Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 99 of 425
Found at i:28667396 original size:27 final size:27
Alignment explanation
Indices: 28667366--28667483 Score: 141
Period size: 27 Copynumber: 4.4 Consensus size: 27
28667356 GGGGCAAAAT
* * *
28667366 GATAATTTTACCCCACAAAGGTATCTC
1 GATAATTTTACCCTACAAGGGTATTTC
* *
28667393 GATAATTCTACCCTACAGGGGTATTTC
1 GATAATTTTACCCTACAAGGGTATTTC
*
28667420 GGT-ATTTCTACCCTACAAGGGTATTTC
1 GATAATTT-TACCCTACAAGGGTATTTC
* *
28667447 GATAATTCTACCCTACAGGGGTATTTC
1 GATAATTTTACCCTACAAGGGTATTTC
28667474 GAT-ATTTTAC
1 GATAATTTTAC
28667484 AAATCGAGAG
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.12
27 65 0.84
28 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (27 bp):
GATAATTTTACCCTACAAGGGTATTTC
Found at i:28667468 original size:54 final size:53
Alignment explanation
Indices: 28667370--28667483 Score: 183
Period size: 54 Copynumber: 2.1 Consensus size: 53
28667360 CAAAATGATA
*
28667370 ATTTTACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGGT
1 ATTTTACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGAT
* * *
28667423 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTATTTCGAT
1 ATTT-TACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGAT
28667477 ATTTTAC
1 ATTTTAC
28667484 AAATCGAGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
53 7 0.12
54 49 0.88
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (53 bp):
ATTTTACCCCACAAAGGTATCTCGATAATTCTACCCTACAGGGGTATTTCGAT
Found at i:28667523 original size:27 final size:27
Alignment explanation
Indices: 28667438--28667618 Score: 122
Period size: 27 Copynumber: 6.7 Consensus size: 27
28667428 TACCCTACAA
* **
28667438 GGGTATTTCGATAATTCTAC-CCTACAG
1 GGGTATTTCGATAATTTTACAAAT-CAG
28667465 GGGTATTTCGAT-ATTTTACAAATC-G
1 GGGTATTTCGATAATTTTACAAATCAG
* *
28667490 AGAGTATTTCGATAATTTCACAAATCAG
1 -GGGTATTTCGATAATTTTACAAATCAG
* * * **
28667518 GGGTATTTTGGTAATTTTATAAGCCAG
1 GGGTATTTCGATAATTTTACAAATCAG
* *
28667545 GGGTATTTTGAAAATTTT-CTAAA-CTAG
1 GGGTATTTCGATAATTTTAC-AAATC-AG
* * *
28667572 GGGTATTT-TAGTAATTTTACAAACCAA
1 GGGTATTTCGA-TAATTTTACAAATCAG
* *
28667599 GGGTATTTTGGTAATTTTAC
1 GGGTATTTCGATAATTTTAC
28667619 TGATTGAGGG
Statistics
Matches: 123, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
25 1 0.01
26 20 0.16
27 99 0.80
28 3 0.02
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCAG
Found at i:28667561 original size:54 final size:54
Alignment explanation
Indices: 28667462--28667660 Score: 172
Period size: 54 Copynumber: 3.7 Consensus size: 54
28667452 TTCTACCCTA
* * * * * * *
28667462 CAGGGGTATTTCGAT-ATTTTACAAATCGAGAGTATTTCGATAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGATAATTTCACAAAT
* * * *
28667515 CAGGGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTGAAAATTTTC-TAAA-
1 CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGATAA-TTTCACAAAT
* * * * **
28667568 CTAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACTGAT
1 C-AGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGATAATTTCACAAAT
* *
28667623 -TGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTT
1 CAG-GGGTATTTTGGTAATTTTATAAACCAAGGGTATTT
28667661 CAGTAATTTT
Statistics
Matches: 115, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
53 18 0.16
54 93 0.81
55 4 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGATAATTTCACAAAT
Found at i:28667655 original size:27 final size:27
Alignment explanation
Indices: 28667518--28667711 Score: 138
Period size: 27 Copynumber: 7.2 Consensus size: 27
28667508 CACAAATCAG
* * *
28667518 GGGTATTTTGGTAATTTTATAAGCCAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
** * * *
28667545 GGGTATTTTGAAAATTTTCTAAACTAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
* **
28667572 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
* * ***
28667599 GGGTATTTTGGTAATTTTACT-GATTGA
1 GGGTATTTTGGTAATTTT-GTAAACCAA
28667626 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
** * *
28667653 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTGTAAACCAA
**** * *
28667680 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
28667707 GGGTA
1 GGGTA
28667712 AAACGGTAAT
Statistics
Matches: 131, Mismatches: 34, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
26 1 0.01
27 130 0.99
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGTAAACCAA
Found at i:28667682 original size:54 final size:53
Alignment explanation
Indices: 28667518--28667684 Score: 167
Period size: 54 Copynumber: 3.1 Consensus size: 53
28667508 CACAAATCAG
* * * * *
28667518 GGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTGAAAATTTTCTAAA-CTA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTAG-TAATTTTCTAAATCGA
* * * * *
28667571 GGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACT-GATTGA
1 -GGGTATTTTGGTAATTTTATAAACCAAGGGTA-TTTAGTAATTTT-CTAAATCGA
* *
28667626 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTT-AGTAATTTTCTAAATCGA
28667680 GGGTA
1 GGGTA
28667685 AAACGGTAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
53 4 0.04
54 81 0.88
55 7 0.08
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTAGTAATTTTCTAAATCGA
Found at i:28667684 original size:81 final size:81
Alignment explanation
Indices: 28667493--28667670 Score: 207
Period size: 81 Copynumber: 2.2 Consensus size: 81
28667483 CAAATCGAGA
* * *
28667493 GTATTTC-GATAATTTCACAAATCAGGGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTGAA
1 GTATTTCAG-TAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTGAA
* *
28667557 AATTTTCTAAACTAGGG
65 AATTTTCTAAACCAAGG
* * *** **
28667574 GTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACTGATTGA-GGGTATTTTGGT
1 GTATTTCAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTA-TAAGCCAGGGGTATTTTGAA
*
28667638 AATTTTGTAAACCAAGG
65 AATTTTCTAAACCAAGG
28667655 GTATTTCAGTAATTTT
1 GTATTTCAGTAATTTT
28667671 GTAAATCGAG
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
81 77 0.95
82 4 0.05
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (81 bp):
GTATTTCAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTGAAA
ATTTTCTAAACCAAGG
Found at i:28667693 original size:81 final size:81
Alignment explanation
