35704855 CATAGGGAAG
Statistics
Matches: 357, Mismatches: 58, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
198 1 0.00
199 166 0.46
200 14 0.04
201 176 0.49
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (200 bp):
GGTCATCTTCCTGATGAGATACAGAGAATAATACCAACTCAACGCTCAAAGCGAGCAAATCTTCG
TACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCTTGATA
AGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATTAAAACAAGT
GATGC
Found at i:35707417 original size:59 final size:59
Alignment explanation
Indices: 35707221--35707486 Score: 333
Period size: 60 Copynumber: 4.5 Consensus size: 59
35707211 GCTCTCTAGT
* * *
35707221 CCCCAAACTTTCCAAAATTCTATTTTTGACCCCGATTTCACCCAAAAATTACCGTTTTA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAAATTACCATTTTA
* * ** *
35707280 CCCCTAAACTTTCCAAAATTCCATTTTTGACCCTGATTTCATACAAAAATTATCATTTTA
1 CCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAAATTACCATTTTA
*
35707340 CCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CCTAAAATTACCATTTTA
1 -CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAAATTACCATTTTA
* * *
35707399 TCCCCAAACTTTCTAAAATT-C-TGTTTTAACCCCAATTTTACCC-AAAATTACCATTTTA
1 -CCCCAAACTTTCCAAAATTCCAT-TTTTAACCCCGATTTCACCCAAAAATTACCATTTTA
* *
35707457 CCCTCGAACTTTCCAAAATTCTATTTTTAA
1 CCC-CAAACTTTCCAAAATTCCATTTTTAA
35707487 ACCCAAATTT
Statistics
Matches: 182, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.02
58 45 0.25
59 45 0.25
60 84 0.46
61 4 0.02
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCCAAAAATTACCATTTTA
Found at i:35707520 original size:59 final size:58
Alignment explanation
Indices: 35707226--35707522 Score: 244
Period size: 60 Copynumber: 5.0 Consensus size: 58
35707216 CTAGTCCCCA
* * * * * *
35707226 AACTTTCCAAAATTCTATTTTTGACCCCGATTTCACCCAAAAATTACCGTTTTACCC-CTA
1 AACTTTCCAAAATTCTATTTTTAACCCCAATTT-TCCC-AAAATTACCATTTTTCCCTC-G
* * ** * * * * * *
35707286 AACTTTCCAAAATTCCATTTTTGACCCTGATTTCATACAAAAATTATCATTTTACCCCCA
1 AACTTTCCAAAATTCTATTTTTAACCCCAATTT--TCCCAAAATTACCATTTTTCCCTCG
* * *
35707346 AACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCTAAAATTACCATTTTATCCC-CA
1 AACTTTCCAAAATTCTATTTTTAACCCCAATTTTC-CC-AAAATTACCATTTT-TCCCTCG
* * *
35707405 AACTTTCTAAAATTCT-GTTTTAACCCCAATTTTACCCAAAATTACCATTTTACCCTCG
1 AACTTTCCAAAATTCTATTTTTAACCCCAATTTT-CCCAAAATTACCATTTTTCCCTCG
* *
35707463 AACTTTCCAAAATTCTATTTTTAAACCCAAATTTTCCCGAAATTA-CATTTTTGCCCTCG
1 AACTTTCCAAAATTCTATTTTT-AACCCCAATTTTCCCAAAATTACCATTTTT-CCCTCG
35707522 A
1 A
35707523 GAGCCAAAAA
Statistics
Matches: 201, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
57 4 0.02
58 48 0.24
59 56 0.28
60 91 0.45
61 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (58 bp):
AACTTTCCAAAATTCTATTTTTAACCCCAATTTTCCCAAAATTACCATTTTTCCCTCG
Found at i:35710826 original size:31 final size:32
Alignment explanation
Indices: 35710757--35710826 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
35710747 TCTTGACATC
*
35710757 AAAC-TTTGAGGAATCCTAATTAAACTTTTCA
1 AAACTTTTGAGGAATCCTAATTAAAATTTTCA
* *
35710788 AAACTTTTGAGGAAT-TTAATTAAAATTTTTA
1 AAACTTTTGAGGAATCCTAATTAAAATTTTCA
35710819 AAACTTTT
1 AAACTTTT
35710827 ACCAGACTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 25 0.71
32 10 0.29
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (32 bp):
AAACTTTTGAGGAATCCTAATTAAAATTTTCA
Found at i:35711500 original size:32 final size:31
Alignment explanation
Indices: 35711464--35711764 Score: 206
Period size: 32 Copynumber: 9.2 Consensus size: 31
35711454 GATTCAAGGA
* * *
35711464 AGGTTCGAGTTTGAGTTTAGTATTGTTGTTCG
1 AGGTT-GAGTTTGGGTTTAGTATCGTGGTTCG
*
35711496 AGGTTTGGGTTTGGGTTTAGTATCGTGGTTCG
1 AGG-TTGAGTTTGGGTTTAGTATCGTGGTTCG
* * *
35711528 AGGTTTAAGTTTGGATTTAGTATCATGGTTCG
1 AGG-TTGAGTTTGGGTTTAGTATCGTGGTTCG
* *
35711560 AGGTTTAGGTTTGGGTTTAGTATCGTGGTTTG
1 AGGTTGA-GTTTGGGTTTAGTATCGTGGTTCG
*
35711592 AGGTTTAGATTTGGGTTTAGTATCGTAGTATAGTGGTTCG
1 AGGTTGAG-TTTGGGTTTAGTATC--------GTGGTTCG
* * * *
35711632 AGATTTAGATTTGAGTTTAGTATCGTTGTTCG
1 AGGTTGAG-TTTGGGTTTAGTATCGTGGTTCG
* * * * *
35711664 AAGTTTAGGTTTGAGTTTAATATCGTGGTTCA
1 AGGTTGA-GTTTGGGTTTAGTATCGTGGTTCG
* * * * *
35711696 AAGTTTAGGTTTGGATTTAGTATAGTGGTTCAA
1 AGGTTGA-GTTTGGGTTTAGTATCGTGGTTC-G
* * *
35711729 AGTTTAAGTTTGGATTTAGTATCGTGGTTCG
1 AGGTTGAGTTTGGGTTTAGTATCGTGGTTCG
35711760 AGGTT
1 AGGTT
35711765 CATAATTTGA
Statistics
Matches: 225, Mismatches: 31, Indels: 27
0.80 0.11 0.10
Matches are distributed among these distances:
31 8 0.04
32 180 0.80
33 8 0.04
40 29 0.13
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (31 bp):
AGGTTGAGTTTGGGTTTAGTATCGTGGTTCG
Found at i:35711548 original size:64 final size:64
Alignment explanation
Indices: 35711471--35711764 Score: 297
Period size: 64 Copynumber: 4.5 Consensus size: 64
35711461 GGAAGGTTCG
* * * *
35711471 AGTTT-GAGTTTAGTATTGTTGTTCGAGGTTTGGGTTTGGGTTTAGTATCGTGGTTCGAGGTTTA
1 AGTTTGGA-TTTAGTATCGTGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTCGAAGTTTA
* * *
35711535 AGTTTGGATTTAGTATCATGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTTGAGGTTT-
1 AGTTTGGATTTAGTATCGTGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTCGAAGTTTA
* * * * *
35711598 AGATTTGGGTTTAGTATCGTAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCGTTGTTC
1 AG-TTT-GG---A-T-T--TAGTATCGTGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTC
35711663 GAAGTTTA
57 GAAGTTTA
* * * * * * *
35711671 GGTTT-GAGTTTAATATCGTGGTTCAAAGTTTAGGTTTGGATTTAGTATAGTGGTTCAAAGTTTA
1 AGTTTGGA-TTTAGTATCGTGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTCGAAGTTTA
