Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 115 of 199
Found at i:35029767 original size:23 final size:23
Alignment explanation
Indices: 35029737--35029780 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
35029727 GGGAAAGATA
*
35029737 AGTTCTTTCTTATCTTTCTCATG
1 AGTTCTTTCTCATCTTTCTCATG
35029760 AGTTCTTTCTCATCTTTCTCA
1 AGTTCTTTCTCATCTTTCTCA
35029781 CGAAAGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.14, C:0.25, G:0.07, T:0.55
Consensus pattern (23 bp):
AGTTCTTTCTCATCTTTCTCATG
Found at i:35029904 original size:2 final size:2
Alignment explanation
Indices: 35029897--35029942 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
35029887 CTTGCTTTAC
*
35029897 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35029939 AT AT
1 AT AT
35029943 CAATAGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35036662 original size:12 final size:12
Alignment explanation
Indices: 35036645--35036669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35036635 CTGGTCTGGA
35036645 AGCTGCTTCAAC
1 AGCTGCTTCAAC
35036657 AGCTGCTTCAAC
1 AGCTGCTTCAAC
35036669 A
1 A
35036670 ATGAGGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
AGCTGCTTCAAC
Found at i:35036833 original size:22 final size:21
Alignment explanation
Indices: 35036770--35036833 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
35036760 TTGCTTCCTT
*
35036770 AACACGCTCCAGGATTTCTTG
1 AACACGCTCCAGGATTTCTTC
* * *
35036791 TACATGCTTCAGGATTTCTTC
1 AACACGCTCCAGGATTTCTTC
*
35036812 AACGCGCTCCAGGATTTTCTTC
1 AACACGCTCCAGGA-TTTCTTC
35036834 TGCAGTTCAG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 27 0.79
22 7 0.21
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (21 bp):
AACACGCTCCAGGATTTCTTC
Found at i:35042527 original size:20 final size:20
Alignment explanation
Indices: 35042502--35042540 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35042492 CACGTGGGAT
35042502 GAATGTCT-TCGATGGGACAA
1 GAATGTCTGT-GATGGGACAA
35042522 GAATGTCTGTGATGGGACA
1 GAATGTCTGTGATGGGACA
35042541 GATATTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.26
Consensus pattern (20 bp):
GAATGTCTGTGATGGGACAA
Found at i:35044516 original size:22 final size:22
Alignment explanation
Indices: 35044484--35044525 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35044474 TATATAAGCA
* *
35044484 ATATTATTTGAATAGTTATGAG
1 ATATTAGTTGAATAATTATGAG
35044506 ATATTAGTTGAATAATTATG
1 ATATTAGTTGAATAATTATG
35044526 TCACTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (22 bp):
ATATTAGTTGAATAATTATGAG
Found at i:35047342 original size:2 final size:2
Alignment explanation
Indices: 35047335--35047360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35047325 ACCTTTAGCA
35047335 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
35047361 TTAAATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35048082 original size:63 final size:63
Alignment explanation
Indices: 35047952--35048182 Score: 245
Period size: 63 Copynumber: 3.7 Consensus size: 63
35047942 TCTTCGTAGC
* * * * * ** ** *
35047952 AAACATACATTCAGATACCATATATATATGTAATTCATACAATTAAATTCTGCTTATAGAACTCA
1 AAACATACATTCGGCTAACATAT-T-TATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
* * *
35048017 AAAAATACATTCGGCTAACATATTTATATAATTTATAAAATTTGTTTCAACTCATAGAACTCA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
* * * *
35048080 AAACATACACT-GGCTAACATATTTATAT--TTCATACAATTAGTTTCAACTTATCA-AACTTA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCAT-AGAACTCA
*
35048140 AAACATACATTCAGCTAACATATTTATATAATTCATAAAATTA
1 AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTA
35048183 AATTCAGCTT
Statistics
Matches: 139, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
60 35 0.25
61 17 0.12
62 17 0.12
63 50 0.36
64 1 0.01
65 19 0.14
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (63 bp):
AAACATACATTCGGCTAACATATTTATATAATTCATAAAATTAGTTTCAACTCATAGAACTCA
Found at i:35048146 original size:60 final size:62
Alignment explanation
Indices: 35048004--35048182 Score: 238
Period size: 60 Copynumber: 2.9 Consensus size: 62
35047994 TTAAATTCTG
* * *
35048004 CTTATAGAACTCAAAAAATACATTCGGCTAACATATTTATATAATTTATAAAATTTGTTTCAA
1 CTTATAGAACTCAAAACATACATTCGGCTAACATATTTATAT-ATTCATAAAATTAGTTTCAA
* * *
35048067 CTCATAGAACTCAAAACATACACT-GGCTAACATATTTATAT-TTCATACAATTAGTTTCAA
1 CTTATAGAACTCAAAACATACATTCGGCTAACATATTTATATATTCATAAAATTAGTTTCAA
* *
35048127 CTTATCA-AACTTAAAACATACATTCAGCTAACATATTTATATAATTCATAAAATTA
1 CTTAT-AGAACTCAAAACATACATTCGGCTAACATATTTATAT-ATTCATAAAATTA
35048183 AATTCAGCTT
Statistics
Matches: 101, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
60 35 0.35
61 17 0.17
62 17 0.17
63 32 0.32
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (62 bp):
CTTATAGAACTCAAAACATACATTCGGCTAACATATTTATATATTCATAAAATTAGTTTCAA
Found at i:35048207 original size:2 final size:2
Alignment explanation
Indices: 35048200--35048239 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35048190 CTTACAGTAC
35048200 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35048240 TCTAATTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35050458 original size:2 final size:2
Alignment explanation
Indices: 35050451--35050481 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35050441 TTCATTAACA
35050451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35050482 AACATAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35052593 original size:18 final size:17
Alignment explanation
Indices: 35052567--35052602 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35052557 TTTGGTTATA
35052567 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
35052585 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
35052602 T
1 T
35052603 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:35056210 original size:21 final size:21
Alignment explanation
Indices: 35056169--35056211 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
35056159 AATAAAGTAG
*
35056169 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
35056190 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
35056211 A
1 A
35056212 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:35056259 original size:35 final size:33
Alignment explanation
Indices: 35056194--35056269 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 33
35056184 TATAGTATTA
*
35056194 TATATTATGATTTTAGTAAATTCATATAATAAT
1 TATATTAAGATTTTAGTAAATTCATATAATAAT
*
35056227 TATATTAAGAATTTTATTAAATT-ATATTTAATAAT
1 TATATTAAG-ATTTTAGTAAATTCATA--TAATAAT
*
35056262 TATGTTAA
1 TATATTAA
35056270 AATATGAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 11 0.30
34 12 0.32
35 14 0.38
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (33 bp):
TATATTAAGATTTTAGTAAATTCATATAATAAT
Found at i:35056269 original size:23 final size:22
Alignment explanation
Indices: 35056224--35056270 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
35056214 TTCATATAAT
*
35056224 AATTATATTAAGAATTTTATTA
1 AATTATATTAAGAATTATATTA
* *
35056246 AATTATATTTAATAATTATGTTA
1 AATTATA-TTAAGAATTATATTA
35056269 AA
1 AA
35056271 ATATGAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTATATTAAGAATTATATTA
Found at i:35056503 original size:16 final size:16
Alignment explanation
Indices: 35056482--35056520 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
35056472 TAAATTACTT
35056482 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
35056498 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
35056514 ATTACAG
1 ATTACAG
35056521 TGAACCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:35078630 original size:69 final size:69
Alignment explanation
Indices: 35078510--35078677 Score: 187
Period size: 69 Copynumber: 2.4 Consensus size: 69
35078500 TTTACTTGCA
* * * *
35078510 AACCTTGATTTTACAGTTGGGAGCTTCGCTCTTACTAACTGCGTTAAAGGTCACGA-CTCTTCGC
1 AACCTTGATTTTACAGTTGGAAGCTTTGCTCTCACTAACTGCATTAAAGGTCAC-ACCTCTTCGC
35078574 CTGTG
65 CTGTG
* * * ** * * *
35078579 AACCTTGCTTTTATAGTTGGAAGCTTTGCTCTCACTAACTGTATTGGAGGTCGCACCTCTTTGCT
1 AACCTTGATTTTACAGTTGGAAGCTTTGCTCTCACTAACTGCATTAAAGGTCACACCTCTTCGCC
35078644 TGTG
66 TGTG
*
35078648 AACCTTGATTTTACAGCT-GAGAGCTTTGCT
1 AACCTTGATTTTACAGTTGGA-AGCTTTGCT
35078678 TGCGCTAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
68 3 0.04
69 79 0.96
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (69 bp):
AACCTTGATTTTACAGTTGGAAGCTTTGCTCTCACTAACTGCATTAAAGGTCACACCTCTTCGCC
TGTG
Found at i:35080840 original size:21 final size:21
Alignment explanation
Indices: 35080816--35080855 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35080806 AGCATTCTAC
35080816 CATGAACTTCATCTATTCCCT
1 CATGAACTTCATCTATTCCCT
*
35080837 CATGAACTTCATCTGTTCC
1 CATGAACTTCATCTATTCC
35080856 TGGAGGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (21 bp):
CATGAACTTCATCTATTCCCT
Found at i:35081314 original size:40 final size:40
Alignment explanation
Indices: 35081259--35081354 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
35081249 AGCGTTAGCG
* * *
35081259 GCGTTTTTCCTATAAACACCGTAAAAGGTAAAGAAATA-AT
1 GCGTTTTTGC-ATAAACACCGTAAAAGGGAAAGAAACAGAT
* * *
35081299 GACGTTTTTGCATAAACTCCGTAAAAGGGAAAGCAACAGCT
1 G-CGTTTTTGCATAAACACCGTAAAAGGGAAAGAAACAGAT
35081340 GCGTTTTTGCATAAA
1 GCGTTTTTGCATAAA
35081355 TGCCGCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 38 0.79
41 10 0.21
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (40 bp):
GCGTTTTTGCATAAACACCGTAAAAGGGAAAGAAACAGAT
Found at i:35084567 original size:66 final size:66
Alignment explanation
Indices: 35084456--35084599 Score: 193
Period size: 66 Copynumber: 2.2 Consensus size: 66
35084446 GCAAATCGCT
** * * *
35084456 CAACTTAAAGCGGATGCAGCATCGAGAGAAGCAGTGGCTAAAAGAAAATATGATGAACTCCAGCT