Indices: 28667545--28667695 Score: 176
Period size: 81 Copynumber: 1.9 Consensus size: 81
28667535 TATAAGCCAG
* * * ****
28667545 GGGTATTTTGAAAATTTTCTAAACTAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGG
1 GGGTATTTTGAAAATTTTCTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACGG
28667610 TAATTTTACTGATTGA
66 TAATTTTACTGATTGA
** * ** * *
28667626 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACGG
1 GGGTATTTTGAAAATTTTCTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACGG
28667691 TAATT
66 TAATT
28667696 CTGTAAATCA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (81 bp):
GGGTATTTTGAAAATTTTCTAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACGG
TAATTTTACTGATTGA
Found at i:28667712 original size:27 final size:27
Alignment explanation
Indices: 28667635--28667872 Score: 253
Period size: 27 Copynumber: 8.9 Consensus size: 27
28667625 AGGGTATTTT
* * ***
28667635 GGTAATTTTGTAAACCAAGGGTATTTC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*
28667662 AGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* *
28667689 GGTAATTCTGTAAATCAAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* * * *
28667716 GGTAATTCTATAAATTGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* *
28667743 GGTAATTTTATAAATCGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* *
28667770 GGTAATTTTGTAAATCGAAGATAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*** * *
28667797 GGTAATTCAATAAATTGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* * *
28667824 GGTAATTCTATAAATTGAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
28667851 -GTAATTTTGTAAATCGAGGGTA
1 GGTAATTTTGTAAATCGAGGGTA
28667873 CTTTGGTAAT
Statistics
Matches: 180, Mismatches: 31, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
26 19 0.11
27 161 0.89
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (27 bp):
GGTAATTTTGTAAATCGAGGGTAAAAC
Found at i:28671366 original size:29 final size:29
Alignment explanation
Indices: 28671334--28671436 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
28671324 GTGACGAGAT
* *
28671334 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
28671363 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
28671392 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
28671421 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28671437 TGATCAAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:28673699 original size:27 final size:27
Alignment explanation
Indices: 28673669--28673785 Score: 130
Period size: 27 Copynumber: 4.4 Consensus size: 27
28673659 GGGCAAAATG
* *
28673669 ATAATTTTACCCCACAAGGGTATCTCA
1 ATAATTTTACCCTACAAGGGTATTTCA
* *
28673696 ATAATTCTACCCTACAAGGGTATTTCG
1 ATAATTTTACCCTACAAGGGTATTTCA
* *
28673723 GT-ATTTCTACCCTACAAGGGTATTTCG
1 ATAATTT-TACCCTACAAGGGTATTTCA
* * *
28673750 ATAATTCTACCCTACAGGGGTTTTTCA
1 ATAATTTTACCCTACAAGGGTATTTCA
28673777 AT-ATTTTAC
1 ATAATTTTAC
28673786 AAATCGAGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
26 9 0.12
27 64 0.84
28 3 0.04
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (27 bp):
ATAATTTTACCCTACAAGGGTATTTCA
Found at i:28673734 original size:54 final size:53
Alignment explanation
Indices: 28673672--28673785 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 53
28673662 CAAAATGATA
28673672 ATTTTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGT
1 ATTTTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGT
* * * * * **
28673725 ATTTCTACCCTACAAGGGTATTTCGATAATTCTACCCTACAGGGGTTTTTCAAT
1 ATTT-TACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGT
28673779 ATTTTAC
1 ATTTTAC
28673786 AAATCGAGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
53 7 0.13
54 46 0.87
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (53 bp):
ATTTTACCCCACAAGGGTATCTCAATAATTCTACCCTACAAGGGTATTTCGGT
Found at i:28673825 original size:27 final size:27
Alignment explanation
Indices: 28673740--28673920 Score: 120
Period size: 27 Copynumber: 6.7 Consensus size: 27
28673730 TACCCTACAA
* **
28673740 GGGTATTTCGATAATTCTACCCTA-CAG
1 GGGTATTTCGATAATTTTA-CAAACCAG
* * *
28673767 GGGTTTTTCAAT-ATTTTACAAATC-G
1 GGGTATTTCGATAATTTTACAAACCAG
* * *
28673792 AGAGTATTTCGATAATTTCACAAATCAG
1 -GGGTATTTCGATAATTTTACAAACCAG
* * * *
28673820 GGGTATTTTGGTAATTTTATAAGCCAG
1 GGGTATTTCGATAATTTTACAAACCAG
* *
28673847 GGGTATTTTC-ATAATTTTCCAAACTAG
1 GGGTA-TTTCGATAATTTTACAAACCAG
* *
28673874 GGGTATTT-TAGTAATTTTACAAACCAA
1 GGGTATTTCGA-TAATTTTACAAACCAG
* *
28673901 GGGTATTTTGGTAATTTTAC
1 GGGTATTTCGATAATTTTAC
28673921 TGATTGAGGG
Statistics
Matches: 119, Mismatches: 27, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.03
26 19 0.16
27 93 0.78
28 4 0.03
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAACCAG
Found at i:28673957 original size:27 final size:27
Alignment explanation
Indices: 28673820--28674013 Score: 129
Period size: 27 Copynumber: 7.2 Consensus size: 27
28673810 CACAAATCAG
* * *
28673820 GGGTATTTTGGTAATTTTATAAGCCAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
** ** * *
28673847 GGGTATTTTCATAATTTTCCAAACTAG
1 GGGTATTTTGGTAATTTTGTAAACCAA
* **
28673874 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
* * ***
28673901 GGGTATTTTGGTAATTTTACT-GATTGA
1 GGGTATTTTGGTAATTTT-GTAAACCAA
28673928 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
** * *
28673955 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTGTAAACCAA
**** * *
28673982 GGGTAAAACGGTAATTCTGTAAATCAA
1 GGGTATTTTGGTAATTTTGTAAACCAA
28674009 GGGTA
1 GGGTA
28674014 AAACGGTAAT
Statistics
Matches: 132, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
26 1 0.01
27 131 0.99
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTGTAAACCAA
Found at i:28673972 original size:54 final size:54
Alignment explanation
Indices: 28673795--28673972 Score: 184
Period size: 54 Copynumber: 3.3 Consensus size: 54
28673785 CAAATCGAGA
* * *
28673795 GTATTTC-GATAATTTCACAAA-TCAGGGGTATTTTGGTAATTTTATAAGCCAGGG
1 GTATTTCAG-TAATTTTACAAACT-AGGGGTATTTTGGTAATTTTATAAACCAAGG
* * *
28673849 GTATTTTCA-TAATTTTCCAAACTAGGGGTATTTTAGTAATTTTACAAACCAAGG
1 GTA-TTTCAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGG
** ** * *
28673903 GTATTTTGGTAATTTTACTGA-TTGAGGGTATTTTGGTAATTTTGTAAACCAAGG