35711735 AGTTTGGATTTAGTATCGTGGTTCGAGGTT
1 AGTTTGGATTTAGTATCGTGGTTCGAGGTT
35711765 CATAATTTGA
Statistics
Matches: 189, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
63 2 0.01
64 124 0.66
65 6 0.03
66 1 0.01
67 3 0.02
68 1 0.01
69 1 0.01
70 2 0.01
72 48 0.25
73 1 0.01
ACGTcount: A:0.19, C:0.05, G:0.31, T:0.45
Consensus pattern (64 bp):
AGTTTGGATTTAGTATCGTGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTCGAAGTTTA
Found at i:35711628 original size:40 final size:40
Alignment explanation
Indices: 35711577--35711657 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
35711567 GGTTTGGGTT
* * * *
35711577 TAGTATCGTGGTTTGAGGTTTAGATTTGGGTTTAGTATCG
1 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCG
35711617 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCG
1 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCG
35711657 T
1 T
35711658 TGTTCGAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (40 bp):
TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCG
Found at i:35711652 original size:104 final size:104
Alignment explanation
Indices: 35711513--35711718 Score: 272
Period size: 104 Copynumber: 2.0 Consensus size: 104
35711503 GGTTTGGGTT
* * * *
35711513 TAGTATCGTGGTTCGAGGTTTAAGTTTGGATTTAGTATCATGGTTCGAGGTTTAGGTTTGGGTTT
1 TAGTATAGTGGTTCGAGATTTAAGTTTGGATTTAGTATCATGGTTCGAAGTTTAGGTTTGAGTTT
* ** * *
35711578 AGTATCGTGGTTTGAGGTTTAGATTTGGGTTTAGTATCG
66 AATATCGTGGTTCAAAGTTTAGATTTGGATTTAGTATCG
* *
35711617 TAGTATAGTGGTTCGAGATTT-AGATTT-GAGTTTAGTATCGTTGTTCGAAGTTTAGGTTTGAGT
1 TAGTATAGTGGTTCGAGATTTAAG-TTTGGA-TTTAGTATCATGGTTCGAAGTTTAGGTTTGAGT
*
35711680 TTAATATCGTGGTTCAAAGTTTAGGTTTGGATTTAGTAT
64 TTAATATCGTGGTTCAAAGTTTAGATTTGGATTTAGTAT
35711719 AGTGGTTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
103 4 0.05
104 84 0.95
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (104 bp):
TAGTATAGTGGTTCGAGATTTAAGTTTGGATTTAGTATCATGGTTCGAAGTTTAGGTTTGAGTTT
AATATCGTGGTTCAAAGTTTAGATTTGGATTTAGTATCG
Found at i:35711725 original size:136 final size:136
Alignment explanation
Indices: 35711481--35711753 Score: 343
Period size: 136 Copynumber: 2.0 Consensus size: 136
35711471 AGTTTGAGTT
* * * * * * *
35711481 TAGTATTGTTGTTCGAGGTTTGGGTTTGGGTTTAGTATCGTGGTTCGAGGTTTAAGTTTGGATTT
1 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCGTGGTTCGAAGTTTAAGTTTGGATTT
* * * * * ** * *
35711546 AGTATCATGGTTCGAGGTTTAGGTTTGGGTTTAGTATCGTGGTTTGAGGTTT-AGATTTGGGTTT
66 AATATCATGGTTCAAAGTTTAGGTTTGGATTTAGTATAGTGGTTCAAAGTTTAAG-TTTGGATTT
35711610 AGTATCG
130 AGTATCG
* *
35711617 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCGTTGTTCGAAGTTTAGGTTT-GAGTT
1 TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCGTGGTTCGAAGTTTAAGTTTGGA-TT
*
35711681 TAATATCGTGGTTCAAAGTTTAGGTTTGGATTTAGTATAGTGGTTCAAAGTTTAAGTTTGGATTT
65 TAATATCATGGTTCAAAGTTTAGGTTTGGATTTAGTATAGTGGTTCAAAGTTTAAGTTTGGATTT
35711746 AGTATCG
130 AGTATCG
35711753 T
1 T
35711754 GGTTCGAGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
135 2 0.02
136 112 0.97
137 2 0.02
ACGTcount: A:0.20, C:0.05, G:0.30, T:0.45
Consensus pattern (136 bp):
TAGTATAGTGGTTCGAGATTTAGATTTGAGTTTAGTATCGTGGTTCGAAGTTTAAGTTTGGATTT
AATATCATGGTTCAAAGTTTAGGTTTGGATTTAGTATAGTGGTTCAAAGTTTAAGTTTGGATTTA
GTATCG
Found at i:35723442 original size:21 final size:19
Alignment explanation
Indices: 35723418--35723458 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35723408 AATATATTTT
35723418 TAAATAATTTTTAATAATTAA
1 TAAATAA-TTTTAA-AATTAA
*
35723439 TAAATTATTTTAAAATTAA
1 TAAATAATTTTAAAATTAA
35723458 T
1 T
35723459 TATACATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATAATTTTAAAATTAA
Found at i:35723506 original size:22 final size:24
Alignment explanation
Indices: 35723468--35723517 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
35723458 TTATACATGA
*
35723468 AATATTTTAAAATTTTA-AAT-AT
1 AATATTTTAAAAATTTACAATAAT
35723490 AATA-TTTAAATAATTTACAATAAT
1 AATATTTTAAA-AATTTACAATAAT
35723514 AATA
1 AATA
35723518 CATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.25
22 9 0.38
23 3 0.12
24 6 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATATTTTAAAAATTTACAATAAT
Found at i:35723526 original size:55 final size:56
Alignment explanation
Indices: 35723377--35723527 Score: 146
Period size: 55 Copynumber: 2.6 Consensus size: 56
35723367 AATTAGATAT
** * *
35723377 TATTTAAATAATTTAGTATAATTATACATAAAATATATTTTTAAATAATTTTTAATAAT
1 TATTTAAATAATTTAAAATAATTATACAT-AAA-ATA-TTTTAAATAATTTTAAATAAA
* * *
35723436 TA-ATAAATTATTTTAAAATTAATTATACATGAAATATTTT-AA-AATTTTAAATATAA
1 TATTTAAA-TAATTTAAAA-TAATTATACATAAAATATTTTAAATAATTTTAAATA-AA
* *
35723492 TATTTAAATAATTTACAATAATAATACATAAAATAT
1 TATTTAAATAATTTAAAATAATTATACATAAAATAT
35723528 AAAATAATCT
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
55 26 0.34
56 13 0.17
57 8 0.11
58 7 0.09
59 11 0.14
60 11 0.14
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (56 bp):
TATTTAAATAATTTAAAATAATTATACATAAAATATTTTAAATAATTTTAAATAAA
Found at i:35724161 original size:15 final size:15
Alignment explanation
Indices: 35724138--35724190 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
35724128 AAGACCAACA
*
35724138 TGAACTAATCAAATC
1 TGAAATAATCAAATC
*
35724153 TGAAATAATCCAAACTT
1 TGAAATAAT-CAAA-TC
* *
35724170 TGAAAGAATCAAACC
1 TGAAATAATCAAATC
35724185 TGAAAT
1 TGAAAT
35724191 CACTTAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 13 0.43
16 8 0.27
17 9 0.30
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (15 bp):