1 CAACTTAAAATGGAGGCAGCATCGAGAGAAGCAGAGGCTAAAAGAAAATATGACGAACTCCAGCT
35084521 A
66 A
*
35084522 CAACTTAAAATGGAGGCAGCAGT-GAGGGAAGCAGAGGC-AACAAGAAAATATGACGAACTCCAG
1 CAACTTAAAATGGAGGCAGCA-TCGAGAGAAGCAGAGGCTAA-AAGAAAATATGACGAACTCCAG
35084585 CTA
64 CTA
35084588 CAACTTCAAAAT
1 CAACTT-AAAAT
35084600 ATGATAGAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
65 2 0.03
66 61 0.88
67 6 0.09
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (66 bp):
CAACTTAAAATGGAGGCAGCATCGAGAGAAGCAGAGGCTAAAAGAAAATATGACGAACTCCAGCT
A
Found at i:35084965 original size:44 final size:44
Alignment explanation
Indices: 35084875--35084971 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
35084865 GCGTTTTCCC
* *
35084875 ACAAACGCCGCTATAGAACATGATCTTTAGCAACACTTTTTACT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCAACACTTTCTACT
* * * *
35084919 ACAAACGCCGCTAAAGAATATGATCTTTTGCAGCGC-TTCTAGCT
1 ACAAACGCCGCTAAAGAACATGATCTTTAGCAACACTTTCTA-CT
35084963 ACAAACGCC
1 ACAAACGCC
35084972 ACAACATGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 4 0.09
44 42 0.91
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (44 bp):
ACAAACGCCGCTAAAGAACATGATCTTTAGCAACACTTTCTACT
Found at i:35087048 original size:25 final size:22
Alignment explanation
Indices: 35087000--35087052 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 22
35086990 TCAAAAGTTC
*
35087000 AAAAGAATTTAAAATAAAATTTT
1 AAAA-AATTTAAAATAAAAATTT
35087023 AAAAAATTCTAAAATATATAAATTT
1 AAAAAATT-TAAAATA-A-AAATTT
35087048 AAAAA
1 AAAAA
35087053 TTAAAAAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 4 0.15
23 11 0.42
24 1 0.04
25 10 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAAAATTTAAAATAAAAATTT
Found at i:35087231 original size:20 final size:21
Alignment explanation
Indices: 35087200--35087243 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
35087190 CCAAATATTC
35087200 AAAATTCTAAAAATTCAAAAA
1 AAAATTCTAAAAATTCAAAAA
35087221 AAAATTC-AAAAATTCAAAAA
1 AAAATTCTAAAAATTCAAAAA
35087241 AAA
1 AAA
35087244 GAAGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATTCTAAAAATTCAAAAA
Found at i:35087243 original size:12 final size:12
Alignment explanation
Indices: 35087208--35087232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35087198 TCAAAATTCT
35087208 AAAAATTCAAAA
1 AAAAATTCAAAA
35087220 AAAAATTCAAAA
1 AAAAATTCAAAA
35087232 A
1 A
35087233 TTCAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATTCAAAA
Found at i:35089104 original size:30 final size:30
Alignment explanation
Indices: 35089070--35089127 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35089060 AGGTGAGATG
*
35089070 GGGAGGGAATAAAAGTTTTAGGGGAAAAGT
1 GGGAGGGAATAAAAATTTTAGGGGAAAAGT
* *
35089100 GGGAGGGAGTAAAAATTTTGGGGGAAAA
1 GGGAGGGAATAAAAATTTTAGGGGAAAA
35089128 TAAAAGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.41, T:0.19
Consensus pattern (30 bp):
GGGAGGGAATAAAAATTTTAGGGGAAAAGT
Found at i:35089437 original size:9 final size:9
Alignment explanation
Indices: 35089420--35089450 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35089410 TCGAGTTGAT
35089420 TCGAATAAC
1 TCGAATAAC
*
35089429 TCGATTAAC
1 TCGAATAAC
35089438 TCGAATAAC
1 TCGAATAAC
35089447 TCGA
1 TCGA
35089451 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:35100475 original size:15 final size:15
Alignment explanation
Indices: 35100457--35100489 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35100447 TTTTATTTTA
*
35100457 TAAATTATTATAAGG
1 TAAACTATTATAAGG
35100472 TAAACTATTATAAGG
1 TAAACTATTATAAGG
35100487 TAA
1 TAA
35100490 TTTTGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.36
Consensus pattern (15 bp):
TAAACTATTATAAGG
Found at i:35106231 original size:14 final size:14
Alignment explanation
Indices: 35106212--35106242 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35106202 CCATGAATTT
*
35106212 CAATAATAGTATTG
1 CAATAATAGCATTG
35106226 CAATAATAGCATTG
1 CAATAATAGCATTG
35106240 CAA
1 CAA
35106243 GAAGCCAAGT
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:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (14 bp):
CAATAATAGCATTG
Found at i:35119997 original size:23 final size:23
Alignment explanation
Indices: 35119971--35120046 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
35119961 ATAAGTGCCA
35119971 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35119994 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
35120017 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
35120040 CACTGAT
1 CACTGAT
35120047 CAATAATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:35120146 original size:8 final size:8
Alignment explanation
Indices: 35120133--35120161 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
35120123 ACCCGGGACT
35120133 CACTGTAA
1 CACTGTAA
35120141 CACTGTAA
1 CACTGTAA
35120149 CACTGTAA
1 CACTGTAA
35120157 CACTG
1 CACTG
35120162 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:35120292 original size:18 final size:17
Alignment explanation
Indices: 35120266--35120304 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35120256 ATTTTCCTTC
35120266 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
35120283 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
35120301 CACA
1 CACA
35120305 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:35127330 original size:8 final size:8
Alignment explanation
Indices: 35127317--35127345 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
35127307 ACCCGGGACT
35127317 CACTGTAA
1 CACTGTAA
35127325 CACTGTAA
1 CACTGTAA
35127333 CACTGTAA
1 CACTGTAA
35127341 CACTG
1 CACTG
35127346 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:35127476 original size:18 final size:17
Alignment explanation
Indices: 35127450--35127488 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35127440 ATTTTCCTTC
35127450 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
35127467 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
35127485 CACA
1 CACA
35127489 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:35138905 original size:26 final size:26
Alignment explanation
Indices: 35138869--35138920 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35138859 TTAAATCTTA
35138869 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
35138895 GTTGAAATCGGGCATGAGAACCTTTT
1 GTTGAAATCGGGCATGAGAACCTTTT
35138921 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (26 bp):
GTTGAAATCGGGCATGAGAACCTTTT
Found at i:35146748 original size:22 final size:22
Alignment explanation
Indices: 35146720--35146761 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
35146710 TCAATTTTGG
35146720 CGTACTAAGCTCTCATGTTTCA
1 CGTACTAAGCTCTCATGTTTCA
35146742 CGTACTAAGCTCTCATGTTT
1 CGTACTAAGCTCTCATGTTT
35146762 GAACAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (22 bp):
CGTACTAAGCTCTCATGTTTCA
Found at i:35148849 original size:3 final size:3
Alignment explanation
Indices: 35148841--35148865 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35148831 TAGGGTTTTT
35148841 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
35148866 AACAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35161022 original size:18 final size:18
Alignment explanation
Indices: 35160999--35161033 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35160989 ACTTAGTCAA
*
35160999 TTTTTTCTTTCTCTTAGT
1 TTTTTTCTTTCCCTTAGT
35161017 TTTTTTCTTTCCCTTAG
1 TTTTTTCTTTCCCTTAG
35161034 AGGATGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.20, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTTTCTTTCCCTTAGT
Found at i:35161699 original size:17 final size:19
Alignment explanation
Indices: 35161674--35161710 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
35161664 AATTACCATC
*
35161674 TTTTTATTA-AGCAA-ATA
1 TTTTCATTATAGCAACATA
35161691 TTTTCATTATAGCAACATA
1 TTTTCATTATAGCAACATA
35161710 T
1 T
35161711 CAAGAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTTCATTATAGCAACATA
Found at i:35162223 original size:29 final size:30
Alignment explanation
Indices: 35162167--35162250 Score: 82
Period size: 30 Copynumber: 2.8 Consensus size: 30
35162157 AATTAAATCG
* * *
35162167 TAAATATGAGAAAATTTTTATGGCTTAAG-TG
1 TAAATATG-GAAAA-TTTGATGGGTTAAGCTA
*
35162198 TAAATACT-TAAAATTTGATGGGTTAAGCTA
1 TAAATA-TGGAAAATTTGATGGGTTAAGCTA
*
35162228 TAAATATGGAAAATTTGAAGGGT
1 TAAATATGGAAAATTTGATGGGT
35162251 CAATAGTGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 13 0.30
30 24 0.55
31 6 0.14
32 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (30 bp):
TAAATATGGAAAATTTGATGGGTTAAGCTA
Found at i:35163196 original size:168 final size:168
Alignment explanation
Indices: 35162918--35163239 Score: 590
Period size: 168 Copynumber: 1.9 Consensus size: 168
35162908 TTTGACATGT
*
35162918 TAATGAAGAGGGAAATTGAGAAAGAGATTCAAGTCGTAGGAGAAGAGAAAAGTAAGAGATTTTGA
1 TAATGAAGAGGGAAATTGAGAAAGAGATTCAAGTCGTAGGAGAAGAGAAAAGCAAGAGATTTTGA
* *
35162983 TAGAAAAGAGGTAAGTACCCGTGGAGTTTTTTAATATTTAAGGATTATAATATAACATGTGAAGT
66 TAGAAAAGAGGTAAGTACCCGTGGACTTTTTTAATATTTAAGGATTATAATATAACATGTGAACT
*
35163048 AGGATATTATAATAAAATTATAATGAAGTAGGATATTA
131 AGGATATTATAATAAAAGTATAATGAAGTAGGATATTA
*
35163086 TAATGAAGAGGGAAATTGAGAAAGAGATTCAAGTGGTAGGAGAAGAGAAAAGCAAGAGATTTTGA
1 TAATGAAGAGGGAAATTGAGAAAGAGATTCAAGTCGTAGGAGAAGAGAAAAGCAAGAGATTTTGA
*
35163151 TAGAAAAGAGGTAAGTACCCGTGGACTTTTTTAATATTTAAGGATTATAATTTAACATGTGAACT
66 TAGAAAAGAGGTAAGTACCCGTGGACTTTTTTAATATTTAAGGATTATAATATAACATGTGAACT
35163216 AGGATATTATAATAAAAGTATAAT
131 AGGATATTATAATAAAAGTATAAT
35163240 AGATGTGTTA
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 148 1.00
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (168 bp):
TAATGAAGAGGGAAATTGAGAAAGAGATTCAAGTCGTAGGAGAAGAGAAAAGCAAGAGATTTTGA