1 GTATTTCAGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTTATAAACCAAGG
28673957 GTATTTCAGTAATTTT
1 GTATTTCAGTAATTTT
28673973 GTAAATCGAG
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
53 5 0.05
54 92 0.90
55 5 0.05
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (54 bp):
GTATTTCAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATAAACCAAGG
Found at i:28673984 original size:54 final size:54
Alignment explanation
Indices: 28673820--28674091 Score: 181
Period size: 54 Copynumber: 5.0 Consensus size: 54
28673810 CACAAATCAG
* * * ** *
28673820 GGGTATTTTGGTAATTTTATAAGCCAGGGGTATTTTC-ATAATTTTCCAAA-CTA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTA-TTTCGGTAATTTTGTAAATCGA
* * * * * *
28673873 GGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACT-GATTGA
1 -GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTCGGTAATTTT-GTAAATCGA
* *
28673928 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTCGGTAATTTTGTAAATCGA
**** * * * *** * **
28673982 GGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTGTAAATTAA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTCGGTAATTTTGTAAATCGA
*** * * ***
28674036 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTCGGTAATTTTGTAAATCGA
28674090 GG
1 GG
28674092 ATAAAACGGT
Statistics
Matches: 176, Mismatches: 38, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
53 4 0.02
54 170 0.97
55 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.36
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTCGGTAATTTTGTAAATCGA
Found at i:28673986 original size:81 final size:81
Alignment explanation
Indices: 28673764--28673972 Score: 201
Period size: 81 Copynumber: 2.6 Consensus size: 81
28673754 TTCTACCCTA
* * * * * * *
28673764 CAGGGGT-TTTTCA-ATATTTTACAAATCGAGAGTATTTC-GATAATTTCACAAATCAGGGGTAT
1 CAGGGGTATTTTCATA-ATTTTCCAAACCAAGGGTATTTCAG-TAATTTTACAAACCAAGGGTAT
28673826 TTTGGTAATTTTATAAGC
64 TTTGGTAATTTTATAAGC
* * *
28673844 CAGGGGTATTTTCATAATTTTCCAAACTAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTT
1 CAGGGGTATTTTCATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTT
* **
28673909 TGGTAATTTTACTGATT
66 TGGTAATTTTA-TAAGC
* ** **
28673926 GA-GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT
1 CAGGGGTATTTTCATAATTTTCCAAACCAAGGGTATTTCAGTAATTTT
28673973 GTAAATCGAG
Statistics
Matches: 104, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
80 7 0.07
81 92 0.88
82 5 0.05
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (81 bp):
CAGGGGTATTTTCATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTT
TGGTAATTTTATAAGC
Found at i:28674012 original size:81 final size:81
Alignment explanation
Indices: 28673964--28674174 Score: 307
Period size: 81 Copynumber: 2.6 Consensus size: 81
28673954 AGGGTATTTC
* * *
28673964 AGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTGT
1 AGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTAT
*
28674029 AAATTAAGGGTAAAAT
66 AAATCAAGGGTAAAAT
* * * *
28674045 GGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGATAAAACGGTAATTCAAT
1 AGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTAT
*
28674110 AAATCGAGGGTAAAAT
66 AAATCAAGGGTAAAAT
* * *
28674126 GGTAATTCTATAAATTGAGGGTAAAAC-GTAATTTTGTAAATCAAGGGTA
1 AGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTA
28674175 CTTTGGTAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 20 0.17
81 97 0.83
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (81 bp):
AGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTAT
AAATCAAGGGTAAAAT
Found at i:28674014 original size:27 final size:27
Alignment explanation
Indices: 28673937--28674174 Score: 271
Period size: 27 Copynumber: 8.9 Consensus size: 27
28673927 AGGGTATTTT
* * ***
28673937 GGTAATTTTGTAAACCAAGGGTATTTC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*
28673964 AGTAATTTTGTAAATCGAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* *
28673991 GGTAATTCTGTAAATCAAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* ** *
28674018 GGTAATTCTGTAAATTAAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*
28674045 GGTAATTTTATAAATCGAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*
28674072 GGTAATTTTGTAAATCGAGGATAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*** *
28674099 GGTAATTCAATAAATCGAGGGTAAAAT
1 GGTAATTTTGTAAATCGAGGGTAAAAC
* * *
28674126 GGTAATTCTATAAATTGAGGGTAAAAC
1 GGTAATTTTGTAAATCGAGGGTAAAAC
*
28674153 -GTAATTTTGTAAATCAAGGGTA
1 GGTAATTTTGTAAATCGAGGGTA
28674175 CTTTGGTAAT
Statistics
Matches: 181, Mismatches: 30, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
26 18 0.10
27 163 0.90
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (27 bp):
GGTAATTTTGTAAATCGAGGGTAAAAC
Found at i:28676858 original size:27 final size:27
Alignment explanation
Indices: 28676780--28676864 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
28676770 GGGGCAAAAT
* * *
28676780 GATAATTTTACCCCACAAGGGTATCTC
1 GATAATTCTACCCTACAAGGGTATTTC
28676807 GATAATTCTACCCTACAAGGGTATTTC
1 GATAATTCTACCCTACAAGGGTATTTC
* *
28676834 GATAATTCTACCCTACAGGGGTATTTT
1 GATAATTCTACCCTACAAGGGTATTTC
28676861 GATA
1 GATA
28676865 TTTTACAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (27 bp):
GATAATTCTACCCTACAAGGGTATTTC
Found at i:28676906 original size:53 final size:54
Alignment explanation
Indices: 28676827--28677002 Score: 157
Period size: 53 Copynumber: 3.3 Consensus size: 54
28676817 CCCTACAAGG
* ** * *
28676827 GTATTTCGATAATTCTACCCTA-CAGGGGTATTTTGAT-ATTTTACAAATCGAGA
1 GTATTTCGATAATT-TTCCAAACCAGGGGTATTTTGATAATTTTACAAAGCCAGA
* * * *
28676880 GTATTTCGATAA-TTTCACAAATCAGGGGTATTTTGGTAATTTTA-TAAGCCAGG
1 GTATTTCGATAATTTTC-CAAACCAGGGGTATTTTGATAATTTTACAAAGCCAGA
* *
28676933 GTATTTTGATAATTTTCCAAACCAGGGGTATTTT-AGTAATTTTACAAA-CCAAGG
1 GTATTTCGATAATTTTCCAAACCAGGGGTATTTTGA-TAATTTTACAAAGCC-AGA
* *
28676987 GTATTTTGGTAATTTT
1 GTATTTCGATAATTTT
28677003 ACTGATTGAG
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
51 2 0.02
52 3 0.03
53 68 0.66
54 30 0.29
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (54 bp):
GTATTTCGATAATTTTCCAAACCAGGGGTATTTTGATAATTTTACAAAGCCAGA
Found at i:28676910 original size:27 final size:27