TGAAATAATCAAATC
Found at i:35724182 original size:16 final size:16
Alignment explanation
Indices: 35724144--35724189 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
35724134 AACATGAACT
*
35724144 AATCAAA-TCTGAAAT
1 AATCAAACTCTGAAAG
*
35724159 AATCCAAACTTTGAAAG
1 AAT-CAAACTCTGAAAG
35724176 AATCAAAC-CTGAAA
1 AATCAAACTCTGAAA
35724190 TCACTTAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 9 0.35
17 9 0.35
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (16 bp):
AATCAAACTCTGAAAG
Found at i:35741820 original size:261 final size:259
Alignment explanation
Indices: 35741356--35742109 Score: 964
Period size: 246 Copynumber: 2.9 Consensus size: 259
35741346 CTGTTGAAAT
* * * * *
35741356 TTCTGAACATAAATCCAAAAGATTAGCCAAAGCCGAAGCCAATGCTAGCCTATCAACTGCAGCAG
1 TTCTGAACACAAATCCAAAATATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCAGCAG
* * *
35741421 GAGAAACTAACAGCTTGAATTACATAAAAAATGGTGAACTGATACAAAATATGCCTCGACAAGAA
66 GAGAAACTAACAGCTTGAA-TACATAAAAAATGGTGAACAGATACAAAATATGTCTCGTCAAGAA
35741486 GGTATCATGGACACATCACAATCAATGGAAGATAAT-TGCAAGGCCATTGATAGCATCCCAGATG
130 GGTATCATGGACACATCACAATCAATGGAAGATAATCT-CAAGGCCATTGATAGCATCCCAGATG
*
35741550 TTGATAATGCTACAAAGGGTACATCTATCGACCATGACATTGCTGTGAAAGCATCAAAGCCAAAA
194 TTGATAATGCTACAAAGGGTACATCTATC-ACCATGACATTGCTGTGAAAGCATCAAAACCAAAA
35741615 GA
258 GA
*
35741617 TTCTGAACACAAATCCAAAATATTAGCCGAAGTTGAAGCCAATGCTAGCCTATCAACTTCAGCAG
1 TTCTGAACACAAATCCAAAATATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCAGCAG
* * * *
35741682 GAGAAACTAACAGCTTGAATAGCATAAAAAATGGTCAACAGATGCAGAATATGTCTTGTCAAGAA
66 GAGAAACTAACAGCTTGAATA-CATAAAAAATGGTGAACAGATACAAAATATGTCTCGTCAAGAA
* *
35741747 GGTATCATGGACACGTCACTATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAGATGT
130 GGTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAGATGT
* *
35741812 TGATAATGCTACAAAGGGTACATCTAT---C---A-A---C----AAAGAATCAAAACCAAACGA
195 TGATAATGCTACAAAGGGTACATCTATCACCATGACATTGCTGTGAAAGCATCAAAACCAAAAGA
* * * * * *
35741863 TTCTGAACACAAGTCCAAAATTTTAGCTGAAGCTGAAGCCAACGCTGGCTTATCAACTTCAGCAG
1 TTCTGAACACAAATCCAAAATATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCAGCAG
* ** * * *
35741928 GAGAAGCTAAGGGCTTGAATAACATAAAAAATGGTGAAAAAATACAAAATATGTCTCGTCGAGAA
66 GAGAAACTAACAGCTTGAAT-ACATAAAAAATGGTGAACAGATACAAAATATGTCTCGTCAAGAA
** * ** * * *
35741993 GGTATCATGGATGCATCACCATCAGGGGAAGATAATCTTAAGGCCATTGATAGCATCCTAGGTGT
130 GGTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAGATGT
* **
35742058 TAATACCGCTACAAAGGGTACATCTATCAACCATGACATTG-TGGTGAAAGCA
195 TGATAATGCTACAAAGGGTACATCTATC-ACCATGACATTGCT-GTGAAAGCA
35742110 CTAGCACCAA
Statistics
Matches: 426, Mismatches: 48, Indels: 38
0.83 0.09 0.07
Matches are distributed among these distances:
246 208 0.49
247 1 0.00
250 2 0.00
253 2 0.00
254 2 0.00
257 1 0.00
260 2 0.00
261 207 0.49
262 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (259 bp):
TTCTGAACACAAATCCAAAATATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCAGCAG
GAGAAACTAACAGCTTGAATACATAAAAAATGGTGAACAGATACAAAATATGTCTCGTCAAGAAG
GTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAGATGTT
GATAATGCTACAAAGGGTACATCTATCACCATGACATTGCTGTGAAAGCATCAAAACCAAAAGA
Found at i:35749505 original size:10 final size:10
Alignment explanation
Indices: 35749479--35749521 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
35749469 TATGTTTTCC
35749479 ATAATATATTA
1 ATAATAT-TTA
*
35749490 ATAATATTTT
1 ATAATATTTA
35749500 ATAATATTTA
1 ATAATATTTA
*
35749510 ATGA-ATTTA
1 ATAATATTTA
35749519 ATA
1 ATA
35749522 CTTTTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 14 0.50
11 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
ATAATATTTA
Found at i:35754067 original size:6 final size:6
Alignment explanation
Indices: 35754053--35754086 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
35754043 TAAATTTAAA
*
35754053 TATATAT TATGAT TATAAT TATAAT TATAAT TAT
1 TATA-AT TATAAT TATAAT TATAAT TATAAT TAT
35754087 TACAACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 22 0.88
7 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TATAAT
Found at i:35756337 original size:18 final size:17
Alignment explanation
Indices: 35756316--35756363 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
35756306 TAGTATGTAT
*
35756316 TTTATTTAATCTTAAAAA
1 TTTATTTAAT-ATAAAAA
*
35756334 TTTAATATAATATAAAAA
1 TTT-ATTTAATATAAAAA
*
35756352 CTTATTTAATAT
1 TTTATTTAATAT
35756364 TTTAGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 11 0.44
19 6 0.24
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTAATATAAAAA
Found at i:35762031 original size:2 final size:2
Alignment explanation
Indices: 35762024--35762057 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
35762014 AAGTGTATTT
35762024 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35762058 CCAAAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35763294 original size:18 final size:19
Alignment explanation
Indices: 35763273--35763310 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
35763263 GATTTTTTTT
35763273 AAATATAAAAT-TTTATAA
1 AAATATAAAATATTTATAA
* *
35763291 AAATGTAAATTATTTATAA
1 AAATATAAAATATTTATAA
35763310 A
1 A
35763311 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
AAATATAAAATATTTATAA
Found at i:35763805 original size:27 final size:27
Alignment explanation
Indices: 35763767--35763822 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
35763757 GCAATGGACT
* *
35763767 AGAGTTTGCTAGATTGATTACCAAACA
1 AGAGTTTGCTAGATTCACTACCAAACA
*
