Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 107 of 182
Found at i:34688487 original size:25 final size:24
Alignment explanation
Indices: 34688440--34688557 Score: 80
Period size: 25 Copynumber: 4.7 Consensus size: 24
34688430 GGATTCGATG
*
34688440 AAGAAAAATAAATAAA-AAGAAAGAA
1 AAGAAAAA-AAA-AAAGAAAAAAGAA
*
34688465 AAGACAAAAAAAAAAGCAAAAAGAAGA
1 AAGA-AAAAAAAAAAGAAAAAAG-A-A
*
34688492 AAGAATAAAGAAAAAAAAAAAAAG-A
1 AAGAA-AAA-AAAAAAGAAAAAAGAA
*
34688517 AAGAGAAAAAGAAAAGAAAAAAAGAA
1 AAGA-AAAAAAAAAAG-AAAAAAGAA
* *
34688543 AA-AAAAGAAGAAAGA
1 AAGAAAAAAAAAAAGA
34688558 TGAGATGTCG
Statistics
Matches: 75, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
23 1 0.01
24 16 0.21
25 28 0.37
26 10 0.13
27 8 0.11
28 12 0.16
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAAAAAGAAAAAAGAA
Found at i:34688494 original size:7 final size:7
Alignment explanation
Indices: 34688484--34688557 Score: 58
Period size: 7 Copynumber: 11.7 Consensus size: 7
34688474 AAAAAAGCAA
34688484 AAAGAAG
1 AAAGAAG
*
34688491 AAAGAAT
1 AAAGAAG
34688498 AAAGAA-
1 AAAGAAG
34688504 AAA-AA-
1 AAAGAAG
*
34688509 AAAAAAG
1 AAAGAAG
34688516 AAAG-AG
1 AAAGAAG
34688522 AAA-AAG
1 AAAGAAG
34688528 AAAAGAA-
1 -AAAGAAG
34688535 AAA-AAG
1 AAAGAAG
34688541 AAA-AA-
1 AAAGAAG
34688546 AAAGAAG
1 AAAGAAG
34688553 AAAGA
1 AAAGA
34688558 TGAGATGTCG
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
5 10 0.18
6 22 0.39
7 23 0.40
8 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAGAAG
Found at i:34688506 original size:59 final size:61
Alignment explanation
Indices: 34688440--34688557 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 61
34688430 GGATTCGATG
*
34688440 AAGAAAAATAAATAAAAAG-AA-AG-AAAAGACAAA-AAAAAAAG-CAAAAAGAAGAAAGAATA
1 AAGAAAAA-AAA-AAAAAGAAAGAGAAAAAGA-AAAGAAAAAAAGAAAAAAAGAAGAAAGAATA
34688499 AAGAAAAAAAAAAAAAGAAAGAGAAAAAGAAAAGAAAAAAAGAAAAAAAAGAAGAAAGA
1 AAGAAAAAAAAAAAAAGAAAGAGAAAAAGAAAAGAAAAAAAG-AAAAAAAGAAGAAAGA
34688558 TGAGATGTCG
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
57 6 0.12
58 5 0.10
59 13 0.25
60 14 0.27
62 14 0.27
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.03
Consensus pattern (61 bp):
AAGAAAAAAAAAAAAAGAAAGAGAAAAAGAAAAGAAAAAAAGAAAAAAAGAAGAAAGAATA
Found at i:34689731 original size:50 final size:50
Alignment explanation
Indices: 34689512--34689789 Score: 154
Period size: 50 Copynumber: 5.6 Consensus size: 50
34689502 CCGGTATCTT
* * * * *** *
34689512 AAAAGAT-TGAAGGGAAAGGTTGAGGTCGCAATGGCGAACCTAATACCTA
1 AAAAGATGCGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACATA
* * * * * * * *
34689561 AGAAGATGCGATGGAAAAGGTTGAGGCCGCAACGTCGAACCCAGTACCATG
1 AAAAGATGCGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTA-CATA
* * * * ** *
34689612 AAGAGAT--GACAGGG--GGGATTGAGGCCGTAACGGCGAATTCGATACATTA
1 AAAAGATGCGA-AGGGAAAGG-TTGAGGTCGTAACGACGAACCCGGTACA-TA
* ** * *
34689661 AAAAGCTGTAAAGGGAAAGGTTGAGGTCGTGACGACGAACCTGGTACATA
1 AAAAGATGCGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACATA
* * * ** *
34689711 AGAAGATGTGAAGGGAAAGGTTGAGGTCGTAATGGTGAACCCGGTACCTA
1 AAAAGATGCGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACATA
*
34689761 AAAAGATGCGATGGG-AAGGATTGAGGTCG
1 AAAAGATGCGAAGGGAAAGG-TTGAGGTCG
34689790 CAACAGCGAA
Statistics
Matches: 173, Mismatches: 46, Indels: 19
0.73 0.19 0.08
Matches are distributed among these distances:
48 4 0.02
49 38 0.22
50 100 0.58
51 29 0.17
52 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.18
Consensus pattern (50 bp):
AAAAGATGCGAAGGGAAAGGTTGAGGTCGTAACGACGAACCCGGTACATA
Found at i:34690681 original size:208 final size:205
Alignment explanation
Indices: 34690296--34691142 Score: 988
Period size: 208 Copynumber: 4.1 Consensus size: 205
34690286 TAAAATGGTC
* * **
34690296 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATATAGAGAAGCAG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
* * * ** * *
34690361 ATTAAAACAAGTTATGCTGTCATCTTCTTGATGAGATATTGAGAAGTAGGCCAAATCAAGGAAAC
66 ATT-AAA-AAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAAATCAATGAAAC
* * * * **
34690426 AAAACTCAATGTGAGCGAAACTTCGAACCCTAGCTTCCGGATGAGATACTGAGAAGCGGGTTAAA
129 AAAGCTCAATGTGAGCAAAACTTCGAACCC-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAA
34690491 GCAATAAAGCAGTT
193 GCAATAAAG-AGTT
* *
34690505 GTCTTCCTGATGAGATACAGAGAAGTGGACTAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
* * * * * * *
34690570 ATTAAAATAGTGATGCGGTCACCTTCTTAATGAGATACAAAGAAGTATGTCAACTTAATGAAACA
66 ATTAAAA-AGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAAATCAATGAAACA
* *
34690635 AAGCTCAATGTGAGCAAAACTTCGAATCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTCGAAG
130 AAGCTCAATGTGAGCAAAACTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
34690700 CAATAAATTG-GTT
194 CAATAAA--GAGTT
34690713 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
*
34690778 ATTAAAACAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGTCAAATCAATGAAACA
66 ATTAAAA-AGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAAATCAATGAAACA
* * * * *
34690843 AACCTCAATGTGAGCGAAACTTTGAATCCAAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAG
130 AAGCTCAATGTGAGCAAAACTTCGAA-CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAG
34690908 ---T---G-GTT
194 CAATAAAGAGTT
* * * * *
34690913 GTCTTCTTGATGAGATATAGAGAAGTAGACCAAATTCGTCTTCCTGATGAGATAACAGATAAGTG
1 GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGAT-ACAGAGAAGTG
** * *
34690978 GATTGAAACAAGTGATGCAATCATCTTCCTGATGAGATACTGAGAGGTA-GACCAAATCAATGAA
65 GATT-AAA-AAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATG-CCAAATCAATGAA
* * *
34691042 ACCAAAGGTCGATGTGAGCGAAAA---C---CCCAGCTCCCTGATGAGATACTGAGAAGCAGGTC
127 A-CAAAGCTCAATGTGAGC-AAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC
*
34691101 GAAGCAATAAA-ATGATC
190 GAAGCAATAAAGA-G-TT
*
34691118 GTCTTCCTGATGAGATACAGAGAAG
1 GTCTTCCTGATGAGATATAGAGAAG
34691143 AAGATCAAGA
Statistics
Matches: 556, Mismatches: 63, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
197 35 0.06
200 54 0.10
201 15 0.03
202 51 0.09
203 15 0.03
204 4 0.01
205 25 0.04
207 1 0.00
208 290 0.52
209 65 0.12
210 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (205 bp):
GTCTTCCTGATGAGATATAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGTGG
ATTAAAAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAAATCAATGAAACAA
AGCTCAATGTGAGCAAAACTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAGAGTT
Found at i:34691584 original size:17 final size:16
Alignment explanation
Indices: 34691537--34691611 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 16
34691527 TTAAATCAAG
34691537 TTTAAATTTATTTTAAA
1 TTTAAA-TTATTTTAAA
*
34691554 TTCAAAAGTTATTTTAAA
1 TT-TAAA-TTATTTTAAA
*
34691572 TTTAAACTTA-TTTGAA
1 TTTAAA-TTATTTTAAA
*
34691588 TTTAAATTCATTTAAAA
1 TTTAAATT-ATTTTAAA
*
34691605 TTAAAAT
1 TTTAAAT
34691612 AAATAAAATG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.04
16 12 0.26
17 18 0.38
18 15 0.32
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:34691608 original size:16 final size:16
Alignment explanation
Indices: 34691537--34691609 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
34691527 TTAAATCAAG
*
34691537 TTTAAATTTATTTTAAA
1 TTTAAACTTA-TTTAAA
* *
34691554 TTCAAAAGTTATTTTAAA
1 TT-TAAACTTA-TTTAAA
*
34691572 TTTAAACTTATTTGAA
1 TTTAAACTTATTTAAA
34691588 TTTAAA-TTCATTTAAA
1 TTTAAACTT-ATTTAAA
*
34691604 ATTAAA
1 TTTAAA
34691610 ATAAATAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 2 0.04
16 22 0.47
17 8 0.17
18 15 0.32
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTAAACTTATTTAAA
Found at i:34693434 original size:30 final size:30
Alignment explanation
Indices: 34693391--34693648 Score: 202
Period size: 30 Copynumber: 8.6 Consensus size: 30
34693381 TGAACTGTCC
34693391 AAAAATCACATTTTGACCCTCAAACTTTCA
1 AAAAATCACATTTTGACCCTCAAACTTTCA
* * * * *
34693421 AAAAATTATATTTTGACCCTCGAACTTACT
1 AAAAATCACATTTTGACCCTCAAACTTTCA
* * * * *
34693451 AAAAATCACGTTTTAACCCCCAAGCTTTCC
1 AAAAATCACATTTTGACCCTCAAACTTTCA
* * * *
34693481 AAAAATTATATTTTGACTCAT-AAACTTTCC
1 AAAAATCACATTTTGAC-CCTCAAACTTTCA
* * *
34693511 AAAAATTACATTTTAAGCCCT-AAACTTTCT
1 AAAAATCACATTTTGA-CCCTCAAACTTTCA
* * *
34693541 AAAAATTACATTTTGACCCTCAAAATTTTA
1 AAAAATCACATTTTGACCCTCAAACTTTCA
* * * *
34693571 TAAAATCACATTTTTACCC-CTAAACTCTCT
1 AAAAATCACATTTTGACCCTC-AAACTTTCA
* * *
34693601 AAAAATCACATTTTTACCCTCATAC-TTCC
1 AAAAATCACATTTTGACCCTCAAACTTTCA
34693630 AAAAATCACATCTTT-ACCC
1 AAAAATCACAT-TTTGACCC
34693649 CGTACTTCCA
Statistics
Matches: 182, Mismatches: 40, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
29 22 0.12
30 157 0.86
31 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAAATCACATTTTGACCCTCAAACTTTCA
Found at i:34693479 original size:60 final size:60
Alignment explanation
Indices: 34693389--34693649 Score: 242
Period size: 60 Copynumber: 4.4 Consensus size: 60
34693379 CCTGAACTGT
* * *
34693389 CCAAAAATCACATTTTGACCCTCAAACTTTCAAAAAATTATATTTTGACCCTCGAACTTA
1 CCAAAAATCACATTTTAACCCCCAAACTTTCAAAAAATTATATTTTGACCCTCAAACTTA
* * * * * *
34693449 CTAAAAATCACGTTTTAACCCCCAAGCTTTCCAAAAATTATATTTTGACTCAT-AAACTTT
1 CCAAAAATCACATTTTAACCCCCAAACTTTCAAAAAATTATATTTTGAC-CCTCAAACTTA
* * * * * *
34693509 CCAAAAATTACATTTTAAGCCCTAAACTTTCTAAAAATTACATTTTGACCCTCAAAATT-
1 CCAAAAATCACATTTTAACCCCCAAACTTTCAAAAAATTATATTTTGACCCTCAAACTTA
** * * * * * * * *
34693568 TTATAAAATCACATTTTTACCCCTAAACTCTCTAAAAATCACATTTTTACCCTCATACTT-
1 CCA-AAAATCACATTTTAACCCCCAAACTTTCAAAAAATTATATTTTGACCCTCAAACTTA
34693628 CCAAAAATCACATCTTT-ACCCC
1 CCAAAAATCACAT-TTTAACCCC
34693650 GTACTTCCAA
Statistics
Matches: 166, Mismatches: 31, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
59 18 0.11
60 146 0.88
61 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.34
Consensus pattern (60 bp):
CCAAAAATCACATTTTAACCCCCAAACTTTCAAAAAATTATATTTTGACCCTCAAACTTA
Found at i:34693576 original size:90 final size:90
Alignment explanation
Indices: 34693388--34693649 Score: 246
Period size: 90 Copynumber: 2.9 Consensus size: 90
34693378 CCCTGAACTG
* * *
34693388 TCCAAAAATCACATTTTGACCC-TCAAACTTTCAAAAAATTATATTTTGACCCTCGAACTTACTA
1 TCCAAAAATCACATTTTGACCCAT-AAACTTTCAAAAAATTACATTTTAACCCTCAAACTTACTA
* **
34693452 AAAATCACGTTTTAACCCCCAAGCTT
65 AAAATCACATTTTAACCCCCAAAATT
* * * * *
34693478 TCCAAAAATTATATTTTGACTCATAAACTTTCCAAAAATTACATTTTAAGCCCT-AAACTTTCTA
1 TCCAAAAATCACATTTTGACCCATAAACTTTCAAAAAATTACATTTTAA-CCCTCAAACTTACTA
* * *
34693542 AAAATTACATTTTGACCCTCAAAATT
65 AAAATCACATTTTAACCCCCAAAATT
* * * * * * * * *
34693568 T-TATAAAATCACATTTTTACCCCTAAACTCTCTAAAAATCACATTTTTACCCTCATACTT-CCA
