Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 17 of 276
Found at i:5116683 original size:24 final size:25
Alignment explanation
Indices: 5116609--5116686 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
5116599 TCATTTTCCT
*
5116609 CTCTTTTGAGCT-ATGAACAGTAAG
1 CTCTATTGAGCTGATGAACAGTAAG
* *
5116633 CTCTTCTTGAGCTGATGGACAGTAAG
1 CTC-TATTGAGCTGATGAACAGTAAG
5116659 CTCTATTGAGCTGA-GAACAGTAAG
1 CTCTATTGAGCTGATGAACAGTAAG
5116683 CTCT
1 CTCT
5116687 TATGAGTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.33
25 18 0.38
26 14 0.29
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (25 bp):
CTCTATTGAGCTGATGAACAGTAAG
Found at i:5118690 original size:33 final size:33
Alignment explanation
Indices: 5118619--5118690 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
5118609 ACAATGAATG
* * *
5118619 CAGTAACAGTCTAGGCCATAGCCCTATTCAGTAC
1 CAGT-ACAGTCTAGGCCATAGCCCTATACAGAAA
* **
5118653 CAGTACAGTCTGGGCTTTAGCCCTATACAGAAA
1 CAGTACAGTCTAGGCCATAGCCCTATACAGAAA
5118686 CAGTA
1 CAGTA
5118691 TGGGCGTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (33 bp):
CAGTACAGTCTAGGCCATAGCCCTATACAGAAA
Found at i:5118702 original size:28 final size:28
Alignment explanation
Indices: 5118657--5118710 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5118647 CAGTACCAGT
* * * *
5118657 ACAGTCTGGGCTTTAGCCCTATACAGAA
1 ACAGTATGGGCGTAAGCCCAATACAGAA
5118685 ACAGTATGGGCGTAAGCCCAATACAG
1 ACAGTATGGGCGTAAGCCCAATACAG
5118711 TATCAGTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (28 bp):
ACAGTATGGGCGTAAGCCCAATACAGAA
Found at i:5118717 original size:28 final size:27
Alignment explanation
Indices: 5118653--5118718 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
5118643 TATTCAGTAC
* * * *
5118653 CAGTACAGTCTGGGCTTTAGCCCTATA
1 CAGTACAGTATGGGCGTAAGCCCAATA
*
5118680 CAGAAACAGTATGGGCGTAAGCCCAATA
1 CAG-TACAGTATGGGCGTAAGCCCAATA
5118708 CAGTATCAGTA
1 CAGTA-CAGTA
5118719 CAGTGTAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (27 bp):
CAGTACAGTATGGGCGTAAGCCCAATA
Found at i:5118939 original size:27 final size:27
Alignment explanation
Indices: 5118879--5118939 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
5118869 CAGAAACAGC
5118879 GAATGTGGCAAAGCCACCAGTATCAAT
1 GAATGTGGCAAAGCCACCAGTATCAAT
** *
5118906 -AATTGTGGCATCGCCACCAGTATCAGT
1 GAA-TGTGGCAAAGCCACCAGTATCAAT
5118933 GAATGTG
1 GAATGTG
5118940 ACATAGTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 25 0.86
28 2 0.07
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (27 bp):
GAATGTGGCAAAGCCACCAGTATCAAT
Found at i:5119118 original size:27 final size:27
Alignment explanation
Indices: 5119088--5119223 Score: 141
Period size: 27 Copynumber: 5.0 Consensus size: 27
5119078 GCACATAAAC
*
5119088 GCATTACAGTCATTTTACCCTACAAGG
1 GCATTACAGTCATTTTACCCTACAGGG
* * *
5119115 GCATTAAAATCATTTTACCGTACAGGG
1 GCATTACAGTCATTTTACCCTACAGGG
**
5119142 GCATTAC-GATCATTTTACCCTATGGGG
1 GCATTACAG-TCATTTTACCCTACAGGG
* * *
5119169 GCATTACGGTAATTTTACTCTAC-GGCG
1 GCATTACAGTCATTTTACCCTACAGG-G
* *
5119196 ACATTACCGTCATTTTACCCTACAGGG
1 GCATTACAGTCATTTTACCCTACAGGG
5119223 G
1 G
5119224 TGTTATGGTC
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.02
27 83 0.94
28 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (27 bp):
GCATTACAGTCATTTTACCCTACAGGG
Found at i:5123462 original size:27 final size:27
Alignment explanation
Indices: 5123399--5123468 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
5123389 TGCCAGAAAT
* *
5123399 AGTGAATGTGGCAAAGCCACCAGTATC
1 AGTGAATGTGGCATAGCAACCAGTATC
5123426 AGT-AATTGTGGCATAGCAACCAGTATC
1 AGTGAA-TGTGGCATAGCAACCAGTATC
* *
5123453 AGTGACTGTGACATAG
1 AGTGAATGTGGCATAG
5123469 TCACCAATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 34 0.92
28 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (27 bp):
AGTGAATGTGGCATAGCAACCAGTATC
Found at i:5123474 original size:27 final size:26
Alignment explanation
Indices: 5123416--5123482 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
5123406 GTGGCAAAGC
* *
5123416 CACCAGTATCAGTAATTGTGGCATAG
1 CACCAGTATCAGTAACTGTGACATAG
*
5123442 CAACCAGTATCAGTGACTGTGACATAG
1 C-ACCAGTATCAGTAACTGTGACATAG
*
5123469 TCACCAATA-CAGTA
1 -CACCAGTATCAGTA
5123483 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.15
27 28 0.82
28 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (26 bp):
CACCAGTATCAGTAACTGTGACATAG
Found at i:5129127 original size:52 final size:52
Alignment explanation
Indices: 5129016--5129127 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 52
5129006 GGTTCATGAT
* *
5129016 ATGCATGTGGCATCTGAGCTCGTTGAGTTGGTTCGAGTTCATAACGAATGCC
1 ATGCATGTGGCATCCGAGCTCATTGAGTTGGTTCGAGTTCATAACGAATGCC
* * * * * *
5129068 ATACATGTGGCATCCGAGGTCATTGGGTTGG-TCTGAGTTCATAATGGATGCG
1 ATGCATGTGGCATCCGAGCTCATTGAGTTGGTTC-GAGTTCATAACGAATGCC
5129120 ATGCATGT
1 ATGCATGT
5129128 AATTTGGTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 2 0.04
52 48 0.96
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.31
Consensus pattern (52 bp):
ATGCATGTGGCATCCGAGCTCATTGAGTTGGTTCGAGTTCATAACGAATGCC
Found at i:5139575 original size:52 final size:52
Alignment explanation
Indices: 5139488--5139596 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
5139478 TCGTGATATG
* * *
5139488 CATGTGGCATCCGAGCTCATTGAGTTGGTCTGAGTTCATAACGGAAGCGATA
1 CATGTGGCATCCGAGCTCATTAAGTTCGTCCGAGTTCATAACGGAAGCGATA
* * *
5139540 CATGTGGCATCTGAGCT-AGTTAAGTTCGTCCGAGTTCATAATGGATGCGATA
1 CATGTGGCATCCGAGCTCA-TTAAGTTCGTCCGAGTTCATAACGGAAGCGATA
5139592 CATGT
1 CATGT
5139597 AATTGGGTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
51 1 0.02
52 49 0.98
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (52 bp):
CATGTGGCATCCGAGCTCATTAAGTTCGTCCGAGTTCATAACGGAAGCGATA
Found at i:5148027 original size:34 final size:34
Alignment explanation
Indices: 5147989--5148062 Score: 123
Period size: 34 Copynumber: 2.2 Consensus size: 34
5147979 AGTGGCAGTC
*
5147989 CAGTATTAGTGTGGGCCTTAGCCCA-TAGCAGTAA
1 CAGTATTAATGTGGGCCTTAGCCCATTA-CAGTAA
5148023 CAGTATTAATGTGGGCCTTAGCCCATTACAGTAA
1 CAGTATTAATGTGGGCCTTAGCCCATTACAGTAA
5148057 CAGTAT
1 CAGTAT
5148063 AAGTAATGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 36 0.95
35 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (34 bp):
CAGTATTAATGTGGGCCTTAGCCCATTACAGTAA
Found at i:5158465 original size:43 final size:43
Alignment explanation
Indices: 5158414--5158543 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
5158404 CATAGGATTT
5158414 TCGATATGTG-TTCTCGTGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGATT-TCGTGTAAGACCACGTCTGGGACATTGGCA
* * * *
5158457 TCGATATGTGATTTCGAGTAAAACC-CTGTTTGGGACAGTGGCA
1 TCGATATGTGATTTCGTGTAAGACCAC-GTCTGGGACATTGGCA
* * *
5158500 TCGACATGTGATTACATGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCA
5158543 T
1 T
5158544 TGTACGATAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 1 0.01
43 69 0.95
44 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
TCGATATGTGATTTCGTGTAAGACCACGTCTGGGACATTGGCA
Found at i:5159530 original size:13 final size:13
Alignment explanation
Indices: 5159512--5159539 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5159502 TAAGATAGCT
5159512 TACTCTGTGTGTG
1 TACTCTGTGTGTG
5159525 TACTCTGTGTGTG
1 TACTCTGTGTGTG
5159538 TA
1 TA
5159540 TTTTTACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.11, C:0.14, G:0.29, T:0.46
Consensus pattern (13 bp):
TACTCTGTGTGTG
Found at i:5162309 original size:51 final size:51
Alignment explanation
Indices: 5162233--5162371 Score: 149
Period size: 51 Copynumber: 2.7 Consensus size: 51
5162223 GGATGCCCGA
* *
5162233 TGGCCTGCACATGGTACCATC-CTTGT-AGTCAAAGCTACCTTCTT-CACAAAG
1 TGGCCTGCACATAGTACCA-CACTTGTGA-CCAAAGCTACCTT-TTACACAAAG
* * *
5162284 TGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTTACACATAG
1 TGGCCTGCACATAGTACCACACTTGTGACCAAAGCTACCTTTTACACAAAG
* * * *
5162335 TGGCCTGCACTTAGTACCACACATGTGATCGAAGCTA
1 TGGCCTGCACATAGTACCACACTTGTGACCAAAGCTA
5162372 TCAGGTACAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 3 0.04
51 71 0.95
52 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.27
Consensus pattern (51 bp):
TGGCCTGCACATAGTACCACACTTGTGACCAAAGCTACCTTTTACACAAAG
Found at i:5162372 original size:51 final size:51
Alignment explanation
Indices: 5162262--5162512 Score: 168
Period size: 51 Copynumber: 4.9 Consensus size: 51
5162252 TCCTTGTAGT
* * * * *
5162262 CAAAGCTACCTTCTT-CACAAAGTGGCCTTCACATAGTACCACACTTGTGAC
1 CAAAGCTATCTT-TTACACATAGTGGCCTGCACTTAGTACCACACATGTGAC
*
5162313 CAAAGCTATCTTTTACACATAGTGGCCTGCACTTAGTACCACACATGTGAT
1 CAAAGCTATCTTTTACACATAGTGGCCTGCACTTAGTACCACACATGTGAC
* *** * * ** *
5162364 CGAAGCTATCAGGTACATATAGTAGCCTGCACTTAGTATTACACATGCGAC
1 CAAAGCTATCTTTTACACATAGTGGCCTGCACTTAGTACCACACATGTGAC
* * * * * * * *
5162415 CTAA-CCAT-TTGGTACACGTAGTAGCCTGGACTTAGTACTACACACGTGAC
1 CAAAGCTATCTT-TTACACATAGTGGCCTGCACTTAGTACCACACATGTGAC
* * * * * * *
5162465 CTAAAACCAT-TTTAAACACATAGTAGCTTGCACATAGTACTACACATG
1 C-AAAGCTATCTTT-TACACATAGTGGCCTGCACTTAGTACCACACATG
5162513 GGTTCTCACA
Statistics
Matches: 161, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
50 39 0.24
51 88 0.55
52 34 0.21
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (51 bp):
CAAAGCTATCTTTTACACATAGTGGCCTGCACTTAGTACCACACATGTGAC
Found at i:5162503 original size:52 final size:50
Alignment explanation
Indices: 5162382--5162510 Score: 150
Period size: 52 Copynumber: 2.5 Consensus size: 50
5162372 TCAGGTACAT
* * **
5162382 ATAGTAGCCTGCACTTAGTATTACACATGCGACCTAACCATTTGGTACAC
1 ATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATTTGAAACAC
* * * *
5162432 GTAGTAGCCTGGACTTAGTACTACACACGTGACCTAAAACCATTTTAAACAC
1 ATAGTAGCCTGCACTTAGTACTACACACGCGACCT--AACCATTTGAAACAC
* *
5162484 ATAGTAGCTTGCACATAGTACTACACA
1 ATAGTAGCCTGCACTTAGTACTACACA
5162511 TGGGTTCTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 30 0.46
52 35 0.54
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (50 bp):
ATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATTTGAAACAC
Found at i:5168115 original size:44 final size:44
Alignment explanation
Indices: 5168060--5168160 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 44
5168050 TTGATATGTG
*
5168060 ATTTCGTGTAAGACCACGTC-TAGGACATTAGCATCG-ATTTGAT
1 ATTTCGTGTAAGACCACGTCTTA-GACATCAGCATCGTATTTGAT
* *
5168103 ATTTACGTGTAAGACCATGTCTTAGACATCAGTATCGTATTTGAT
1 ATTT-CGTGTAAGACCACGTCTTAGACATCAGCATCGTATTTGAT
5168148 -TTT-GTGTAAGACC
1 ATTTCGTGTAAGACC
5168161 CTGTTTAGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 10 0.19
43 4 0.08
44 29 0.56
45 9 0.17
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (44 bp):
ATTTCGTGTAAGACCACGTCTTAGACATCAGCATCGTATTTGAT
Found at i:5177113 original size:40 final size:39
Alignment explanation
Indices: 5177069--5177169 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 39
5177059 ACTATGTTTG
*
5177069 GCACTAAATGTGCGATTTGATATAGCTTTGGCTATAAATA
1 GCACTAAGTGTGCGATTTGA-ATAGCTTTGGCTATAAATA
* ** *
5177109 GCACTAAGTGTGCGAATTGGAATAGCTTTGGCTATATGTG
1 GCACTAAGTGTGCG-ATTTGAATAGCTTTGGCTATAAATA
5177149 GCACTAAGTGTGCGATATTGA
1 GCACTAAGTGTGCGAT-TTGA
5177170 GATAATTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.04
40 46 0.87
41 5 0.09
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (39 bp):
GCACTAAGTGTGCGATTTGAATAGCTTTGGCTATAAATA
Found at i:5181612 original size:46 final size:46
Alignment explanation
Indices: 5181562--5181733 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
5181552 TGAGCATCCA
5181562 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
5181608 AACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCG
* * * *
5181655 AAATCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
* * *
5181701 AGCTCGTTGAGTTTAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5181734 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 57 0.55
47 27 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCG
Found at i:5181719 original size:93 final size:93
Alignment explanation
Indices: 5181555--5181726 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
5181545 GGATGATTGA
* * *
5181555 GCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCAAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5181620 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5181648 GCATCCGAAA-TCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GCATCC-AAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
5181712 TTTAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
5181727 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 70 0.96
94 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCAAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5189259 original size:27 final size:27
Alignment explanation
Indices: 5189219--5189317 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 27
5189209 AGATAAGTTG
* *
5189219 TAGAATTATCGAAATACCCCTACAGGA
1 TAGAATTACCGAAATACCCCTATAGGA
* * *
5189246 TAGAATTACTGAAATACCCTTGTAGGA
1 TAGAATTACCGAAATACCCCTATAGGA
* *
5189273 TAGAAATACCGAAATACCCCTATAGGG
1 TAGAATTACCGAAATACCCCTATAGGA
*
5189300 TAGAATTACCGAGATACC
1 TAGAATTACCGAAATACC
5189318 TTTGTGGGGT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCCTATAGGA
Found at i:5189293 original size:54 final size:54
Alignment explanation
Indices: 5189219--5189322 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
5189209 AGATAAGTTG
* * *
5189219 TAGAATTATCGAAATACCCCTACAGGATAGAATTACTGAAATACCCTTGTAGGA
1 TAGAAATACCGAAATACCCCTACAGGATAGAATTACCGAAATACCCTTGTAGGA
* * * *
5189273 TAGAAATACCGAAATACCCCTATAGGGTAGAATTACCGAGATACCTTTGT
1 TAGAAATACCGAAATACCCCTACAGGATAGAATTACCGAAATACCCTTGT
5189323 GGGGTAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (54 bp):
TAGAAATACCGAAATACCCCTACAGGATAGAATTACCGAAATACCCTTGTAGGA
Found at i:5189327 original size:27 final size:27
Alignment explanation
Indices: 5189218--5189336 Score: 112
Period size: 27 Copynumber: 4.4 Consensus size: 27
5189208 TAGATAAGTT
* * **
5189218 GTAGAATTATCGAAATACCCCTACAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* *
5189245 ATAGAATTACTGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * * *
5189272 ATAGAAATACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCTTGTAGG
* * *
5189299 GTAGAATTACCGAGATACCTTTGTGGG
1 GTAGAATTACCGAAATACCCTTGTAGG
*
5189326 GTAAAATTACC
1 GTAGAATTACC
5189337 ATTTTGCCCC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAGG
Found at i:5190030 original size:27 final size:26
Alignment explanation
Indices: 5189986--5190037 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5189976 CTCGCTGCAA
*
5189986 TCTGGTGGCCTTGCCACATATATCTGT
1 TCTGGTGACCTTGCCACA-ATATCTGT
* *
5190013 TCTGGTGACTTTGTCACAATATCTG
1 TCTGGTGACCTTGCCACAATATCTG
5190038 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
TCTGGTGACCTTGCCACAATATCTGT
Found at i:5190105 original size:26 final size:27
Alignment explanation
Indices: 5190076--5190135 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
5190066 CCACATATAT
*
5190076 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
5190102 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
5190129 ATATCTG
1 ATATCTG
5190136 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:5193643 original size:45 final size:44
Alignment explanation
Indices: 5193592--5193676 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
5193582 TTTAATACGT
* * *
5193592 TGGCATCAATATGTGATTCCGATATGTGATGTGCGAGTAAGACCA
1 TGGCATCAATATATGATTCCAATATATG-TGTGCGAGTAAGACCA
* *
5193637 TGGCATCGATATATGATTCTAATATATGTGTGCGAGTAAG
1 TGGCATCAATATATGATTCCAATATATGTGTGCGAGTAAG
5193677 TCCACATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 12 0.34
45 23 0.66
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (44 bp):
TGGCATCAATATATGATTCCAATATATGTGTGCGAGTAAGACCA
Found at i:5193691 original size:101 final size:101
Alignment explanation
Indices: 5193500--5193720 Score: 311
Period size: 101 Copynumber: 2.2 Consensus size: 101
5193490 AGACATCGAC
* * *
5193500 ATGTGAATTCCGATATGTGATGTGCGAGTAAGACCCTAGAATCGATGTGTGATTCCTATATATGT
1 ATGTG-ATTCCGATATGTGATGTGCGAGTAAGACCATAGAATCGATATATGATTCCTATATATGT
* *
5193565 GCACGAGTAAGACCACGTTTAATACGTTGGCATCAAT
65 GCACGAGTAAGACCACATTTAATACGTTGGCATCAAA
* *
5193602 ATGTGATTCCGATATGTGATGTGCGAGTAAGACCATGGCATCGATATATGATT-CTAATATATGT
1 ATGTGATTCCGATATGTGATGTGCGAGTAAGACCATAGAATCGATATATGATTCCT-ATATATGT
** *
5193666 GTGCGAGTAAGTCCACATTCT-ATACGTTGGCATCAAA
65 GCACGAGTAAGACCACATT-TAATACGTTGGCATCAAA
5193703 ATGTGATTCCGATATGTG
1 ATGTGATTCCGATATGTG
5193721 TACGAGTAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
100 2 0.02
101 99 0.93
102 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (101 bp):
ATGTGATTCCGATATGTGATGTGCGAGTAAGACCATAGAATCGATATATGATTCCTATATATGTG
CACGAGTAAGACCACATTTAATACGTTGGCATCAAA
Found at i:5204998 original size:68 final size:68
Alignment explanation
Indices: 5204851--5205006 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
5204841 AGCCGATTTG
* * * * *
5204851 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
5204916 TATC
65 TATA
* *
5204920 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
5204982 ATATAGTA
62 ATATA-TA
5204990 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
5205007 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:5208847 original size:45 final size:45
Alignment explanation
Indices: 5208795--5208927 Score: 196
Period size: 45 Copynumber: 3.0 Consensus size: 45
5208785 CCTGATTATC
*
5208795 ATTTCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCTGAATAGT
1 ATTTCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAGT
* *
5208840 ATTTCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCCAATAGT
1 ATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
* * *
5208885 GTCTCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 ATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
5208928 TAATACCAGC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 3 0.04
45 77 0.96
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (45 bp):
ATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
Found at i:5208973 original size:38 final size:38
Alignment explanation
Indices: 5208920--5209882 Score: 1696
Period size: 38 Copynumber: 25.3 Consensus size: 38
5208910 GGCTCAAAGG
* *
5208920 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5208958 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5208996 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209034 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209072 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209110 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209148 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209186 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209224 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209262 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209300 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209338 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209376 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209414 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209452 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209490 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209528 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5209566 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5209604 CCCGGATGTATTACCAACACGAAGCCCGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5209642 CCCGAATGTATTACCAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
5209680 CCCAGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5209718 CCCGGATGTATTACCAACACGAAGCCCGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5209756 CCCGAATGTATTACCAGCACGAAGCCTACGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
5209794 CCCAGATATATTACCAGCACGAAGCCTGCGAGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
5209832 CCCGGATATAATT-CCAGCA-TATAGCCTGCGGGTCTTTAA