TAGAAAAGAGGTAAGTACCCGTGGACTTTTTTAATATTTAAGGATTATAATATAACATGTGAACT
AGGATATTATAATAAAAGTATAATGAAGTAGGATATTA
Found at i:35167089 original size:59 final size:60
Alignment explanation
Indices: 35166994--35167116 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 60
35166984 AGCAAAATTC
*
35166994 ACTAAATTAATTAACAAATAGTCGGGATTATAATTATTTTTAAGTAAAAAGGTGGTAAAA
1 ACTAAATTAATTAACAAATACTCGGGATTATAATTATTTTTAAGTAAAAAGGTGGTAAAA
* *
35167054 ACTAAATTAATTAA-AAATTCTCGGGATTATTATTATTTTTAAGTAAAAAGGTGGTAAAA
1 ACTAAATTAATTAACAAATACTCGGGATTATAATTATTTTTAAGTAAAAAGGTGGTAAAA
35167113 ACTA
1 ACTA
35167117 CTAGAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
59 46 0.77
60 14 0.23
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.35
Consensus pattern (60 bp):
ACTAAATTAATTAACAAATACTCGGGATTATAATTATTTTTAAGTAAAAAGGTGGTAAAA
Found at i:35169466 original size:25 final size:25
Alignment explanation
Indices: 35169377--35169504 Score: 118
Period size: 25 Copynumber: 5.1 Consensus size: 25
35169367 TCATTAGGGT
* *
35169377 TACCGATTTATGGCTCGTGAA-AGCA
1 TACCGATTTATAGCTCG-AAAGAGCA
**
35169402 TACCGATTTATAGCTCGTGAGAGCA
1 TACCGATTTATAGCTCGAAAGAGCA
*
35169427 TACCAATTTATAGCTCGAAAGAGCA
1 TACCGATTTATAGCTCGAAAGAGCA
*
35169452 TACCGATCTT-CAGCTC-AAATGAGCA
1 TACCGAT-TTATAGCTCGAAA-GAGCA
* * * *
35169477 TACCGATTCACAGCTCGTATGAGCA
1 TACCGATTTATAGCTCGAAAGAGCA
35169502 TAC
1 TAC
35169505 ATGTACATGA
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
24 5 0.06
25 79 0.91
26 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (25 bp):
TACCGATTTATAGCTCGAAAGAGCA
Found at i:35171985 original size:16 final size:16
Alignment explanation
Indices: 35171964--35171995 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35171954 AAAATTTATT
*
35171964 TTAAAATATTTTAAAA
1 TTAAAAAATTTTAAAA
35171980 TTAAAAAATTTTAAAA
1 TTAAAAAATTTTAAAA
35171996 GTATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:35172003 original size:11 final size:11
Alignment explanation
Indices: 35171987--35172098 Score: 143
Period size: 11 Copynumber: 9.8 Consensus size: 11
35171977 AAATTAAAAA
35171987 ATTTTAAAAGT
1 ATTTTAAAAGT
*
35171998 ATTTTAAAAAT
1 ATTTTAAAAGT
*
35172009 ATTTTAAAAAT
1 ATTTTAAAAGT
*
35172020 ATTTTAAAATT
1 ATTTTAAAAGT
**
35172031 AAAAATTAAAAAAGT
1 ----ATTTTAAAAGT
35172046 ATTTTAAAAGT
1 ATTTTAAAAGT
35172057 ATTTTAAAAGT
1 ATTTTAAAAGT
35172068 ATTTTAAAAGT
1 ATTTTAAAAGT
35172079 ATTTTAAAAGT
1 ATTTTAAAAGT
35172090 ATTTTAAAA
1 ATTTTAAAA
35172099 TTTAAAAAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
11 82 0.91
15 8 0.09
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
ATTTTAAAAGT
Found at i:35172027 original size:59 final size:59
Alignment explanation
Indices: 35171960--35172108 Score: 205
Period size: 59 Copynumber: 2.5 Consensus size: 59
35171950 ATAAAAAATT
35171960 TATTTTAAAATATTTTAAAATTAAAAAATTTTAAAAGTATTTTAAAAATATTTTAAAAA
1 TATTTTAAAATATTTTAAAATTAAAAAATTTTAAAAGTATTTTAAAAATATTTTAAAAA
* * *
35172019 TATTTT-AAA-A-TTAAAAATTAAAAAAGTATTTTAAAAGTATTTTAAAAGTATTTTAAAAG
1 TATTTTAAAATATTTTAAAATT-AAAAA--ATTTTAAAAGTATTTTAAAAATATTTTAAAAA
35172078 TATTTTAAAAGTATTTTAAAATTTAAAAAAT
1 TATTTTAAAA-TATTTTAAAA-TTAAAAAAT
35172109 AAAAAATTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
56 8 0.10
57 6 0.08
58 3 0.04
59 42 0.54
60 3 0.04
61 2 0.03
62 1 0.01
63 11 0.14
64 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (59 bp):
TATTTTAAAATATTTTAAAATTAAAAAATTTTAAAAGTATTTTAAAAATATTTTAAAAA
Found at i:35179150 original size:26 final size:26
Alignment explanation
Indices: 35179121--35179179 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
35179111 TACCCCCAGC
* *
35179121 AAAATTTTGATAATTTTATCCT-TGGT
1 AAAATTTTGACAATTTT-GCCTCTGGT
*
35179147 AAAATTTTGACGATTTTGCCTCTGGT
1 AAAATTTTGACAATTTTGCCTCTGGT
35179173 AAAATTT
1 AAAATTT
35179180 CGAGAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.10
26 26 0.90
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (26 bp):
AAAATTTTGACAATTTTGCCTCTGGT
Found at i:35189523 original size:12 final size:13
Alignment explanation
Indices: 35189493--35189522 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
35189483 AGGGATTCAC
35189493 AAAAATATTAGTG
1 AAAAATATTAGTG
35189506 AAAAATATTAGTG
1 AAAAATATTAGTG
35189519 AAAA
1 AAAA
35189523 TTAACAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (13 bp):
AAAAATATTAGTG
Found at i:35203252 original size:109 final size:109
Alignment explanation
Indices: 35203061--35203278 Score: 436
Period size: 109 Copynumber: 2.0 Consensus size: 109
35203051 ACGGTCTCCA
35203061 TTCATTAAGGAAAAACTAGAGCATCTACTCAAGTTTTTTCCATAACCACAATTTCGGATGAATTC
1 TTCATTAAGGAAAAACTAGAGCATCTACTCAAGTTTTTTCCATAACCACAATTTCGGATGAATTC
35203126 TTCTATTCCTAACTCATCCAATAGTCCTTCTTACTCCTTTGCCC
66 TTCTATTCCTAACTCATCCAATAGTCCTTCTTACTCCTTTGCCC
35203170 TTCATTAAGGAAAAACTAGAGCATCTACTCAAGTTTTTTCCATAACCACAATTTCGGATGAATTC
1 TTCATTAAGGAAAAACTAGAGCATCTACTCAAGTTTTTTCCATAACCACAATTTCGGATGAATTC
35203235 TTCTATTCCTAACTCATCCAATAGTCCTTCTTACTCCTTTGCCC
66 TTCTATTCCTAACTCATCCAATAGTCCTTCTTACTCCTTTGCCC
35203279 AATTAGGTAT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (109 bp):
TTCATTAAGGAAAAACTAGAGCATCTACTCAAGTTTTTTCCATAACCACAATTTCGGATGAATTC
TTCTATTCCTAACTCATCCAATAGTCCTTCTTACTCCTTTGCCC
Found at i:35216645 original size:17 final size:17
Alignment explanation
Indices: 35216625--35216666 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
35216615 TCAAATTAAA
*
35216625 TTAATTCAATAATCAAT
1 TTAATTCAACAATCAAT
*
35216642 TTAATTCAACAATTAAT
1 TTAATTCAACAATCAAT
35216659 TTAATTCA
1 TTAATTCA
35216667 TGTGATAGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTCAACAATCAAT
Found at i:35224099 original size:25 final size:25
Alignment explanation
Indices: 35224018--35224101 Score: 114
Period size: 25 Copynumber: 3.4 Consensus size: 25
35224008 TATGTTCATT
* *
35224018 CGAGCTGTAAATCGATATGCTCTCA
1 CGAGCTATAAATCGGTATGCTCTCA
* * * *
35224043 CAAGCTATAAATTGGTTTGCTCTTA
1 CGAGCTATAAATCGGTATGCTCTCA
35224068 CGAGCTATAAATCGGTATGCTCTCA
1 CGAGCTATAAATCGGTATGCTCTCA
35224093 CGAGCTATA
1 CGAGCTATA
35224102 GAGTATCCGT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (25 bp):
CGAGCTATAAATCGGTATGCTCTCA
Found at i:35225530 original size:49 final size:49
Alignment explanation
Indices: 35225443--35225539 Score: 126
Period size: 49 Copynumber: 2.0 Consensus size: 49
35225433 ACTTGAACCC
*
35225443 ATGACCGTATAACCACTGCCAACTGGGGGCCCGTGTTATACT-TCAACTA
1 ATGACCGTATAACCACTGCCAACTGGGAGCCCGTGTTATA-TGTCAACTA
* * *
35225492 ATGACCGTATAACCATTGTCAACTGGGAG-CCTTAGTTATATGTCAACT
1 ATGACCGTATAACCACTGCCAACTGGGAGCCCGT-GTTATATGTCAACT
35225540 CGTGACCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 4 0.10
49 38 0.90
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (49 bp):
ATGACCGTATAACCACTGCCAACTGGGAGCCCGTGTTATATGTCAACTA
Found at i:35232246 original size:24 final size:26
Alignment explanation
Indices: 35232114--35232267 Score: 83
Period size: 25 Copynumber: 6.2 Consensus size: 26
35232104 TGAGCTCTCG
*
35232114 TATATGGCTCTTCGTGAGCTTCCCGAT
1 TATATGGCTCTTCGTGAGCTACCC-AT
* * **
35232141 TATA-GGCTCTTTGTGAGCTTCCTGT
1 TATATGGCTCTTCGTGAGCTACCCAT
* * * ** *
35232166 TA-GT-GCT-TTCTTGAACTTTCCGT
1 TATATGGCTCTTCGTGAGCTACCCAT
*
35232189 TATATGGCT-ATC-TGATGCTACCCAT
1 TATATGGCTCTTCGTGA-GCTACCCAT
*
35232214 TA-ATTGCTCTTCG-GAGCTACCCAT
1 TATATGGCTCTTCGTGAGCTACCCAT
* * *
35232238 TATA-GGCTCTTTGTGAGCTTCCCGT
1 TATATGGCTCTTCGTGAGCTACCCAT
35232263 TATAT
1 TATAT
35232268 TGCCTGGATA
Statistics
Matches: 97, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
23 13 0.13
24 30 0.31
25 33 0.34
26 17 0.18
27 4 0.04
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (26 bp):
TATATGGCTCTTCGTGAGCTACCCAT
Found at i:35232265 original size:25 final size:26
Alignment explanation
Indices: 35232114--35232267 Score: 94
Period size: 24 Copynumber: 6.2 Consensus size: 26
35232104 TGAGCTCTCG
*
35232114 TATATGGCTCTTCGTGAGCTTCCCGAT
1 TATATGGCTCTTTGTGAGCTTCCCG-T
*
35232141 TATA-GGCTCTTTGTGAGCTTCCTGT
1 TATATGGCTCTTTGTGAGCTTCCCGT
* * *
35232166 TA-GT-GCT-TTCT-TGAACTTTCCGT
1 TATATGGCTCTT-TGTGAGCTTCCCGT
* * * *
35232189 TATATGG--CTATCTGATGCTACCCAT
1 TATATGGCTCTTTGTGA-GCTTCCCGT
* * * *
35232214 TA-ATTGCTCTTCG-GAGCTACCCAT
1 TATATGGCTCTTTGTGAGCTTCCCGT
35232238 TATA-GGCTCTTTGTGAGCTTCCCGT
1 TATATGGCTCTTTGTGAGCTTCCCGT
35232263 TATAT
1 TATAT
35232268 TGCCTGGATA
Statistics
Matches: 95, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
23 14 0.15
24 30 0.32
25 27 0.28
26 20 0.21
27 4 0.04
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (26 bp):
TATATGGCTCTTTGTGAGCTTCCCGT
Found at i:35236573 original size:25 final size:25
Alignment explanation
Indices: 35236545--35236593 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
35236535 TACATTGATC
35236545 CATTCACATTATG-ATAACA-TAATAA
1 CATTCA-ATT-TGAATAACATTAATAA
35236570 CATTCAATTTGAATAACATTAATA
1 CATTCAATTTGAATAACATTAATA
35236594 CAATAACTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.09
24 9 0.41
25 11 0.50
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (25 bp):
CATTCAATTTGAATAACATTAATAA
Found at i:35246766 original size:15 final size:14
Alignment explanation
Indices: 35246718--35246755 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
35246708 ATATATTCAA
35246718 ATATATTTT-AAAT
1 ATATATTTTAAAAT
35246731 A-AT-TTTTAAAAT
1 ATATATTTTAAAAT
35246743 ATATATTTTAAAA
1 ATATATTTTAAAA
35246756 CTGATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.18
12 7 0.32
13 3 0.14
14 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATTTTAAAAT
Found at i:35246891 original size:8 final size:8
Alignment explanation
Indices: 35246878--35246902 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35246868 TTTTCTATAA
35246878 TACATTTT