1 TCCA-AAAATCACATTTTGACCCATAAACTTTCAAAAAATTACATTTTAACCCTCAAACTTACTA
34693631 AAAATCACATCTTT-ACCCC
65 AAAATCACAT-TTTAACCCC
34693650 GTACTTCCAA
Statistics
Matches: 139, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
89 20 0.14
90 114 0.82
91 5 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (90 bp):
TCCAAAAATCACATTTTGACCCATAAACTTTCAAAAAATTACATTTTAACCCTCAAACTTACTAA
AAATCACATTTTAACCCCCAAAATT
Found at i:34693655 original size:28 final size:27
Alignment explanation
Indices: 34693572--34693676 Score: 113
Period size: 28 Copynumber: 3.7 Consensus size: 27
34693562 AAAATTTTAT
*
34693572 AAAATCACATTTTTACCCCTAAACTCTCTA
1 AAAATCACATTTTTACCCCT--ACT-TCCA
34693602 AAAATCACATTTTTACCCTCATACTTCCA
1 AAAATCACATTTTTACCC-C-TACTTCCA
*
34693631 AAAATCACATCTTTACCCCGTACTTCCA
1 AAAATCACATTTTTACCCC-TACTTCCA
*
34693659 AAAATTACCA-TTTTACCC
1 AAAATCA-CATTTTTACCC
34693677 TCGAATATCG
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
28 22 0.33
29 22 0.33
30 21 0.31
31 1 0.01
32 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.32
Consensus pattern (27 bp):
AAAATCACATTTTTACCCCTACTTCCA
Found at i:34693697 original size:29 final size:28
Alignment explanation
Indices: 34693627--34693868 Score: 175
Period size: 29 Copynumber: 8.4 Consensus size: 28
34693617 CCCTCATACT
* *
34693627 TCCAAAAATCA-CATCTTTACCCCGTACT-
1 TCCAAAAATTACCAT-TTTACCCCG-AATA
34693655 TCCAAAAATTACCATTTTACCCTCGAATA
1 TCCAAAAATTACCATTTTACCC-CGAATA
* * *
34693684 TCGAAAAATTACCATTTTACTCCCGGATG
1 TCCAAAAATTACCATTTTAC-CCCGAATA
* * *
34693713 TCCAAAAAATA-TATTTTTGACCCCGAACTT
1 TCCAAAAATTACCA-TTTT-ACCCCGAA-TA
* *
34693743 TCCAAAAATTACCATTTTACCCTCGAGTG
1 TCCAAAAATTACCATTTTACCC-CGAATA
** * ** *
34693772 TCCAAAAATTACTTTTTTACCTCGGGTG
1 TCCAAAAATTACCATTTTACCCCGAATA
* * *
34693800 TCCAAAAATTATCATTTTACCCCCGGACA
1 TCCAAAAATTACCATTTTA-CCCCGAATA
* * * *
34693829 TCCAAAAATTACCGTTTTGCCCCTAGTA
1 TCCAAAAATTACCATTTTACCCCGAATA
34693857 TCCAAAAATTAC
1 TCCAAAAATTAC
34693869 ATTCTTGACT
Statistics
Matches: 172, Mismatches: 32, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
28 58 0.34
29 91 0.53
30 22 0.13
31 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
TCCAAAAATTACCATTTTACCCCGAATA
Found at i:34693703 original size:57 final size:57
Alignment explanation
Indices: 34693627--34693868 Score: 199
Period size: 57 Copynumber: 4.2 Consensus size: 57
34693617 CCCTCATACT
* *
34693627 TCCAAAAATCA-CATCTTTACCCCGTACT-TCCAAAAATTACCATTTTACCCTCGAATA
1 TCCAAAAATTACCAT-TTTACCCCGGACTGTCCAAAAATTACCATTTTACCC-CGAATA
* * * *
34693684 TCGAAAAATTACCATTTTACTCCCGGA-TGTCCAAAAAATA-TATTTTTGACCCCGAACTT
1 TCCAAAAATTACCATTTTAC-CCCGGACTGTCCAAAAATTACCA-TTTT-ACCCCGAA-TA
* ** * ** *
34693743 TCCAAAAATTACCATTTTACCCTC-GAGTGTCCAAAAATTACTTTTTTACCTCGGGTG
1 TCCAAAAATTACCATTTTACCC-CGGACTGTCCAAAAATTACCATTTTACCCCGAATA
* * * * * *
34693800 TCCAAAAATTATCATTTTACCCCCGGAC-ATCCAAAAATTACCGTTTTGCCCCTAGTA
1 TCCAAAAATTACCATTTTA-CCCCGGACTGTCCAAAAATTACCATTTTACCCCGAATA
34693857 TCCAAAAATTAC
1 TCCAAAAATTAC
34693869 ATTCTTGACT
Statistics
Matches: 150, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
57 68 0.45
58 40 0.27
59 41 0.27
60 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.31
Consensus pattern (57 bp):
TCCAAAAATTACCATTTTACCCCGGACTGTCCAAAAATTACCATTTTACCCCGAATA
Found at i:34711596 original size:23 final size:23
Alignment explanation
Indices: 34711563--34711883 Score: 263
Period size: 23 Copynumber: 13.5 Consensus size: 23
34711553 ATTAAATGTG
34711563 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* ** *
34711586 TAAAAAATTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
*
34711609 TTAAATGTTAATACGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* *
34711632 TTAAATGTTAATGTAATTTATGC
1 TTAAATGTTAATATGATTTATGC
34711655 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* *
34711678 TTAAAAGTTAATGTGATTTATG-
1 TTAAATGTTAATATGATTTATGC
* * * *
34711700 TTGATTTATGCTTGA-ATG-TTAATAC
1 TT-A--AATG-TTAATATGATTTATGC
*
34711725 AATT-TATGCTTAAAAGTTAATGTGATTTATGC
1 --TTAAATG-TT--AA--T-A--TGATTTATGC
* * *
34711757 ATAAATGTTAATGTGATTTTTGC
1 TTAAATGTTAATATGATTTATGC
* *
34711780 ATAAATGTTAATATAATTTATGC
1 TTAAATGTTAATATGATTTATGC
* *
34711803 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
34711826 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* * *
34711849 TTAAAAGTTAATGTGATTTATGT
1 TTAAATGTTAATATGATTTATGC
*
34711872 TTAAGTGTTAAT
1 TTAAATGTTAAT
34711884 GTGACTAATG
Statistics
Matches: 238, Mismatches: 43, Indels: 34
0.76 0.14 0.11
Matches are distributed among these distances:
22 2 0.01
23 205 0.86
24 4 0.02
25 5 0.02
26 4 0.02
27 2 0.01
28 2 0.01
29 1 0.00
30 3 0.01
31 5 0.02
32 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (23 bp):
TTAAATGTTAATATGATTTATGC
Found at i:34711614 original size:46 final size:46
Alignment explanation
Indices: 34711563--34711870 Score: 303
Period size: 46 Copynumber: 6.5 Consensus size: 46
34711553 ATTAAATGTG
*
34711563 TTAAATGTTAATATGATTTATGCTAAAAAATTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTAAAAAGTTAATGTGATTTATGC
* * * *
34711609 TTAAATGTTAATACGATTTATGCTTAAATGTTAATGTAATTTATGC
1 TTAAATGTTAATATGATTTATGCTAAAAAGTTAATGTGATTTATGC
*
34711655 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGTTGATTTATGC
1 TTAAATGTTAATATGATTTATGC-T-AAA---AA---G-TTAATG-TGATTTATGC
* ** *
34711711 TTGAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTAAAAAGTTAATGTGATTTATGC
* * * * * *
34711757 ATAAATGTTAATGTGATTTTTGC-ATAAATGTTAATATAATTTATGC
1 TTAAATGTTAATATGATTTATGCTA-AAAAGTTAATGTGATTTATGC
* * * * *
34711803 TTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGCTAAAAAGTTAATGTGATTTATGC
* *
34711849 TTAAAAGTTAATGTGATTTATG
1 TTAAATGTTAATATGATTTATG
34711871 TTTAAGTGTT
Statistics
Matches: 220, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
46 170 0.77
47 6 0.03
48 3 0.01
51 3 0.01
54 3 0.01
55 6 0.03
56 29 0.13
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (46 bp):
TTAAATGTTAATATGATTTATGCTAAAAAGTTAATGTGATTTATGC
Found at i:34711674 original size:69 final size:69
Alignment explanation
Indices: 34711563--34711887 Score: 380
Period size: 69 Copynumber: 4.6 Consensus size: 69
34711553 ATTAAATGTG
* * * *
34711563 TTAAATGTTAATATGATTTATGCTAAAAAATTAATGTGATTTATGCTTAAATGTTAATACGATTT
1 TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTT
34711628 ATGC
66 ATGC
* * * *
34711632 TTAAATGTTAATGTAATTTATGCTTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTT
1 TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTT-A----A--T
34711697 ATGTTGATTTATGC
59 A---TGATTTATGC
* * * *
34711711 TTGAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATGCATAAATGTTAATGTGATTT
1 TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTT
*
34711776 TTGC
66 ATGC
*
34711780 ATAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTT
1 TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTT
34711845 ATGC
66 ATGC
* * * * **
34711849 TTAAAAGTTAATGTGATTTATGTTTAAGTGTTAATGTGA
1 TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGA
34711888 CTAATGTGTA
Statistics
Matches: 216, Mismatches: 30, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
69 152 0.70
70 1 0.00
72 1 0.00
74 2 0.01
76 2 0.01
78 1 0.00
79 57 0.26
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (69 bp):
TTAAATGTTAATATAATTTATGCTTAAAAGTTAATGTGATTTATGCTTAAATGTTAATATGATTT
ATGC
Found at i:34711718 original size:56 final size:56
Alignment explanation
Indices: 34711647--34711755 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
34711637 TGTTAATGTA
**
34711647 ATTTATGCTTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGTTG
1 ATTTATGCTTAAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATGTTG
*
34711703 ATTTATGCTTGAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATG
1 ATTTATGCTTAAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATG
34711756 CATAAATGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (56 bp):
ATTTATGCTTAAATGTTAATACAATTTATGCTTAAAAGTTAATGTGATTTATGTTG
Found at i:34711730 original size:33 final size:33
Alignment explanation
Indices: 34711668--34711732 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
34711658 AATGTTAATA
***
34711668 TGATTTATGCTTAAAAGTTAATGTGATTTATGT
1 TGATTTATGCTTAAAAGTTAATACAATTTATGT
* *
34711701 TGATTTATGCTTGAATGTTAATACAATTTATG
1 TGATTTATGCTTAAAAGTTAATACAATTTATG
34711733 CTTAAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (33 bp):
TGATTTATGCTTAAAAGTTAATACAATTTATGT
Found at i:34720180 original size:23 final size:23
Alignment explanation
Indices: 34720085--34720180 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
34720075 CTTTACAACG
* * **
34720085 TATTCTGATTGGCCTTAATGGCA
1 TATTTTGATTAGCCTTTGTGGCA
* ** *
34720108 TATTTTGATGAGCCTTTGCAGCG
1 TATTTTGATTAGCCTTTGTGGCA
* * *
34720131 TATTTT-ATTTGGCCCTTGTTGCA
1 TATTTTGA-TTAGCCTTTGTGGCA
*
34720154 TATTTTGATTAGCCTTTGTGGCT
1 TATTTTGATTAGCCTTTGTGGCA
34720177 TATT
1 TATT
34720181 CTATTTTGCC
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
22 1 0.02
23 51 0.96
24 1 0.02
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.47
Consensus pattern (23 bp):
TATTTTGATTAGCCTTTGTGGCA
Found at i:34720186 original size:46 final size:46
Alignment explanation
Indices: 34720105--34720206 Score: 123
Period size: 46 Copynumber: 2.2 Consensus size: 46
34720095 GGCCTTAATG
* * *
34720105 GCATATTTTGATGAGCCTTTGCAGCGTATTTTATTTGGCCCTTGTT
1 GCATATTTTGATGAGCCTTTGCAGCGTATTCTATTTGGCCATTGTA
* ** * *
34720151 GCATATTTTGATTAGCCTTTGTGGCTTATTCTATTTTGCCATTGTA
1 GCATATTTTGATGAGCCTTTGCAGCGTATTCTATTTGGCCATTGTA
*
34720197 GCGTATTTTG
1 GCATATTTTG
34720207 TGAAGTCTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.48
Consensus pattern (46 bp):
GCATATTTTGATGAGCCTTTGCAGCGTATTCTATTTGGCCATTGTA
Found at i:34722764 original size:38 final size:37
Alignment explanation
Indices: 34722716--34722809 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 37
34722706 CCAAATTTAT
* *
34722716 GCCCAAAACTATCGCCGCATGAGTACTTCTAAATTTGC
1 GCCCAAAACTATCGCCGCATGAGAACTTCCAAA-TTGC
* * ** *
34722754 GCCCAGAACTATTGCCGTGTGAGAACTTCCAGATTGC
1 GCCCAAAACTATCGCCGCATGAGAACTTCCAAATTGC
*
34722791 ACCCAAAACTATCGCCGCA
1 GCCCAAAACTATCGCCGCA
34722810 GGAATATTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
37 18 0.41
38 26 0.59
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (37 bp):
GCCCAAAACTATCGCCGCATGAGAACTTCCAAATTGC
Found at i:34722918 original size:37 final size:38
Alignment explanation
Indices: 34722837--34722922 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
34722827 CTCTCAAGAT
* *