1 CCCGGATAT-ATTACCAGCACGA-AGCCTGCGGG-ATTTAA
*
5209871 GCCAGGATATAT
1 -CCCGGATATAT
5209883 ATCAAATATC
Statistics
Matches: 890, Mismatches: 31, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
37 1 0.00
38 871 0.98
39 10 0.01
40 8 0.01
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:5215335 original size:45 final size:45
Alignment explanation
Indices: 5215279--5215411 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
5215269 CCTGATTATC
* * *
5215279 ATTTCACCGGCATTATAGCCTGCCAGGCTCGAAA-GCCCAAATAGT
1 ATTTCACCGGCATAATAGCCTGCTAGGCTC-AAAGGCCCGAATAGT
*
5215324 ATTTCACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
1 ATTTCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
* * *
5215369 GTCTCACCGACATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 ATTTCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
5215412 TAATACCAGC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 3 0.04
45 77 0.96
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
ATTTCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGT
Found at i:5215457 original size:38 final size:38
Alignment explanation
Indices: 5215404--5215739 Score: 478
Period size: 38 Copynumber: 8.8 Consensus size: 38
5215394 GGCTCAAAGG
* *
5215404 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
5215442 CCCGGATATATTACCACCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5215480 CCCGGATGTATTACCAGCACGAAGCCTACGGAATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5215518 CTCGGATGTATTACCAGCACGAAGCTTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5215556 CCCGAATGTATTACCAGCACGAAGCCTGCGAGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
5215594 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* * *
5215632 CCCGGATGTATTACCAGCACGAAGCTTGCAGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
5215670 CCTGGATATATTACCAGCACGAAGCTTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
5215708 CCCGGATATAATT-CCAGCA-TATAGCCTGCGGG
1 CCCGGATAT-ATTACCAGCACGA-AGCCTGCGGG
5215740 TCTTTAAGCC
Statistics
Matches: 269, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
37 1 0.00
38 265 0.99
39 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:5220963 original size:48 final size:48
Alignment explanation
Indices: 5220895--5221318 Score: 429
Period size: 48 Copynumber: 8.8 Consensus size: 48
5220885 CATCGATGTT
* *
5220895 GATGCCATG-TCCTAGACATGGTCTTACACTGGCTCACATAACAATACC
1 GATGCCATGTTCC-AAACATGGTCTTACACTGGCTCACATAACAATGCC
* *
5220943 GATGCCATGTTCCAAACATGGTCTTACACTGGCTTACATAACAATACC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* ** * *** *
5220991 GATGCCACGTTCCAAACATCATCTTACACTGGCTCGCATATTGAGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* * * * *
5221039 GATGCCATG-TCTTAGACATGGTCTTACACTAGCTCTCATAACAATGCT
1 GATGCCATGTTC-CAAACATGGTCTTACACTGGCTCACATAACAATGCC
* *
5221087 GATGTCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGTC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* ** * *** *
5221135 GATGCCATGTTCCAAAAATGGTCTTACACTATCTCGCATATTGAGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* *** *
5221183 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCC
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* * * * * * * *
5221231 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAGAATAATACA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
* * *
5221279 GATGCCATGTTTCAAACATGATCTTACACTAGCTCACATA
1 GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATA
5221319 TAACCTTAGT
Statistics
Matches: 313, Mismatches: 60, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
47 2 0.01
48 306 0.98
49 5 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (48 bp):
GATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAACAATGCC
Found at i:5221160 original size:144 final size:143
Alignment explanation
Indices: 5220895--5221319 Score: 546
Period size: 144 Copynumber: 3.0 Consensus size: 143
5220885 CATCGATGTT
* *
5220895 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCACATAACAATACCGATGCCATGTTCCAAAC
1 GATGCCATGTCTTAGACATGGTCTTACACTGGCTCACATAACAATGCCGATGCCATGTTCCAAAC
* * * *
5220960 ATGGTCTTACACTGGCTTACATAACAATACCGATGCCACGTTCCAAACATCATCTTACACTGGCT
66 ATGGTCTTACACTGGCTCACATAACAATA-CGATGCCATGTTCCAAACATGATCTTACACTAGCT
5221025 CGCATATTGAGGCC
130 CGCATATTGAGGCC
* * * *
5221039 GATGCCATGTCTTAGACATGGTCTTACACTAGCTCTCATAACAATGCTGATGTCATGTTCCAAAC
1 GATGCCATGTCTTAGACATGGTCTTACACTGGCTCACATAACAATGCCGATGCCATGTTCCAAAC
* * * *
5221104 ATGGTCTTACACTGGCTCACATAACAATGTCGATGCCATGTTCCAAAAATGGTCTTACACTATCT
66 ATGGTCTTACACTGGCTCACATAACAAT-ACGATGCCATGTTCCAAACATGATCTTACACTAGCT
5221169 CGCATATTGAGGCC
130 CGCATATTGAGGCC
* * * *** * * *
5221183 GATGCCATGT-TCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCCGATGCCATGTCCCAGA
1 GATGCCATGTCT-TAGACATGGTCTTACACTGGCTCACATAACAATGCCGATGCCATGTTCCAAA
* * * * *
5221247 CATGGTCTTACACTAGCTCTCAGAATAATACAGATGCCATGTTTCAAACATGATCTTACACTAGC
65 CATGGTCTTACACTGGCTCACATAACAATAC-GATGCCATGTTCCAAACATGATCTTACACTAGC
*
5221312 TCACATAT
129 TCGCATAT
5221320 AACCTTAGTA
Statistics
Matches: 242, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
143 2 0.01
144 240 0.99
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (143 bp):
GATGCCATGTCTTAGACATGGTCTTACACTGGCTCACATAACAATGCCGATGCCATGTTCCAAAC
ATGGTCTTACACTGGCTCACATAACAATACGATGCCATGTTCCAAACATGATCTTACACTAGCTC
GCATATTGAGGCC
Found at i:5225412 original size:26 final size:25
Alignment explanation
Indices: 5225369--5225425 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5225359 TCGCTTTTTC
*
5225369 GAGCT-ATGAATAGTAAGCT-TATCCT
1 GAGCTGATGAATAATAAGCTCTAT--T
*
5225394 GAGCTGATGGATAATAAGCTCTATT
1 GAGCTGATGAATAATAAGCTCTATT
5225419 GAGCTGA
1 GAGCTGA
5225426 AACGGTAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.46
26 12 0.43
27 3 0.11
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (25 bp):
GAGCTGATGAATAATAAGCTCTATT
Found at i:5234814 original size:49 final size:49
Alignment explanation
Indices: 5234746--5234985 Score: 293
Period size: 49 Copynumber: 4.8 Consensus size: 49
5234736 TAGCCAAAGC
* *
5234746 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACAC-CTGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAC-GCGACCAAT
* * * *
5234795 TATCCGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * * *
5234845 CATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* ** *
5234896 TATCGGGTACACACAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
*
5234945 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
1 TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACG
5234986 TGACGTCACA
Statistics
Matches: 160, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
49 76 0.47
50 47 0.29
51 37 0.23
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (49 bp):
TATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:5234983 original size:100 final size:99
Alignment explanation
Indices: 5234747--5234989 Score: 319
Period size: 100 Copynumber: 2.4 Consensus size: 99
5234737 AGCCAAAGCT
* * * **
5234747 ATCTGGTACGCATAGTAGCCTGCACTTAGTACTACAC-CTGCGACCAATTATCCGGTACACGTAG
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAC-GTGACCAATTATCCGGTACACACAG
* * *
5234811 TAGCTTGCACTTAGTACTACACACGTGACCTAACC
65 TAGCCTGCACTTAGTACTACACACGCGACCTAACA
* * * *
5234846 ATCTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTATCGGGTACACACA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACACA
* *
5234911 GTAGCCTGCACTTAGTACTACACATGCGACC-AATA
64 GTAGCCTGCACTTAGTACTACACACGCGACCTAACA
5234946 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
5234990 GTCACAATAG
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
99 37 0.30
100 47 0.38
101 41 0.33
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.25
Consensus pattern (99 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACACAGT
AGCCTGCACTTAGTACTACACACGCGACCTAACA
Found at i:5238789 original size:27 final size:28
Alignment explanation
Indices: 5238705--5238802 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
5238695 CATGAGATTG
* * * *
5238705 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
5238734 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
5238762 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
5238789 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
5238803 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:5238813 original size:27 final size:27
Alignment explanation
Indices: 5238733--5238813 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
5238723 TAAATTGTAC
* *
5238733 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
5238761 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
5238788 AGCACTGAGTGTGCGGACTT-AATATA
1 AGCACTAAGTGTGC-GACTTGAATATA
5238814 CATTTTTGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
27 28 0.58
28 20 0.42
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:5240342 original size:189 final size:189
Alignment explanation
Indices: 5240022--5240384 Score: 690
Period size: 189 Copynumber: 1.9 Consensus size: 189
5240012 GTATTGAAGC
5240022 CCTGTACAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCAATCCCTGTAACATGG
1 CCTGTACAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCAATCCCTGTAACATGG
5240087 GAGACTTTGACTAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATATGTAGAT
66 GAGACTTTGACTAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATATGTAGAT
* * *
5240152 GGGAATATGAGTCTAGTTTCAGGGAAAATTTATGGAACTGGATTCCGAGTTTCTGAACT
131 GGGAATATGAGTCTAGTTTCAGGAAAAATTTACGGAACTAGATTCCGAGTTTCTGAACT
5240211 CCTGTACAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCAATCCCTGTAACATGG
1 CCTGTACAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCAATCCCTGTAACATGG
*
5240276 GAGACTTTGACTAATAAACTGTACTAATTGGCCCGACCAAAAATTCTAGAAAAAAATATGTAGAT
66 GAGACTTTGACTAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATATGTAGAT
5240341 GGGAATATGAGTCTAGTTTCAGGAAAAATTTACGGAACTAGATT
131 GGGAATATGAGTCTAGTTTCAGGAAAAATTTACGGAACTAGATT