Alignment explanation
Indices: 28676849--28677004 Score: 167
Period size: 27 Copynumber: 5.9 Consensus size: 27
28676839 TTCTACCCTA
*
28676849 CAGGGGTATTTTGAT-ATTTTACAAAT
1 CAGGGGTATTTTGATAATTTTACAAAC
* * * *
28676875 C-GAGAGTATTTCGATAATTTCACAAAT
1 CAG-GGGTATTTTGATAATTTTACAAAC
* * *
28676902 CAGGGGTATTTTGGTAATTTTATAAGC
1 CAGGGGTATTTTGATAATTTTACAAAC
*
28676929 CA-GGGTATTTTGATAATTTTCCAAAC
1 CAGGGGTATTTTGATAATTTTACAAAC
28676955 CAGGGGTATTTT-AGTAATTTTACAAAC
1 CAGGGGTATTTTGA-TAATTTTACAAAC
* *
28676982 CAAGGGTATTTTGGTAATTTTAC
1 CAGGGGTATTTTGATAATTTTAC
28677005 TGATTGAGGG
Statistics
Matches: 107, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
25 1 0.01
26 34 0.32
27 71 0.66
28 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTGATAATTTTACAAAC
Found at i:28677016 original size:54 final size:54
Alignment explanation
Indices: 28676849--28677056 Score: 190
Period size: 54 Copynumber: 3.9 Consensus size: 54
28676839 TTCTACCCTA
* * * * * * * *
28676849 CAGGGGTATTTTGAT-ATTTTACAAATCGAGAGTATTTCGATAA-TTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTC-CAAAC
* *
28676902 CAGGGGTATTTTGGTAATTTTATAAGCC-AGGGTATTTTGATAATTTTCCAAAC
1 CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTCCAAAC
* * * **
28676955 CAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACTGA-
1 CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTCCAAAC
** * **
28677008 TTGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT
1 CAG-GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTT
28677057 GTAAATCGAG
Statistics
Matches: 130, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
53 57 0.44
54 73 0.56
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTCCAAAC
Found at i:28677041 original size:27 final size:27
Alignment explanation
Indices: 28676852--28677097 Score: 156
Period size: 27 Copynumber: 9.2 Consensus size: 27
28676842 TACCCTACAG
* * * *
28676852 GGGTATTTTGAT-ATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * * * * *
28676878 GAGTATTTCGATAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
*
28676905 GGGTATTTTGGTAATTTTATAAGCC-A
1 GGGTATTTTGGTAATTTTATAAACCAA
* ** *
28676931 GGGTATTTTGATAATTTTCCAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
28676958 GGGTATTTTAGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* ***
28676985 GGGTATTTTGGTAATTTTACT-GATTGA
1 GGGTATTTTGGTAATTTTA-TAAACCAA
*
28677012 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
** * * *
28677039 GGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
**** * *
28677066 GGGTAAAACGGTAATTCTATAAATCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
28677093 GGGTA
1 GGGTA
28677098 AAACGATAAT
Statistics
Matches: 172, Mismatches: 44, Indels: 7
0.77 0.20 0.03
Matches are distributed among these distances:
26 32 0.19
27 140 0.81
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:28677070 original size:81 final size:80
Alignment explanation
Indices: 28676852--28677056 Score: 234
Period size: 80 Copynumber: 2.6 Consensus size: 80
28676842 TACCCTACAG
* * * * * * *
28676852 GGGTATTTTGAT-ATTTTACAAATCGAGAGTATTTC-GATAATTTCACAAATCAGGGGTATTTTG
1 GGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAG-TAATTTTACAAACCAAGGGTATTTTG
28676915 GTAATTTTATAAGCCA
65 GTAATTTTATAAGCCA
* *
28676931 GGGTATTTTGATAATTTTCCAAACCAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTGG
1 GGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTTGG
* ***
28676996 TAATTTTACTGATTGA
66 TAATTTTA-TAAGCCA
* **
28677012 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTT
1 GGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTT
28677057 GTAAATCGAG
Statistics
Matches: 105, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 12 0.11
80 49 0.47
81 44 0.42
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (80 bp):
GGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTATTTTGG
TAATTTTATAAGCCA
Found at i:28677079 original size:81 final size:81
Alignment explanation
Indices: 28676930--28677081 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 81
28676920 TTTATAAGCC
* * ****
28676930 AGGGTATTTTGATAATTTTCCAAACCAGGGGTATTTTAGTAATTTTACAAACCAAGGGTATTTTG
1 AGGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACG
28676995 GTAATTTTACTGATTG
66 GTAATTTTACTGATTG
* ** ** * *
28677011 AGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACG
1 AGGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACG
28677076 GTAATT
66 GTAATT
28677082 CTATAAATCA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 58 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.39
Consensus pattern (81 bp):
AGGGTATTTTGATAATTTTCCAAACCAAGGGTATTTCAGTAATTTTACAAACCAAGGGTAAAACG
GTAATTTTACTGATTG
Found at i:28677098 original size:27 final size:27
Alignment explanation
Indices: 28677049--28677258 Score: 260
Period size: 27 Copynumber: 7.8 Consensus size: 27
28677039 GGGTATTTCA
* *
28677049 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
28677076 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
* * * *
28677103 ATAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
* *
28677130 GTAATTTTATAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
* * *
28677157 GTAATTTTGTAAATCGAGGATAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
* *
28677184 GTAATTCAATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
28677211 GTAATTCTATAAATTGAGGGTAAAAC-
1 GTAATTCTATAAATCGAGGGTAAAACG
* *
28677237 GTAATTTTGTAAATCGAGGGTA
1 GTAATTCTATAAATCGAGGGTA
28677259 CTTTGGTAAT
Statistics
Matches: 157, Mismatches: 26, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 19 0.12
27 138 0.88
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAACG
Found at i:28677108 original size:81 final size:81
Alignment explanation
Indices: 28677023--28677251 Score: 228
Period size: 81 Copynumber: 2.8 Consensus size: 81
28677013 GGTATTTTGG
* ** *
28677023 TAATTTTGTAAACCAAGGGT-ATTTCAGTAATTTTGTAAATCGAGGGTAAAACGGTAATTCTATA
1 TAATTCTGTAAACCAAGGGTAAAAT-AGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATA
*
28677087 AATCAAGGGTAAAACGA
65 AATCAAGGATAAAACGA
*** * * * *
28677104 TAATTCTGTAAATTGAGGGTAAAATGGTAATTTTATAAATTGAGGGTAAAACGGTAATTTTGTAA