35763794 AGAGTTTGCTAGATTCACTACCATACA
1 AGAGTTTGCTAGATTCACTACCAAACA
35763821 AG
1 AG
35763823 GAATGACGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (27 bp):
AGAGTTTGCTAGATTCACTACCAAACA
Found at i:35765562 original size:21 final size:21
Alignment explanation
Indices: 35765538--35765585 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35765528 TTCTATTAAA
*
35765538 AAAATTATTAAAT-GAATTTAT
1 AAAATTAATAAATAGAATTT-T
35765559 AAAA-TAATAAATAAGAATTTT
1 AAAATTAATAAAT-AGAATTTT
35765580 AAAATT
1 AAAATT
35765586 TATATATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 7 0.30
21 9 0.39
22 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAATTAATAAATAGAATTTT
Found at i:35771875 original size:33 final size:33
Alignment explanation
Indices: 35771831--35771897 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
35771821 TCGTTTTCGG
* *
35771831 GAAAGGGTTGGTGGGAGGAGAAAGATACAGTTC
1 GAAAGGCTTGGTGGGAGGAGAAAAATACAGTTC
35771864 GAAAGGCTTGGTGGGAGGAGAAAAATACAGTTC
1 GAAAGGCTTGGTGGGAGGAGAAAAATACAGTTC
35771897 G
1 G
35771898 GCTATGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.40, T:0.18
Consensus pattern (33 bp):
GAAAGGCTTGGTGGGAGGAGAAAAATACAGTTC
Found at i:35775695 original size:42 final size:42
Alignment explanation
Indices: 35775636--35775838 Score: 210
Period size: 42 Copynumber: 4.8 Consensus size: 42
35775626 AGCTGAATCA
* * * *
35775636 TAGGACCGGTCCCGCCTTCTATAGTATTGATCATCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGAGAG
* *
35775678 TAGGAACGATCCCGCCTTCTGTAGTATCGATCATCAGGTGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGAGAG
* * * * *
35775720 TAGGAACGGTCCCGCCTGCGGTAGTAAC-AGTCATCGGGAGTG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGA-TCATCAGGAGAG
* * ** *
35775762 TAAGATCTATCACGCCTTCTGTAGTATCGATCATCAGGAGAG
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGAGAG
* * * *
35775804 TAGGAACGGTCCCGTCTTCTATAGTAGCGGTCATC
1 TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATC
35775839 TGACGATCTG
Statistics
Matches: 129, Mismatches: 30, Indels: 4
0.79 0.18 0.02
Matches are distributed among these distances:
41 1 0.01
42 127 0.98
43 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (42 bp):
TAGGAACGGTCCCGCCTTCTGTAGTATCGATCATCAGGAGAG
Found at i:35778540 original size:22 final size:25
Alignment explanation
Indices: 35778492--35778539 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
35778482 TGTTGATCTC
*
35778492 TTTTTTTTGCTTATTATGTGTTGTG
1 TTTTTTTTGATTATTATGTGTTGTG
*
35778517 TTTTTTTTTATTATTAT-TGTTGT
1 TTTTTTTTGATTATTATGTGTTGT
35778540 TAAAACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.10, C:0.02, G:0.15, T:0.73
Consensus pattern (25 bp):
TTTTTTTTGATTATTATGTGTTGTG
Found at i:35779299 original size:13 final size:13
Alignment explanation
Indices: 35779281--35779330 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
35779271 CTTAAATCAA
*
35779281 ACTTTTCAAAAAT
1 ACTTTTCAAAAAC
35779294 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
35779307 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
35779320 ACTTTTCAAAA
1 ACTTTTCAAAA
35779331 GCAATGCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:35781899 original size:16 final size:15
Alignment explanation
Indices: 35781855--35781923 Score: 50
Period size: 16 Copynumber: 4.3 Consensus size: 15
35781845 ACAAGTCAAC
35781855 AATTCAATATTAAATT
1 AATTCAA-ATTAAATT
35781871 AA-TCGAAACTTAAATT
1 AATTC-AAA-TTAAATT
35781887 AATTCAACATTAAAATT
1 AATTCAA-ATT-AAATT
* * *
35781904 GATACAAATTTAAAAT
1 AATTCAAA-TTAAATT
35781920 AATT
1 AATT
35781924 TAATCTTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 3 0.07
16 24 0.57
17 15 0.36
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (15 bp):
AATTCAAATTAAATT
Found at i:35781917 original size:33 final size:32
Alignment explanation
Indices: 35781855--35781923 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 32
35781845 ACAAGTCAAC
* *
35781855 AATTCAATATTAAATTAATCGAAACTTAAATT
1 AATTCAACATTAAATTAATCGAAACTTAAAAT
* *
35781887 AATTCAACATTAAAATTGATAC-AAATTTAAAAT
1 AATTCAACATT-AAATTAAT-CGAAACTTAAAAT
35781920 AATT
1 AATT
35781924 TAATCTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 10 0.32
33 20 0.65
34 1 0.03
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (32 bp):
AATTCAACATTAAATTAATCGAAACTTAAAAT
Found at i:35802300 original size:31 final size:31
Alignment explanation
Indices: 35802264--35802322 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
35802254 AGTAGCCCAA
*
35802264 TGACTTAAAT-AAAAGCTTTCGAATAATTTAG
1 TGACTTAAATGAAAA-CTTTCAAATAATTTAG
35802295 TGACTTAAATGAAAACTTTCAAATAATT
1 TGACTTAAATGAAAACTTTCAAATAATT
35802323 CAGTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAATTTAG
Found at i:35802514 original size:2 final size:2
Alignment explanation
Indices: 35802493--35802540 Score: 62
Period size: 2 Copynumber: 23.5 Consensus size: 2
35802483 TTATGCATAA
*
35802493 AT AT AT AC AT GAT AT GAT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35802536 AT AT A
1 AT AT A
35802541 AGTTATAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 36 0.88
3 4 0.10
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:35808282 original size:6 final size:6
Alignment explanation
Indices: 35808271--35808300 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35808261 AAGAAAGGAA
35808271 AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG
1 AGGGGG AGGGGG AGGGGG AGGGGG AGGGGG
35808301 GAGACTATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.83, T:0.00