5240385 TCAGGTTTCA
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 170 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (189 bp):
CCTGTACAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCAATCCCTGTAACATGG
GAGACTTTGACTAATAAACTGTACTAATTGGCCCAACCAAAAATTCTAGAAAAAAATATGTAGAT
GGGAATATGAGTCTAGTTTCAGGAAAAATTTACGGAACTAGATTCCGAGTTTCTGAACT
Found at i:5244047 original size:49 final size:48
Alignment explanation
Indices: 5243973--5244199 Score: 249
Period size: 49 Copynumber: 4.6 Consensus size: 48
5243963 ATCTGGTATG
5243973 CATAGTAGCCTGCACTTAGTACTACACATGCAACCAATCATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATG-AACCAATCATCCGGTACA
* * * *
5244022 CGTAGTAGCCTGCACTTAGTACTACACACGTG-ACCTAAGCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACA--TGAACC-AATCATCCGGTACA
* * * * * * * *
5244072 CGTAGTAGCTTGCATTTAGTACTACACATGTGATCGAAGTTATCGGGTACG
1 CATAGTAGCCTGCACTTAGTACTACACA--TGAACCAA-TCATCCGGTACA
* *
5244123 CACAGTAGCCTGCACTTAGTACTACACATGAGACCAATAATCCGGTACA
1 CATAGTAGCCTGCACTTAGTACTACACATGA-ACCAATCATCCGGTACA
5244172 CATAGTAGCCTGCACTTAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
5244200 CGTGACCTCA
Statistics
Matches: 148, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
49 69 0.47
50 45 0.30
51 34 0.23
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (48 bp):
CATAGTAGCCTGCACTTAGTACTACACATGAACCAATCATCCGGTACA
Found at i:5245580 original size:6 final size:6
Alignment explanation
Indices: 5245573--5245606 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5245563 CCAAATATGG
* *
5245573 AAATGG AAATGA AAATGA AAATGA GAATGA AAAT
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAAT
5245607 TTTCAGTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (6 bp):
AAATGA
Found at i:5248206 original size:23 final size:22
Alignment explanation
Indices: 5248167--5248212 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
5248157 GCATATATCC
*
5248167 AAACCAAAGCATACCAAATCAT
1 AAACCAAAGCATACCAAAACAT
5248189 AAACCAAAGTCATACCAAAACAT
1 AAACCAAAG-CATACCAAAACAT
5248212 A
1 A
5248213 TGATTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.57, C:0.26, G:0.04, T:0.13
Consensus pattern (22 bp):
AAACCAAAGCATACCAAAACAT
Found at i:5252199 original size:195 final size:195
Alignment explanation
Indices: 5251853--5252238 Score: 691
Period size: 195 Copynumber: 2.0 Consensus size: 195
5251843 ACGTCTCTTT
5251853 CATCTCGAGTATTCCTCCATTTGAGTAGAATTTTACCCGTTGAACACATCGGAATATAATCCGGA
1 CATCTCGAGTATTCCTCCATTTGAGTAGAATTTTACCCGTTGAACACATCGGAATATAATCCGGA
5251918 TACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAG
66 TACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAG
* * * * * *
5251983 TGAACTCGGACTCAGCTCAACGAGCTCGGGCGTTCGCATCCACGAGTGAACTCAGACTCAAGTCA
131 TGAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATACACAAGTGAACTCAGACTCAAGTCA
5252048 CATCTCGAGTATTCCTCCATTTGAGTAGAATTTTACCCGTTGAACACATCGGAATATAATCCGGA
1 CATCTCGAGTATTCCTCCATTTGAGTAGAATTTTACCCGTTGAACACATCGGAATATAATCCGGA
5252113 TACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAG
66 TACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAG
* * *
5252178 TGAACTCAGACTCAACTCAACGAGTTCAGGCATTCGCATACATAAGTGAACTCGGACTCAA
131 TGAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATACACAAGTGAACTCAGACTCAA
5252239 CTCAATGAGT
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 182 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (195 bp):
CATCTCGAGTATTCCTCCATTTGAGTAGAATTTTACCCGTTGAACACATCGGAATATAATCCGGA
TACATGGAAAGTTTGCACATAAGTGCCACATATGTAGCCAAGCTACCATGTAACCCGCCCATAAG
TGAACTCAGACTCAACTCAACGAGCTCAGGCATTCGCATACACAAGTGAACTCAGACTCAAGTCA
Found at i:5252346 original size:46 final size:46
Alignment explanation
Indices: 5252171--5252346 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
5252161 TGTAACCCGC
*
5252171 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCAGG-CATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* * *
5252217 ACATAAGTGAACTCGGACTCAACTCAATGAGTTCGGACGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
5252267 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5252310 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5252347 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.25
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5253062 original size:34 final size:34
Alignment explanation
Indices: 5252997--5253065 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5252987 CGAGTAGTAC
5252997 AAGTTGTATAACATAATTTAAAACCTCATATTCT
1 AAGTTGTATAACATAATTTAAAACCTCATATTCT
5253031 AAGTTGTATAACATAATTTAAAACCTCATATTCT
1 AAGTTGTATAACATAATTTAAAACCTCATATTCT
5253065 A
1 A
5253066 TCATAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (34 bp):
AAGTTGTATAACATAATTTAAAACCTCATATTCT
Found at i:5253462 original size:31 final size:31
Alignment explanation
Indices: 5253424--5253486 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
5253414 TAAAATTACT
5253424 ATTTAAGACCTCCTAATTAATATTCCAAAAC
1 ATTTAAGACCTCCTAATTAATATTCCAAAAC
* *
5253455 ATTTAAGACCTCTTAATTAATATTTCAAAAC
1 ATTTAAGACCTCCTAATTAATATTCCAAAAC
5253486 A
1 A
5253487 ATTTCATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (31 bp):
ATTTAAGACCTCCTAATTAATATTCCAAAAC
Found at i:5256382 original size:29 final size:29
Alignment explanation
Indices: 5256343--5256442 Score: 146
Period size: 29 Copynumber: 3.4 Consensus size: 29
5256333 TGGTCCATCT
5256343 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
5256372 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* * * *
5256401 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCCATCAGGCCCAATTCA
* *
5256430 CCTTTATATGGCC
1 CATTCATATGGCC
5256443 TGTTAGGCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (29 bp):
CATTCATATGGCCCATCAGGCCCAATTCA
Found at i:5256462 original size:29 final size:29
Alignment explanation
Indices: 5256343--5256459 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
5256333 TGGTCCATCT
* * *
5256343 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCTATTAGGCCCAAATCA
* * *
5256372 CATTCATATGGCCCATCAGGCCCAATTCA
1 CATTCATATGGCCTATTAGGCCCAAATCA
*
5256401 TATTCATATGGCCTATTAGGCCCAAATCA
1 CATTCATATGGCCTATTAGGCCCAAATCA
* * *
5256430 CCTTTATATGGCCTGTTAGGCCCAAATCA
1 CATTCATATGGCCTATTAGGCCCAAATCA
5256459 C
1 C
5256460 CTTATATTCA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CATTCATATGGCCTATTAGGCCCAAATCA
Found at i:5276090 original size:27 final size:27
Alignment explanation
Indices: 5276040--5276129 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 27
5276030 NNNNNNNNNN
** *
5276040 ACTTAGTGCCGCATGGTCAATTCGCAC
1 ACTTAGTGCAACATAGTCAATTCGCAC
* * *
5276067 ACTTAGTGCATCATATTCATTTCGCAC
1 ACTTAGTGCAACATAGTCAATTCGCAC
*
5276094 ACTTAGTGCAACATAGTCAAATCGCAC
1 ACTTAGTGCAACATAGTCAATTCGCAC
5276121 ACTTAGTGC
1 ACTTAGTGC
5276130 TGTACAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (27 bp):
ACTTAGTGCAACATAGTCAATTCGCAC
Found at i:5279400 original size:44 final size:42
Alignment explanation
Indices: 5279324--5279423 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 42
5279314 GATGTTACAA
5279324 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGGCAT
1 GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGGCAT
* ***
5279366 GGTCTTACACGTAAATCTCAAAT-TGATGCCAATGTCCCAGATGT
1 GGTCTTACACG-AAA--TCAAATACGATGCCAATGTCCCAGGCAT
*
5279410 GGTCTTACATGAAA
1 GGTCTTACACGAAA
5279424 ACACATATCG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
42 11 0.22
43 6 0.12
44 27 0.54
45 6 0.12
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCAATGTCCCAGGCAT
Found at i:5287700 original size:40 final size:40
Alignment explanation
Indices: 5287623--5287840 Score: 316
Period size: 40 Copynumber: 5.5 Consensus size: 40
5287613 AAACCAAGTA
* *
5287623 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
5287662 TCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
5287702 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
5287742 CCTTCGGGACTTAGCCCGGAGATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
5287782 CCTTTGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
5287822 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5287841 TTATCATCCG
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 14 0.09
40 149 0.91
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:5289758 original size:23 final size:22
Alignment explanation
Indices: 5289719--5289764 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5289709 GCATATATCC
*
5289719 AAACCAAAACATACCAAATCAT
1 AAACCAAAACATACCAAAACAT
*
5289741 AAACCAAATTCATACCAAAACAT
1 AAACCAAA-ACATACCAAAACAT
5289764 A
1 A
5289765 TGATTCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACCAAAACATACCAAAACAT
Found at i:5290521 original size:43 final size:42
Alignment explanation
Indices: 5290474--5290572 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
5290464 TCTCAGATGT
* * **
5290474 GGTCTTACATGTAATCAAGTATCGATGCCACTATCCTAGGCAG
1 GGTCTTACATGTAATCAAATAT-GATGCCAATATCCTACACAG
* * *
5290517 GGTCTTACATGAAATCAAATATGATGCCAATGTCCTACACAT
1 GGTCTTACATGTAATCAAATATGATGCCAATATCCTACACAG
*
5290559 GGTCTTACACGTAA
1 GGTCTTACATGTAA
5290573 ATATCAAATC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 27 0.57
43 20 0.43
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAATATGATGCCAATATCCTACACAG
Found at i:5290563 original size:42 final size:42
Alignment explanation
Indices: 5290455--5290609 Score: 134
Period size: 43 Copynumber: 3.6 Consensus size: 42
5290445 AGCTCGTACA
** * *
5290455 ATGCCAATGT-CTCAGATGTGGTCTTACATGTAATCAAGTATCG
1 ATGCCAATGTCCT-AGACATGGTCTTACATGAAATCAAATAT-G
* * * *
5290498 ATGCCACTATCCTAGGCAGGGTCTTACATGAAATCAAATATG
1 ATGCCAATGTCCTAGACATGGTCTTACATGAAATCAAATATG
* * *
5290540 ATGCCAATGTCCTACACATGGTCTTACACGTAAATATCAAAT-CG
1 ATGCCAATGTCCTAGACATGGTCTTACA--TGAA-ATCAAATATG
* *
5290584 ATGCCAATGTCCCAGACGTGGTCTTA
1 ATGCCAATGTCCTAGACATGGTCTTA
5290610 GACCAAAACA
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 24 0.27