1 TAATTCTGTAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAA
* *
28677169 ATCGAGGATAAAACGG
66 ATCAAGGATAAAACGA
** * * * * * * *
28677185 TAATTCAATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAAC-GTAATTTTGTAA
1 TAATTCTGTAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAA
28677249 ATC
66 ATC
28677252 GAGGGTACTT
Statistics
Matches: 129, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
80 15 0.12
81 112 0.87
82 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (81 bp):
TAATTCTGTAAACCAAGGGTAAAATAGTAATTTTATAAATCGAGGGTAAAACGGTAATTCTATAA
ATCAAGGATAAAACGA
Found at i:28678985 original size:31 final size:31
Alignment explanation
Indices: 28678913--28678985 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
28678903 CTCTCCTTAT
28678913 ATATTTAA-TAAAATAATAATAAATAATAAA
1 ATATTTAATTAAAATAATAATAAATAATAAA
* * * *
28678943 ATATCTCATTAAAATATTAATAAACTAAT-AT
1 ATATTTAATTAAAATAATAATAAA-TAATAAA
*
28678974 TTATTTAATTAA
1 ATATTTAATTAA
28678986 TCTAAAATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 6 0.18
31 24 0.71
32 4 0.12
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (31 bp):
ATATTTAATTAAAATAATAATAAATAATAAA
Found at i:28685033 original size:58 final size:58
Alignment explanation
Indices: 28684969--28685088 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 58
28684959 TATCACATAC
* *
28684969 AAGGCCAGATATAGTTTTTGCAGTGAGCTTAGTGAGTCAATTTATGCACTCCCCAATG
1 AAGGCCAGACATAGTTTTTGCAGTGAGCTTAATGAGTCAATTTATGCACTCCCCAATG
28685027 AAGGCCAGACATAGTTTTTGCAGTGAGCTTAATGAGTCAATTTATGCACTCCCCAATG
1 AAGGCCAGACATAGTTTTTGCAGTGAGCTTAATGAGTCAATTTATGCACTCCCCAATG
28685085 AAGG
1 AAGG
28685089 AACATGAAGA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (58 bp):
AAGGCCAGACATAGTTTTTGCAGTGAGCTTAATGAGTCAATTTATGCACTCCCCAATG
Found at i:28686376 original size:16 final size:16
Alignment explanation
Indices: 28686357--28686387 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28686347 CTTCTTCACT
28686357 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28686373 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28686388 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28686393 original size:20 final size:20
Alignment explanation
Indices: 28686354--28686393 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28686344 AAACTTCTTC
* *
28686354 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28686374 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28686394 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28690076 original size:27 final size:27
Alignment explanation
Indices: 28690011--28690076 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
28690001 TACCCTTAGT
* *
28690011 TTGTAAAAATACTGAAATACCCTCGAT
1 TTGTAAAATTACTGAAATACCCTCGAC
* *
28690038 TTGTAAATTTACTGAAATACCTTCGAC
1 TTGTAAAATTACTGAAATACCCTCGAC
28690065 TTGTAAAATTAC
1 TTGTAAAATTAC
28690077 CAAAGTACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (27 bp):
TTGTAAAATTACTGAAATACCCTCGAC
Found at i:28690085 original size:27 final size:27
Alignment explanation
Indices: 28689988--28690085 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
28689978 TTTAGTTTAC
*
28689988 TAAAATTAC-CAAATACCCTTAG-TTTG
1 TAAAATTACTCAAATA-CCTTCGATTTG
* * *
28690014 TAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACTCAAATACCTTCGATTTG
* * *
28690041 TAAATTTACTGAAATACCTTCGACTTG
1 TAAAATTACTCAAATACCTTCGATTTG
28690068 TAAAATTAC-CAAAGTACC
1 TAAAATTACTCAAA-TACC
28690086 CCCGATTTAC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
26 15 0.25
27 44 0.75
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
TAAAATTACTCAAATACCTTCGATTTG
Found at i:28690112 original size:27 final size:27
Alignment explanation
Indices: 28690089--28690319 Score: 291
Period size: 27 Copynumber: 8.6 Consensus size: 27
28690079 AAGTACCCCC
*
28690089 GATTTACAGAATTACCGTTTTACCCCT
1 GATTTACAGAATTACCGTTTTACCCTT
* * *
28690116 AATTTACATAATTACCGTTTTACCCCT
1 GATTTACAGAATTACCGTTTTACCCTT
* * *
28690143 GATTTACATAATTATCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28690170 GACTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28690197 GATTTACTGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
* **
28690224 GATTTATAGAATTACTATTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28690251 GATTTATAGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28690278 GATTTACAGAATTACTGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
*
28690305 GATTTACAAAATTAC
1 GATTTACAGAATTAC
28690320 TAAAATACCC
Statistics
Matches: 184, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 184 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
GATTTACAGAATTACCGTTTTACCCTT
Found at i:28690328 original size:27 final size:27
Alignment explanation
Indices: 28690217--28690464 Score: 110
Period size: 27 Copynumber: 9.1 Consensus size: 27
28690207 ATTACTGTTT
* * ***
28690217 TACCCTTGATTTATAGAATTACTATTT
1 TACCCTTGATTTACAAAATTACTAAAA
* * ****
28690244 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
* ****
28690271 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
*
28690298 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *** *
28690325 TACCCTTGGTTTGTGAAATTACCGAAAA
1 TACCCTTGATTTACAAAATTA-CTAAAA
** ** *
28690353 -ACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* * *
28690379 TACCAC-TAATTTATAAAGTTAC-AAAA
1 TACC-CTTGATTTACAAAATTACTAAAA
28690405 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACTA-AAA
* * *
28690434 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
28690461 TACC
1 TACC
28690465 TTTGGTTTGT
Statistics
Matches: 182, Mismatches: 28, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 15 0.08
27 138 0.76
28 17 0.09
29 11 0.06
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:28690357 original size:81 final size:81
Alignment explanation
Indices: 28690191--28690363 Score: 186
Period size: 81 Copynumber: 2.1 Consensus size: 81
28690181 TTACCGTTTT
* * * * ***
28690191 ACCCTCGATTTACTGAATTACTGTTTTACCCTTGATTTATAGAATTACTATTTTACCCTTGATTT
1 ACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
* ****
28690256 ATAGAATTACTGTTTT
66 ATAGAATTACCGAAAA
* *