Consensus pattern (6 bp):
AGGGGG
Found at i:35810292 original size:13 final size:13
Alignment explanation
Indices: 35810274--35810298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35810264 TTCTTTTCTA
35810274 ATTTTAAATCTTG
1 ATTTTAAATCTTG
35810287 ATTTTAAATCTT
1 ATTTTAAATCTT
35810299 TTCTCACCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTTAAATCTTG
Found at i:35813023 original size:18 final size:18
Alignment explanation
Indices: 35813000--35813036 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35812990 TTTGTGATCA
35813000 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
35813018 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
35813036 A
1 A
35813037 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:35814566 original size:14 final size:15
Alignment explanation
Indices: 35814537--35814569 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35814527 ACATTAACAA
35814537 TATTTATTACTTTTT
1 TATTTATTACTTTTT
*
35814552 TATTTA-TAGTTTTT
1 TATTTATTACTTTTT
35814566 TATT
1 TATT
35814570 AGAGTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (15 bp):
TATTTATTACTTTTT
Found at i:35815648 original size:28 final size:28
Alignment explanation
Indices: 35815594--35815648 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
35815584 AATTGTCTGA
*
35815594 TTATTTTGTTAATTAAAAATAATTTTAT
1 TTATTTTGTTAATTAAAAATAAATTTAT
35815622 TTATTTAT-TTAATATAAAAA-AAATTTA
1 TTATTT-TGTTAAT-TAAAAATAAATTTA
35815649 GCAACAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATTTTGTTAATTAAAAATAAATTTAT
Found at i:35828578 original size:24 final size:24
Alignment explanation
Indices: 35828546--35828595 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
35828536 ATATTATGTT
35828546 ATAAAAATTA-ATTATATATATTAA
1 ATAAAAATTATA-TATATATATTAA
* *
35828570 ATAATAATTATATATTTATATTAA
1 ATAAAAATTATATATATATATTAA
35828594 AT
1 AT
35828596 CAGTAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAAAATTATATATATATATTAA
Found at i:35830799 original size:12 final size:12
Alignment explanation
Indices: 35830786--35830860 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 12
35830776 TCAAATAACC
*
35830786 AAAATAACAACC
1 AAAATAACAACA
* * *
35830798 AAAACAGCAGCA
1 AAAATAACAACA
*
35830810 AAAATAATAGA-A
1 AAAATAACA-ACA
*
35830822 AAAATAGCAACA
1 AAAATAACAACA
*
35830834 AAAATAACAATA
1 AAAATAACAACA
*
35830846 AAAATAACACCA
1 AAAATAACAACA
35830858 AAA
1 AAA
35830861 TAGTAAAAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
11 1 0.02
12 46 0.98
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.09
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:35830850 original size:24 final size:23
Alignment explanation
Indices: 35830786--35830882 Score: 79
Period size: 24 Copynumber: 4.1 Consensus size: 23
35830776 TCAAATAACC
* * *
35830786 AAAATAACAACCAAAACAGCAGCA
1 AAAATAACAA-AAAAATAGCAACA
*
35830810 AAAATAATAGAAAAAATAGCAACA
1 AAAATAACA-AAAAAATAGCAACA
* *
35830834 AAAATAACAATAAAAATAAC-ACC
1 AAAATAACAA-AAAAATAGCAACA
** *
35830857 AAAATAGTAAAAAAATAGCACCA
1 AAAATAACAAAAAAATAGCAACA
35830880 AAA
1 AAA
35830883 CAACAACCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
22 8 0.14
23 15 0.26
24 34 0.59
25 1 0.02
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAATAACAAAAAAATAGCAACA
Found at i:35830904 original size:22 final size:21
Alignment explanation
Indices: 35830879--35830960 Score: 69
Period size: 22 Copynumber: 3.9 Consensus size: 21
35830869 AAATAGCACC
* *
35830879 AAAACAACAACCAAAACAAT-A
1 AAAATAAC-ACCAAAACAGTAA
* *
35830900 AAAA-AACACTAAAATAGTAA
1 AAAATAACACCAAAACAGTAA
*
35830920 AAACATAACACCAAAACAGCAA
1 AAA-ATAACACCAAAACAGTAA
*
35830942 AAAATAGCAACCAAAACAG
1 AAAATAAC-ACCAAAACAG
35830961 CACCACAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.16
20 7 0.14
21 9 0.18
22 26 0.52
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAATAACACCAAAACAGTAA
Found at i:35834260 original size:4 final size:4
Alignment explanation
Indices: 35834251--35834280 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
35834241 CTAATTTCTC
35834251 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT
35834281 TTATTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:35835257 original size:38 final size:38
Alignment explanation
Indices: 35835206--35835287 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
35835196 GTGACAAAGC
35835206 TTTTTTAATTATGTTCTTTTCAACATATAGATTCAACG
1 TTTTTTAATTATGTTCTTTTCAACATATAGATTCAACG
* * * *
35835244 TTTTTTAGTTATGTTTTTTTCAACATATGGTTTCAACG
1 TTTTTTAATTATGTTCTTTTCAACATATAGATTCAACG
35835282 TTTTTT
1 TTTTTT
35835288 CTCCCAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.56
Consensus pattern (38 bp):
TTTTTTAATTATGTTCTTTTCAACATATAGATTCAACG
Found at i:35854278 original size:43 final size:43
Alignment explanation
Indices: 35854179--35854278 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 43
35854169 TAATATGTGT
* * * * * *
35854179 AATTTAAATTATTTTTAAATGTGTGATTATCATAATTTTTATTA
1 AATTTTAATT-TTTTCAAATGTATAATTATCACAACTTTTATTA
* * *
35854223 AATTATATTTTTTTCAAATGTATAATTATCACAACTTTTATTT
1 AATTTTAATTTTTTCAAATGTATAATTATCACAACTTTTATTA
*
35854266 TATTTTAATTTTT
1 AATTTTAATTTTT
35854279 AAGTAATAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
43 37 0.84
44 7 0.16
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (43 bp):
AATTTTAATTTTTTCAAATGTATAATTATCACAACTTTTATTA
Found at i:35860792 original size:6 final size:6
Alignment explanation
Indices: 35860783--35860816 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35860773 TCAGCCTCTG