43 30 0.33
44 29 0.32
45 7 0.08
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGAAATCAAATATG
Found at i:5297581 original size:15 final size:16
Alignment explanation
Indices: 5297563--5297596 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5297553 AAATTAAATT
*
5297563 AATTAA-CTAGATGCA
1 AATTAACCTAAATGCA
5297578 AATTAACCTAAATGCA
1 AATTAACCTAAATGCA
5297594 AAT
1 AAT
5297597 AAGATGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (16 bp):
AATTAACCTAAATGCA
Found at i:5300347 original size:6 final size:6
Alignment explanation
Indices: 5300338--5300380 Score: 59
Period size: 6 Copynumber: 6.7 Consensus size: 6
5300328 TTTAAAAAGA
5300338 AAAAAT AAAAAT AAAAAT AAAACCAT AAAAAT AATAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAA--AT AAAAAT AA-AAAT AAAA
5300381 GTCTTTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 22 0.65
7 6 0.18
8 6 0.18
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5300365 original size:20 final size:21
Alignment explanation
Indices: 5300342--5300380 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5300332 AAAAGAAAAA
5300342 ATAAAAATAA-AAATAAAACC
1 ATAAAAATAATAAATAAAACC
5300362 ATAAAAATAATAAATAAAA
1 ATAAAAATAATAAATAAAA
5300381 GTCTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (21 bp):
ATAAAAATAATAAATAAAACC
Found at i:5306007 original size:73 final size:73
Alignment explanation
Indices: 5305887--5306032 Score: 229
Period size: 73 Copynumber: 2.0 Consensus size: 73
5305877 TTTATCGATT
* *
5305887 TGACTTGATCCATAGAAATCCATAAGTTATATTATTATCTCTATCGAGACTAATAACGCCTAACC
1 TGACTTGATACATAGAAATCCATAAGTTATATTATTATCTCTATCGAGACTAACAACGCCTAACC
5305952 CTAGGTTG
66 CTAGGTTG
* * * * *
5305960 TGACTTGATACGTAGAAATCCCTAATTTATATTATTATCTCTCTCGAGACTAACAACGTCTAACC
1 TGACTTGATACATAGAAATCCATAAGTTATATTATTATCTCTATCGAGACTAACAACGCCTAACC
5306025 CTAGGTTG
66 CTAGGTTG
5306033 ATTAATTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (73 bp):
TGACTTGATACATAGAAATCCATAAGTTATATTATTATCTCTATCGAGACTAACAACGCCTAACC
CTAGGTTG
Found at i:5316303 original size:28 final size:27
Alignment explanation
Indices: 5316239--5316390 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
5316229 TTATTAAGTC
* *
5316239 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
5316266 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
*
5316294 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
5316321 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
5316349 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
5316376 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5316391 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:5316323 original size:55 final size:55
Alignment explanation
Indices: 5316239--5316415 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
5316229 TTATTAAGTC
* * *
5316239 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* *
5316294 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
5316349 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
5316405 CGCACACTTAG
1 CGCACACTTAG
5316416 CGCCAATCTC
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 93 0.85
56 16 0.15
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:5316893 original size:50 final size:50
Alignment explanation
Indices: 5316817--5316924 Score: 207
Period size: 50 Copynumber: 2.1 Consensus size: 50
5316807 ATCAAAACCT
5316817 TAACCATATTCGATTAATGCTTCAAGGCCGAATGCATTATCGCTATTATGG
1 TAACC-TATTCGATTAATGCTTCAAGGCCGAATGCATTATCGCTATTATGG
5316868 TAACCTATTCGATTAATGCTTCAAGGCCGAATGCATTATCGCTATTATGG
1 TAACCTATTCGATTAATGCTTCAAGGCCGAATGCATTATCGCTATTATGG
5316918 TAACCTA
1 TAACCTA
5316925 GTCTTGAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 52 0.91
51 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (50 bp):
TAACCTATTCGATTAATGCTTCAAGGCCGAATGCATTATCGCTATTATGG
Found at i:5332747 original size:28 final size:29
Alignment explanation
Indices: 5332710--5332805 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
5332700 AAGTCTACAT
*
5332710 ACATGCATATGGCCCACTAGGCCC-AATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
* *
5332738 TCATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
** * * *
5332767 ACATTCATACAGCCTATTAGGCCTAAATC
1 ACATTCATATGGCCCACTAGGCCCAAATC
5332796 ACATTCATAT
1 ACATTCATAT
5332806 ACATGCTCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 21 0.36
29 37 0.64
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.26
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAAATC
Found at i:5337235 original size:28 final size:28
Alignment explanation
Indices: 5337194--5337281 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 28
5337184 ATACATGCAC
* * *
5337194 ATGGTCCACTAGGCCCAATCTCATTCAT
1 ATGGCCCATTAGGCCCAATCACATTCAT
5337222 ATGGCCCATTAGGCCCAAATCACATTCAT
1 ATGGCCCATTAGGCCC-AATCACATTCAT
** * *
5337251 ACAGCCCGTTAGGCCCAAACCACATTCAT
1 ATGGCCCATTAGGCCC-AATCACATTCAT
5337280 AT
1 AT
5337282 ACACGCTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 14 0.27
29 37 0.73
ACGTcount: A:0.30, C:0.33, G:0.14, T:0.24
Consensus pattern (28 bp):
ATGGCCCATTAGGCCCAATCACATTCAT
Found at i:5337257 original size:29 final size:29
Alignment explanation
Indices: 5337203--5337280 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
5337193 CATGGTCCAC
* **
5337203 TAGGCCC-AATCTCATTCATATGGCCCAT
1 TAGGCCCAAATCACATTCATACAGCCCAT
*
5337231 TAGGCCCAAATCACATTCATACAGCCCGT
1 TAGGCCCAAATCACATTCATACAGCCCAT
*
5337260 TAGGCCCAAACCACATTCATA
1 TAGGCCCAAATCACATTCATA
5337281 TACACGCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.23
Consensus pattern (29 bp):
TAGGCCCAAATCACATTCATACAGCCCAT
Found at i:5337361 original size:17 final size:18
Alignment explanation
Indices: 5337339--5337373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5337329 TGCCTATTAT
5337339 GGGCCCA-ACAGCCCATC
1 GGGCCCACACAGCCCATC
*
5337356 GGGCCCACTCAGCCCATC
1 GGGCCCACACAGCCCATC
5337374 CTGGCCCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.20, C:0.49, G:0.23, T:0.09
Consensus pattern (18 bp):
GGGCCCACACAGCCCATC
Found at i:5341448 original size:20 final size:20
Alignment explanation
Indices: 5341423--5341469 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
5341413 ATTCTAATAT
5341423 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
5341443 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
5341463 ACATGAT
1 ACATGAT
5341470 GTATTCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:5341551 original size:26 final size:26
Alignment explanation
Indices: 5341515--5341587 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 26
5341505 GGAGGAAGTG
5341515 CAAAAAGGGCTTTTGCCCCAGTTTAC
1 CAAAAAGGGCTTTTGCCCCAGTTTAC
**
5341541 CAAAAAGGGCTTTTGCCCCAGTTTTT
1 CAAAAAGGGCTTTTGCCCCAGTTTAC
*
5341567 C-AAAAGGGC-TTTGCCCTAGTT
1 CAAAAAGGGCTTTTGCCCCAGTT
5341588 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 11 0.25
25 8 0.18
26 25 0.57
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (26 bp):
CAAAAAGGGCTTTTGCCCCAGTTTAC
Found at i:5341577 original size:25 final size:25
Alignment explanation
Indices: 5341517--5341600 Score: 100
Period size: 26 Copynumber: 3.4 Consensus size: 25
5341507 AGGAAGTGCA
**
5341517 AAAAGGGCTTTTGCCCCAGTTTACC
1 AAAAGGGCTTTTGCCCCAGTTTTTC
5341542 AAAAAGGGCTTTTGCCCCAGTTTTTC
1 -AAAAGGGCTTTTGCCCCAGTTTTTC
* *
5341568 AAAAGGGC-TTTGCCCTAGTTATT-
1 AAAAGGGCTTTTGCCCCAGTTTTTC
5341591 AAAAGAGGCT
1 AAAAG-GGCT
5341601 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
23 5 0.10
24 16 0.31
25 8 0.15
26 23 0.44
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTTTC
Found at i:5341843 original size:31 final size:34
Alignment explanation
Indices: 5341808--5341930 Score: 153
Period size: 38 Copynumber: 3.5 Consensus size: 34
5341798 CGTTTACAGT
5341808 AAAGGCTTCGGCCCA-G-T-AATATGAAATATGA
1 AAAGGCTTCGGCCCAGGTTGAATATGAAATATGA
5341839 AAAGGCTTCGGCCCAGTGTTATGAAATATGAAATATGA
1 AAAGGCTTCGGCCCAG-G-T-TG-AATATGAAATATGA
5341877 AAAGGCTTCGGCCCAGTGTTATGGAATATGAAATATGA
1 AAAGGCTTCGGCCCAG-G-T-T-GAATATGAAATATGA
5341915 AAAGGCTTCGGCCCAG
1 AAAGGCTTCGGCCCAG
5341931 TATATGCTGA
Statistics
Matches: 84, Mismatches: 0, Indels: 9
0.90 0.00 0.10
Matches are distributed among these distances:
31 15 0.18
33 1 0.01
36 1 0.01
38 66 0.79
39 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (34 bp):
AAAGGCTTCGGCCCAGGTTGAATATGAAATATGA
Found at i:5341876 original size:38 final size:38
Alignment explanation
Indices: 5341825--5341931 Score: 205
Period size: 38 Copynumber: 2.8 Consensus size: 38
5341815 TCGGCCCAGT
5341825 AATATGAAATATGAAAAGGCTTCGGCCCAGTGTTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTGTTATGA
*
5341863 AATATGAAATATGAAAAGGCTTCGGCCCAGTGTTATGG
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTGTTATGA
5341901 AATATGAAATATGAAAAGGCTTCGGCCCAGT
1 AATATGAAATATGAAAAGGCTTCGGCCCAGT
5341932 ATATGCTGAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 68 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (38 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGTGTTATGA
Found at i:5364850 original size:19 final size:19
Alignment explanation
Indices: 5364826--5364863 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5364816 ATCTCTCAAG
5364826 GCATGGGACAGATGACTCC
1 GCATGGGACAGATGACTCC
5364845 GCATGGGACAGATGACTCC
1 GCATGGGACAGATGACTCC
5364864 TTACTCATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (19 bp):
GCATGGGACAGATGACTCC
Found at i:5366558 original size:30 final size:30
Alignment explanation
Indices: 5366500--5366559 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5366490 TTCCCGAGCC
*
5366500 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATACAAAAGTT
* *
5366530 TAGGGGCAAAAA-TGTAATTTTACCAAAGTT
1 TAGGGG-AAAAAGTGTAATTATACAAAAGTT
5366560 CACATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATACAAAAGTT
Found at i:5373416 original size:22 final size:22
Alignment explanation
Indices: 5373388--5373463 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