28690272 ACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTT
1 ACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
*
28690337 GT-GAAATTACCGAAAA
66 ATAG-AATTACCGAAAA
*
28690353 ACCCTCAATTT
1 ACCCTCGATTT
28690364 GTAAAATTAC
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
80 1 0.01
81 73 0.99
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (81 bp):
ACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
ATAGAATTACCGAAAA
Found at i:28690469 original size:27 final size:27
Alignment explanation
Indices: 28690421--28690472 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28690411 TGACTTTCTA
28690421 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
28690448 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
28690473 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:28690566 original size:27 final size:27
Alignment explanation
Indices: 28690526--28690589 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
28690516 ACCTCTAAAA
*
28690526 GGTAAAA-CACCGTAA-AGCCCCTGTAG
1 GGTAAAATGACCGTAATA-CCCCTGTAG
* *
28690552 GGTAAAGTGACCGTAATACCCCTGTAT
1 GGTAAAATGACCGTAATACCCCTGTAG
28690579 GGTAAAATGAC
1 GGTAAAATGAC
28690590 GAATATGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 6 0.19
27 25 0.78
28 1 0.03
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAATACCCCTGTAG
Found at i:28691779 original size:25 final size:25
Alignment explanation
Indices: 28691750--28691797 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28691740 TTATAATATG
* *
28691750 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
28691775 AAAATTACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28691798 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28691848 original size:9 final size:9
Alignment explanation
Indices: 28691836--28691892 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28691826 TTTGATAAAC
28691836 ATGATATGT
1 ATGATATGT
*
28691845 ATGATATGCAC
1 ATGATATG--T
*
28691856 ATGACATGT
1 ATGATATGT
*
28691865 ATGATATGCAC
1 ATGATATG--T
28691876 ATGATATGT
1 ATGATATGT
28691885 ATGATATG
1 ATGATATG
28691893 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:28691859 original size:20 final size:20
Alignment explanation
Indices: 28691834--28691904 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
28691824 ATTTTGATAA
28691834 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28691854 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28691874 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28691894 ACATGAGATGT
1 ACATGATATGT
28691905 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28691881 original size:11 final size:11
Alignment explanation
Indices: 28691845--28691899 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28691835 CATGATATGT
28691845 ATGATATGCAC
1 ATGATATGCAC
* *
28691856 ATGACATG--T
1 ATGATATGCAC
28691865 ATGATATGCAC
1 ATGATATGCAC
*
28691876 ATGATATG--T
1 ATGATATGCAC
28691885 ATGATATGCAC
1 ATGATATGCAC
28691896 ATGA
1 ATGA
28691900 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28691981 original size:23 final size:23
Alignment explanation
Indices: 28691951--28692116 Score: 251
Period size: 23 Copynumber: 7.1 Consensus size: 23
28691941 AGGAAGTGCA
28691951 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28691974 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28691997 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
28692021 AAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
* * *
28692044 AAAGGGCTTATGCCCTAGTGATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
28692068 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28692091 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28692114 AAA
1 AAA
28692117 AGAGGCAAGG
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
23 88 0.69
24 40 0.31
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28692043 original size:47 final size:47
Alignment explanation
Indices: 28691951--28692118 Score: 266
Period size: 47 Copynumber: 3.6 Consensus size: 47
28691941 AGGAAGTGCA
*
28691951 AAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
28691997 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
28692044 AAAGGGCTTATGCCCTAGTGATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* *
28692091 AAAGGGCTTTTGCCCCAGTTATTAAAAG
1 AAAGGGCTTATGCCCCAGTTATCAAAAG
28692119 AGGCAAGGCC
Statistics
Matches: 111, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 22 0.20
47 89 0.80
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:28692095 original size:70 final size:70
Alignment explanation
Indices: 28691949--28692116 Score: 257
Period size: 70 Copynumber: 2.4 Consensus size: 70
28691939 GGAGGAAGTG
* * *
28691949 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTGATAAAAGGGCTTACGCCCCA
28692014 GTTAT
66 GTTAT
* *
28692019 CAAAAGGGCTTATGCCCCAATTATTAAAGGGCTTATGCCCTAGTGATCAAAAGGGCTTACGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTGAT-AAAAGGGCTTACGCCCC
28692084 AGTTAT
65 AGTTAT
* *
28692090 -TAAAGGGCTTTTGCCCCAGTTATTAAA
1 CAAAAGGGCTTATGCCCCAGTTATTAAA
28692117 AGAGGCAAGG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 68 0.76
71 21 0.24
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (70 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTGATAAAAGGGCTTACGCCCCA
GTTAT
Found at i:28692321 original size:42 final size:42
Alignment explanation
Indices: 28692258--28692349 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
28692248 TAGTCTCCCC
* **
28692258 AAATGGGTTTGCATACATTCATTGGTATT-TCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTAT-ATGTGATATTG
* *
28692300 AAATGGGCTTGCATTCTTTCATTGACATTATATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
28692342 AAATGGGC
1 AAATGGGC
28692350 CTCTGGGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTATATGTGATATTG
Found at i:28693968 original size:29 final size:28
Alignment explanation
Indices: 28693935--28694034 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 28
28693925 ATAGTGAATC
*
28693935 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-A-TCAAACT