* *
35860783 CCCCCT CCCCCT CTCCCT CCCCCT CTCCCT CCCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCCC
35860817 AGCCCCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.79, G:0.00, T:0.21
Consensus pattern (6 bp):
CCCCCT
Found at i:35860802 original size:12 final size:12
Alignment explanation
Indices: 35860785--35860816 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
35860775 AGCCTCTGCC
35860785 CCCTCCCCCTCT
1 CCCTCCCCCTCT
35860797 CCCTCCCCCTCT
1 CCCTCCCCCTCT
35860809 CCCTCCCC
1 CCCTCCCC
35860817 AGCCCCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (12 bp):
CCCTCCCCCTCT
Found at i:35875244 original size:10 final size:10
Alignment explanation
Indices: 35875231--35875289 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
35875221 TATAAAGTCG
35875231 TAAAAAATTA
1 TAAAAAATTA
* *
35875241 TAAAAAAATG
1 TAAAAAATTA
35875251 TAAAGAAA-TA
1 TAAA-AAATTA
* *
35875261 T-AAAATTTG
1 TAAAAAATTA
35875270 TAAAAAATTA
1 TAAAAAATTA
35875280 T-AAAAATTA
1 TAAAAAATTA
35875289 T
1 T
35875290 CGTACCAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 2 0.05
9 13 0.33
10 21 0.54
11 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:35875287 original size:20 final size:20
Alignment explanation
Indices: 35875230--35875287 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
35875220 TTATAAAGTC
**
35875230 GTAAAAAATTATAAAAAAAT
1 GTAAAAAATTATAAAAATTT
35875250 GTAAAGAAA-TAT-AAAATTT
1 GTAAA-AAATTATAAAAATTT
35875269 GTAAAAAATTATAAAAATT
1 GTAAAAAATTATAAAAATT
35875288 ATCGTACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 14 0.42
21 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
GTAAAAAATTATAAAAATTT
Found at i:35875500 original size:23 final size:23
Alignment explanation
Indices: 35875470--35875517 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
35875460 ATTTTTTATG
35875470 TTTTTTATAAAATTTTACAATTT
1 TTTTTTATAAAATTTTACAATTT
* *
35875493 TTTTTTATAAATTTTTACGATTT
1 TTTTTTATAAAATTTTACAATTT
35875516 TT
1 TT
35875518 ATATTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTATAAAATTTTACAATTT
Found at i:35875504 original size:22 final size:24
Alignment explanation
Indices: 35875470--35875535 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
35875460 ATTTTTTATG
35875470 TTTTTTATAAAA-TTTTACAATTT
1 TTTTTTATAAAATTTTTACAATTT
*
35875493 TTTTTTAT-AAATTTTTACGATTT
1 TTTTTTATAAAATTTTTACAATTT
* *
35875516 TTATATTTTTATAATTTTTA
1 TT-T-TTTATAAAATTTTTA
35875536 ATAAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.08
23 20 0.56
24 1 0.03
25 4 0.11
26 8 0.22
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTTTTATAAAATTTTTACAATTT
Found at i:35875507 original size:10 final size:9
Alignment explanation
Indices: 35875494--35875608 Score: 65
Period size: 9 Copynumber: 12.3 Consensus size: 9
35875484 TTACAATTTT
35875494 TTTTTATAAA
1 TTTTTAT-AA
**
35875504 TTTTTACGA
1 TTTTTATAA
35875513 TTTTTAT-A
1 TTTTTATAA
35875521 TTTTTATAA
1 TTTTTATAA
35875530 TTTTTAATAA
1 TTTTT-ATAA
*
35875540 ATTTTA-AA
1 TTTTTATAA
35875548 TATTTTAT-A
1 T-TTTTATAA
*
35875557 TTCTTTGTTAAA
1 TT-TTT-AT-AA
* *
35875569 ATTTAATAA
1 TTTTTATAA
35875578 TTTTTATAA
1 TTTTTATAA
* *
35875587 CTTTTATTA
1 TTTTTATAA
*
35875596 TTTATTATTA
1 TTT-TTATAA
35875606 TTT
1 TTT
35875609 ATATTTTTTT
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
8 11 0.13
9 42 0.51
10 25 0.30
11 2 0.02
12 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:35875543 original size:28 final size:27
Alignment explanation
Indices: 35875514--35875592 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 27
35875504 TTTTTACGAT
35875514 TTTTATATTTTTATAATTTTTAATAAA
1 TTTTATATTTTTATAATTTTTAATAAA
* **
35875541 TTTTAAATATTTTAT-ATTCTTTGTTAAAA
1 TTTTATAT-TTTTATAATT-TTTAAT-AAA
* *
35875570 TTTAATAATTTTTATAACTTTTA
1 TTTTAT-ATTTTTATAATTTTTA
35875593 TTATTTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
27 10 0.25
28 10 0.25
29 16 0.40
30 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTATATTTTTATAATTTTTAATAAA
Found at i:35876519 original size:3 final size:3
Alignment explanation
Indices: 35876466--35876500 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35876456 CCTATTTTAC
35876466 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35876501 ATTAATAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35876523 original size:9 final size:10
Alignment explanation
Indices: 35876467--35876531 Score: 58
Period size: 9 Copynumber: 7.3 Consensus size: 10
35876457 CTATTTTACA
35876467 ATAATAATA-
1 ATAATAATAT
35876476 ATAATAATA-
1 ATAATAATAT
35876485 ATAATAATA-
1 ATAATAATAT
35876494 ATAATAA-AT
1 ATAATAATAT
35876503 -TAATAACT-T
1 ATAATAA-TAT
35876512 A-AATAATAT
1 ATAATAATAT
35876521 A-AA-AATAT
1 ATAATAATAT
35876529 ATA
1 ATA
35876532 TATATTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
8 14 0.28
9 36 0.72
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAATAATAT
Found at i:35880215 original size:67 final size:67
Alignment explanation
Indices: 35880134--35880263 Score: 199
Period size: 67 Copynumber: 1.9 Consensus size: 67
35880124 TAAGGTTTTG
35880134 TGAATTGTAAGGGTTTA-AATTTTAAGGTTTTAAGGATTTAAGATTTAAAGTGATGAGTTTAGGG
1 TGAATTGTAAGGGTTTAGAATTTTAAGGTTTTAAGG-TTTAAGATTTAAAGTGATGAGTTTAGGG
35880198 TAT
65 TAT
* * * **
35880201 TGAATTTTATGGGTTTAGGATTTTAAGGTTTTAAGGTTTGGGATTTAAAGTGATGAGTTTAGG
1 TGAATTGTAAGGGTTTAGAATTTTAAGGTTTTAAGGTTTAAGATTTAAAGTGATGAGTTTAGG
35880264 ATTTTAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 40 0.70