5373378 AAGTGTATAT
5373388 ATGTGATAAGGCCGAGTGGCCA
1 ATGTGATAAGGCCGAGTGGCCA
** ***
5373410 ATGTGATGAATGTG-AAAGTGTATA
1 ATGTGAT-AA-G-GCCGAGTGGCCA
5373434 TATGTGATAAGGCCGAGTGGCCA
1 -ATGTGATAAGGCCGAGTGGCCA
5373457 ATGTGAT
1 ATGTGAT
5373464 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.30, C:0.11, G:0.33, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAGTGGCCA
Found at i:5373416 original size:47 final size:47
Alignment explanation
Indices: 5373363--5373824 Score: 744
Period size: 47 Copynumber: 9.7 Consensus size: 47
5373353 TTAGGATTCT
* * *
5373363 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
5373410 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
5373457 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5373504 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
5373553 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
5373602 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5373649 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
5373696 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
5373743 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
5373790 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
5373825 TCCCGAAGGG
Statistics
Matches: 400, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 306 0.76
49 94 0.23
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:5373749 original size:239 final size:235
Alignment explanation
Indices: 5373363--5373824 Score: 753
Period size: 239 Copynumber: 1.9 Consensus size: 235
5373353 TTAGGATTCT
*
5373363 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
*
5373428 TGTATATATGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * * *
5373493 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTG
131 CCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGACAAGGCCGAATGGCCAACGTG
5373558 ATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
194 ATGAATGTGAAAGTGTATA-A-ATGTGATAAGGCCTAATGGCCG
* *
5373602 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
5373667 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* * * *
5373732 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGAT
131 CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGAT
*
5373797 GGATGTGAAAGTGTATAAATGTGATAAG
196 GAATGTGAAAGTGTATAAATGTGATAAG
5373825 TCCCGAAGGG
Statistics
Matches: 208, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
235 10 0.05
236 1 0.00
237 44 0.21
239 153 0.74
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (235 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGAT
GAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCG
Found at i:5376868 original size:125 final size:124
Alignment explanation
Indices: 5376711--5376964 Score: 436
Period size: 125 Copynumber: 2.0 Consensus size: 124
5376701 TACTTACTTT
* ** *
5376711 ATCAACTATCACGCATTTGCCTAGTGGATTCGACACTCTAATCATAAATTCTGTGTTCTCAACAG
1 ATCAACTATCACCCATTTGCCTAACGGATTCGACACTCTAATCATAAATTATGTGTTCTCAACAG
*
5376776 GTATATTCATACTAGACACCAGTTTAATGCATACGTATGAATGAGTAGAACCAGGATCA
66 GTATATTCATACTAGACACCAGTTTAATGCATACATATGAATGAGTAGAACCAGGATCA
5376835 ATCAAGCTATCACCCATTTGCCTAACGGATTCGACACTCTAATCATAAATTATGTGTTCTCAACA
1 ATCAA-CTATCACCCATTTGCCTAACGGATTCGACACTCTAATCATAAATTATGTGTTCTCAACA
* *
5376900 GGTATATTCATACTAGACACCAGTTTCATGCATACATATGAATGAGTAGAACCGGGATCA
65 GGTATATTCATACTAGACACCAGTTTAATGCATACATATGAATGAGTAGAACCAGGATCA
5376960 ATCAA
1 ATCAA
5376965 AGCAATAACA
Statistics
Matches: 122, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
124 5 0.04
125 117 0.96
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (124 bp):
ATCAACTATCACCCATTTGCCTAACGGATTCGACACTCTAATCATAAATTATGTGTTCTCAACAG
GTATATTCATACTAGACACCAGTTTAATGCATACATATGAATGAGTAGAACCAGGATCA
Found at i:5377097 original size:79 final size:80
Alignment explanation
Indices: 5376963--5377122 Score: 232
Period size: 79 Copynumber: 2.0 Consensus size: 80
5376953 GGGATCAATC
** * ** *
5376963 AAAGCAATAACATTAGTATCATAAAGAGAAAATGTACCGGTAATCACATCGGGTGAGGAAGCATC
1 AAAGCAATAACATTAACATCATAAAGAGAAAATATACCAATAATCACATCAGGTGAGGAAGCATC
5377028 TTCACGCG-CTTTAT
66 TTCACGCGCCTTTAT
* *
5377042 AAAGCAATAACATTAACATCATAAAGAGAAAATATACCAATAATCACGTCAGGTGATGAAGCATC
1 AAAGCAATAACATTAACATCATAAAGAGAAAATATACCAATAATCACATCAGGTGAGGAAGCATC
*
5377107 TTCACGTGCCTTTAT
66 TTCACGCGCCTTTAT
5377122 A
1 A
5377123 GCATAAGTTC
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 64 0.90
80 7 0.10
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (80 bp):
AAAGCAATAACATTAACATCATAAAGAGAAAATATACCAATAATCACATCAGGTGAGGAAGCATC
TTCACGCGCCTTTAT
Found at i:5396318 original size:35 final size:35
Alignment explanation
Indices: 5396272--5396345 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
5396262 CTAAAAAAAA
5396272 TTCTGCTAAGGGTATTATGGTCATTTTAGTTTTTT
1 TTCTGCTAAGGGTATTATGGTCATTTTAGTTTTTT
5396307 TTCTGCTAAGGGTATTATGGTCATTTTAGTTTTTT
1 TTCTGCTAAGGGTATTATGGTCATTTTAGTTTTTT
5396342 TTCT
1 TTCT
5396346 TTATGCTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.16, C:0.09, G:0.19, T:0.55
Consensus pattern (35 bp):
TTCTGCTAAGGGTATTATGGTCATTTTAGTTTTTT
Found at i:5399440 original size:57 final size:57
Alignment explanation
Indices: 5399352--5399524 Score: 328
Period size: 57 Copynumber: 3.0 Consensus size: 57
5399342 ATTTAGAGGA
5399352 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
1 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
5399409 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
1 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
* *
5399466 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCCATTGGGGAAAATTTTGAC
1 ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
5399523 AT
1 AT
5399525 CAGACCCTCC
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 114 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (57 bp):
ATTAATCATGGAAAAGGAACTCAACTATGTTGAGGACCTATTGGGGTAAATTTTGAC
Found at i:5401466 original size:42 final size:43
Alignment explanation
Indices: 5401407--5401499 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 43
5401397 GATTTACGTA
** *
5401407 TAAGACCATGTCTGGGACATCGGCATCG-TATCT-AATTTCATG
1 TAAGACCATGTCTGGGACAGAGGCATCGACAT-TGAATTTCATG
* * *
5401449 TAAGACCTTGTTTGGGACAGAGGCATCGACATTGGATTTCATG
1 TAAGACCATGTCTGGGACAGAGGCATCGACATTGAATTTCATG
5401492 TAAGACCA
1 TAAGACCA
5401500 CATCCGGGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 25 0.60
43 17 0.40
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACAGAGGCATCGACATTGAATTTCATG
Found at i:5403451 original size:11 final size:10
Alignment explanation
Indices: 5403390--5403450 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
5403380 TAACATGCTG
*
5403390 AATTTTAATT
1 AATTTTGATT
5403400 AATTTT-ATAAT
1 AATTTTGAT--T
5403411 AAATTTTGATT
1 -AATTTTGATT
5403422 AATTTTGATT
1 AATTTTGATT
5403432 AATTTTGACTT
1 AATTTTGA-TT
*
5403443 ATTTTTGA
1 AATTTTGA
5403451 CAGATTCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
9 2 0.04
10 24 0.53
11 11 0.24
12 6 0.13
13 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (10 bp):
AATTTTGATT
Found at i:5404815 original size:21 final size:21
Alignment explanation
Indices: 5404791--5404835 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5404781 ACTACAGGGG
5404791 TCAGAACAGGGGATCACGTAA
1 TCAGAACAGGGGATCACGTAA
5404812 TCAGAACAGGGGATCACGTAA
1 TCAGAACAGGGGATCACGTAA
5404833 TCA
1 TCA
5404836 TTCTGAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (21 bp):
TCAGAACAGGGGATCACGTAA
Found at i:5422355 original size:27 final size:27
Alignment explanation
Indices: 5422317--5422618 Score: 354
Period size: 27 Copynumber: 11.2 Consensus size: 27
5422307 NNNNNNNNNN
* *
5422317 TAATTTTACAAACTAGGGGTATTTTGA
1 TAATTTTACAAACCAGGGGTATTTTGG
*
5422344 TAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
*
5422371 TAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* ** **
5422398 TAATTTTATAAACCAATGGTATTTTAC
1 TAATTTTACAAACCAGGGGTATTTTGG
5422425 TAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
** * *
5422452 TAATTTTGTAAACCAAGGGTATTTTGA
1 TAATTTTACAAACCAGGGGTATTTTGG
* *
5422479 TAATTTTATAAACTAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
** *
5422506 TAATTTTGTAAACCAAGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* *
5422533 TAATTTTACAAACAAAGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* * *** *
5422560 TGATTTTATAAACCAAAAG-ATTTTAG
1 TAATTTTACAAACCAGGGGTATTTTGG
*
5422586 TAATTTTACAAACCAGTGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
5422613 TAATTT
1 TAATTT
5422619 GGTAAACTAA
Statistics
Matches: 236, Mismatches: 38, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
26 20 0.08
27 216 0.92
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (27 bp):
TAATTTTACAAACCAGGGGTATTTTGG
Found at i:5422402 original size:54 final size:54
Alignment explanation
Indices: 5422317--5422618 Score: 417
Period size: 54 Copynumber: 5.6 Consensus size: 54
5422307 NNNNNNNNNN
* * * *
5422317 TAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTAGGGGTATTTTGG
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
* **
5422371 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAATGGTATTTTAC
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
* * *
5422425 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGA
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
* *
5422479 TAATTTTATAAACTAGGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTGG
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
* * * ** *
5422533 TAATTTTACAAACAAAGGGTATTTTGGTGATTTTATAAACCAAAAG-ATTTTAG
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
* *
5422586 TAATTTTACAAACCAGTGGTATTTTGGTAATTT
1 TAATTTTACAAACTAGGGGTATTTTGGTAATTT
5422619 GGTAAACTAA
Statistics
Matches: 221, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
53 35 0.16
54 186 0.84
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (54 bp):
TAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGG
Found at i:5425048 original size:74 final size:74
Alignment explanation
Indices: 5424927--5425070 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
5424917 TCTCTTCACT
5424927 AAAAATTAATTATCTCACAGTACAGAACTTAGATAATGTTCTTGTTGATTTATCTTGAAAATAGA
1 AAAAATTAATTATCTCACAGTACAGAACTTAGATAATGTTCTTGTTGATTTATCTTGAAAATAGA
5424992 CTCATTATG
66 CTCATTATG
* *
5425001 AAAAATTAATTATCTCACAGTATAGAACTTGGATAATGTTCTTGTTGATTTATCTTGAAAATAGA
1 AAAAATTAATTATCTCACAGTACAGAACTTAGATAATGTTCTTGTTGATTTATCTTGAAAATAGA
5425066 CTCAT
66 CTCAT
5425071 AGTATAGAAC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (74 bp):
AAAAATTAATTATCTCACAGTACAGAACTTAGATAATGTTCTTGTTGATTTATCTTGAAAATAGA
CTCATTATG
Found at i:5438381 original size:40 final size:41
Alignment explanation
Indices: 5438306--5438401 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 41
5438296 TGACTATGTT
* **
5438306 TGGCACTAGGTGTGCGGTTCGAAATAGCTTTGGCTACA-AA
1 TGGCACTAAGTGTGCGGTTCGAAATAGCTCCGGCTACATAA
* * * *
5438346 TGGCACTAAGTGTGCGTGTT-GGAATTGCTCCGGCTATATGA
1 TGGCACTAAGTGTGCG-GTTCGAAATAGCTCCGGCTACATAA
5438387 T-GCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
5438402 ATACCAAGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 42 0.89
41 5 0.11
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGGTTCGAAATAGCTCCGGCTACATAA
Found at i:5439923 original size:46 final size:46
Alignment explanation
Indices: 5439873--5440045 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
5439863 TGGTTGAGCA
5439873 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
5439919 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
5439964 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5440012 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
5440046 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5440029 original size:93 final size:93
Alignment explanation
Indices: 5439870--5440040 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5439860 GGATGGTTGA
* *
5439870 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5439935 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5439963 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5440028 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5440041 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5445784 original size:40 final size:40
Alignment explanation
Indices: 5445700--5445943 Score: 280
Period size: 40 Copynumber: 6.1 Consensus size: 40
5445690 TCGAATGATG
* * * * * *
5445700 TCCGAGCTAAATCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5445740 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5445780 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5445819 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5445859 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* ** * *
5445900 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
5445939 TCCGG
1 TCCGG
5445944 TTAAATTCCG
Statistics
Matches: 177, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
39 35 0.20
40 132 0.75
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5453959 original size:40 final size:40
Alignment explanation
Indices: 5453728--5453952 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
5453718 TCGAATGATG
* * * *
5453728 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
5453768 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5453808 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
5453847 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
5453887 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
5453928 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
5453953 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 120 0.74
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5453974 original size:119 final size:119
Alignment explanation
Indices: 5453735--5453985 Score: 278
Period size: 119 Copynumber: 2.1 Consensus size: 119
5453725 ATGTCCGGGC
*
5453735 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
* ** *
5453800 ATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCTGGGT
66 ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATCTCGGT
* * * **
5453854 TAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
* * * *
5453917 AGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATC-CGGT
64 AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAATCTCGGT
* *
5453973 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
5453986 TACGTGATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 78 0.70
120 30 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAG
ATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAATCTCGGT
Found at i:5456750 original size:40 final size:40
Alignment explanation
Indices: 5456693--5456933 Score: 169
Period size: 40 Copynumber: 5.7 Consensus size: 40
5456683 GTTATGATTA
5456693 TCGGCTAAAA-TGGCACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGCTAAAAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
* * ** * *
5456732 TTGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
* **
5456772 TCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGC------TA-A-AAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
* ** * *
5456820 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
* **
5456860 TCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGC------TA-A-AAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
*
5456908 TCGGCTAAAAGTGGCACTTGGTGTGC
1 TCGGCTAAAAGTGGCACTTAGTGTGC
5456934 AATTTGAGAT
Statistics
Matches: 150, Mismatches: 35, Indels: 33
0.69 0.16 0.15
Matches are distributed among these distances:
39 9 0.06
40 71 0.47
41 2 0.01
42 4 0.03
46 4 0.03
47 2 0.01
48 58 0.39
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (40 bp):
TCGGCTAAAAGTGGCACTTAGTGTGCGGTTCGAAATAGCT
Found at i:5456818 original size:48 final size:48
Alignment explanation
Indices: 5456766--5456914 Score: 170
Period size: 48 Copynumber: 3.3 Consensus size: 48
5456756 GCAATTTGAG
5456766 ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
1 ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
* ** * ** * *
5456814 ATAGCTTCGGC------TA-A-AAGTGGCACTTGGTGTGCAATTTGAG
1 ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
5456854 ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
1 ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
5456902 ATAGCTTCGGCTA
1 ATAGCTTCGGCTA
5456915 AAAGTGGCAC
Statistics
Matches: 77, Mismatches: 16, Indels: 16
0.71 0.15 0.15
Matches are distributed among these distances:
40 29 0.38
41 1 0.01
42 2 0.03
46 2 0.03
47 1 0.01
48 42 0.55
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (48 bp):
ATAGCTTCGGCTATATATATATAAATTTCACTTAGTGTGCGGTTCGAA
Found at i:5456855 original size:88 final size:88
Alignment explanation
Indices: 5456706--5456964 Score: 500
Period size: 88 Copynumber: 2.9 Consensus size: 88
5456696 GCTAAAATGG
*
5456706 CACTTAGTGTGCGGTTCGAAATAGCTTTGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
1 CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
5456771 TTCGGCTATATATATATAAATTT
66 TTCGGCTATATATATATAAATTT
5456794 CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
1 CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
5456859 TTCGGCTATATATATATAAATTT
66 TTCGGCTATATATATATAAATTT
5456882 CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
1 CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
*
5456947 TTCAGCTATATATATATA
66 TTCGGCTATATATATATA
5456965 TATATATAAA
Statistics
Matches: 169, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 169 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (88 bp):
CACTTAGTGTGCGGTTCGAAATAGCTTCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
TTCGGCTATATATATATAAATTT
Found at i:5457857 original size:15 final size:15
Alignment explanation
Indices: 5457837--5457867 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5457827 GTAAAAATGC
5457837 AAATATGATTGTATT
1 AAATATGATTGTATT
*
5457852 AAATATGGTTGTATT
1 AAATATGATTGTATT
5457867 A
1 A
5457868 CCTTGAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (15 bp):
AAATATGATTGTATT
Found at i:5461368 original size:24 final size:24
Alignment explanation
Indices: 5461341--5461397 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
5461331 AAGAATTAGT
*
5461341 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
5461365 ATTTATTAGCATAATATATTTCAC
1 ATTTATTAGCATAATATATTTAAC
*
5461389 ATTGATTAG
1 ATTTATTAG
5461398 AATTAGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:5464352 original size:54 final size:54
Alignment explanation
Indices: 5464294--5464421 Score: 141
Period size: 54 Copynumber: 2.4 Consensus size: 54
5464284 CGTGTCTTAA
* * *
5464294 ACCGTGTAACTCACTGAGTT-AGATCACACGGCCGTGTCGCAGGTCGTGTGCCAG
1 ACCGTGTAACTCACTGACTTGAGA-CACACGGCCATGTCGCAAGTCGTGTGCCAG
** * * **
5464348 ACCGTGTAACTCTTTGACTTGTGACACACTGCCATGTCGCAAGTCGTGTGTTAG
1 ACCGTGTAACTCACTGACTTGAGACACACGGCCATGTCGCAAGTCGTGTGCCAG
* *
5464402 ACCATGTAACTCACTAACTT
1 ACCGTGTAACTCACTGACTT
5464422 CAAATAATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 58 0.97
55 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (54 bp):
ACCGTGTAACTCACTGACTTGAGACACACGGCCATGTCGCAAGTCGTGTGCCAG
Found at i:5465755 original size:36 final size:37
Alignment explanation
Indices: 5465700--5465769 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
5465690 AATTAATCAA
* *
5465700 AACATCAATATATTCATATAATCAAGTCAATTTATACT
1 AACATCAATATATACATATAATCAA-TCAAATTATACT
5465738 AACAT-AATATA-ACATATAATCAATCAAATTAT
1 AACATCAATATATACATATAATCAATCAAATTAT
5465770 CATTAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 8 0.27
36 11 0.37
37 6 0.20
38 5 0.17
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.34
Consensus pattern (37 bp):
AACATCAATATATACATATAATCAATCAAATTATACT
Found at i:5468105 original size:20 final size:20
Alignment explanation
Indices: 5468077--5468121 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5468067 CTCATTTTTC
* *
5468077 CTCTCAAATGCTCT-TTAATT