34722837 TATCACTGCATAAATATTCTTCAAATTGCATCTAGAAC
1 TATCGCTGCATAAATATTCTTCAAATTGCACCTAGAAC
*
34722875 TATCGCTGCATAAGTATTCTTC-AATTGCACCTAGGAA-
1 TATCGCTGCATAAATATTCTTCAAATTGCACCTA-GAAC
*
34722912 TGTCGCTGCAT
1 TATCGCTGCAT
34722923 GAACATGTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 20 0.47
38 23 0.53
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (38 bp):
TATCGCTGCATAAATATTCTTCAAATTGCACCTAGAAC
Found at i:34733423 original size:24 final size:21
Alignment explanation
Indices: 34733384--34733427 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
34733374 AAAAATAGAA
34733384 AAGAAGAAAAAGAAAACAAAG
1 AAGAAGAAAAAGAAAACAAAG
34733405 AAGAAGAGAAAAGCAAAAACAAA
1 AAGAAGA-AAAAG--AAAACAAA
34733428 TTTGCAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
24 8 0.40
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (21 bp):
AAGAAGAAAAAGAAAACAAAG
Found at i:34739306 original size:12 final size:11
Alignment explanation
Indices: 34739289--34739324 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
34739279 TTAGTCACAT
34739289 AAAAAAAGAAGA
1 AAAAAAAGAA-A
34739301 AAAAAAAGAAA
1 AAAAAAAGAAA
*
34739312 AGAAAAAGAAA
1 AAAAAAAGAAA
34739323 AA
1 AA
34739325 TATTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:34739314 original size:17 final size:17
Alignment explanation
Indices: 34739292--34739324 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34739282 GTCACATAAA
34739292 AAAAGAAGAAA-AAAAAG
1 AAAAGAA-AAAGAAAAAG
34739309 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
34739325 TATTTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAAG
Found at i:34739915 original size:38 final size:38
Alignment explanation
Indices: 34739864--34739943 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
34739854 TAAAATAGCA
*
34739864 TCCAAATTTGTGCCCAAAACTATTG-CTGCATGAGCACT
1 TCCAAATTTGTGCCCAAAACTATCGTC-GCATGAGCACT
* *
34739902 TCCAAATTTGTGCCCAAAATTGTCGTCGCATGAGCACT
1 TCCAAATTTGTGCCCAAAACTATCGTCGCATGAGCACT
34739940 TCCA
1 TCCA
34739944 GATTGCACCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (38 bp):
TCCAAATTTGTGCCCAAAACTATCGTCGCATGAGCACT
Found at i:34744189 original size:38 final size:38
Alignment explanation
Indices: 34744137--34744212 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
34744127 TGTGGATATC
*
34744137 ATCTTCAAGCTTTTTCTTAGCAAGTTTTCTTTCTTGGA
1 ATCTTCAAGCTTTTTCTTACCAAGTTTTCTTTCTTGGA
* *
34744175 ATCTTTAAGTTTTTTCTTACCAAGTTTTCTTTCTTGGA
1 ATCTTCAAGCTTTTTCTTACCAAGTTTTCTTTCTTGGA
34744213 GGGGAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.18, C:0.17, G:0.12, T:0.53
Consensus pattern (38 bp):
ATCTTCAAGCTTTTTCTTACCAAGTTTTCTTTCTTGGA
Found at i:34751249 original size:20 final size:20
Alignment explanation
Indices: 34751212--34751250 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34751202 GCTAATAATT
*
34751212 TGAAACAACAAAATGAAAAG
1 TGAAACAACAAAAAGAAAAG
34751232 TGAAACAA-ATAAAAGAAAA
1 TGAAACAACA-AAAAGAAAA
34751251 TAAATGAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.69, C:0.08, G:0.13, T:0.10
Consensus pattern (20 bp):
TGAAACAACAAAAAGAAAAG
Found at i:34761843 original size:11 final size:11
Alignment explanation
Indices: 34761821--34761853 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
34761811 TTGAAAATAT
34761821 ATTTTG-GAGA
1 ATTTTGAGAGA
34761831 ATTTTGAGAGA
1 ATTTTGAGAGA
*
34761842 ATTTGGAGAGA
1 ATTTTGAGAGA
34761853 A
1 A
34761854 CAAAAGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.30, T:0.33
Consensus pattern (11 bp):
ATTTTGAGAGA
Found at i:34772302 original size:27 final size:26
Alignment explanation
Indices: 34772252--34772302 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
34772242 GTGTCGTATC
*
34772252 TTGTTTTGGCTTCTTCACTGTGGAAT
1 TTGTTTTGGCTTCTTCAATGTGGAAT
*
34772278 TTGTTTTGTGCTTCTTCAATTTGGA
1 TTGTTTTG-GCTTCTTCAATGTGGA
34772303 TCGAGGAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.12, C:0.14, G:0.22, T:0.53
Consensus pattern (26 bp):
TTGTTTTGGCTTCTTCAATGTGGAAT
Found at i:34773406 original size:23 final size:23
Alignment explanation
Indices: 34773370--34773535 Score: 159
Period size: 23 Copynumber: 7.5 Consensus size: 23
34773360 AGTGCTGGGC
*
34773370 AACAGAAAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
34773393 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
**
34773412 ---ATTGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
34773432 ATCAGAGTGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* ** *
34773455 ATCAGAGAGCACACGCAGTGCTG
1 AACAGAGAGCACACAAAGTGCTA
* *
34773478 AACAAAGAGCACACATAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
34773501 AACAGAGAGCACACACAAG-GCTA
1 AACAGAGAGCACACA-AAGTGCTA
34773524 AACAGAGAGCAC
1 AACAGAGAGCAC
34773536 GCTAGTGTTC
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
16 11 0.09
18 1 0.01
19 1 0.01
20 1 0.01
21 1 0.01
23 99 0.85
24 2 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:34780700 original size:27 final size:28
Alignment explanation
Indices: 34780668--34780725 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
34780658 TGTCGGGGTA
34780668 TCTTTCTTCTCTTCATTATTATCC-TCT
1 TCTTTCTTCTCTTCATTATTATCCTTCT
* *
34780695 TCTTTCTTCTCTTCTTTATTTTCCTTCT
1 TCTTTCTTCTCTTCATTATTATCCTTCT
34780723 TCT
1 TCT
34780726 CCTCAGGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (28 bp):
TCTTTCTTCTCTTCATTATTATCCTTCT
Found at i:34795222 original size:131 final size:131
Alignment explanation
Indices: 34794988--34795251 Score: 528
Period size: 131 Copynumber: 2.0 Consensus size: 131
34794978 ATAAACAAGT
34794988 AAAAGATCAAGTGAAGTAACAACATATCACTATATTGAAACAATTTAATCACAAAAATCTCTCAA
1 AAAAGATCAAGTGAAGTAACAACATATCACTATATTGAAACAATTTAATCACAAAAATCTCTCAA
34795053 GTTATGCAAGGTTAATGTATTGTTAATATCGTCGCTAATTTAACCTTCAACTCCCGTAGAACATT
66 GTTATGCAAGGTTAATGTATTGTTAATATCGTCGCTAATTTAACCTTCAACTCCCGTAGAACATT
34795118 A
131 A
34795119 AAAAGATCAAGTGAAGTAACAACATATCACTATATTGAAACAATTTAATCACAAAAATCTCTCAA
1 AAAAGATCAAGTGAAGTAACAACATATCACTATATTGAAACAATTTAATCACAAAAATCTCTCAA
34795184 GTTATGCAAGGTTAATGTATTGTTAATATCGTCGCTAATTTAACCTTCAACTCCCGTAGAACATT
66 GTTATGCAAGGTTAATGTATTGTTAATATCGTCGCTAATTTAACCTTCAACTCCCGTAGAACATT
34795249 A
131 A
34795250 AA
1 AA
34795252 CATGCACCAA
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 133 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (131 bp):
AAAAGATCAAGTGAAGTAACAACATATCACTATATTGAAACAATTTAATCACAAAAATCTCTCAA
GTTATGCAAGGTTAATGTATTGTTAATATCGTCGCTAATTTAACCTTCAACTCCCGTAGAACATT
A
Found at i:34800986 original size:13 final size:14
Alignment explanation
Indices: 34800968--34800997 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34800958 GTCAACGCAA
34800968 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
34800981 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
34800995 TCA
1 TCA
34800998 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:34820096 original size:24 final size:24
Alignment explanation
Indices: 34820069--34820115 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
34820059 TTTGAGGAAT
34820069 TTTGTGTTT-ACGTTTTCAGGGTTC
1 TTTGT-TTTCACGTTTTCAGGGTTC
*
34820093 TTTGTTTTCAGGTTTTCAGGGTT
1 TTTGTTTTCACGTTTTCAGGGTT
34820116 TAGTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.09, C:0.11, G:0.26, T:0.55
Consensus pattern (24 bp):
TTTGTTTTCACGTTTTCAGGGTTC
Found at i:34828659 original size:25 final size:25
Alignment explanation
Indices: 34828611--34828659 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
34828601 TGAGAAGAGA
* * * *
34828611 GAAAAATAAAGAGAAAGAAGAAATG
1 GAAAAAAAAAAAGAAAAAAAAAATG
34828636 GAAAAAAAAAAAGAAAAAAAAAAT
1 GAAAAAAAAAAAGAAAAAAAAAAT
34828660 AAATTGTTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (25 bp):
GAAAAAAAAAAAGAAAAAAAAAATG
Found at i:34830077 original size:13 final size:14
Alignment explanation
Indices: 34830052--34830080 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
34830042 GAAGAGCATA
34830052 GAGGGAGAAGAAGG
1 GAGGGAGAAGAAGG
34830066 GAGGGA-AAGAAGG
1 GAGGGAGAAGAAGG
34830079 GA
1 GA
34830081 AGTAAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (14 bp):
GAGGGAGAAGAAGG
Found at i:34830796 original size:19 final size:19
Alignment explanation
Indices: 34830769--34830805 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34830759 AATTACTTTA
34830769 AAATATAAAAAAAATTATC
1 AAATATAAAAAAAATTATC
*
34830788 AAATTTAAAAAAAATTAT
1 AAATATAAAAAAAATTAT
34830806 GAGATTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (19 bp):
AAATATAAAAAAAATTATC
Found at i:34831441 original size:32 final size:32
Alignment explanation
Indices: 34831400--34831460 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
34831390 ATATATTTTG
34831400 AACCTATCTCAATGTCTGAAAATAATGCAGTT
1 AACCTATCTCAATGTCTGAAAATAATGCAGTT
*
34831432 AACCTATCTCAATGTTTGAAAATAATGCA
1 AACCTATCTCAATGTCTGAAAATAATGCA
34831461 CTGTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (32 bp):
AACCTATCTCAATGTCTGAAAATAATGCAGTT
Found at i:34831682 original size:14 final size:13
Alignment explanation
Indices: 34831659--34831689 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
34831649 TTTACATCTC
34831659 AAAAAATATATAA
1 AAAAAATATATAA
34831672 AAAAGAATATATAA
1 AAAA-AATATATAA
34831686 AAAA
1 AAAA
34831690 CTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAAAAATATATAA
Found at i:34831717 original size:20 final size:20
Alignment explanation
Indices: 34831672--34831718 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
34831662 AAATATATAA
*
34831672 AAAAGAATATATAAAAAACTT
1 AAAA-AATATATAAAAAACCT
34831693 AAAAAATAT-TAAAAAACCT
1 AAAAAATATATAAAAAACCT
*
34831712 ATAAAAT
1 AAAAAAT
34831719 CCTAAACCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 5 0.21
21 4 0.17
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAATATATAAAAAACCT
Found at i:34832457 original size:6 final size:6
Alignment explanation
Indices: 34832446--34832503 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
34832436 AAAAGTTGTG
* *
34832446 ATAATT ATAATT ACAATT ATAATT -TAATTT ACAATT ATTAATT A-AA--
1 ATAATT ATAATT ATAATT ATAATT ATAA-TT ATAATT A-TAATT ATAATT
34832492 ATAATT ATAATT
1 ATAATT ATAATT
34832504 TAAATATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 1 0.02
4 2 0.05
5 5 0.12
6 27 0.64
7 7 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:34832469 original size:18 final size:19
Alignment explanation
Indices: 34832446--34832489 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
34832436 AAAAGTTGTG
34832446 ATAATTATAA-TTACAATT
1 ATAATTATAATTTACAATT
34832464 ATAATT-TAATTTACAATT
1 ATAATTATAATTTACAATT
34832482 ATTAATTA