1 TACATTTT
35246886 TACATTTT
1 TACATTTT
35246894 TACATTTT
1 TACATTTT
35246902 T
1 T
35246903 GATAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TACATTTT
Found at i:35248735 original size:17 final size:18
Alignment explanation
Indices: 35248702--35248735 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35248692 ACAAGATAGA
*
35248702 AAATAAAAAAGGAAAAAC
1 AAATAAAAAAGAAAAAAC
35248720 AAAT-AAAAAGAAAAAA
1 AAATAAAAAAGAAAAAA
35248736 ATGAACAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.03, G:0.09, T:0.06
Consensus pattern (18 bp):
AAATAAAAAAGAAAAAAC
Found at i:35249729 original size:100 final size:100
Alignment explanation
Indices: 35249614--35249886 Score: 420
Period size: 100 Copynumber: 2.7 Consensus size: 100
35249604 AAACAAGATT
* * *
35249614 CGCCGCCGTGACTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
1 CGCCGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
35249679 AATCTTTTAAATTACAATGCCGGGGAAACCAGAGC
66 AATCTTTTAAATTACAATGCCGGGGAAACCAGAGC
* * * * * *
35249714 CGCCGTCGTGGCTTCAATCTGCTCTACTACACCACTAGGGAAGTAAAATCTGCCGTTGTGGCTTC
1 CGCCGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
* * * *
35249779 AATCTTTTTAATTGCAATGTCGGGGAAACCAGATC
66 AATCTTTTAAATTACAATGCCGGGGAAACCAGAGC
*
35249814 CGCCGTTGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
1 CGCCGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
35249879 AATCTTTT
66 AATCTTTT
35249887 CCACTGTAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 153 1.00
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (100 bp):
CGCCGTCGTGGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTC
AATCTTTTAAATTACAATGCCGGGGAAACCAGAGC
Found at i:35249889 original size:50 final size:50
Alignment explanation
Indices: 35249625--35249891 Score: 255
Period size: 50 Copynumber: 5.3 Consensus size: 50
35249615 GCCGCCGTGA
*
35249625 CTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
** * ** * *** * *
35249675 CTTCAATCTTTTAAATTACAATGCCGGGGAAACCAGAGCCGCCGTCGTGG
1 CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
** * * * * *
35249725 CTTCAATCTGCTCTACTACACCACTAGGGAAGTAAAATCTGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
** * * ** * * ***
35249775 CTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
*
35249825 CTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
35249875 CTTCAATCTTTTCCACT
1 CTTCAATCTTTTCCACT
35249892 GTAATGCTAA
Statistics
Matches: 158, Mismatches: 59, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 158 1.00
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
CTTCAATCTTTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGG
Found at i:35250234 original size:88 final size:88
Alignment explanation
Indices: 35250085--35250399 Score: 459
Period size: 88 Copynumber: 3.6 Consensus size: 88
35250075 AGGACTGATG
* * * ** * * *
35250085 TCTTCGATCTACTTCGCTGCCAGTACAAAAAGGCAAGATCTGCCATTTTCGACCTACTCCACTGC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
35250150 TGCCCAGAGAGACAAGGCTGGTA
66 TGCCCAGAGAGACAAGGCTGGTA
*
35250173 TCTTCGATCTGCTTCTTTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
* * *
35250238 TGCCTAGGGAGACAAGGCTGTTA
66 TGCCCAGAGAGACAAGGCTGGTA
* **
35250261 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCTATTTTCAACCCGCTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
35250326 TGCCCAGAGAGACAAGGCTGGTA
66 TGCCCAGAGAGACAAGGCTGGTA
* * * *
35250349 TCTTCCATCTGCTTCTCTATCAGTACAGGAAGGCAAGATCTGTTATCTTCA
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCA
35250400 GTCTGCTCTG
Statistics
Matches: 203, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 203 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTAC
TGCCCAGAGAGACAAGGCTGGTA
Found at i:35255208 original size:27 final size:27
Alignment explanation
Indices: 35255152--35255208 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
35255142 AATGATGTAG
* *
35255152 AAAAAGAATAAAAGAATAATTACTCGA
1 AAAAAGAATAAAAGAATAATGACTCAA
* *
35255179 AAAAAGAATAAAAGAATACTGGCTCAA
1 AAAAAGAATAAAAGAATAATGACTCAA
35255206 AAA
1 AAA
35255209 TGCATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.63, C:0.09, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAAAGAATAAAAGAATAATGACTCAA
Found at i:35263296 original size:17 final size:16
Alignment explanation
Indices: 35263268--35263305 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
35263258 AACAAGATAG
35263268 AAAATAAAAAAGGAAAA
1 AAAATAAAAAA-GAAAA
35263285 ACAAAT-AAAAAGAAAA
1 A-AAATAAAAAAGAAAA
35263301 AAAAT
1 AAAAT
35263306 GAACAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 6 0.30
18 4 0.20
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (16 bp):
AAAATAAAAAAGAAAA
Found at i:35265784 original size:27 final size:25
Alignment explanation
Indices: 35265740--35265793 Score: 63
Period size: 27 Copynumber: 2.1 Consensus size: 25
35265730 TACCTTTTTA
**
35265740 TTAATTTTATATTTTTTAATTTTTATT
1 TTAATTTTATATAATTT-A-TTTTATT
*
35265767 TTAATTTTCTATAATTTATTTTATT
1 TTAATTTTATATAATTTATTTTATT
35265792 TT
1 TT
35265794 TTTTACTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
26 1 0.04
27 14 0.58
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (25 bp):
TTAATTTTATATAATTTATTTTATT
Found at i:35265785 original size:36 final size:34
Alignment explanation
Indices: 35265696--35265798 Score: 97
Period size: 35 Copynumber: 3.0 Consensus size: 34
35265686 AGGTCATAGA
* *
35265696 TAATTTTCTAGAATTTTTTATTTTTTATTTTTAT
1 TAATTTTCTATAATTTTATATTTTTTATTTTTAT
*
35265730 TACCTTTT-TATTAATTTTATATTTTTTAATTTTTATTT
1 TA-ATTTTCTA-TAATTTTATATTTTTT-ATTTTTA--T
35265768 TAATTTTCTATAA-TTTAT-TTTATTT-TTTTTA
1 TAATTTTCTATAATTTTATATTT-TTTATTTTTA
35265799 CTTTTCTAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
34 10 0.17
35 21 0.36
36 15 0.26
37 7 0.12
38 5 0.09
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (34 bp):
TAATTTTCTATAATTTTATATTTTTTATTTTTAT
Found at i:35265979 original size:9 final size:10
Alignment explanation
Indices: 35265936--35266011 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
35265926 TTCTATAAAT
35265936 TTTTTTATAA
1 TTTTTTATAA
***
35265946 TTTTAGGTAA
1 TTTTTTATAA
35265956 TTTTTTATAA
1 TTTTTTATAA
*
35265966 TTTTTTATGA
1 TTTTTTATAA
*
35265976 TTTTGTATTAA
1 TTTTTTA-TAA
* *
35265987 ATTTTAATAA
1 TTTTTTATAA
* *
35265997 TCATTTTATTA
1 T-TTTTTATAA
35266008 TTTT
1 TTTT
35266012 CTATTTTTTT
Statistics
Matches: 47, Mismatches: 17, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
10 34 0.72
11 13 0.28
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.64
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:35270566 original size:22 final size:22
Alignment explanation
Indices: 35270543--35270585 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35270533 ATAAACTAAT
35270543 AATAATACAGTAATAATAATATA
1 AATAA-ACAGTAATAATAATATA
* *
35270566 AATAAACAGTATTAGTAATA
1 AATAAACAGTAATAATAATA
35270586 AAAAATTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (22 bp):
AATAAACAGTAATAATAATATA
Found at i:35279183 original size:19 final size:20
Alignment explanation
Indices: 35279160--35279204 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35279150 TTTTGTTCCA
* *
35279160 ATTTTTT-ATT-TTTAATTT
1 ATTTTTTAATTATTAAATAT
35279178 ATTTTTTAATTATTAAATAT
1 ATTTTTTAATTATTAAATAT
35279198 ATTTTTT
1 ATTTTTT
35279205 GAAGTATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 3 0.13
20 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTTAATTATTAAATAT
Found at i:35289517 original size:16 final size:16
Alignment explanation
Indices: 35289496--35289564 Score: 95
Period size: 16 Copynumber: 4.3 Consensus size: 16
35289486 TTGGTTCGCT
35289496 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGAC
*
35289512 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGAC
35289528 GTAATGGAATAGA-AGC
1 GTAATGGAATAGAGA-C
* *
35289544 GTAATTGAATAGAGGC
1 GTAATGGAATAGAGAC
35289560 GTAAT
1 GTAAT
35289565 AGCAATTCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGAC
Found at i:35289532 original size:32 final size:32
Alignment explanation
Indices: 35289496--35289564 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
35289486 TTGGTTCGCT
35289496 GTAATGGAATAG-AGACGTAATGGAATAGAGGC
1 GTAATGGAATAGAAG-CGTAATGGAATAGAGGC
*
35289528 GTAATGGAATAGAAGCGTAATTGAATAGAGGC
1 GTAATGGAATAGAAGCGTAATGGAATAGAGGC
35289560 GTAAT
1 GTAAT
35289565 AGCAATTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.41, C:0.06, G:0.32, T:0.22
Consensus pattern (32 bp):
GTAATGGAATAGAAGCGTAATGGAATAGAGGC
Found at i:35289603 original size:45 final size:44
Alignment explanation
Indices: 35289544--35289640 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
35289534 GAATAGAAGC
*
35289544 GTAATTGAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* * *
35289589 GTAATGGAATAGAGGTGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
35289633 GGAATGGA
1 GTAATGGA
35289641 GGTGTAATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.52
45 21 0.46
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:35289818 original size:18 final size:17
Alignment explanation
Indices: 35289797--35289831 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35289787 TTATTATTAA
*
35289797 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35289815 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35289832 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:35291692 original size:4 final size:4
Alignment explanation
Indices: 35291683--35291717 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
35291673 GATGTTTATA
*
35291683 TATG TATG TATG TATG TATG TATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
35291718 TTGGTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:35292753 original size:46 final size:46