28693964 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28693992 C-CACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28694021 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28694035 CAATCTTGTC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
27 19 0.31
28 5 0.08
29 26 0.42
30 12 0.19
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28694029 original size:30 final size:28
Alignment explanation
Indices: 28693934--28694034 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 28
28693924 TATAGTGAAT
* *
28693934 CCGCACACTTAGTGCTATATACATTC-AGC
1 CCGCACACTTAGTGC--TATACAATCAAAC
* *
28693963 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
28693991 TC-CACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATACAA--TCAAAC
28694020 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28694035 CAATCTTGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 24 0.40
28 4 0.07
29 20 0.33
30 12 0.20
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.29
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:28698266 original size:28 final size:27
Alignment explanation
Indices: 28698233--28698288 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
28698223 TTAGAATACT
*
28698233 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-CTAAAAATACCGAAATACCC
* *
28698261 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTCTAAAAATACCGAAATACCC
28698288 T
1 T
28698289 CGATTTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (27 bp):
TTAGTTTCTAAAAATACCGAAATACCC
Found at i:28698272 original size:27 final size:28
Alignment explanation
Indices: 28698242--28698341 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
28698232 TTTAGTTTAC
28698242 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
28698269 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * * *
28698296 TAAATTTACTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
28698323 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
28698342 CCGATTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.11
27 52 0.85
28 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:28698367 original size:27 final size:27
Alignment explanation
Indices: 28698344--28698574 Score: 282
Period size: 27 Copynumber: 8.6 Consensus size: 27
28698334 AAGTACCCCC
*
28698344 GATTTACAGAATTACCGTTTTACCCCT
1 GATTTACAGAATTACCGTTTTACCCTT
* * *
28698371 AATTTACATAATTACCGTTTTACCCCT
1 GATTTACAGAATTACCGTTTTACCCTT
* * *
28698398 GATTTACATAATTATCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28698425 GACTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28698452 GATTTACTGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
* **
28698479 GATTTATAGAATTACTATTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
* *
28698506 GATTTATAGAATTACTGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTT
** *
28698533 GATTTACAGAATTACTATTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTT
*
28698560 GATTTACAAAATTAC
1 GATTTACAGAATTAC
28698575 TAAAATACCC
Statistics
Matches: 183, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 183 1.00
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (27 bp):
GATTTACAGAATTACCGTTTTACCCTT
Found at i:28698583 original size:27 final size:27
Alignment explanation
Indices: 28698472--28698720 Score: 112
Period size: 27 Copynumber: 9.1 Consensus size: 27
28698462 ATTACTGTTT
* * ***
28698472 TACCCTTGATTTATAGAATTACTATTT
1 TACCCTTGATTTACAAAATTACTAAAA
* * ****
28698499 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTTGATTTACAAAATTACTAAAA
* ***
28698526 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTTGATTTACAAAATTACTAAAA
*
28698553 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* *** *
28698580 TACCCTTGGTTTGTGAAATTACCGAAAA
1 TACCCTTGATTTACAAAATTA-CTAAAA
** ** *
28698608 -ACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* * *
28698634 TACCAC-TAATTTATAAAGTTAC-AGAAA
1 TACC-CTTGATTTACAAAATTACTA-AAA
28698661 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACTA-AAA
* * *
28698690 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
28698717 TACC
1 TACC
28698721 TTTGGTTTGT
Statistics
Matches: 183, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.04
27 144 0.79
28 13 0.07
29 19 0.10
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:28698612 original size:81 final size:81
Alignment explanation
Indices: 28698446--28698618 Score: 177
Period size: 81 Copynumber: 2.1 Consensus size: 81
28698436 TTACCGTTTT
* * * * * ***
28698446 ACCCTCGATTTACTGAATTACTGTTTTACCCTTGATTTATAGAATTACTATTTTACCCTTGATTT
1 ACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
* ****
28698511 ATAGAATTACTGTTTT
66 ATAGAATTACCGAAAA
* *
28698527 ACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTT
1 ACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
*
28698592 GT-GAAATTACCGAAAA
66 ATAG-AATTACCGAAAA
*
28698608 ACCCTCAATTT
1 ACCCTCGATTT
28698619 GTAAAATTAC
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
80 1 0.01
81 72 0.99
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (81 bp):
ACCCTCGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGATTT
ATAGAATTACCGAAAA
Found at i:28698725 original size:27 final size:27
Alignment explanation
Indices: 28698677--28698728 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28698667 TGACTTTCTA
28698677 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
28698704 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
28698729 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:28698820 original size:26 final size:27
Alignment explanation
Indices: 28698791--28698845 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
28698781 AGGTAACAAC
* *
28698791 ACCGTAA-AGCCCTGTAGGGTAAAGTG
1 ACCGTAATACCCCTGTAGGGTAAAATG
*
28698817 ACCGTAATACCCCTGTATGGTAAAATG
1 ACCGTAATACCCCTGTAGGGTAAAATG
28698844 AC
1 AC
28698846 GAATATGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (27 bp):
ACCGTAATACCCCTGTAGGGTAAAATG
Found at i:28700031 original size:25 final size:25
Alignment explanation
Indices: 28700002--28700049 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28699992 TTATAATATG
* *
28700002 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