1 A-TAATTA
34832490 AAATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATTATAATTTACAATT
Found at i:34843985 original size:15 final size:15
Alignment explanation
Indices: 34843954--34844000 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
34843944 GATCTCCTAC
*
34843954 TCTTCATA-ATACCCA
1 TCTTCATAGATA-TCA
34843969 TCTTCATAGATATCA
1 TCTTCATAGATATCA
* *
34843984 TCATCAGAGATATCA
1 TCTTCATAGATATCA
34843999 TC
1 TC
34844001 ATAAATGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 25 0.89
16 3 0.11
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (15 bp):
TCTTCATAGATATCA
Found at i:34853472 original size:20 final size:20
Alignment explanation
Indices: 34853444--34853485 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
34853434 ACTGAGAGGT
*
34853444 ATGGTAATTGAGTGCACAAC
1 ATGGCAATTGAGTGCACAAC
34853464 ATGGCAATTGAGTGCACAAC
1 ATGGCAATTGAGTGCACAAC
34853484 AT
1 AT
34853486 TGCCAACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGGCAATTGAGTGCACAAC
Found at i:34861981 original size:21 final size:21
Alignment explanation
Indices: 34861939--34861982 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34861929 TGATTCGAAG
*
34861939 GATAAGAAGAGAAAGCATAAA
1 GATAAGAAGAGAAAGCACAAA
*
34861960 GATAAGAAGA-AGAAGCGCAAA
1 GATAAGAAGAGA-AAGCACAAA
34861981 GA
1 GA
34861983 AGAAGGCGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.59, C:0.07, G:0.27, T:0.07
Consensus pattern (21 bp):
GATAAGAAGAGAAAGCACAAA
Found at i:34862114 original size:17 final size:17
Alignment explanation
Indices: 34862088--34862146 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
34862078 CATGCATTTT
*
34862088 ATTT-ATTTGTCATTAC
1 ATTTCATTTGTCAATAC
*
34862104 ATTTCATTTGTCACTAC
1 ATTTCATTTGTCAATAC
*
34862121 ATTTCATTTGTTAATAC
1 ATTTCATTTGTCAATAC
34862138 ATTTGCATT
1 ATTT-CATT
34862147 GTAGTTGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 4 0.11
17 30 0.79
18 4 0.11
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (17 bp):
ATTTCATTTGTCAATAC
Found at i:34862745 original size:10 final size:10
Alignment explanation
Indices: 34862730--34862763 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
34862720 AAATTCATAG
34862730 AAAGAAAGAA
1 AAAGAAAGAA
34862740 AAAGAAAGAA
1 AAAGAAAGAA
*
34862750 GAAGAAAAGAA
1 AAAG-AAAGAA
34862761 AAA
1 AAA
34862764 ATGAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:34868823 original size:15 final size:16
Alignment explanation
Indices: 34868798--34868828 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
34868788 TGTCAGGGCA
34868798 TCTTCCTTCTCTTCCT
1 TCTTCCTTCTCTTCCT
34868814 TCTT-CTTCTCTTCCT
1 TCTTCCTTCTCTTCCT
34868829 CATTTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (16 bp):
TCTTCCTTCTCTTCCT
Found at i:34881346 original size:16 final size:16
Alignment explanation
Indices: 34881327--34881357 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34881317 CAATAATGTG
34881327 AAATAAAGATAAAATA
1 AAATAAAGATAAAATA
*
34881343 AAATAAAGGTAAAAT
1 AAATAAAGATAAAAT
34881358 GGGATCCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (16 bp):
AAATAAAGATAAAATA
Found at i:34889277 original size:40 final size:40
Alignment explanation
Indices: 34889233--34889313 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
34889223 CATTGCAGGG
*
34889233 AAAAGCTCGAACACGATTTTTAGGATCCTTGACTGGATCT
1 AAAAGCTCGAACACGATTTTTAGGATCATTGACTGGATCT
* * *
34889273 AAAAGCTCGAACAGGGTTTTTAGGATTATTGACTGGATCT
1 AAAAGCTCGAACACGATTTTTAGGATCATTGACTGGATCT
34889313 A
1 A
34889314 GTACATCATG
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:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (40 bp):
AAAAGCTCGAACACGATTTTTAGGATCATTGACTGGATCT
Found at i:34901083 original size:37 final size:37
Alignment explanation
Indices: 34901037--34901214 Score: 239
Period size: 37 Copynumber: 4.8 Consensus size: 37
34901027 TGCATCAAAA
*
34901037 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * * * *
34901074 TATTTAGGCTTTATGCCTAGTAGGCTTTATACCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * * *
34901111 TATTCAGGTTGTATGCCTAGTAGGCTTTGTGCCTGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
34901148 TATTCAGGCTATGTGCCTACTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
34901185 TATTCAAGCTGTGTGCCTAGTAGGCTTTGT
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGT
34901215 ATCGATGAAT
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 121 1.00
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:34901156 original size:21 final size:21
Alignment explanation
Indices: 34901132--34901202 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
34901122 TATGCCTAGT
34901132 AGGCTTTGTGCCTGTGTATTC
1 AGGCTTTGTGCCTGTGTATTC
* *
34901153 AGGCTATGTGCC----TACT-
1 AGGCTTTGTGCCTGTGTATTC
*
34901169 AGGCTTTGTGCCGGTGTATTC
1 AGGCTTTGTGCCTGTGTATTC
* *
34901190 AAGCTGTGTGCCT
1 AGGCTTTGTGCCT
34901203 AGTAGGCTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
16 11 0.29
17 3 0.08
20 3 0.08
21 21 0.55
ACGTcount: A:0.13, C:0.21, G:0.30, T:0.37
Consensus pattern (21 bp):
AGGCTTTGTGCCTGTGTATTC
Found at i:34903659 original size:21 final size:21
Alignment explanation
Indices: 34903619--34903671 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
34903609 GGATTTTTAG
*
34903619 TATCGGTAGAAGCACGACTTG
1 TATCGGTAGAAGCACGACTTA
* *
34903640 TTTCGGTAGAAGCTTC-ACTTA
1 TATCGGTAGAAGC-ACGACTTA
34903661 TATCGGTAGAA
1 TATCGGTAGAA
34903672 CTGTCACAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (21 bp):
TATCGGTAGAAGCACGACTTA
Found at i:34904445 original size:12 final size:12
Alignment explanation
Indices: 34904404--34904460 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
34904394 TAAAAATCAT
*
34904404 AAAATATTTTAA
1 AAAATAATTTAA
*
34904416 AAAGTTAGATTTAA
1 AAA-ATA-ATTTAA
*
34904430 AAAATAATTTAT
1 AAAATAATTTAA
* *
34904442 AAAATTATTAAA
1 AAAATAATTTAA
34904454 AAAATAA
1 AAAATAA
34904461 GTTTTGTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
12 23 0.66
13 4 0.11
14 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
AAAATAATTTAA
Found at i:34911264 original size:21 final size:21
Alignment explanation
Indices: 34911212--34911264 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
34911202 GACACAATTT
*
34911212 TATCGATACCTTTTTAAAGAAT
1 TATCGATA-CTTTTTAAAGAAG
34911234 TATCGATACTTGTTTAAA-AAG
1 TATCGATACTT-TTTAAAGAAG
*
34911255 TATTGATACT
1 TATCGATACT
34911265 CATGGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (21 bp):
TATCGATACTTTTTAAAGAAG
Found at i:34922914 original size:19 final size:19
Alignment explanation
Indices: 34922861--34922923 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
34922851 TTTTATAATT
*
34922861 TTTTAAAAATTATAATATGAA
1 TTTTAAAAATTAT--TTTGAA
* *
34922882 TTTTTATAGA-TATTTTGAA
1 -TTTTAAAAATTATTTTGAA
*
34922901 TTTTAAAAATTATTTTTAA
1 TTTTAAAAATTATTTTGAA
34922920 TTTT
1 TTTT
34922924 TTTTGTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 7 0.21
19 17 0.50
21 3 0.09
22 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:34924081 original size:65 final size:66
Alignment explanation
Indices: 34924005--34924135 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
34923995 CCAAATCAAG
*
34924005 TGACCCAAACCAAGACCCAACCTATGGCCC-AAAATTTATCCCAACTATAACCCAAGCTTATACC
1 TGACCCAAACCAAGACCCAACCTAAGGCCCAAAAATTTATCCCAACTATAACCCAAGCTTATACC
34924069 C
66 C
*
34924070 TGACCCAAACCAAGACCCAACCTAAGGCCCAAAAATTTATCCCAACTATGACCCAAGCTTATACC
1 TGACCCAAACCAAGACCCAACCTAAGGCCCAAAAATTTATCCCAACTATAACCCAAGCTTATACC
34924135 C
66 C
34924136 AATACCCATG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 29 0.46
66 34 0.54
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.18
Consensus pattern (66 bp):
TGACCCAAACCAAGACCCAACCTAAGGCCCAAAAATTTATCCCAACTATAACCCAAGCTTATACC
C
Found at i:34925850 original size:44 final size:41
Alignment explanation
Indices: 34925800--34925895 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 41
34925790 ATATTTCAGT
* *
34925800 TGTTTGGTTAAATGAAATGAAATAGAGTTGTAATAGTATTCTTG
1 TGTTTGGTT-AATG-AATG-AATAGAGCTGTAATAGCATTCTTG
*
34925844 TGTTTGG-T--TGAATGAATAGTGCTGTAATAGCATTCTTG
1 TGTTTGGTTAATGAATGAATAGAGCTGTAATAGCATTCTTG
34925882 TGTTTGGTTGAATG
1 TGTTTGGTT-AATG
34925896 TAATAGTGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
38 28 0.62
39 5 0.11
40 2 0.04
42 2 0.04
43 1 0.02
44 7 0.16
ACGTcount: A:0.27, C:0.04, G:0.26, T:0.43
Consensus pattern (41 bp):
TGTTTGGTTAATGAATGAATAGAGCTGTAATAGCATTCTTG
Found at i:34925870 original size:38 final size:39
Alignment explanation
Indices: 34925828--34925911 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 39
34925818 GAAATAGAGT
*
34925828 TGTAATAGTATTCTTGTGTTTGGTTGAATG-AATAGTGC
1 TGTAATAGCATTCTTGTGTTTGGTTGAATGTAATAGTGC
34925866 TGTAATAGCATTCTTGTGTTTGGTTGAATGTAATAGTGC
1 TGTAATAGCATTCTTGTGTTTGGTTGAATGTAATAGTGC
34925905 TG-AATAG
1 TGTAATAG
34925912 GATAAGAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 34 0.77
39 10 0.23
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.43
Consensus pattern (39 bp):
TGTAATAGCATTCTTGTGTTTGGTTGAATGTAATAGTGC
Found at i:34929561 original size:21 final size:21
Alignment explanation
Indices: 34929537--34929576 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34929527 TAAAAGGAAA
*
34929537 AAAAAGAAGCTAAAAATGGTG
1 AAAAAGAACCTAAAAATGGTG
*
34929558 AAAATGAACCTAAAAATGG
1 AAAAAGAACCTAAAAATGG
34929577 ACAAATCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.20, T:0.15
Consensus pattern (21 bp):
AAAAAGAACCTAAAAATGGTG
Found at i:34931494 original size:30 final size:30
Alignment explanation
Indices: 34931460--34931524 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
34931450 GCTACTACCC
*
34931460 ATTTGAGGTATGTTTCTAT-TCGTGCTACAT
1 ATTTGAGGTATGTTTCTATCT-ATGCTACAT
** *
34931490 ATTTGCTGTGTGTTTCTATCTATGCTACAT
1 ATTTGAGGTATGTTTCTATCTATGCTACAT
34931520 -TTTGA
1 ATTTGA
34931525 TGTGTGACGG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
29 4 0.14
30 24 0.83
31 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (30 bp):
ATTTGAGGTATGTTTCTATCTATGCTACAT
Found at i:34938368 original size:21 final size:21
Alignment explanation
Indices: 34938344--34938389 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
34938334 TCTTCCAAAA
34938344 GCCCGTGTGAACCTCCCACAC
1 GCCCGTGTGAACCTCCCACAC
34938365 GCCCGTGTGAACCTCCCACAC
1 GCCCGTGTGAACCTCCCACAC
34938386 GCCC
1 GCCC
34938390 ATGTCTCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.50, G:0.20, T:0.13
Consensus pattern (21 bp):
GCCCGTGTGAACCTCCCACAC
Found at i:34938459 original size:42 final size:42
Alignment explanation