Alignment explanation
Indices: 35292686--35292778 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
35292676 CCTCAAAGAA
*
35292686 CAAAGACTTGCAATCAGAAACTATTAGGCTTCACAGAATAAACTTT
1 CAAAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTT
*
35292732 CAAAGACTTGCAATCAGAAACTATGATGCTTCACAGAATAAACTTT
1 CAAAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTT
35292778 C
1 C
35292779 TAGGATACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (46 bp):
CAAAGACTTGCAATCAGAAACTATGAGGCTTCACAGAATAAACTTT
Found at i:35293790 original size:17 final size:17
Alignment explanation
Indices: 35293769--35293822 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
35293759 AAAAATAAAT
35293769 TAAAAA-ACAAAATTTA
1 TAAAAATACAAAATTTA
* *
35293785 TAAAAATTTCAAAATATA
1 TAAAAA-TACAAAATTTA
* *
35293803 TAATATTACAAAATTTA
1 TAAAAATACAAAATTTA
35293820 TAA
1 TAA
35293823 TAAGATTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 6 0.20
17 12 0.40
18 12 0.40
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAATACAAAATTTA
Found at i:35293823 original size:17 final size:17
Alignment explanation
Indices: 35293775--35293824 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
35293765 AAATTAAAAA
*
35293775 ACAAAATTTATAAAAATT
1 ACAAAATTTAT-AATATT
* *
35293793 TCAAAATATATAATATT
1 ACAAAATTTATAATATT
35293810 ACAAAATTTATAATA
1 ACAAAATTTATAATA
35293825 AGATTGTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
ACAAAATTTATAATATT
Found at i:35298987 original size:43 final size:43
Alignment explanation
Indices: 35298926--35299195 Score: 416
Period size: 43 Copynumber: 6.3 Consensus size: 43
35298916 TTATGTAAAA
* **
35298926 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* *
35298969 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTCACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
*
35299012 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* *
35299055 AAACGCTGCTAAAGAACATCACCTTTAGCGGCGCTTTACACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTAC-CCAC
*
35299099 AAACGCCGCTAAAGAACATGACATTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
* * *
35299142 AAATGCCGCTAAAGAACATGATCTTTAGCGGTGCTTTA-CCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
35299184 AAACGCCGCTAA
1 AAACGCCGCTAA
35299196 TTTTGACAAA
Statistics
Matches: 209, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
42 15 0.07
43 154 0.74
44 40 0.19
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
Found at i:35299134 original size:87 final size:87
Alignment explanation
Indices: 35298926--35299195 Score: 411
Period size: 87 Copynumber: 3.1 Consensus size: 87
35298916 TTATGTAAAA
* **
35298926 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTACCCACAAACGCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAC
* *
35298991 CTTTAGCAGCGCTTCAC-CCAC
66 CTTTAGCGGCGCTTTACACCAC
* * *
35299012 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCACCCACAAACGCTGCTAAAGAACATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAC
35299077 CTTTAGCGGCGCTTTACACCAC
66 CTTTAGCGGCGCTTTACACCAC
* * *
35299099 AAACGCCGCTAAAGAACATGACATTTAGCGGCGCTTTACCCACAAATGCCGCTAAAGAACATGAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAC
*
35299164 CTTTAGCGGTGCTTT--ACCAC
66 CTTTAGCGGCGCTTTACACCAC
35299184 AAACGCCGCTAA
1 AAACGCCGCTAA
35299196 TTTTGACAAA
Statistics
Matches: 168, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 17 0.10
86 74 0.44
87 77 0.46
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (87 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTACACCAC
Found at i:35299158 original size:130 final size:128
Alignment explanation
Indices: 35298926--35299195 Score: 414
Period size: 130 Copynumber: 2.1 Consensus size: 128
35298916 TTATGTAAAA
* * *
35298926 AAACGTCGCTAAAGAACATGACCTTTAGCGGCATTTTACCCACAAACGCCGCTAAAGAACATGAC
1 AAACGCCGCTAAAGAACATCACCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAACATGAC
*
35298991 CTTTAGCAGCGCTTCACCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCACCCAC
66 ATTTAGCAGCGCTTCACCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCA-CCAC
* *
35299055 AAACGCTGCTAAAGAACATCACCTTTAGCGGCGCTTTACACCACAAACGCCGCTAAAGAACATGA
1 AAACGCCGCTAAAGAACATCACCTTTAGCGGCACTTTAC-CCACAAACGCCGCTAAAGAACATGA
* * * * * *
35299120 CATTTAGCGGCGCTTTACCCACAAATGCCGCTAAAGAACATGATCTTTAGCGGTGCTTTACCAC
65 CATTTAGCAGCGCTTCACCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCACCAC
35299184 AAACGCCGCTAA
1 AAACGCCGCTAA
35299196 TTTTGACAAA
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
129 49 0.39
130 78 0.61
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.20
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATCACCTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAACATGAC
ATTTAGCAGCGCTTCACCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTCACCAC
Found at i:35309577 original size:10 final size:10
Alignment explanation
Indices: 35309562--35309589 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
35309552 CTTTCATCAG
35309562 TGTACTTCGA
1 TGTACTTCGA
35309572 TGTACTTCGA
1 TGTACTTCGA
35309582 TGTACTTC
1 TGTACTTC
35309590 TGAACTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (10 bp):
TGTACTTCGA
Found at i:35315364 original size:10 final size:10
Alignment explanation
Indices: 35315349--35315378 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
35315339 GAAAGCTTTA
35315349 ATTTAAAATT
1 ATTTAAAATT
35315359 ATTTAAAATT
1 ATTTAAAATT
35315369 ATTTAAAATT
1 ATTTAAAATT
35315379 GTATGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:35319635 original size:47 final size:48
Alignment explanation
Indices: 35319577--35319675 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
35319567 CATAGTTTTG
*
35319577 TTTAAGTAATATTTATAAAAATTAGATAAAATTATAAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
35319624 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
35319672 TTTA
1 TTTA
35319676 TTTTTTTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
Found at i:35320730 original size:7 final size:7
Alignment explanation
Indices: 35320720--35320758 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
35320710 CTCTAACTCT
35320720 TAACCCC
1 TAACCCC
**
35320727 TAACATC
1 TAACCCC
35320734 TAACCCC
1 TAACCCC
35320741 TAAACCCC
1 T-AACCCC
35320749 TAACCCC
1 TAACCCC
35320756 TAA
1 TAA
35320759 ACCTTCAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (7 bp):
TAACCCC
Found at i:35320732 original size:318 final size:313
Alignment explanation
Indices: 35319975--35320899 Score: 1297
Period size: 318 Copynumber: 2.9 Consensus size: 313
35319965 TAAATTATAC
*
35319975 ATCTTTTACAATTACATAAGAACATATTTAAAATATAAATAAAAAATTAATCTAAACCCAAAACC
1 ATCTTTTACAATTACATAATAACATATTTAAAATATAAAT-AAAAA-TAATCTAAACCCAAAACC
* * *
35320040 CTAACCCGACCCTTGAAACCCTAAATCCTAAATCCCTAACTCTTAACCACTAACGTCTAACCCCT
64 CTAACCCGACCCTTGAAACCATAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCT
* *
35320105 AAACCCCTAACCCTTAAACCTTAAATCTCGACCAACCCTTAATTAAACCGTAATCCCTAATCTAT
129 AAACCCCTAACCCTTAAACCTTAAATC-CG-CCAACCCTTAATTAAACCATAATCCCTAATCCAT
* * * *
35320170 AATCCCTAAATCCATATATATATAGTACTCCCTAAACCTTTAAATATGAACTCCTAAACCAGCAT
192 AATCCCT-AA-CTAAATATATATA-TACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCAT
35320235 TAAATCTT-AA-TTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
254 TAAATCTTAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
*
35320293 ATCTTTTACAACTACATAATAACATATTTAAAATATAAATAAAAAAATTAATCTAAACCCAAAAC
1 ATCTTTTACAATTACATAATAACATATTTAAAATATAAAT--AAAAA-TAATCTAAACCCAAAAC
* * * *
35320358 CCTATCCCGACCCTTGAAACCTTAAACCCTAAATCCCTAACCCTTAACCACTAACATCTAACTCC
63 CCTAACCCGACCCTTGAAACCATAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCC
35320423 TAAACCCCTAACCCTTAAACCTTAAATCCAGGCCAACCCTTAATTAAACCATAATCCCTAATCCA
128 TAAACCCCTAACCCTTAAACCTTAAATCC--GCCAACCCTTAATTAAACCATAATCCCTAATCCA
* ** * *
35320488 TAATCCCTAGCTAAATCCATATATACTACCTAAACCTTAAAATATGAACTCCTAGACCGGCATTA
191 TAATCCCTAACTAAATATATATATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCATTA
35320553 AATCTTAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
256 AATCTTAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
35320611 ATCTCTTTTACAATAATTACATAATAACATATTTAAAATATAAAT-AAAA-AATCTAAACCCAAA
1 A--TCTTTTAC---AATTACATAATAACATATTTAAAATATAAATAAAAATAATCTAAACCCAAA
* * * * * *
35320674 ACCCTAACTCGACCCCT-AAATTCATAAACCCCAAATCTCTAACTCTTAACCCCTAACATCTAAC
61 ACCCTAACCCGACCCTTGAAA-CCATAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAAC
* *
35320738 CCCTAAACCCCTAACCCCTAAACCTTCAAT-C-CCAACCCTTAATTAAACCATAATCCCTAATCC
125 CCCTAAACCCCTAACCCTTAAACCTTAAATCCGCCAACCCTTAATTAAACCATAATCCCTAATCC
* ** * * *
35320801 ATAATCCCTAAATCCATATATATATACTCCCTAAAACCTTAAAATATGAACTCTTAAACCGACCT
190 ATAATCCCTAACTAAATATATATATACTCCCT-AAACCTTAAAATATGAACTCCTAAACCGGCAT
**
35320866 TAAATCTTAAATAAAATCATATACCCTAAACTAA
254 TAAATCTTAAAT-TTATCATATACCCTAAACTAA
35320900 AAACCATAAA
Statistics
Matches: 549, Mismatches: 45, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
314 57 0.10
315 40 0.07
316 63 0.11
317 15 0.03
318 181 0.33
319 150 0.27
320 13 0.02
323 30 0.05
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (313 bp):
ATCTTTTACAATTACATAATAACATATTTAAAATATAAATAAAAATAATCTAAACCCAAAACCCT
AACCCGACCCTTGAAACCATAAACCCTAAATCCCTAACTCTTAACCACTAACATCTAACCCCTAA
ACCCCTAACCCTTAAACCTTAAATCCGCCAACCCTTAATTAAACCATAATCCCTAATCCATAATC
CCTAACTAAATATATATATACTCCCTAAACCTTAAAATATGAACTCCTAAACCGGCATTAAATCT
TAAATTTATCATATACCCTAAACTAATTAAAAACCCTAAACAATTTTATTATT
Found at i:35320753 original size:15 final size:15
Alignment explanation
Indices: 35320720--35320761 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
35320710 CTCTAACTCT
**
35320720 TAACCCCT-AACATC