68 17 0.30
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (67 bp):
TGAATTGTAAGGGTTTAGAATTTTAAGGTTTTAAGGTTTAAGATTTAAAGTGATGAGTTTAGGGT
AT
Found at i:35884040 original size:20 final size:19
Alignment explanation
Indices: 35884017--35884057 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
35884007 AAAAAAAATA
*
35884017 AAAATAGTTTTCAAAAATTC
1 AAAATAATTTT-AAAAATTC
*
35884037 AAAATAATTTTTAAAATTC
1 AAAATAATTTTAAAAATTC
35884056 AA
1 AA
35884058 GATATTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:35884125 original size:20 final size:20
Alignment explanation
Indices: 35884088--35884124 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35884078 AATTTATATT
35884088 TTAAAAAACATATAAAAATA
1 TTAAAAAACATATAAAAATA
*
35884108 TTAAAAAATAT-TAAAAA
1 TTAAAAAACATATAAAAA
35884125 AAAGTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAAAACATATAAAAATA
Found at i:35884134 original size:10 final size:10
Alignment explanation
Indices: 35884088--35884125 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
35884078 AATTTATATT
*
35884088 TTAAAAAACA
1 TTAAAAAATA
35884098 -TATAAAAATA
1 TTA-AAAAATA
35884108 TTAAAAAATA
1 TTAAAAAATA
35884118 TTAAAAAA
1 TTAAAAAA
35884126 AAGTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:35887374 original size:22 final size:22
Alignment explanation
Indices: 35887322--35887374 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
35887312 TTGCTGGGGA
35887322 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* *
35887344 AGCAAAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
35887366 AACAGAAGC
1 AACAGAAGC
35887375 GCGCTAGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.26, G:0.23, T:0.08
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:35891697 original size:22 final size:22
Alignment explanation
Indices: 35891667--35891719 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
35891657 TTGCTAGGGA
*
35891667 AACAGAAGCACACATAATGCTG
1 AACAGAAGCACACACAATGCTG
* * *
35891689 AGCAGAAGCATACACAGTGCTG
1 AACAGAAGCACACACAATGCTG
35891711 AACAGAAGC
1 AACAGAAGC
35891720 GCGCTAGCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAATGCTG
Found at i:35897568 original size:14 final size:15
Alignment explanation
Indices: 35897540--35897571 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35897530 TATACTTTTC
35897540 AACCTTTTAAAATTT
1 AACCTTTTAAAATTT
*
35897555 AACCTTTTAAATTTT
1 AACCTTTTAAAATTT
35897570 AA
1 AA
35897572 TTTCAGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
AACCTTTTAAAATTT
Found at i:35906689 original size:23 final size:24
Alignment explanation
Indices: 35906663--35906710 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
35906653 CAACCAATCA
*
35906663 AATTCGCCAGC-CTTTCGCTTCTT
1 AATTCGCCAACGCTTTCGCTTCTT
*
35906686 AATTGGCCAACTGCTTTCGCTTCTT
1 AATTCGCCAAC-GCTTTCGCTTCTT
35906711 CCTATAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
25 12 0.57
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTCGCCAACGCTTTCGCTTCTT
Found at i:35908298 original size:124 final size:125
Alignment explanation
Indices: 35908076--35908317 Score: 369
Period size: 124 Copynumber: 1.9 Consensus size: 125
35908066 TTATTTATTT
* * * * *
35908076 ATATTTTATTATTTTACATCTAAAAATTGAAATATATAAAGAAAATATTGCATGAAATAGATACA
1 ATATTTTATCATTTTACATCTAAAAATTAAAATATATAAAGAAAATATTACATAAAATAGAGACA
** *
35908141 TTGCATCATCCTATGTCTTTTATTAATTATTTAATATCATTTCAACATTTTTTCATGTCA
66 TCACATCATCCTATGTCTTTTACTAATTATTTAATATCATTTCAACATTTTTTCATGTCA
* *
35908201 ATATTTTATCATTTTACATTTAAAAATTAAAATATATAAAG-AAATATTATATAAAATAGAGACA
1 ATATTTTATCATTTTACATCTAAAAATTAAAATATATAAAGAAAATATTACATAAAATAGAGACA
* *
35908265 TCACATCATCTTATGTTTTTTACTAATTATTTAATATCATTTCAACATTTTTT
66 TCACATCATCCTATGTCTTTTACTAATTATTTAATATCATTTCAACATTTTTT
35908318 TTCATACCAC
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
124 67 0.64
125 38 0.36
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (125 bp):
ATATTTTATCATTTTACATCTAAAAATTAAAATATATAAAGAAAATATTACATAAAATAGAGACA
TCACATCATCCTATGTCTTTTACTAATTATTTAATATCATTTCAACATTTTTTCATGTCA
Found at i:35917061 original size:12 final size:12
Alignment explanation
Indices: 35917041--35917076 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35917031 AATCTCCTCG
*
35917041 AAAACAAAAACA
1 AAAATAAAAACA
*
35917053 AAAATAAAAATA
1 AAAATAAAAACA
35917065 AAAATAAAAACA
1 AAAATAAAAACA
35917077 CTACAGCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.83, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAATAAAAACA
Found at i:35922423 original size:5 final size:5
Alignment explanation
Indices: 35922387--35922463 Score: 52
Period size: 5 Copynumber: 15.0 Consensus size: 5
35922377 ATTGAAAAAC
* * *
35922387 TTTAA TTTAA ATAAA TTT-A TTT-G TTATAA TTTAA TTTAA TTTAA TTCT-A
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA TT-TAA
*
35922436 TTGTTA TATTAA TTTAA TTTTAA TTTAA
1 TT-TAA T-TTAA TTTAA -TTTAA TTTAA
35922464 AAGTATCCCA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
4 6 0.10
5 38 0.66
6 13 0.22
7 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:35922432 original size:29 final size:27
Alignment explanation
Indices: 35922387--35922462 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
35922377 ATTGAAAAAC
* *
35922387 TTTAATTTAAATAAATTTATTTGTTATAA
1 TTTAATTTAATTTAATTTA-TTGTTAT-A
35922416 TTTAATTTAATTTAATTCTATTGTTATA
1 TTTAATTTAATTTAATT-TATTGTTATA
35922444 -TTAATTTAATTTTAATTTA
1 TTTAATTTAA-TTTAATTTA
35922463 AAAGTATCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 11 0.26