Indices: 34938412--34938501 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
34938402 GTGTGCTAGA
* *
34938412 CCGTGTAACTCACTGACTTGGACCACACGCCCATGTCTCAAC
1 CCGTGTAACTCACTAAATTGGACCACACGCCCATGTCTCAAC
* * *
34938454 CCGTGTAACTCACTAAATTGGGCCACACGCCCGTGTGTCAAC
1 CCGTGTAACTCACTAAATTGGACCACACGCCCATGTCTCAAC
34938496 CCGTGT
1 CCGTGT
34938502 GAACCCTGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (42 bp):
CCGTGTAACTCACTAAATTGGACCACACGCCCATGTCTCAAC
Found at i:34940207 original size:21 final size:21
Alignment explanation
Indices: 34940181--34940221 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
34940171 TTCACATGTT
34940181 TTCTTACTCATGATTCTTTTG
1 TTCTTACTCATGATTCTTTTG
**
34940202 TTCTTACTCATTTTTCTTTT
1 TTCTTACTCATGATTCTTTT
34940222 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.05, T:0.63
Consensus pattern (21 bp):
TTCTTACTCATGATTCTTTTG
Found at i:34949589 original size:107 final size:107
Alignment explanation
Indices: 34949399--34949654 Score: 300
Period size: 107 Copynumber: 2.4 Consensus size: 107
34949389 TTCACAATGC
* * * *
34949399 TGCTCACACAAGCTGTTGAGAATTCGTAAATTATGCAGGATCTCAACCATCGCAAGGATTCATAT
1 TGCTCACACAAGCTATTGAGAATCCGCAACTTATGCAGGATCTCAACCATCGCAAGGATTCATAT
*
34949464 CATAAGAACACAATAACCATTCAGTATTCACCGTCTCACGA-
66 CATAAGAACACAATAACCATTCAGTATTCACCGACTCACGAT
* * * **
34949505 TGCTACACACAAGCTATTGAGAATCCGCAACGTATGCAGGATCTCAGCCATCGTAGAGG-TTTGT
1 TGCT-CACACAAGCTATTGAGAATCCGCAACTTATGCAGGATCTCAACCATCGCA-AGGATTCAT
* * * * *
34949569 ATCATCATAAGACAATAACCATTCAGTATTCACTGACTCATGATGT
64 ATCATAAGAACACAATAACCATTCAGTATTCACCGACTCACGA--T
** *
34949615 TGCTCACACAAGCTATCAAGAATCCGCAACTTATGTAGGA
1 TGCTCACACAAGCTATTGAGAATCCGCAACTTATGCAGGA
34949655 CCTTAGCTAT
Statistics
Matches: 126, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
106 4 0.03
107 83 0.66
108 3 0.02
109 32 0.25
110 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (107 bp):
TGCTCACACAAGCTATTGAGAATCCGCAACTTATGCAGGATCTCAACCATCGCAAGGATTCATAT
CATAAGAACACAATAACCATTCAGTATTCACCGACTCACGAT
Found at i:34949667 original size:109 final size:107
Alignment explanation
Indices: 34949473--34949667 Score: 266
Period size: 109 Copynumber: 1.8 Consensus size: 107
34949463 TCATAAGAAC
* **
34949473 ACAATAACCATTCAGTATTCACCGTCTCACGATGCTACACACAAGCTATTGAGAATCCGCAACGT
1 ACAATAACCATTCAGTATTCACCGACTCACGATGCTACACACAAGCTATCAAGAATCCGCAACGT
*
34949538 ATGCAGGATCTCAGCCATCGTAGAGGTTTGTATCATCATAAG
66 ATGCAGGACCTCAGCCATCGTAGAGGTTTGTATCATCATAAG
* *
34949580 ACAATAACCATTCAGTATTCACTGACTCATGATGTTGCT-CACACAAGCTATCAAGAATCCGCAA
1 ACAATAACCATTCAGTATTCACCGACTCACGA---TGCTACACACAAGCTATCAAGAATCCGCAA
* * * *
34949644 CTTATGTAGGACCTTAGCTATCGT
63 CGTATGCAGGACCTCAGCCATCGT
34949668 GGCAATTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
107 29 0.39
109 42 0.56
110 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (107 bp):
ACAATAACCATTCAGTATTCACCGACTCACGATGCTACACACAAGCTATCAAGAATCCGCAACGT
ATGCAGGACCTCAGCCATCGTAGAGGTTTGTATCATCATAAG
Found at i:34949681 original size:109 final size:107
Alignment explanation
Indices: 34949430--34949681 Score: 258
Period size: 107 Copynumber: 2.3 Consensus size: 107
34949420 ATTCGTAAAT
* * * * * * *
34949430 TATGCAGGATCTCAACCATCGCA-AGGATTCATATCATAAGAACACAATAACCATTCAGTATTCA
1 TATGCAGGACCTCAGCCATCGTAGA-GATTTATATCATCATAAGACAATAACCATTCAGTATTCA
* **
34949494 CCGTCTCACGATGCTACACACAAGCTATTGAGAATCCGCAACG
65 CCGACTCACGATGCTACACACAAGCTATCAAGAATCCGCAACG
* * *
34949537 TATGCAGGATCTCAGCCATCGTAGAGGTTTGTATCATCATAAGACAATAACCATTCAGTATTCAC
1 TATGCAGGACCTCAGCCATCGTAGAGATTTATATCATCATAAGACAATAACCATTCAGTATTCAC
* * *
34949602 TGACTCATGATGTTGCT-CACACAAGCTATCAAGAATCCGCAACT
66 CGACTCACGA---TGCTACACACAAGCTATCAAGAATCCGCAACG
* * * *
34949646 TATGTAGGACCTTAGCTATCGTGGCA-ATTTATATCA
1 TATGCAGGACCTCAGCCATCGTAG-AGATTTATATCA
34949682 CCGACCCAAG
Statistics
Matches: 119, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
107 62 0.52
108 1 0.01
109 51 0.43
110 5 0.04
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (107 bp):
TATGCAGGACCTCAGCCATCGTAGAGATTTATATCATCATAAGACAATAACCATTCAGTATTCAC
CGACTCACGATGCTACACACAAGCTATCAAGAATCCGCAACG
Found at i:34957307 original size:21 final size:20
Alignment explanation
Indices: 34957281--34957319 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
34957271 CATTCATCAT
34957281 TCAATTATCTCTTCTATTCTC
1 TCAATTATCTCTTC-ATTCTC
*
34957302 TCAATTCTCTCTTCATTC
1 TCAATTATCTCTTCATTC
34957320 CCACACCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (20 bp):
TCAATTATCTCTTCATTCTC
Found at i:34975977 original size:106 final size:102
Alignment explanation
Indices: 34975793--34975980 Score: 270
Period size: 102 Copynumber: 1.8 Consensus size: 102
34975783 CTCACCCCTC
* *
34975793 AACCTCACTTCTCAAATCATCCCTTCATTCATCATCATCTCTTCTATTCTCTCAATTTTCTCTTC
1 AACCTCACTTCTCAAATAATCCCTTCATTCATCATCATCTCTTCTATTATCTCAATTTTCTCTTC
34975858 ATTCTCACGCCTAGCATCTCTTATAAATAGAGCCTTT
66 ATTCTCACGCCTAGCATCTCTTATAAATAGAGCCTTT
* * *
34975895 AACCTTACTTCTCAAATAATCTCTTCATTCATCATTTAGTTATCTCTTCTATTATCTC-ATTTTC
1 AACCTCACTTCTCAAATAATCCCTTCATTCATC----A-TCATCTCTTCTATTATCTCAATTTTC
*
34975959 TCTTCATTCTCATGCCTAGCAT
61 TCTTCATTCTCACGCCTAGCAT
34975981 ATCCTTTCTT
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
102 30 0.40
106 28 0.37
107 17 0.23
ACGTcount: A:0.23, C:0.30, G:0.04, T:0.43
Consensus pattern (102 bp):
AACCTCACTTCTCAAATAATCCCTTCATTCATCATCATCTCTTCTATTATCTCAATTTTCTCTTC
ATTCTCACGCCTAGCATCTCTTATAAATAGAGCCTTT
Found at i:34983868 original size:31 final size:32
Alignment explanation
Indices: 34983830--34983913 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 32
34983820 AAATTCAAAA
34983830 TTCGAATTATTCGAATCGAGTTGAATTTTT-T
1 TTCGAATTATTCGAATCGAGTTGAATTTTTAT
*
34983861 TTCGAATTTCGAGTTCGAATCGAGTTTAATTTTTGAAT
1 TTCGAA-TT--A-TTCGAATCGAGTTGAATTTTT--AT
34983899 TT-GAATTATTCGAAT
1 TTCGAATTATTCGAAT
34983914 AATTCGAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
31 6 0.13
32 2 0.04
33 7 0.16
34 2 0.04
35 20 0.44
36 2 0.04
37 3 0.07
38 3 0.07
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (32 bp):
TTCGAATTATTCGAATCGAGTTGAATTTTTAT
Found at i:34984152 original size:42 final size:42
Alignment explanation
Indices: 34984093--34984186 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
34984083 CAAATATTTT
* *
34984093 TAAACCCAAATATAATTTCATTCTTAAAAAACATCCATAAAC
1 TAAACCCAAATATAATTTCATTATTAAAAAACACCCATAAAC
* * *
34984135 TAAACCCAAATATAATTTTATTATTATAAAACACCCATAAAT
1 TAAACCCAAATATAATTTCATTATTAAAAAACACCCATAAAC
*
34984177 TAAACTCAAA
1 TAAACCCAAA
34984187 ACCAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTATTAAAAAACACCCATAAAC
Found at i:34984194 original size:42 final size:42
Alignment explanation
Indices: 34984093--34984226 Score: 121
Period size: 42 Copynumber: 3.2 Consensus size: 42
34984083 CAAATATTTT
* * * *
34984093 TAAACCCAAATATAATTTCATTCTTAAAAAACATCCATAAAC
1 TAAACCCAAATACAATTTTATTATTAAAAAACACCCATAAAC
* * *
34984135 TAAACCCAAATATAATTTTATTATTATAAAACACCCATAAAT
1 TAAACCCAAATACAATTTTATTATTAAAAAACACCCATAAAC
* * *
34984177 TAAACTCAAA-ACCAATTTT-TTCATCCTAAAAAA-ACCCCTAAAT
1 TAAACCCAAATA-CAATTTTATT-AT--TAAAAAACACCCATAAAC
34984220 TAAACCC
1 TAAACCC
34984227 CCATTTAATC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
41 3 0.04
42 54 0.69
43 15 0.19
44 6 0.08
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (42 bp):
TAAACCCAAATACAATTTTATTATTAAAAAACACCCATAAAC
Found at i:34984255 original size:24 final size:24
Alignment explanation
Indices: 34984226--34984272 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
34984216 AAATTAAACC
*
34984226 CCCATTTAATCGAAGAGGCTGAAA
1 CCCATTTAATCAAAGAGGCTGAAA
*
34984250 CCCATTTAGTCAAAGAGGCTGAA
1 CCCATTTAATCAAAGAGGCTGAA
34984273 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
CCCATTTAATCAAAGAGGCTGAAA
Found at i:34986540 original size:29 final size:27
Alignment explanation
Indices: 34986483--34986542 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
34986473 AAAATACATG
* *
34986483 AAAAATAGAAAAAATTAGGGCTAATTT
1 AAAAATAGAAAAAATGAGGGCTAAATT
34986510 AAAATATA-AAAAAATGAGAGGACTAAATT
1 AAAA-ATAGAAAAAATGAG-GG-CTAAATT
34986539 AAAA
1 AAAA
34986543 CCAAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.46
28 5 0.18
29 10 0.36
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.22
Consensus pattern (27 bp):
AAAAATAGAAAAAATGAGGGCTAAATT
Found at i:34988852 original size:98 final size:98
Alignment explanation
Indices: 34988750--34989077 Score: 381
Period size: 98 Copynumber: 3.4 Consensus size: 98
34988740 TTGCTGTTAC
* * * * **
34988750 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTATATTCGCTATTGTGGGTTAAATATTTTTC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTATATTCGCTGTTGCGGCTTAAATCTTTCCC
* * * *
34988815 GTCATGTTCCTAAGGTACAAGGTTCACCGTTGT
66 TTCATGTTTCTGAGGTACAAGGTTCGCCGTTGT
* * ** * * *
34988848 GACTTAAACCTTTCCCT-CATATCTTCGTGCTAATGGACTCG-TCGTTACGGCTTAAATCCTTCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTATATTCGCT-GTTGCGGCTTAAATCTTTCC
* * * *
34988911 CTTCATGTTTATGAGGTGCAAGGTTCGCCATTGC
65 CTTCATGTTTCTGAGGTACAAGGTTCGCCGTTGT
* * **
34988945 GACTTAAACCTTTCCTTCCATAGCTTTATGGTACTATATTCGCTGTTGCGGCTTAAATCTTTCCC
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTATATTCGCTGTTGCGGCTTAAATCTTTCCC
34989010 TTCATGTTTCTGAGGTACAAGGTTCGCCGTTGT
66 TTCATGTTTCTGAGGTACAAGGTTCGCCGTTGT
* * *
34989043 GACTTAAATCTTTCCCTCCACACCTTCGTGGTACT
1 GACTTAAACCTTTCCCTCCATATCTTCGTGGTACT
34989078 GAAACCTATA
Statistics
Matches: 185, Mismatches: 42, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
96 1 0.01
97 73 0.39
98 110 0.59
99 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (98 bp):
GACTTAAACCTTTCCCTCCATATCTTCGTGGTACTATATTCGCTGTTGCGGCTTAAATCTTTCCC
TTCATGTTTCTGAGGTACAAGGTTCGCCGTTGT
Found at i:34989027 original size:49 final size:48
Alignment explanation
Indices: 34988827--34989059 Score: 168
Period size: 49 Copynumber: 4.8 Consensus size: 48
34988817 CATGTTCCTA
* * * * *
34988827 AGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCC-TCATATCTTCG
1 AGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGT-TTTG
* * * * * * * *
34988875 TGCTA-ATGGACTCGTCGTTACGGCTTAAATCCTTCCCTTCATGTTTATG
1 AGGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTT-TG
* * * *
34988924 AGGTGCAAGGTTCGCCATTGCGACTTAAACCTTT-CCTTCCATAGCTTT-
1 AGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTT-CAT-GTTTTG
* ** * *
34988972 ATGGTACTATATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTTTCTG
1 A-GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTT-TG
*
34989022 AGGTACAAGGTTCGCCGTTGTGACTTAAATCTTTCCCT