1 TAACCCCTAAACCCC
35320734 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
35320749 TAACCCCTAAACC
1 TAACCCCTAAACC
35320762 TTCAATCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.17
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Found at i:35320816 original size:15 final size:15
Alignment explanation
Indices: 35320781--35320818 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
35320771 AACCCTTAAT
35320781 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
35320795 T-AATCCATAATCCC
1 TAAATCCATAATCCC
35320809 TAAATCCATA
1 TAAATCCATA
35320819 TATATATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:35321848 original size:31 final size:29
Alignment explanation
Indices: 35321813--35321890 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
35321803 CTAACGGCTC
* *
35321813 AGTGACTAAAATGTTACGACATGATAACATA
1 AGTGACTAAAATGTAAC-ACATCA-AACATA
* **
35321844 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACATCAAACATA
35321873 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
35321891 TGAACCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.56
30 3 0.07
31 15 0.37
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACATCAAACATA
Found at i:35321907 original size:31 final size:29
Alignment explanation
Indices: 35321838--35321911 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
35321828 ACGACATGAT
**
35321838 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATACCA
*
35321867 AACATAAGTGACTAAAATGTAACATGAACCA
1 AACATAAGTGACTAAAACGTAACAT--ACCA
*
35321898 AACAAAAGTGACTA
1 AACATAAGTGACTA
35321912 TTTTAGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATACCA
Found at i:35322017 original size:41 final size:41
Alignment explanation
Indices: 35321972--35322413 Score: 514
Period size: 41 Copynumber: 10.8 Consensus size: 41
35321962 GTGTTTTAAC
* *
35321972 AAAAACGACGCTAAAACCCCGAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * * *
35322013 AAAAACGCTGCTAAAACCCCGAGCATTAGCAGTGCTT-TTCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTT-A
* * *
35322054 GAAAATGCCGCTAAAACCCCGAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * * *
35322095 GAAAACGCTGCTAAAACCCAGAGCATTAGTGGCGCTTTTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * *
35322136 GAAAACGCCGCTAAAACCTAGAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
*
35322177 GAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* *
35322218 AAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTT-TCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * * * *
35322258 CAAAAACACCGCTAAAACCAAGAGCATTAGTGACACTTCTTA
1 -AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * *
35322300 AAAAACGCTGCTAAAACCCCGAGCATTAGCGGCGCTT-TCA
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
* * * * * *
35322340 CAAAAATGTCGGTAAAACCCAAAGAATTAGCGGTGCTTTCTT-
1 -AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGC-TTCTTA
*
35322382 AAAAACGCCGCTAAAACCCTGAGCATTAGCGG
1 AAAAACGCCGCTAAAACCCAGAGCATTAGCGG
35322414 TAATTTCTCA
Statistics
Matches: 342, Mismatches: 52, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
40 6 0.02
41 329 0.96
42 6 0.02
43 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAACCCAGAGCATTAGCGGCGCTTCTTA
Found at i:35325896 original size:25 final size:25
Alignment explanation
Indices: 35325826--35325894 Score: 106
Period size: 23 Copynumber: 2.8 Consensus size: 25
35325816 AAAACTCTTC
*
35325826 TAAAAGAAAACTCAAGAGAAATTCT
1 TAAAAAAAAACTCAAGAGAAATTCT
35325851 T-AAAAAAAA-TCAAGAGAAATTCT
1 TAAAAAAAAACTCAAGAGAAATTCT
35325874 TAAAAAAAAACTCAAAGAGAA
1 TAAAAAAAAACTC-AAGAGAA
35325895 TTTTACTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 15 0.38
24 15 0.38
25 3 0.08
26 7 0.17
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (25 bp):
TAAAAAAAAACTCAAGAGAAATTCT
Found at i:35326113 original size:8 final size:8
Alignment explanation
Indices: 35326100--35326133 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
35326090 CAAAATTCAG
35326100 AATAATAA
1 AATAATAA
35326108 AATAATAA
1 AATAATAA
35326116 AATAATAA
1 AATAATAA
35326124 AATAATAA
1 AATAATAA
35326132 AA
1 AA
35326134 CTTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:35329620 original size:20 final size:20
Alignment explanation
Indices: 35329595--35329635 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35329585 CACTATTGTC
35329595 ACTTCATTTCATACTTATTG
1 ACTTCATTTCATACTTATTG
35329615 ACTTCATTTCATACTTATTG
1 ACTTCATTTCATACTTATTG
35329635 A
1 A
35329636 ACTCAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.49
Consensus pattern (20 bp):
ACTTCATTTCATACTTATTG
Found at i:35330324 original size:29 final size:29
Alignment explanation
Indices: 35330259--35330327 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
35330249 TACAGAGATG
* *
35330259 CATTGAAGTGCAATAAGAAAACAAAGTGA
1 CATTGAAGTGCAATAACAAAACAAAATGA
** * *
35330288 TGTCGAAGTGCAATACCAAAACAAAATGA
1 CATTGAAGTGCAATAACAAAACAAAATGA
35330317 CATTGAAGTGC
1 CATTGAAGTGC
35330328 TTTAGCAGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.19
Consensus pattern (29 bp):
CATTGAAGTGCAATAACAAAACAAAATGA
Found at i:35331772 original size:42 final size:42
Alignment explanation
Indices: 35331648--35331961 Score: 377
Period size: 42 Copynumber: 7.4 Consensus size: 42
35331638 ACGTCGCTAA
* *
35331648 CTTTTGCGGCGCTTATAGAAAAAAATGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAT-G-AAAAAACGCCGCTAAAGATCATGTT
* * *
35331692 CTTTAGCGGCACTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAA-AAACGCCGCTAAAGATCATGTT
35331735 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
*
35331777 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
*
35331819 CTTTAGCGGCACTT-TGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAT-GAAAAAACGCCGCTAAAGATCATGTT
* * *
35331861 CTTTAGCGACGCTT-TGGAAGAAAACGCCACTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT-GAA-AAAACGCCGCTAAAGA-TCATGTT
* * ** *
35331904 CTATAGCGGCGCTTGTTCAAAAACGCCGTTAACAG-T-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TGTT
35331946 CTTTAGCGGCGCTTAT
1 CTTTAGCGGCGCTTAT
35331962 TTCACAAACG
Statistics
Matches: 239, Mismatches: 23, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
41 1 0.00
42 153 0.64
43 72 0.30
44 13 0.05
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:35331809 original size:127 final size:127
Alignment explanation
Indices: 35331648--35331955 Score: 394
Period size: 127 Copynumber: 2.4 Consensus size: 127
35331638 ACGTCGCTAA
* *
35331648 CTTTTGCGGCGCTTATAGAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAAT
1 CTTTAGCGGCGC-T-TAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAA-
* * *
35331713 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT-GAA-AAAACGCCGCT-AAAGATCATG
63 AAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTT-TGGAAGAAAACGCCACTAAAAG-TAATG
35331775 TT
126 TT
* **
35331777 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTGGAAAAAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAAAAA
35331842 CGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTGGAAGAAAACGCCACTAAAAGTAATGTT
66 CGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTGGAAGAAAACGCCACTAAAAGTAATGTT
* ** *
35331904 CTATAGCGGCGCTT-GTTCAAAAACGCCGTTAACAG-T-AGTGTTCTTTAGCGGC
1 CTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGC
35331956 GCTTATTTCA
Statistics
Matches: 161, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
125 1 0.01
126 40 0.25
127 102 0.63
128 7 0.04
129 11 0.07
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (127 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAAAAA
CGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTGGAAGAAAACGCCACTAAAAGTAATGTT
Found at i:35331841 original size:85 final size:84
Alignment explanation
Indices: 35331648--35331960 Score: 384
Period size: 85 Copynumber: 3.7 Consensus size: 84
35331638 ACGTCGCTAA
* * * * *
35331648 CTTTTGCGGCGCTTATAGAAAAAAATGCCGCTAAAGATCATGTTCTTTAGCGGCACTAAGGAAAT
1 CTTTAGCGGCGCTT-T-GGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-
35331713 AAACGCCGCTAAAGATCATGTT
63 AAACGCCGCTAAAGATCATGTT
35331735 CTTTAGCGGCGCTTAT-GAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
1 CTTTAGCGGCGCTT-TGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAA
35331799 ACGCCGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTT
* * *
35331819 CTTTAGCGGCACTTTGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTTGGAAGAAA
1 CTTTAGCGGCGCTTTGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-AAA
* *
35331884 ACGCCACTAAA-AGTAATGTT
65 ACGCCGCTAAAGA-TCATGTT
* ** *
35331904 CTATAGCGGCGC-TTGTTCAAAAACGCCGTTAACAG-T-AGTGTTCTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTTG-GAAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTA
35331961 TTTCACAAAC
Statistics
Matches: 203, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
83 1 0.00
84 83 0.41
85 102 0.50
86 2 0.01
87 15 0.07
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (84 bp):
CTTTAGCGGCGCTTTGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
CGCCGCTAAAGATCATGTT
Found at i:35332466 original size:33 final size:33
Alignment explanation
Indices: 35332394--35332475 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
35332384 TCTTTTGAAC
* * *
35332394 CTCTGCTTCTATCGCTGCTTCTCTCACTGCTAT
1 CTCTGCTTCTCTCGCTACTTCTCTCACTGCTAG
*
35332427 CGCTGCTTCTCTCGCTACTTCTCTCACTGC-AGG
1 CTCTGCTTCTCTCGCTACTTCTCTCACTGCTA-G
35332460 CTCTGCTTCTCTCGCT
1 CTCTGCTTCTCTCGCT
35332476 GTAGCCTCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.07, C:0.39, G:0.15, T:0.39
Consensus pattern (33 bp):
CTCTGCTTCTCTCGCTACTTCTCTCACTGCTAG
Found at i:35332468 original size:21 final size:21
Alignment explanation