28 8 0.19
29 22 0.51
30 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTAATTTAATTTAATTTATTGTTATA
Found at i:35925541 original size:19 final size:20
Alignment explanation
Indices: 35925494--35925541 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
35925484 ACAAATTGAA
35925494 ATACATTAACAAAAGTTTTT
1 ATACATTAACAAAAGTTTTT
35925514 ATACATTAACAAAAGTTTTT
1 ATACATTAACAAAAGTTTTT
35925534 ATAC-TTAA
1 ATACATTAA
35925542 ATAACATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (20 bp):
ATACATTAACAAAAGTTTTT
Found at i:35926519 original size:16 final size:16
Alignment explanation
Indices: 35926498--35926530 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35926488 CAGTTGGAGT
*
35926498 AGTTAGTTTGTTTAGA
1 AGTTAGTCTGTTTAGA
35926514 AGTTAGTCTGTTTAGA
1 AGTTAGTCTGTTTAGA
35926530 A
1 A
35926531 TTTGTTAGCA
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:0.27, C:0.03, G:0.24, T:0.45
Consensus pattern (16 bp):
AGTTAGTCTGTTTAGA
Found at i:35931231 original size:17 final size:18
Alignment explanation
Indices: 35931191--35931231 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35931181 ATAGTATTTT
*
35931191 TTAAAAATATTTTTGACA
1 TTAAAAATATTTTTGAAA
*
35931209 TAAAAAATATTTTT-AAA
1 TTAAAAATATTTTTGAAA
35931226 TTAAAA
1 TTAAAA
35931232 GTAATGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TTAAAAATATTTTTGAAA
Found at i:35937493 original size:24 final size:24
Alignment explanation
Indices: 35937458--35937514 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
35937448 ATATTTATGA
* *
35937458 TTAAAAAATATAATTTTATTA-TT
1 TTAAAAATTATAATTTTATAATTT
*
35937481 TTAATAAATTATATTTTTATAATTT
1 TTAA-AAATTATAATTTTATAATTT
35937506 TTAAAAATT
1 TTAAAAATT
35937515 TAAATCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.14
24 19 0.66
25 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAAAATTATAATTTTATAATTT
Found at i:35945782 original size:17 final size:20
Alignment explanation
Indices: 35945739--35945785 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 20
35945729 AAAACATTCT
35945739 TACAAAAAAGTGATCAAAAA
1 TACAAAAAAGTGATCAAAAA
35945759 TGA-AAAAAA-T-A-CAAAAA
1 T-ACAAAAAAGTGATCAAAAA
35945776 TACAAAAAAG
1 TACAAAAAAG
35945786 AAAGGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
16 1 0.04
17 13 0.54
18 1 0.04
19 1 0.04
20 7 0.29
21 1 0.04
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.13
Consensus pattern (20 bp):
TACAAAAAAGTGATCAAAAA
Found at i:35953147 original size:18 final size:17
Alignment explanation
Indices: 35953120--35953155 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35953110 GTTTATAGTA
*
35953120 TTTAATATTATGTTATT
1 TTTAATATTATGTAATT
35953137 TTTATATATTATGTAATT
1 TTTA-ATATTATGTAATT
35953155 T
1 T
35953156 AGAACTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTAATATTATGTAATT
Found at i:35962687 original size:22 final size:22
Alignment explanation
Indices: 35962662--35962733 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
35962652 ACAACAACAA
35962662 GAAATAAAACAACCTTGATTTT
1 GAAATAAAACAACCTTGATTTT
* *
35962684 GAAA-AATAACTAA-TTTAATTACTT
1 GAAATAA-AAC-AACCTTGATT--TT
*
35962708 GAAATAAAGCAACCTTGATTTT
1 GAAATAAAACAACCTTGATTTT
35962730 GAAA
1 GAAA
35962734 AATAGTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.05
22 18 0.46
23 4 0.10
24 13 0.33
25 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (22 bp):
GAAATAAAACAACCTTGATTTT
Found at i:35962690 original size:24 final size:24
Alignment explanation
Indices: 35962663--35962737 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
35962653 CAACAACAAG
35962663 AAATAAAACAACCTTGATTTTGAA
1 AAATAAAACAACCTTGATTTTGAA
* *
35962687 AAAT--AACTAA-TTTAATTACTTG--
1 AAATAAAAC-AACCTTGATT--TTGAA
*
35962709 AAATAAAGCAACCTTGATTTTGAA
1 AAATAAAACAACCTTGATTTTGAA
35962733 AAATA
1 AAATA
35962738 GTTAATTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
22 15 0.39
23 4 0.11
24 19 0.50
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (24 bp):
AAATAAAACAACCTTGATTTTGAA
Found at i:35962714 original size:46 final size:46
Alignment explanation
Indices: 35962662--35962763 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
35962652 ACAACAACAA
*
35962662 GAAATAAAACAACCTTGATTTTGAAAAATAACTAATTTAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAACTAATTCAATTACTT
* **
35962708 GAAATAAAGCAACCTTGATTTTGAAAAATAGTTAATTCAATTACTT
1 GAAATAAAACAACCTTGATTTTGAAAAATAACTAATTCAATTACTT
35962754 GAAAATAAAA
1 G-AAATAAAA
35962764 AAAATATTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 43 0.86
47 7 0.14
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (46 bp):
GAAATAAAACAACCTTGATTTTGAAAAATAACTAATTCAATTACTT
Found at i:35969085 original size:20 final size:20
Alignment explanation
Indices: 35969060--35969097 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35969050 GGAAGTTCTG
* *
35969060 AAATATTTTAATTTTTTATA
1 AAATATTTCAATATTTTATA
35969080 AAATATTTCAATATTTTA
1 AAATATTTCAATATTTTA
35969098 AAATTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATATTTCAATATTTTATA
Found at i:35974065 original size:32 final size:32
Alignment explanation
Indices: 35974024--35974089 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
35974014 GTTTTTCTTA
35974024 GCTCACTTGATTTTGGTAAAATTACCATAGAG
1 GCTCACTTGATTTTGGTAAAATTACCATAGAG
35974056 GCTCACTTGATTTTGGTAAAATTACCATAGAG
1 GCTCACTTGATTTTGGTAAAATTACCATAGAG
35974088 GC
1 GC
35974090 CCTATATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (32 bp):
GCTCACTTGATTTTGGTAAAATTACCATAGAG
Done.