1 AGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCT
34989060 CCACACCTTC
Statistics
Matches: 135, Mismatches: 40, Indels: 19
0.70 0.21 0.10
Matches are distributed among these distances:
47 3 0.02
48 32 0.24
49 89 0.66
50 11 0.08
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (48 bp):
AGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTTTTG
Found at i:35006046 original size:16 final size:17
Alignment explanation
Indices: 35006015--35006051 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
35006005 ATTACTATTT
*
35006015 TAAAATATTATAAATTA
1 TAAAAAATTATAAATTA
35006032 TAAAAAATT-TAAATTA
1 TAAAAAATTATAAATTA
35006048 -AAAA
1 TAAAA
35006052 TTTATCATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 7 0.37
17 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAATTATAAATTA
Found at i:35007101 original size:39 final size:40
Alignment explanation
Indices: 35007057--35007139 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
35007047 ACTCGAACTC
* *
35007057 AAAACTTGAATTACTT-ATTCAAGTTAATT-AAAAATAAAA
1 AAAACTCGAATCACTTAATTCAA-TTAATTCAAAAATAAAA
* * *
35007096 AAAACTCGAGTCACTTAATTCGATTAATTCAAAATTAAAA
1 AAAACTCGAATCACTTAATTCAATTAATTCAAAAATAAAA
35007136 AAAA
1 AAAA
35007140 TAGATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 19 0.51
40 18 0.49
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.30
Consensus pattern (40 bp):
AAAACTCGAATCACTTAATTCAATTAATTCAAAAATAAAA
Found at i:35010421 original size:27 final size:26
Alignment explanation
Indices: 35010379--35010436 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
35010369 TTACCATGGC
*
35010379 AACATAGAGAGTCCACCAGGATAGAA
1 AACATAGAGAGTCCACCAGGACAGAA
* * *
35010405 AACATAGGGAAGTCCACTAGGACATAA
1 AACATAGAG-AGTCCACCAGGACAGAA
35010432 AACAT
1 AACAT
35010437 GGGTTACACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (26 bp):
AACATAGAGAGTCCACCAGGACAGAA
Found at i:35011664 original size:78 final size:78
Alignment explanation
Indices: 35011582--35011735 Score: 182
Period size: 78 Copynumber: 2.0 Consensus size: 78
35011572 ATAGCTACAC
* * * * *
35011582 AGTGTTGACAATGTCATTGTCAGCTCAATATAGTATTACGGTGTTTACAGTGTCACCGTCAGTTT
1 AGTGTTGACAATGTCACTGCCAACTCAATATAGTATTACGGTGTTTACAATGTCACCGTCAGTTC
*
35011647 AATTTTGTATTGT
66 AATGTTGTATTGT
* * * * * * * *
35011660 AGTGTTTATAGTGTTACTGCCAATTCGATATAGTATTACGGTGTTTACAATTTTACCGTCAGTTC
1 AGTGTTGACAATGTCACTGCCAACTCAATATAGTATTACGGTGTTTACAATGTCACCGTCAGTTC
35011725 AATGTTGTATT
66 AATGTTGTATT
35011736 CTAAATTACG
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (78 bp):
AGTGTTGACAATGTCACTGCCAACTCAATATAGTATTACGGTGTTTACAATGTCACCGTCAGTTC
AATGTTGTATTGT
Found at i:35011735 original size:39 final size:39
Alignment explanation
Indices: 35011600--35011727 Score: 121
Period size: 39 Copynumber: 3.3 Consensus size: 39
35011590 CAATGTCATT
* *
35011600 GTCAGCTCAATATAGTATTACGGTGTTTACAGTGTCACC
1 GTCAGTTCAATATAGTATTACGGTGTTTACAGTGTTACC
* * * *** * *
35011639 GTCAGTTTAATTTTGTATTGTAGTGTTTATAGTGTTACT
1 GTCAGTTCAATATAGTATTACGGTGTTTACAGTGTTACC
* * * * *
35011678 GCCAATTCGATATAGTATTACGGTGTTTACAATTTTACC
1 GTCAGTTCAATATAGTATTACGGTGTTTACAGTGTTACC
35011717 GTCAGTTCAAT
1 GTCAGTTCAAT
35011728 GTTGTATTCT
Statistics
Matches: 63, Mismatches: 26, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (39 bp):
GTCAGTTCAATATAGTATTACGGTGTTTACAGTGTTACC
Found at i:35018691 original size:78 final size:78
Alignment explanation
Indices: 35018609--35018753 Score: 184
Period size: 78 Copynumber: 1.9 Consensus size: 78
35018599 TATAGCTACA
* * *
35018609 TAGTGTTGACAGTGTCACTGTAAGCTCTG-TATAGTATTACCGTGTTTACAGTGTCAGCATCAGT
1 TAGTGTTGACAGTGTCACTGCAAG-TCTGATACAGTATTACCGTGTTTACAGTGTCACCATCAGT
35018673 TCAATGTTGTATTG
65 TCAATGTTGTATTG
* * * * * * *
35018687 TAGTGTTTACATTGTCATTGCCAGTTTGATACAGTATTACGGTGTTTACAGTGTCACCGTCAGTT
1 TAGTGTTGACAGTGTCACTGCAAGTCTGATACAGTATTACCGTGTTTACAGTGTCACCATCAGTT
35018752 CA
66 CA
35018754 GTATTATATT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 3 0.05
78 53 0.95
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (78 bp):
TAGTGTTGACAGTGTCACTGCAAGTCTGATACAGTATTACCGTGTTTACAGTGTCACCATCAGTT
CAATGTTGTATTG
Found at i:35018861 original size:29 final size:29
Alignment explanation
Indices: 35018829--35018893 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
35018819 TGTACTAACC
35018829 CGTGTGTGTCACACGATCATGCACATACT
1 CGTGTGTGTCACACGATCATGCACATACT
* *
35018858 CGTGTGTGTCACACGATCATGCATATGCT
1 CGTGTGTGTCACACGATCATGCACATACT
35018887 CGTGTGT
1 CGTGTGT
35018894 TCAGACCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.31
Consensus pattern (29 bp):
CGTGTGTGTCACACGATCATGCACATACT
Found at i:35035961 original size:11 final size:10
Alignment explanation
Indices: 35035933--35035969 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
35035923 TTTTACCCAC
35035933 AAAAAATACA
1 AAAAAATACA
35035943 AAAAAATACA
1 AAAAAATACA
*
35035953 AAATCAATACA
1 AAA-AAATACA
35035964 AAAAAA
1 AAAAAA
35035970 AAAAGGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (10 bp):
AAAAAATACA
Found at i:35037088 original size:59 final size:58
Alignment explanation
Indices: 35036992--35037110 Score: 168
Period size: 59 Copynumber: 2.0 Consensus size: 58
35036982 CAAGAGGTCC
* * *
35036992 CCTAAACTTTTCCAAAATTACATTTTGACTCCTAAACTTTTCCAAAATTACATTTTGAA
1 CCTAAACTTTTCCAAAATCACATTTTAACTCCTAAACTTTTCCAAAATCACATTTT-AA
* *
35037051 CCTAATCTTTTCCAAAATCATATTTTAAC-CCTCAAACTTTTCCAAAATCACATTTTAA
1 CCTAAACTTTTCCAAAATCACATTTTAACTCCT-AAACTTTTCCAAAATCACATTTTAA
35037109 CC
1 CC
35037111 CTCGAGCTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 7 0.13
59 47 0.87
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
CCTAAACTTTTCCAAAATCACATTTTAACTCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:35037121 original size:30 final size:29
Alignment explanation
Indices: 35036991--35037112 Score: 165
Period size: 30 Copynumber: 4.1 Consensus size: 29
35036981 TCAAGAGGTC
* *
35036991 CCCTAAACTTTTCCAAAATTACATTTTGA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
*
35037020 CTCCTAAACTTTTCCAAAATTACATTTTGAA
1 C-CCTAAACTTTTCCAAAATCACATTTT-AA
* *
35037051 -CCTAATCTTTTCCAAAATCATATTTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
35037079 CCCTCAAACTTTTCCAAAATCACATTTTAA
1 CCCT-AAACTTTTCCAAAATCACATTTTAA
35037109 CCCT
1 CCCT
35037113 CGAGCTTTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
28 2 0.02
29 27 0.33
30 53 0.64
31 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:35043229 original size:49 final size:49
Alignment explanation
Indices: 35043153--35043632 Score: 263
Period size: 49 Copynumber: 9.8 Consensus size: 49
35043143 GGTTTCATTG
* * *
35043153 CCACGAAGATATGAAAGGAAAGATTTAAGCCGCAACGGTAAATTCAGTA
1 CCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTCAGTA
* * ** * * *
35043202 CCACGAAGATAT-AGAGGGAAAGGTTTAAGTTGCAATGGTGAACCTT--GTA
1 CCACGAAGACATGA-AGGGAAAGATTTAAGCCGCAACGG-CAA-ATTCAGTA
* * * * *
35043251 CCTCAGAA-ACATGAAGGAAAAGATTTAAGCCGTAACGGCGAATCCAGTA
1 CCAC-GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTCAGTA
* * * * * *
35043300 CCATGAGGACATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTT-A-TA
1 CCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGC-AA-ATTCAGTA
* * * *
35043349 CCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTA
1 CCAC-GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTCAGTA
* * * *
35043398 CCACGAAGATATGAAGTGAAAGGTTTAAGTCGCAACGGCAAACCTT--GTA
1 CCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAA--TTCAGTA
** *
35043447 CCTTA-GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTA
1 CC--ACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTCAGTA
* * * * * *
35043496 CCACGAAAATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTT--GTA
1 CCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGC-AA-ATTCAGTA
** * ** *
35043545 CCTTGGAAG-CATGAAAGGAAAGATTTAAGTTGCAACGGCGAA-TCTAGTA
1 CC-ACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTC-AGTA
* * * * *
35043594 CCACAAAGATATGGAGGGAAAG-GTTACGACCGCAACGGC
1 CCACGAAGACATGAAGGGAAAGATTTAAG-CCGCAACGGC
35043633 GAACCCGATA
Statistics
Matches: 317, Mismatches: 84, Indels: 60
0.69 0.18 0.13
Matches are distributed among these distances:
46 1 0.00
47 4 0.01
48 21 0.07
49 266 0.84
50 19 0.06
51 6 0.02
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (49 bp):
CCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCAAATTCAGTA
Found at i:35043645 original size:98 final size:98
Alignment explanation
Indices: 35043163--35043650 Score: 649
Period size: 98 Copynumber: 5.0 Consensus size: 98
35043153 CCACGAAGAT
** * *
35043163 ATGAAAGGAAAGATTTAAGCCGCAACGGTAAATTCAGTACCACGAAGATATAGAGGGAAAGGTTT
1 ATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
* * * * *
35043228 AAGTTGCAATGGTGAACCTTGTACCTCAGAAAC
66 AAGTCGCAACGGCGAACCTTGTACCTTAGAAGC
* * * *
35043261 ATG-AAGGAAAAGATTTAAGCCGTAACGGCGAATCCAGTACCATGAGGACATGGAGGGAAAGGTT
1 ATGAAAGG-AAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTT
* *
35043325 TAAGTCGCAACGGCGAACCTTATACCTCAGAAGC
65 TAAGTCGCAACGGCGAACCTTGTACCTTAGAAGC
* * * *
35043359 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATATGAAGTGAAAGGTTT
1 ATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
*
35043424 AAGTCGCAACGGCAAACCTTGTACCTTAGAAGC
66 AAGTCGCAACGGCGAACCTTGTACCTTAGAAGC
* * *
35043457 ATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCCAGTACCACGAAAATATGGAGGGAAAGGTTT
1 ATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
*
35043522 AAGTCGCAACGGCGAACCTTGTACCTTGGAAGC
66 AAGTCGCAACGGCGAACCTTGTACCTTAGAAGC
** * *
35043555 ATGAAAGGAAAGATTTAAGTTGCAACGGCGAATCTAGTACCACAAAGATATGGAGGGAAAGG-TT
1 ATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
* * *
35043619 ACGACCGCAACGGCGAACC-CGATACCTTAGAA
66 AAG-TCGCAACGGCGAACCTTG-TACCTTAGAA
35043651 AATGACGAGA
Statistics
Matches: 344, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
97 9 0.03
98 332 0.97
99 3 0.01
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
ATGAAAGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
AAGTCGCAACGGCGAACCTTGTACCTTAGAAGC
Found at i:35044680 original size:11 final size:10
Alignment explanation
Indices: 35044653--35044686 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
35044643 TTTACCCACG
35044653 AAAAATACAA
1 AAAAATACAA
35044663 AAAAATACAA
1 AAAAATACAA
*
35044673 AATCAATACAA
1 AA-AAATACAA
35044684 AAA
1 AAA
35044687 GGAGCATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAATACAA
Found at i:35045836 original size:30 final size:29
Alignment explanation
Indices: 35045705--35045825 Score: 161