Indices: 35332444--35332509 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
35332434 TCTCTCGCTA
* *
35332444 CTTCTCTCACTGCAGGCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
*
35332465 CTTCTCTCGCTGTAGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
* *
35332486 CTTCCCTCGCTGCCGCCTCTG
1 CTTCTCTCGCTGCAGCCTCTG
35332507 CTT
1 CTT
35332510 TAAGTTGTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.05, C:0.42, G:0.18, T:0.35
Consensus pattern (21 bp):
CTTCTCTCGCTGCAGCCTCTG
Found at i:35337978 original size:7 final size:7
Alignment explanation
Indices: 35337968--35338013 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
35337958 TGATATATTT
35337968 TTATGTA
1 TTATGTA
35337975 TTATGTAA
1 TTATGT-A
35337983 GTTATGTAA
1 -TTATGT-A
35337992 GTTATGTA
1 -TTATGTA
35338000 TTATGTA
1 TTATGTA
35338007 TTATGTA
1 TTATGTA
35338014 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:35337989 original size:9 final size:9
Alignment explanation
Indices: 35337975--35338307 Score: 325
Period size: 9 Copynumber: 36.8 Consensus size: 9
35337965 TTTTTATGTA
35337975 TTATGTAAG
1 TTATGTAAG
35337984 TTATGTAAG
1 TTATGTAAG
35337993 TTATGT-A-
1 TTATGTAAG
35338000 TTATGT-A-
1 TTATGTAAG
35338007 TTATGTAAG
1 TTATGTAAG
35338016 -TACTGTAAG
1 TTA-TGTAAG
*
35338025 TAATGTAAG
1 TTATGTAAG
* *
35338034 TTATTTAAT
1 TTATGTAAG
*
35338043 TTATGTAGG
1 TTATGTAAG
35338052 TTATGTAAG
1 TTATGTAAG
* * * *
35338061 TCCACGGAAT
1 T-TATGTAAG
35338071 TTATGTAAG
1 TTATGTAAG
35338080 TTATGTAAG
1 TTATGTAAG
* *
35338089 TTATTTAAT
1 TTATGTAAG
35338098 TTATGTAAG
1 TTATGTAAG
35338107 TTATGTAAG
1 TTATGTAAG
* *
35338116 TTATTTAAT
1 TTATGTAAG
*
35338125 TTATGTAGG
1 TTATGTAAG
35338134 TTATGTAAG
1 TTATGTAAG
35338143 TTATGTAAG
1 TTATGTAAG
* *
35338152 TTATTTAAT
1 TTATGTAAG
*
35338161 TTATGCAAG
1 TTATGTAAG
35338170 TTTATGTAAG
1 -TTATGTAAG
35338180 TTATGTAAG
1 TTATGTAAG
* *
35338189 TTATTTAAT
1 TTATGTAAG
*
35338198 TTATGTAGG
1 TTATGTAAG
35338207 TTATGTAAG
1 TTATGTAAG
* *
35338216 TTATTTAAT
1 TTATGTAAG
*
35338225 TTATGTAGG
1 TTATGTAAG
35338234 TTATGTAAG
1 TTATGTAAG
35338243 TTATGTAAG
1 TTATGTAAG
* *
35338252 TTATTTAAT
1 TTATGTAAG
*
35338261 TTATGCAAG
1 TTATGTAAG
35338270 TTTATGTAAG
1 -TTATGTAAG
*
35338280 TTATGCAAG
1 TTATGTAAG
*
35338289 CTTATATACAAG
1 -TTATGT--AAG
35338301 TTATGTA
1 TTATGTA
35338308 TTATAACATA
Statistics
Matches: 260, Mismatches: 54, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
7 13 0.05
8 4 0.02
9 209 0.80
10 26 0.10
11 5 0.02
12 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:35338147 original size:100 final size:100
Alignment explanation
Indices: 35337975--35338293 Score: 398
Period size: 100 Copynumber: 3.2 Consensus size: 100
35337965 TTTTTATGTA
* * * * *
35337975 TTATGTAAGTTATGTAAGTTATGT-A-TTATGT-A-TTATGTAAG-TACTGTAAGTAATGTAAGT
1 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTA-TTTAATTTATGTAGGT
* * * *
35338035 TATTTAATTTATGTAGGTTATGTAAGTCCACGGAA-T
65 TATGTAAGTTATGTAAGTTATGTAA-TCCACGCAAGT
35338071 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTT
1 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTT
* ** *
35338136 ATGTAAGTTATGTAAGTTATTTAATTTATGCAAGT
66 ATGTAAGTTATGTAAGTTATGTAATCCACGCAAGT
*
35338171 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTTATGTAAGTTATTTAATTTATGTAGGTT
1 TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTT
* ** *
35338236 ATGTAAGTTATGTAAGTTATTTAATTTATGCAAGT
66 ATGTAAGTTATGTAAGTTATGTAATCCACGCAAGT
*
35338271 TTATGTAAGTTATGCAAGCTTAT
1 TTATGTAAGTTATGTAAG-TTAT
35338294 ATACAAGTTA
Statistics
Matches: 201, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
96 23 0.11
97 1 0.00
98 6 0.03
99 6 0.03
100 159 0.79
101 6 0.03
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.48
Consensus pattern (100 bp):
TTATGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATGTAGGTT
ATGTAAGTTATGTAAGTTATGTAATCCACGCAAGT
Found at i:35338303 original size:21 final size:19
Alignment explanation
Indices: 35338261--35338305 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
35338251 GTTATTTAAT
**
35338261 TTATGCAAGTTTATGTAAG
1 TTATGCAAGTTTATACAAG
35338280 TTATGCAAGCTTATATACAAG
1 TTATGCAAG-TT-TATACAAG
35338301 TTATG
1 TTATG
35338306 TATTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.41
20 2 0.09
21 11 0.50
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (19 bp):
TTATGCAAGTTTATACAAG
Found at i:35338494 original size:16 final size:16
Alignment explanation
Indices: 35338469--35338506 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35338459 GAAAACGAAG
*
35338469 TAAA-TTTAATACTAA
1 TAAATTTTAATACAAA
35338484 TAAATTTTAATACAAA
1 TAAATTTTAATACAAA
35338500 TAAATTT
1 TAAATTT
35338507 AGAAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTTAATACAAA
Found at i:35338521 original size:13 final size:13
Alignment explanation
Indices: 35338503--35338530 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35338493 ATACAAATAA
35338503 ATTTAGAAAACTT
1 ATTTAGAAAACTT
35338516 ATTTAGAAAACTT
1 ATTTAGAAAACTT
35338529 AT
1 AT
35338531 AAATTTAGAA
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:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAGAAAACTT
Found at i:35338538 original size:17 final size:17
Alignment explanation
Indices: 35338499--35338548 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
35338489 TTTAATACAA
35338499 ATAAATTTAGAAAAC-T
1 ATAAATTTAGAAAACTT
35338515 -T--ATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
35338529 ATAAATTTAGAAAACTT
1 ATAAATTTAGAAAACTT
35338546 ATA
1 ATA
35338549 TAGATATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.37
14 1 0.03
15 2 0.07
17 16 0.53
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTTAGAAAACTT
Found at i:35340288 original size:191 final size:191
Alignment explanation
Indices: 35339953--35340331 Score: 587
Period size: 191 Copynumber: 2.0 Consensus size: 191
35339943 AAGCAACACA
* *
35339953 AATTTAAAGCGAAAGGAAAAACAAAGCGAGCATTAGAGAAAGAAAAAATCAAACAGAAAAATGAA
1 AATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGAA
* *
35340018 AAGCCATATACGTATTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAGTCAGCCCAGAC
66 AAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAGTCAGCCCAGAC
* * ** *
35340083 GAGAAGCAATATTCGATCGAAAAGAGGGGAAATCGTCGTTGAAGGGGTGAATGGTCTATAG
131 GAAAAGCAATATTCGACCGAAAAGAGGGGAAATCGTCGTTGAAAAGGTGAAAGGTCTATAG
* * *
35340144 AATTTAAAGAGAAAGGAAAAACAAAGCGGGCATTACAGAAAGAAAAAATCGAACATAAAAATGAA
1 AATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGAA
* * * * *
35340209 CAGCCATATATGGAGTCAACGGAGAAATTAGGGATTTGGAAAGTTTTTTACCAGTCAGCCCAGAC
66 AAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAGTCAGCCCAGAC
* *
35340274 GAAAAGCGATATTCGACCGAGAAGAGGGGAAATCGTCGTTGAAAAGGTGAAAGGTCTA
131 GAAAAGCAATATTCGACCGAAAAGAGGGGAAATCGTCGTTGAAAAGGTGAAAGGTCTA
35340332 GGGATTTGCA
Statistics
Matches: 169, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
191 169 1.00
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.18
Consensus pattern (191 bp):
AATTTAAAGAGAAAGGAAAAACAAAGCGAGCATTACAGAAAGAAAAAATCAAACAGAAAAATGAA
AAGCCATATACGGAGTCAACGAAGAAATTAAGGATTTGGAAAGATTTTTACCAGTCAGCCCAGAC
GAAAAGCAATATTCGACCGAAAAGAGGGGAAATCGTCGTTGAAAAGGTGAAAGGTCTATAG
Found at i:35340931 original size:14 final size:15
Alignment explanation
Indices: 35340909--35340942 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35340899 TAGCCCCAAC
35340909 CCCTAAACCCA-AAT
1 CCCTAAACCCATAAT
*
35340923 CCCTGAACCCATAAT
1 CCCTAAACCCATAAT
35340938 CCCTA
1 CCCTA
35340943 GTCCACAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.35, C:0.44, G:0.03, T:0.18
Consensus pattern (15 bp):
CCCTAAACCCATAAT
Found at i:35341191 original size:15 final size:15
Alignment explanation
Indices: 35341171--35341199 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35341161 CCATAATCTT
35341171 TAAACCCTAAACCTA
1 TAAACCCTAAACCTA
35341186 TAAACCCTAAACCT
1 TAAACCCTAAACCT
35341200 TGACTCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCCTAAACCTA
Found at i:35341854 original size:114 final size:114
Alignment explanation
Indices: 35341702--35342577 Score: 1275
Period size: 114 Copynumber: 7.7 Consensus size: 114
35341692 GTTTTGGTTT
* *
35341702 AAAACGATGCATTTTGGTTAAGATTTGTTTGCGGCGCTTTGTATAATGCGCCGCTAATGATGTAC
1 AAAACGATGCATTTTGGTTAAGATTT-TTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
*
35341767 TTTAGCGGCGTTTTACTAT-AGCGCCACTAATTCTAAAAATACCTCAACCA
65 TTTAGCGGCGTTTTACTATAAGCGCCACTAATTCT-AAAATACCTCAACCC
* * *
35341817 AAAACGATGCGTTTTGGTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCACTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
35341882 TTAGCGGCATTTATCCT-TAAGCGCCACTAAATCTAAAATACCTCAACCC
66 TTAGCGGCGTTT-TACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
*
35341931 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
** * * *
35341996 TTAATGGC-ATTTATCCATAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCGTTTTA-CTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* *
35342045 AAAACGATGCATTTCGGTTAAGATTTTTTGCGGCGCTTTGTATGATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
35342110 TTAGCGGCGTTTTTACT-TAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCG-TTTTACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* ** *
35342159 AGAACGATGTGTTTTGGTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* * *
35342224 TTAGCGGC-ATTTATCCATAAGCGCCACTAATTCTAATATACCTCAACCC
66 TTAGCGGCGTTTTA-CTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* * *
35342273 AAAACGATGCATTTCGGTTAAGATTTTTTGCGGCGCTTTGTATGATGCGCCGCTAATGGTGTGCG
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
35342338 TTAGCGGCGTTTTTTCT-TAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCG-TTTTACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