1 CTCTTAAAT-CTCTCTTAAAT
5468097 CTCTTAAATCTCTCTTAAAT
1 CTCTTAAATCTCTCTTAAAT
5468117 CTCTT
1 CTCTT
5468122 TTCAGTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.24, C:0.27, G:0.02, T:0.47
Consensus pattern (20 bp):
CTCTTAAATCTCTCTTAAAT
Found at i:5468112 original size:11 final size:11
Alignment explanation
Indices: 5468087--5468120 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5468077 CTCTCAAATG
*
5468087 CTCTTTAAT-T
1 CTCTTAAATCT
5468097 CTCTTAAATCT
1 CTCTTAAATCT
5468108 CTCTTAAATCT
1 CTCTTAAATCT
5468119 CT
1 CT
5468121 TTTCAGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTTAAATCT
Found at i:5468143 original size:18 final size:19
Alignment explanation
Indices: 5468120--5468161 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5468110 CTTAAATCTC
*
5468120 TTTTCAGTATTTTT-CTAT
1 TTTTCAATATTTTTGCTAT
*
5468138 TTTTCAATATTTTTGTTAT
1 TTTTCAATATTTTTGCTAT
5468157 TTTTC
1 TTTTC
5468162 TTCCTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTTCAATATTTTTGCTAT
Found at i:5468828 original size:14 final size:14
Alignment explanation
Indices: 5468809--5468839 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5468799 TTTGGACTTG
5468809 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
*
5468823 ATTTTTGTTTTTTT
1 ATTTTTATTTTTTT
5468837 ATT
1 ATT
5468840 GTTTTTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:5469023 original size:2 final size:2
Alignment explanation
Indices: 5469016--5469040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5469006 GTAATTTAAA
5469016 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
5469041 TTAGGGGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5474635 original size:50 final size:50
Alignment explanation
Indices: 5474576--5474692 Score: 164
Period size: 50 Copynumber: 2.3 Consensus size: 50
5474566 GCCAAATCCT
*
5474576 AGACATGGTCTTACACTAACTCTT-ATATATCGAGACTGATACCATGTCCC
1 AGACATGGTCTTACACTAACT-TTCAGATATCGAGACTGATACCATGTCCC
* * * * *
5474626 AGACATGGTCTTACACTAGCTTTCAGGTCTCGAGGCTGATGCCATGTCCC
1 AGACATGGTCTTACACTAACTTTCAGATATCGAGACTGATACCATGTCCC
5474676 AGACATGGTCTTACACT
1 AGACATGGTCTTACACT
5474693 GGATCTCATA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 2 0.03
50 58 0.97
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (50 bp):
AGACATGGTCTTACACTAACTTTCAGATATCGAGACTGATACCATGTCCC
Found at i:5486420 original size:20 final size:18
Alignment explanation
Indices: 5486397--5486444 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
5486387 GTAGTATTTA
5486397 ATTAATTTAATATTAAAGT
1 ATTAATTTAATATTAAA-T
5486416 GATT-ATCTTAATATTAAAT
1 -ATTAAT-TTAATATTAAAT
5486435 -TTAATTTAAT
1 ATTAATTTAAT
5486445 GTTTACCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.27
18 2 0.08
19 3 0.12
20 14 0.54
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (18 bp):
ATTAATTTAATATTAAAT
Found at i:5489286 original size:42 final size:43
Alignment explanation
Indices: 5489231--5489312 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 43
5489221 TGTGTCTCAT
5489231 AATCATGAACTCAG-ACTACAACTC-ATGAGTTCAAATCACATA
1 AATCATGAACTCAGAAC-ACAACTCAATGAGTTCAAATCACATA
*
5489273 AATCATGAACTCAGAACACAACTCAATGAGTTCAGATCAC
1 AATCATGAACTCAGAACACAACTCAATGAGTTCAAATCAC
5489313 GTAATTCTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 21 0.57
43 16 0.43
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (43 bp):
AATCATGAACTCAGAACACAACTCAATGAGTTCAAATCACATA
Found at i:5497154 original size:42 final size:43
Alignment explanation
Indices: 5497091--5497172 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
5497081 TGTGTCTCGT
*
5497091 AATCATAAACTCAAACTACAACTC-ATGAGTTCAAATCACATA
1 AATCATAAACTCAAACCACAACTCAATGAGTTCAAATCACATA
* * *
5497133 AATCATGAACTCAGACCACAACTCAATGAGTTCAGATCAC
1 AATCATAAACTCAAACCACAACTCAATGAGTTCAAATCAC
5497173 GTAATTCCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.22
Consensus pattern (43 bp):
AATCATAAACTCAAACCACAACTCAATGAGTTCAAATCACATA
Found at i:5497901 original size:21 final size:21
Alignment explanation
Indices: 5497875--5497930 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
5497865 AACAGCGGTG
* *
5497875 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTATA
*
5497896 GCGGTGAGATTGGATACTATA
1 GCGGTGAGATTAGATACTATA
5497917 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
5497931 AATAGCGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:5497937 original size:18 final size:20
Alignment explanation
Indices: 5497875--5497940 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
5497865 AACAGCGGTG
* *
5497875 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATAC-ATA
*
5497896 GCGGTGAGATTGGATACTATA
1 GCGGTGAGATTAGATAC-ATA
5497917 GCGGTGAGATTAGA-A-ATA
1 GCGGTGAGATTAGATACATA
5497935 GCGGTG
1 GCGGTG
5497941 GAGTGTGTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 9 0.22
20 1 0.02
21 31 0.76
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (20 bp):
GCGGTGAGATTAGATACATA
Found at i:5499275 original size:13 final size:13
Alignment explanation
Indices: 5499257--5499283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5499247 CAGGTAGAGT
5499257 AACAATATCTTAA
1 AACAATATCTTAA
5499270 AACAATATCTTAA
1 AACAATATCTTAA
5499283 A
1 A
5499284 TTTTTGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AACAATATCTTAA
Found at i:5501286 original size:5 final size:5
Alignment explanation
Indices: 5501276--5501301 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5501266 TGGTAATTAT
5501276 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
5501302 GCCAAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:5502616 original size:22 final size:24
Alignment explanation
Indices: 5502570--5502616 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5502560 TATTTTAGTA
*
5502570 ATATGTATATTCTTCATATATTAT
1 ATATGTATATTCTTCATATACTAT
*
5502594 ATATGTGTATTCTT-A-ATACTAT
1 ATATGTATATTCTTCATATACTAT
5502616 A
1 A
5502617 CTTTATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (24 bp):
ATATGTATATTCTTCATATACTAT
Found at i:5502663 original size:21 final size:22
Alignment explanation
Indices: 5502637--5502680 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5502627 ATCATGTATT
*
5502637 TTTTAATGTTACATTAT-TATA
1 TTTTAATATTACATTATATATA
*
5502658 TTTTAATATTATATTATATATA
1 TTTTAATATTACATTATATATA
5502680 T
1 T
5502681 ATTTTCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAATATTACATTATATATA
Found at i:5502685 original size:24 final size:25
Alignment explanation
Indices: 5502654--5502755 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 25
5502644 GTTACATTAT
5502654 TATATTTTAATATTA-TATTATATA
1 TATATTTTAATATTATTATTATATA
**
5502678 TATATTTTCCTATTA-TATTATATTCA
1 TATATTTTAATATTATTATTATA-T-A
* * *
5502704 TATATCTTTTATA-TATTACTATGTA
1 TATAT-TTTAATATTATTATTATATA
* *
5502729 AATATTTTGATATTATTAGTTATATA
1 TATATTTTAATATTATTA-TTATATA
5502755 T
1 T
5502756 TACTTATATA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
24 26 0.43
25 11 0.18
26 14 0.23
27 10 0.16
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
TATATTTTAATATTATTATTATATA
Found at i:5502785 original size:23 final size:23
Alignment explanation
Indices: 5502749--5502805 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
5502739 TATTATTAGT
5502749 TATATATTACTTATATAT-TTCCATG
1 TATATATT--TTATAT-TGTTCCATG
5502774 TATATATTTTATATTGTTCCATG
1 TATATATTTTATATTGTTCCATG
*
5502797 TACATATTT
1 TATATATTT
5502806 GAGTAGTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 21 0.70
25 8 0.27
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (23 bp):
TATATATTTTATATTGTTCCATG
Found at i:5503098 original size:15 final size:15
Alignment explanation
Indices: 5503080--5503113 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5503070 TATATACTAT
5503080 GTATACATATATTTA
1 GTATACATATATTTA
**
5503095 GTATGTATATATTTA
1 GTATACATATATTTA
5503110 GTAT
1 GTAT
5503114 TATTACACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (15 bp):
GTATACATATATTTA
Found at i:5503459 original size:25 final size:25
Alignment explanation
Indices: 5503431--5503481 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
5503421 TATTATCATA
5503431 TTTA-TTATTTACTTTAATATATTTT
1 TTTAGTTATTT-CTTTAATATATTTT
* * *
5503456 TTTAGTTCTTTCTTTTATCTATTTT
1 TTTAGTTATTTCTTTAATATATTTT
5503481 T
1 T
5503482 ATTTCATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTAGTTATTTCTTTAATATATTTT
Found at i:5512106 original size:27 final size:27
Alignment explanation
Indices: 5512076--5512251 Score: 183
Period size: 27 Copynumber: 6.5 Consensus size: 27
5512066 AATTGTACAT
*
5512076 CACTAAGTGTGCGATTTGACTATGTTG
1 CACTAAGTGTGCGATTTGACTATGTAG
** *
5512103 CACTAAGTGTGCGAAATGAATATG-ATG
1 CACTAAGTGTGCGATTTGACTATGTA-G
* * **
5512130 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGATTTGACTATGTAG
*
5512157 CACTAAGTGTGGGAGTTTGACTATGTAG
1 CACTAAGTGTGCGA-TTTGACTATGTAG
* *
5512185 CACTAAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGATTTGACTATGTAG
* * *
5512212 CACTAAGTGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGATTTGACTATGTAG
* *
5512239 TACTGAGTGTGCG
1 CACTAAGTGTGCG
5512252 GACTCAATAT
Statistics
Matches: 125, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.82
28 22 0.18
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
CACTAAGTGTGCGATTTGACTATGTAG
Found at i:5512188 original size:82 final size:81
Alignment explanation
Indices: 5512076--5512230 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 81
5512066 AATTGTACAT
* *
5512076 CACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGT
5512140 GCGAATTGACCATGCGG
65 GCGAATTGACCATGCGG
* ** *
5512157 CACTAAGTGTGGGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGT
1 CACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
*
5512222 GCGAGTTGA
65 GCGAATTGA
5512231 TTATATAGTA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 13 0.20
82 51 0.78
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
CGAATTGACCATGCGG
Done.