Period size: 30 Copynumber: 4.1 Consensus size: 29
35045695 CTCAAGAGGT
* * *
35045705 CCCAAACCTTTCCAAAATTACATTTTGAC
1 CCCAAACTTTTCCAAAATCACATTTTAAC
* *
35045734 CCCTAAACTTTTCCAAAATTACATTTTGAGC
1 CCC-AAACTTTTCCAAAATCACATTTT-AAC
*
35045765 CCCAAACTTTTCCAAAATCATATTTTAAC
1 CCCAAACTTTTCCAAAATCACATTTTAAC
35045794 CCGCAAACTTTTCCAAAATCACATTTTAAC
1 CC-CAAACTTTTCCAAAATCACATTTTAAC
35045824 CC
1 CC
35045826 TTGAGCTTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
29 7 0.09
30 71 0.87
31 4 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
CCCAAACTTTTCCAAAATCACATTTTAAC
Found at i:35045850 original size:60 final size:60
Alignment explanation
Indices: 35045705--35045850 Score: 154
Period size: 60 Copynumber: 2.4 Consensus size: 60
35045695 CTCAAGAGGT
* * * * *
35045705 CCCAAACCTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGAGC
1 CCCAAACTTTTCCAAAATTTCATTTTAACCCCTAAACTTTTCCAAAATCACATTTTGAAC
*
35045765 CCCAAACTTTTCCAAAATCAT-ATTTTAACCCGC-AAACTTTTCCAAAATCACATTTT-AAC
1 CCCAAACTTTTCCAAAAT-TTCATTTTAACCC-CTAAACTTTTCCAAAATCACATTTTGAAC
** * *
35045824 CCTTGAGCTTTTCTAAAATTTCATTTT
1 CC-CAAACTTTTCCAAAATTTCATTTT
35045851 CATCCCGAGT
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
59 5 0.07
60 65 0.92
61 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (60 bp):
CCCAAACTTTTCCAAAATTTCATTTTAACCCCTAAACTTTTCCAAAATCACATTTTGAAC
Found at i:35047522 original size:20 final size:21
Alignment explanation
Indices: 35047481--35047522 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
35047471 ATGTCATACA
35047481 TATATATCGATTTGATGAGTTT
1 TATATATCGATTTGAT-AGTTT
35047503 TATATATCGATTTGAT-GTTT
1 TATATATCGATTTGATAGTTT
35047523 CGATTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (21 bp):
TATATATCGATTTGATAGTTT
Found at i:35073302 original size:30 final size:29
Alignment explanation
Indices: 35073279--35073358 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
35073269 AAATTGAATC
*
35073279 AAATCAAAATTTCATGTATAAAATTATACA
1 AAATCAAAA-TTCATATATAAAATTATACA
* *
35073309 AAATCAAAATTCATATATACAATTACACA
1 AAATCAAAATTCATATATAAAATTATACA
* *
35073338 CTAAACCATAATTCATATATA
1 --AAATCAAAATTCATATATA
35073359 GTTTTAGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 17 0.40
30 9 0.21
31 17 0.40
ACGTcount: A:0.53, C:0.15, G:0.01, T:0.31
Consensus pattern (29 bp):
AAATCAAAATTCATATATAAAATTATACA
Found at i:35074350 original size:19 final size:18
Alignment explanation
Indices: 35074323--35074402 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 18
35074313 CCACATCAGC
* *
35074323 AAATGATTTTAAAATTATT
1 AAATTATTTTAAAA-TATA
35074342 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
*
35074362 AAATTA--TTGAAAT-TA
1 AAATTATTTTAAAATATA
* *
35074377 ATATT-TTTTGAAATAATA
1 AAATTATTTTAAAAT-ATA
35074395 AAATTATT
1 AAATTATT
35074403 AAATAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
15 6 0.12
16 13 0.27
18 6 0.12
19 7 0.14
20 9 0.18
21 8 0.16
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:35074365 original size:20 final size:21
Alignment explanation
Indices: 35074329--35074369 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
35074319 CAGCAAATGA
*
35074329 TTTTAAAATTATTAAATTATT
1 TTTTAAAATTATAAAATTATT
35074350 TTTTAAAA-TATAAAATTATT
1 TTTTAAAATTATAAAATTATT
35074370 GAAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAAAATTATAAAATTATT
Found at i:35074396 original size:33 final size:29
Alignment explanation
Indices: 35074332--35074406 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 29
35074322 CAAATGATTT
35074332 TAAAATTATTAAA-TTATTTTTTAAAATA
1 TAAAATTATTAAATTTATTTTTTAAAATA
*
35074360 TAAAATTATTGAAATTAATATTTTTTGAAATAA
1 TAAAATTATT-AAATT--TATTTTTTAAAAT-A
35074393 TAAAATTATTAAAT
1 TAAAATTATTAAAT
35074407 AATTTTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
28 10 0.24
29 3 0.07
30 1 0.02
32 16 0.39
33 11 0.27
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAAATTATTAAATTTATTTTTTAAAATA
Found at i:35083788 original size:16 final size:16
Alignment explanation
Indices: 35083767--35083797 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35083757 CCAAGAACTC
35083767 ATAGTGACCATACCTT
1 ATAGTGACCATACCTT
35083783 ATAGTGACCATACCT
1 ATAGTGACCATACCT
35083798 CGTACGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAGTGACCATACCTT
Found at i:35087998 original size:2 final size:2
Alignment explanation
Indices: 35087991--35088020 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35087981 CTTTTATGTC
35087991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35088021 TAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35092926 original size:12 final size:12
Alignment explanation
Indices: 35092909--35092942 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35092899 TAAAGAGCAT
35092909 AAAATAAAAGAG
1 AAAATAAAAGAG
*
35092921 AAAATAAAATAG
1 AAAATAAAAGAG
*
35092933 AAATTAAAAG
1 AAAATAAAAG
35092943 TAAGATTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (12 bp):
AAAATAAAAGAG
Found at i:35101692 original size:19 final size:19
Alignment explanation
Indices: 35101668--35101718 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
35101658 AAATTACAAA
35101668 AAAATTCAAAATGAA-TTTC
1 AAAATTCAAAAT-AATTTTC
* *
35101687 AAAATTCGAAATAATTTTT
1 AAAATTCAAAATAATTTTC
*
35101706 AAAATTAAAAATA
1 AAAATTCAAAATA
35101719 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:35101721 original size:18 final size:19
Alignment explanation
Indices: 35101666--35101735 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
35101656 GAAAATTACA
*
35101666 AAAAAATTCAAAATGAATTT
1 AAAAAATTAAAAAT-AATTT
* **
35101686 -CAAAATTCGAAATAATTT
1 AAAAAATTAAAAATAATTT
**
35101704 TTAAAATTAAAAAT-ATTT
1 AAAAAATTAAAAATAATTT
*
35101722 AAAAAATTACAAAT
1 AAAAAATTAAAAAT
35101736 TTAATTTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 20 0.49
19 21 0.51
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAAATTAAAAATAATTT
Found at i:35101735 original size:25 final size:25
Alignment explanation
Indices: 35101707--35101755 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
35101697 ATAATTTTTA
35101707 AAATTAAAAATATTTAAAAAATTAC
1 AAATTAAAAATATTTAAAAAATTAC
* ** *
35101732 AAATTTAATTTTTTTAAAAAATTA
1 AAATTAAAAATATTTAAAAAATTA
35101756 TAAAAATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATTAAAAATATTTAAAAAATTAC
Found at i:35101812 original size:35 final size:32
Alignment explanation
Indices: 35101746--35101813 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 32
35101736 TTAATTTTTT
* * *
35101746 TAAAAAATTATAAAAATTTCAAAAAACAATTC
1 TAAAAAATTATAAAAAGTTAAAAAAAAAATTC
35101778 TAAAAAATATATAAAGAAAGTTAAAAAAAAAATTC
1 TAAAAAAT-TAT-AA-AAAGTTAAAAAAAAAATTC
35101813 T
1 T
35101814 TGAATAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 8 0.27
33 3 0.10
34 2 0.07
35 17 0.57
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (32 bp):
TAAAAAATTATAAAAAGTTAAAAAAAAAATTC
Found at i:35102436 original size:18 final size:18
Alignment explanation
Indices: 35102413--35102448 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35102403 GTTCTTCTCC
35102413 CTTCTTTCATTTTATTTG
1 CTTCTTTCATTTTATTTG
*
35102431 CTTCTTTCATTTTCTTTG
1 CTTCTTTCATTTTATTTG
35102449 AATTAGTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.19, G:0.06, T:0.67
Consensus pattern (18 bp):
CTTCTTTCATTTTATTTG
Found at i:35112967 original size:9 final size:9
Alignment explanation
Indices: 35112949--35112978 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35112939 TATAGTAATG
35112949 GTAA-TTTT
1 GTAATTTTT
35112957 GTAATTTTT
1 GTAATTTTT
35112966 GTAATTTTT
1 GTAATTTTT
35112975 GTAA
1 GTAA
35112979 CTTTCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (9 bp):
GTAATTTTT
Found at i:35113357 original size:18 final size:18
Alignment explanation
Indices: 35113315--35113362 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
35113305 CATACATAAT
35113315 AACTAAATAAAAATTAAA
1 AACTAAATAAAAATTAAA
*
35113333 AATTAAATAAAAATTAAA
1 AACTAAATAAAAATTAAA
**
35113351 TGCTAAATAAAA
1 AACTAAATAAAA
35113363 TAATGCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (18 bp):
AACTAAATAAAAATTAAA
Found at i:35114162 original size:7 final size:7
Alignment explanation
Indices: 35114150--35114177 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35114140 AAATTCAATT
35114150 GTGTTGA
1 GTGTTGA
35114157 GTGTTGA
1 GTGTTGA
35114164 GTGTTGA
1 GTGTTGA
35114171 GTGTTGA
1 GTGTTGA
35114178 ATATTTAAAT
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:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:35115142 original size:19 final size:19
Alignment explanation
Indices: 35115114--35115157 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35115104 TTAGATTTTA
* *
35115114 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
35115133 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
35115152 AAATTA
1 AAATTA
35115158 CACTCATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:35115454 original size:135 final size:129
Alignment explanation
Indices: 35115266--35115659 Score: 725
Period size: 135 Copynumber: 3.0 Consensus size: 129
35115256 TGGTGTAAAA
35115266 GTTTATAAAGGTTATTATTATTATTAAATATATATATATATTTATAAGTTAGTGGACAAGGATGG
1 GTTTATAAAGGTTATTATTATTATTAAATATATATATATATTTATAAGTTAGTGGACAAGGATGG
35115331 AAGGAATTATAAAATTCTATTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAGAAGAT
66 AAGGAATTATAAAATTCTATTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAGAAGAT
35115395 GTTTATAAAGGTTATTATTATTATTAAATATATATATATATATATATTTATAAGTTAGTGGACAA
1 GTTTATAAAGGTTATTATTATTA-T---TA-A-ATATATATATATATTTATAAGTTAGTGGACAA
35115460 GGATGGAAGGAATTATAAAATTCTATTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAG
60 GGATGGAAGGAATTATAAAATTCTATTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAG
35115525 AAGAT
125 AAGAT
35115530 GTTTATAAAGGTTATTATTATTATTAAATATATATATATATTTATAAGTTAGTGGACAAGGATGG
1 GTTTATAAAGGTTATTATTATTATTAAATATATATATATATTTATAAGTTAGTGGACAAGGATGG
35115595 AAGGAATTATAAAATTCTATTTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAGAAGAT
66 AAGGAATTATAAAATTCTA-TTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAGAAGAT
35115660 AAAGACTAGA
Statistics
Matches: 258, Mismatches: 0, Indels: 13
0.95 0.00 0.05
Matches are distributed among these distances:
129 80 0.31
130 47 0.18
131 2 0.01
133 2 0.01
134 2 0.01
135 125 0.48
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (129 bp):
GTTTATAAAGGTTATTATTATTATTAAATATATATATATATTTATAAGTTAGTGGACAAGGATGG
AAGGAATTATAAAATTCTATTTTTTTATTTTAAGTAAGGAAAATAAAAGAAATTAAAAGAAGAT
Found at i:35116504 original size:16 final size:16
Alignment explanation