* *
35342387 AGAACGATGCGTTTTGGTTAAGA-TTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
35342451 TTAGCGGC-ATTTATCT-TAAAGCGCCACTAATTCTAAAATACCTCAACCC
66 TTAGCGGCGTTTTA-CTAT-AAGCGCCACTAATTCTAAAATACCTCAACCC
** * * *
35342500 AAAACGATGTGTTTTGGTTAAGATTTTTTGCAGCGCTTTGTGTAATGCGCCGCTAATGGTGTGAT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
35342565 TTAGCGGTGTTTT
66 TTAGCGGCGTTTT
35342578 TCGAAGGTCG
Statistics
Matches: 685, Mismatches: 62, Indels: 28
0.88 0.08 0.04
Matches are distributed among these distances:
111 3 0.00
112 8 0.01
113 103 0.15
114 518 0.76
115 46 0.07
116 7 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (114 bp):
AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCGTTTTACTATAAGCGCCACTAATTCTAAAATACCTCAACCC
Found at i:35342328 original size:342 final size:342
Alignment explanation
Indices: 35341702--35342571 Score: 1406
Period size: 342 Copynumber: 2.5 Consensus size: 342
35341692 GTTTTGGTTT
* *
35341702 AAAACGATGCATTTTGGTTAAGATTTGTTTGCGGCGCTTTGTATAATGCGCCGCTAATGATGTAC
1 AAAACGATGCATTTTGGTTAAGATTT-TTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGC
* *
35341767 TTTAGCGGCG-TTTTAC-TATAGCGCCACTAATTCTAAAAATACCTCAACCAAAAACGATGCGTT
65 TTTAGCGGCGTTTTTACTTA-AGCGCCACTAATTCT-AAAATACCTCAACCCAAAACGATGTGTT
*
35341830 TTGGTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCACTAATGGTGTGCTTTAGCGGCATTTA
128 TTGGTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCTTTAGCGGCATTTA
* *
35341895 TCCTTAAGCGCCACTAAATCTAAAATACCTCAACCCAAAACGATGCATTTTGGTTAAGATTTTTT
193 TCCATAAGCGCCACTAAATCTAAAATACCTCAACCCAAAACGATGCATTTCGGTTAAGATTTTTT
* *
35341960 GCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCTTTAATGGCATTTATCCATAAGCGCCACTA
258 GCGGCGCTTTGAATAATGCGCCGCTAATGGTGTGCGTTAACGGCATTTATCCATAAGCGCCACTA
*
35342025 ATTCTAATATACCTCAACCC
323 ATTCTAAAATACCTCAACCC
* *
35342045 AAAACGATGCATTTCGGTTAAGATTTTTTGCGGCGCTTTGTATGATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
*
35342110 TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCCAGAACGATGTGTTTTG
66 TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCCAAAACGATGTGTTTTG
35342175 GTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCTTTAGCGGCATTTATCC
131 GTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCTTTAGCGGCATTTATCC
* *
35342240 ATAAGCGCCACTAATTCTAATATACCTCAACCCAAAACGATGCATTTCGGTTAAGATTTTTTGCG
196 ATAAGCGCCACTAAATCTAAAATACCTCAACCCAAAACGATGCATTTCGGTTAAGATTTTTTGCG
* * * * * * *
35342305 GCGCTTTGTATGATGCGCCGCTAATGGTGTGCGTTAGCGGCGTTTTTTCTTAAGCGCCACTAATT
261 GCGCTTTGAATAATGCGCCGCTAATGGTGTGCGTTAACGGCATTTATCCATAAGCGCCACTAATT
35342370 CTAAAATACCTCAACCC
326 CTAAAATACCTCAACCC
* *
35342387 AGAACGATGCGTTTTGGTTAAGA-TTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
1 AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
* *
35342451 TTAGCGGCATTTAT-CTTAAAGCGCCACTAATTCTAAAATACCTCAACCCAAAACGATGTGTTTT
66 TTAGCGGCGTTTTTACTT-AAGCGCCACTAATTCTAAAATACCTCAACCCAAAACGATGTGTTTT
* * * *
35342515 GGTTAAGATTTTTTGCAGCGCTTTGTGTAATGCGCCGCTAATGGTGTGATTTAGCGG
130 GGTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCTTTAGCGG
35342572 TGTTTTTCGA
Statistics
Matches: 491, Mismatches: 33, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
340 3 0.01
341 150 0.31
342 290 0.59
343 46 0.09
344 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (342 bp):
AAAACGATGCATTTTGGTTAAGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCT
TTAGCGGCGTTTTTACTTAAGCGCCACTAATTCTAAAATACCTCAACCCAAAACGATGTGTTTTG
GTTATGATTTTTTGCGGCGCTTTGTATAATGCGCCGCTAATGGTGTGCTTTAGCGGCATTTATCC
ATAAGCGCCACTAAATCTAAAATACCTCAACCCAAAACGATGCATTTCGGTTAAGATTTTTTGCG
GCGCTTTGAATAATGCGCCGCTAATGGTGTGCGTTAACGGCATTTATCCATAAGCGCCACTAATT
CTAAAATACCTCAACCC
Found at i:35342982 original size:126 final size:126
Alignment explanation
Indices: 35342827--35343061 Score: 373
Period size: 126 Copynumber: 1.9 Consensus size: 126
35342817 ATAAAAATAT
* * *
35342827 TCATAATGTTTCATGATAATTATTCTAATTGAGAAATAACTTTTTTA-TCTTTCAATATTCTCTA
1 TCATAATGTTTAATCATAATTATTCTAATTGAGAAATAACTATTTTACT-TTTCAATATTCTCTA
* *
35342891 TAATTCCTTCCTTTAATTATCACTTAATTTGATAAAATTAAGATTAACAATATTCATAATTA
65 CAATTCCCTCCTTTAATTATCACTTAATTTGATAAAATTAAGATTAACAATATTCATAATTA
* * *
35342953 TCATAATTTTTAATCATAATTATTTTAATTGAGAAATGACTATTTTACTTTTCAATATTCTCTAC
1 TCATAATGTTTAATCATAATTATTCTAATTGAGAAATAACTATTTTACTTTTCAATATTCTCTAC
*
35343018 AATTCCCTCCTTTAATTATCACTTAATTTGATAAAATTATGATT
66 AATTCCCTCCTTTAATTATCACTTAATTTGATAAAATTAAGATT
35343062 TAATCCCATA
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 98 0.99
127 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (126 bp):
TCATAATGTTTAATCATAATTATTCTAATTGAGAAATAACTATTTTACTTTTCAATATTCTCTAC
AATTCCCTCCTTTAATTATCACTTAATTTGATAAAATTAAGATTAACAATATTCATAATTA
Found at i:35346166 original size:3 final size:3
Alignment explanation
Indices: 35346158--35346200 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
35346148 AAAATAAAAC
* *
35346158 TAA TAA TAA TAAA TAG TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35346201 CATTAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35348488 original size:3 final size:3
Alignment explanation
Indices: 35348480--35348518 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
35348470 TTTTTTGTGC
35348480 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35348519 TTAGATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35351236 original size:124 final size:124
Alignment explanation
Indices: 35351008--35351255 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
35350998 AACTTAAAAC
35351008 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
1 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
*
35351073 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTGCTCAAACCCTCTCAAAT
66 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
*
35351132 GGGTCGGGTCAAGCTTGAGCCTTGAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
1 GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
* * *
35351197 AATTTTTTTGTCCAAGCTCATTTTTCGAGGCTAATATTTTTACTCAAACCTTCTCAAAT
66 AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
35351256 TTTGAATAAG
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (124 bp):
GGGTCGGGTCAAGCTTGAGCCTTAAATGTTCAAACCCGAGCCTAACCCATATTTTAAACGAGCTT
AATTTTTTTGTCCAAGCTCATTTTTCGAGCCTAACATTTTTACTCAAACCCTCTCAAAT
Found at i:35357636 original size:21 final size:20
Alignment explanation
Indices: 35357606--35357656 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35357596 CAGGGGTCAA
*
35357606 GTATCGATACTTAAACAAAAG
1 GTATCAATACTT-AACAAAAG
* *
35357627 GTATCAATACTTTATAAAAG
1 GTATCAATACTTAACAAAAG
*
35357647 GTATCTATAC
1 GTATCAATAC
35357657 CTTTGCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCAATACTTAACAAAAG
Found at i:35357666 original size:21 final size:20
Alignment explanation
Indices: 35357606--35357666 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
35357596 CAGGGGTCAA
* *
35357606 GTATCGATACTTAAACAAAAG
1 GTATCAATACTT-TACAAAAG
*
35357627 GTATCAATACTTTATAAAAG
1 GTATCAATACTTTACAAAAG
* *
35357647 GTATCTATACCTTTGCAAAA
1 GTATCAATA-CTTTACAAAA
35357667 AATTGATACC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (20 bp):
GTATCAATACTTTACAAAAG
Found at i:35359530 original size:19 final size:19
Alignment explanation
Indices: 35359502--35359538 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35359492 ATGACTACTT
35359502 TTCATATTTTTCTCCACTC
1 TTCATATTTTTCTCCACTC
*
35359521 TTCATCTTTTTCTCCACT
1 TTCATATTTTTCTCCACT
35359539 TTTCTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.54
Consensus pattern (19 bp):
TTCATATTTTTCTCCACTC
Found at i:35364469 original size:55 final size:55
Alignment explanation
Indices: 35364385--35364494 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
35364375 TCAAACCTCT
35364385 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
1 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
* *
35364440 TATACCACTGTCGTGGTGACTGTTTCAAACCGTAAAGGGACTTTTTTAGCAAGCA
1 TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
35364495 AACATAGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (55 bp):
TATACCACTGTCGTGGTGACTATTTCAAACCGTAAAGGGACTTTTTCAGCAAGCA
Found at i:35374266 original size:28 final size:28
Alignment explanation
Indices: 35374207--35374273 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
35374197 GTATCATGTT
* * *
35374207 TTAACATAAATATAAATTTAGTAATTAT
1 TTAACATAAATATAAATTTAGCAACTAA
*
35374235 TTAACATAAATATAATTTTA-CAACTACA
1 TTAACATAAATATAAATTTAGCAACTA-A
35374263 TTAAC-TAAATA
1 TTAACATAAATA
35374274 GTTTAATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.29
28 24 0.71
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (28 bp):
TTAACATAAATATAAATTTAGCAACTAA
Found at i:35376977 original size:47 final size:47
Alignment explanation
Indices: 35376926--35377019 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
35376916 AAAAGTATAG
*
35376926 GGACTAGTTTTGACAAATGGAAAACATAGAAAAACTATGTTAAAAGA
1 GGACTAGTTTTAACAAATGGAAAACATAGAAAAACTATGTTAAAAGA
*
35376973 GGACTTGTTTTAACAAATGGAAAACATAGAAAAACTATGTTAAAAGA
1 GGACTAGTTTTAACAAATGGAAAACATAGAAAAACTATGTTAAAAGA
35377020 AATGGAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (47 bp):
GGACTAGTTTTAACAAATGGAAAACATAGAAAAACTATGTTAAAAGA
Found at i:35378724 original size:24 final size:24
Alignment explanation
Indices: 35378696--35378748 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
35378686 CCCTTAAATC
* *
35378696 ATTTTCCCCAAATT-CCTAATTTA
1 ATTTTTCCCAAATTCCCTAACTTA
*
35378719 ATTTTTCCCTAATTCCCTAACTTA
1 ATTTTTCCCAAATTCCCTAACTTA
35378743 ATTTTT
1 ATTTTT
35378749 TCTTTCCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTTCCCAAATTCCCTAACTTA
Done.