Indices: 35116483--35116584 Score: 55
Period size: 16 Copynumber: 5.8 Consensus size: 16
35116473 ACACAAATTC
35116483 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
*
35116499 AGGCTTTATGCCGGT-GTTTT
1 AGGCTTTGTGCC--TAG---T
35116519 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
*
35116536 AGGCTTTATG-CTGATGTTTT
1 AGGCTTTGTGCCT-A-G---T
35116556 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
*
35116573 AGGCCTTGTGCC
1 AGGCTTTGTGCC
35116585 GGTGTATTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 28
0.67 0.05 0.28
Matches are distributed among these distances:
15 2 0.03
16 32 0.48
17 4 0.06
18 1 0.01
19 1 0.01
20 4 0.06
21 21 0.31
22 2 0.03
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.39
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:35116523 original size:37 final size:37
Alignment explanation
Indices: 35116480--35116608 Score: 186
Period size: 37 Copynumber: 3.5 Consensus size: 37
35116470 TTTACACAAA
35116480 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTT
* *
35116517 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCTGATGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTT
* * *
35116554 TTCAGGCTTTGTGCCTAGTAGGCCTTGTGCCGGTGTA
1 TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTT
* * *
35116591 TTCGGGCTATATGCCTAG
1 TTCAGGCTTTGTGCCTAG
35116609 CAAGCATTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 82 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.39
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTT
Found at i:35119471 original size:50 final size:50
Alignment explanation
Indices: 35119309--35119681 Score: 301
Period size: 50 Copynumber: 7.5 Consensus size: 50
35119299 CTTTGCAGCT
* * ** *
35119309 TTAGGGGTATAAGATTTACCTTTAC-GACTTTAATCAATCCCTTTTACAG-C
1 TTAGGGGTATAAGATTCACCTTTACAG-CTTCAATCTTTCCC-TCTACAGTC
* * * * * * * *
35119359 TTTAGGGATATAAGATTCATCTTTGCTA-CTT-TATTTTATCCTTCTATAGTT
1 -TTAGGGGTATAAGATTCACCTTTAC-AGCTTCAATCTT-TCCCTCTACAGTC
* * * * *
35119410 TTAAGGATATAAGATTCGCCTTTCCAGCTTCAATCTTTCCCTCTACAATC
1 TTAGGGGTATAAGATTCACCTTTACAGCTTCAATCTTTCCCTCTACAGTC
** * * * *
35119460 TTAGGGGTATAAGATTTGCCTTTACGGATTCAATCTCTCCCTCTACAATC
1 TTAGGGGTATAAGATTCACCTTTACAGCTTCAATCTTTCCCTCTACAGTC
* *
35119510 TTAGGGGTATAAGATTCGCCTTTACAGCTTCAATCTGTCCCTCTACAGTC
1 TTAGGGGTATAAGATTCACCTTTACAGCTTCAATCTTTCCCTCTACAGTC
* * * *
35119560 TTAGGGGTATAAGTTTCACCTTTGCAACTTCAATCTATT-CCTCTACAGTT
1 TTAGGGGTATAAGATTCACCTTTACAGCTTCAATCT-TTCCCTCTACAGTC
* * * * * *
35119610 TTAGGGGTATAA-ATTCACCTTTTC-GACTTTAACCTATCCCTTTACAGTT
1 TTAGGGGTATAAGATTCACCTTTACAG-CTTCAATCTTTCCCTCTACAGTC
*
35119659 TTAGGGGTAAAAGATTCACCTTT
1 TTAGGGGTATAAGATTCACCTTT
35119682 TTGACTTCAA
Statistics
Matches: 264, Mismatches: 48, Indels: 21
0.79 0.14 0.06
Matches are distributed among these distances:
48 1 0.00
49 39 0.15
50 192 0.73
51 32 0.12
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (50 bp):
TTAGGGGTATAAGATTCACCTTTACAGCTTCAATCTTTCCCTCTACAGTC
Found at i:35119706 original size:50 final size:50
Alignment explanation
Indices: 35119308--35119812 Score: 288
Period size: 50 Copynumber: 10.1 Consensus size: 50
35119298 TCTTTGCAGC
* * * * * * *
35119308 TTTAGGGGTATAAGATTTACCTTTACGACTTTAATCAATCCCTTTTACAGC
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCC-TCTACAGT
* * * * * * * * * *
35119359 TTTAGGGATATAAGATTCATCTTTGCTACTTTATTTTATCCTTCTATAGT
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCCTCTACAGT
* * * * ** *
35119409 TTTAAGGATATAAGATTCGCC-TTTCCAGCTTCAATCTTTCCCTCTACAAT
1 TTTAGGGGTATAAGATTCACCTTTTCGA-CTTCAATCTAGCCCTCTACAGT
* ** * ** *
35119459 CTTAGGGGTATAAGATTTGCCTTTACGGA-TTCAATCTCTCCCTCTACAAT
1 TTTAGGGGTATAAGATTCACCTTTTC-GACTTCAATCTAGCCCTCTACAGT
* * *
35119509 CTTAGGGGTATAAGATTCGCCTTTAC-AGCTTCAATCT-GTCCCTCTACAGT
1 TTTAGGGGTATAAGATTCACCTTTTCGA-CTTCAATCTAG-CCCTCTACAGT
* * * * **
35119559 CTTAGGGGTATAAGTTTCACCTTTGCAACTTCAATCTATTCCTCTACAGT
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCCTCTACAGT
* * * *
35119609 TTTAGGGGTATAA-ATTCACCTTTTCGACTTTAACCTATCCCTTTACAGT
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCCTCTACAGT
* * * *
35119658 TTTAGGGGTAAAAGATTCACCTTTTTGACTTCAATCT-GCCCTTGTACAGC
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCC-TCTACAGT
* * * ** * * * **
35119708 TTTAGGCGTGTATGATTTGCCTTTGCGGCTTCAATCT-GCCCCTTTACAAC
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAG-CCCTCTACAGT
** * * * * * *
35119758 TTTAGAAGTGTATGATTCACCTTTACGGCTTCAATCT-GCCCCTCTTCAGC
1 TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAG-CCCTCTACAGT
35119808 TTTAG
1 TTTAG
35119813 AGATGTACGA
Statistics
Matches: 370, Mismatches: 73, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.00
49 48 0.13
50 280 0.76
51 40 0.11
52 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (50 bp):
TTTAGGGGTATAAGATTCACCTTTTCGACTTCAATCTAGCCCTCTACAGT
Found at i:35119731 original size:149 final size:148
Alignment explanation
Indices: 35119422--35119791 Score: 331
Period size: 149 Copynumber: 2.5 Consensus size: 148
35119412 AAGGATATAA
* * **
35119422 GATTCGCCTTTCCAGCTTCAATCTTTCCCTCTACAATCTTAGGGGTATAAGATTTGCCTTTACGG
1 GATTTGCCTTTGCAGCTTCAATCTTTCCCTCTACAATCTTAGGGGTATAAGATTCACCTTTACGG
* * * *
35119487 ATTCAATCTCTCCCTCTACAATCTTAGGGGTATAAGATTCGCCTTTACAGCTTCAATCTGTCCCT
66 ATTCAACCTATCCCTCTACAATCTTAGGGGTAAAAGATTCACCTTTACAGCTTCAATCTGTCCCT
35119552 CTACAGTCTTAGGGGTAT
131 CTACAGTCTTAGGGGTAT
* * * * * *
35119570 AAGTTTCACCTTTGCAACTTCAATCTATT-CCTCTACAGTTTTAGGGGTATAA-ATTCACCTTTT
1 GA-TTT-GCCTTTGCAGCTTCAATCT-TTCCCTCTACAATCTTAGGGGTATAAGATTCACCTTTA
* * * * **
35119633 C-GACTTTAACCTATCCCTTTACAGTTTTAGGGGTAAAAGATTCACCTTT-TTGACTTCAATCTG
63 CGGA-TTCAACCTATCCCTCTACAATCTTAGGGGTAAAAGATTCACCTTTACAG-CTTCAATCTG
*
35119696 -CCCTTGTACAG-CTTTAGGCGTGTAT
126 TCCC-TCTACAGTC-TTAGG-G-GTAT
* ** * ** * *
35119721 GATTTGCCTTTGCGGCTTCAATCTGCCCCTTTACAA-CTTTAGAAGTGTATGATTCACCTTTACG
1 GATTTGCCTTTGCAGCTTCAATCTTTCCCTCTACAATC-TTAGGGGTATAAGATTCACCTTTACG
*
35119785 GCTTCAA
65 GATTCAA
35119792 TCTGCCCCTC
Statistics
Matches: 172, Mismatches: 37, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
148 8 0.05
149 100 0.58
150 56 0.33
151 8 0.05
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (148 bp):
GATTTGCCTTTGCAGCTTCAATCTTTCCCTCTACAATCTTAGGGGTATAAGATTCACCTTTACGG
ATTCAACCTATCCCTCTACAATCTTAGGGGTAAAAGATTCACCTTTACAGCTTCAATCTGTCCCT
CTACAGTCTTAGGGGTAT
Found at i:35119780 original size:100 final size:100
Alignment explanation
Indices: 35119671--35119862 Score: 251
Period size: 100 Copynumber: 1.9 Consensus size: 100
35119661 AGGGGTAAAA
** * * * * * *
35119671 GATTCACCTTTTTGACTTCAATCTGCCCTTGTACAGCTTTAG-GCGTGTATGATTTGCCTTTGCG
1 GATTCACCTTTACGACTTCAATCTGCCCCTCTACAGCTTTAGAG-ATGTACGATTTGCATATGCG
* *
35119735 GCTTCAATCTGCCCCTTTACAACTTTAGAAGTGTAT
65 GCTTCAATCTACCCCTCTACAACTTTAGAAGTGTAT
* *
35119771 GATTCACCTTTACGGCTTCAATCTGCCCCTCTTCAGCTTTAGAGATGTACGATTTGCATATGCGG
1 GATTCACCTTTACGACTTCAATCTGCCCCTCTACAGCTTTAGAGATGTACGATTTGCATATGCGG
*
35119836 CTTTAATCTACCCCTCTACAACTTTAG
66 CTTCAATCTACCCCTCTACAACTTTAG
35119863 GATTTGGTGT
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 77 0.99
101 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (100 bp):
GATTCACCTTTACGACTTCAATCTGCCCCTCTACAGCTTTAGAGATGTACGATTTGCATATGCGG
CTTCAATCTACCCCTCTACAACTTTAGAAGTGTAT
Found at i:35119837 original size:50 final size:50
Alignment explanation
Indices: 35119686--35119862 Score: 187
Period size: 50 Copynumber: 3.5 Consensus size: 50
35119676 ACCTTTTTGA
* * * *
35119686 CTTCAATCTGCCCTTGTACAGCTTTAG-GCGTGTATGATTTGCCTTTGCGG
1 CTTCAATCTGCCCCTCTACAACTTTAGAG-ATGTATGATTTGCCTTTGCGG
* ** *
35119736 CTTCAATCTGCCCCTTTACAACTTTAGA-AGTGTATGATTCACCTTTACGG
1 CTTCAATCTGCCCCTCTACAACTTTAGAGA-TGTATGATTTGCCTTTGCGG
* * * * *
35119786 CTTCAATCTGCCCCTCTTCAGCTTTAGAGATGTACGATTTGCATATGCGG
1 CTTCAATCTGCCCCTCTACAACTTTAGAGATGTATGATTTGCCTTTGCGG
* *
35119836 CTTTAATCTACCCCTCTACAACTTTAG
1 CTTCAATCTGCCCCTCTACAACTTTAG
35119863 GATTTGGTGT
Statistics
Matches: 104, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
50 103 0.99
51 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (50 bp):
CTTCAATCTGCCCCTCTACAACTTTAGAGATGTATGATTTGCCTTTGCGG
Found at i:35133696 original size:43 final size:43
Alignment explanation
Indices: 35133614--35133696 Score: 98
Period size: 43 Copynumber: 1.9 Consensus size: 43
35133604 GTCGAAATGG
* * *
35133614 TACTGTTTTGAGGCACACAGGCATGCGTCAGGGTTTGTGTGTA
1 TACTGTCTTGAGGCACACAGGCATGCGACAGGGTGTGTGTGTA
*
35133657 TACTGTCTTGAGGCACACGGGC-TG-GCACACGGGTGTGTGT
1 TACTGTCTTGAGGCACACAGGCATGCG-ACA-GGGTGTGTGT
35133697 CAGGGTGTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 1 0.03
42 4 0.12
43 29 0.85
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (43 bp):
TACTGTCTTGAGGCACACAGGCATGCGACAGGGTGTGTGTGTA
Found at i:35133724 original size:53 final size:53
Alignment explanation
Indices: 35133625--35133784 Score: 196
Period size: 53 Copynumber: 3.0 Consensus size: 53
35133615 ACTGTTTTGA
* *
35133625 GGCACAC-AGGCATGCGTCAGGGTTTGTGTGTATACTGTCTTGAGGCACACGGGCT
1 GGCACACGA-GCATGTGTCAGGG--TGTGTGTATACTGTTTTGAGGCACACGGGCT
* ** * **
35133680 GGCACACGGGTGTGTGTCAGGGTGTGTGTATACTATTTTGAGGCACACAAGCT
1 GGCACACGAGCATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACGGGCT
* *
35133733 GGCACACGAGCATGTGTCAAGGTGTGTGTATATTGTTTTGAGGCACACGGGC
1 GGCACACGAGCATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACGGGC
35133785 ATGTGTCAGG
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 71 0.81
55 17 0.19
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (53 bp):
GGCACACGAGCATGTGTCAGGGTGTGTGTATACTGTTTTGAGGCACACGGGCT
Found at i:35133725 original size:41 final size:41
Alignment explanation
Indices: 35133680--35133868 Score: 173
Period size: 41 Copynumber: 4.3 Consensus size: 41
35133670 CACACGGGCT
*
35133680 GGCACACGGGTGTGTGTCAGGGTGTGTGTATACTATTTTGA
1 GGCACACGGGCGTGTGTCAGGGTGTGTGTATACTATTTTGA
* * *
35133721 GGCACACAAGCTGGCACACGAGCATGTGTCAAGGTGTGTGTATATTGTTTTGA
1 GGCACAC--G--GG----C--G--TGTGTCAGGGTGTGTGTATACTATTTTGA
*
35133774 GGCACACGGGCATGTGTCAGGGTGTGTGTATACTATTTTGA
1 GGCACACGGGCGTGTGTCAGGGTGTGTGTATACTATTTTGA
*
35133815 GGCACACGGGCGTGTGTTAAGGTGTGTGTGTATAC-AGTTTTGA
1 GGCACACGGGCGTGTG-TCAGG-GTGTGTGTATACTA-TTTTGA
*
35133858 GGCACATGGGC
1 GGCACACGGGC
35133869 TGGTACACGA
Statistics
Matches: 122, Mismatches: 11, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
41 48 0.39
42 5 0.04
43 29 0.24
45 3 0.02
49 2 0.02
51 2 0.02
53 33 0.27
ACGTcount: A:0.20, C:0.15, G:0.35, T:0.30
Consensus pattern (41 bp):
GGCACACGGGCGTGTGTCAGGGTGTGTGTATACTATTTTGA
Done.