28700027 AAAATTACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28700050 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28700100 original size:9 final size:9
Alignment explanation
Indices: 28700088--28700144 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28700078 TTTGATAAAC
28700088 ATGATATGT
1 ATGATATGT
*
28700097 ATGATATGCAC
1 ATGATATG--T
*
28700108 ATGACATGT
1 ATGATATGT
*
28700117 ATGATATGCAC
1 ATGATATG--T
28700128 ATGATATGT
1 ATGATATGT
28700137 ATGATATG
1 ATGATATG
28700145 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:28700111 original size:20 final size:20
Alignment explanation
Indices: 28700086--28700156 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
28700076 ATTTTGATAA
28700086 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28700106 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28700126 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28700146 ACATGAGATGT
1 ACATGATATGT
28700157 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28700133 original size:11 final size:11
Alignment explanation
Indices: 28700097--28700151 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
28700087 CATGATATGT
28700097 ATGATATGCAC
1 ATGATATGCAC
* *
28700108 ATGACATG--T
1 ATGATATGCAC
28700117 ATGATATGCAC
1 ATGATATGCAC
*
28700128 ATGATATG--T
1 ATGATATGCAC
28700137 ATGATATGCAC
1 ATGATATGCAC
28700148 ATGA
1 ATGA
28700152 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28700233 original size:23 final size:23
Alignment explanation
Indices: 28700203--28700368 Score: 242
Period size: 23 Copynumber: 7.1 Consensus size: 23
28700193 AGGAAGTGCA
28700203 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28700226 AAAGGGCTTATGCCTCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28700249 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
28700273 AAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
* * *
28700296 AAAGGGCTTACGCCCCAGTGATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
28700320 AAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
28700343 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
28700366 AAA
1 AAA
28700369 AGAGGCAAGG
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
23 86 0.67
24 42 0.33
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:28700295 original size:47 final size:47
Alignment explanation
Indices: 28700203--28700370 Score: 257
Period size: 47 Copynumber: 3.6 Consensus size: 47
28700193 AGGAAGTGCA
* *
28700203 AAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCTCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
28700249 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* * *
28700296 AAAGGGCTTACGCCCCAGTGATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
* *
28700343 AAAGGGCTTTTGCCCCAGTTATTAAAAG
1 AAAGGGCTTATGCCCCAGTTATCAAAAG
28700371 AGGCAAGGCC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
46 22 0.20
47 88 0.80
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:28700347 original size:70 final size:70
Alignment explanation
Indices: 28700201--28700368 Score: 248
Period size: 70 Copynumber: 2.4 Consensus size: 70
28700191 GGAGGAAGTG
* * * * *
28700201 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCTCAGTTATTAAAGGGCTTATGCCCCA
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTACGCCCCAGTGATAAAAGGGCTTACGCCCCA
28700266 GTTAT
66 GTTAT
*
28700271 CAAAAGGGCTTATGCCCCAATTATTAAAGGGCTTACGCCCCAGTGATCAAAAGGGCTTACGCCCC
1 CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTACGCCCCAGTGAT-AAAAGGGCTTACGCCCC
28700336 AGTTAT
65 AGTTAT
* *
28700342 -TAAAGGGCTTTTGCCCCAGTTATTAAA
1 CAAAAGGGCTTATGCCCCAGTTATTAAA
28700369 AGAGGCAAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
70 67 0.76
71 21 0.24
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (70 bp):
CAAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTACGCCCCAGTGATAAAAGGGCTTACGCCCCA
GTTAT
Found at i:28701662 original size:55 final size:54
Alignment explanation
Indices: 28701480--28701734 Score: 238
Period size: 55 Copynumber: 4.8 Consensus size: 54
28701470 ACACGGGTAC
* * * * * *
28701480 CTTACCATTGCCATGACTTGTCATGGTCGTACGTGGTATCCTT---TT-GA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
* * ** **
28701529 CTTACCATTGCCATGTCTCAACATGGTCTTACATGGTATCCTTGTTTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
* * * *
28701582 CTCACCAATGCCATGCCTTGGCATGGTCTTACTTGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AA
* * *
28701637 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
*
28701690 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28701735 AAACCCTAAT
Statistics
Matches: 168, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
49 37 0.22
52 4 0.02
53 41 0.24
54 8 0.05
55 76 0.45
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAA
Found at i:28701671 original size:108 final size:110
Alignment explanation
Indices: 28701527--28701723 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 110
28701517 ATCCTTTTGA
* **
28701527 AACTTACCATTGCCATGTCTCAACATGGTCTTACATGGTATCCTTGTTTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAA
28701590 -TGCCATGCCTTGGCATGGTCTTACTTGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACTTGGGACCTTTGCCTTATAGT
* ** *
28701635 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
28701700 TGCCATGCCTTGGCATGGTCTTAC
66 TGCCATGCCTTGGCATGGTCTTAC
28701724 ATGGTATCCT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 47 0.59
109 7 0.09
110 24 0.30
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCAACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACTTGGGACCTTTGCCTTATAGT
Found at i:28703529 original size:19 final size:19
Alignment explanation
Indices: 28703483--28703530 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
28703473 GTATATATTT
28703483 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
28703501 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
28703520 TAAGTTTTATT
1 TAAATTTTATT
28703531 AATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:28706172 original size:21 final size:21
Alignment explanation
Indices: 28706146--28706185 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28706136 TTAAAATTTT
28706146 GTTGACAAGCTAATTCTATCC
1 GTTGACAAGCTAATTCTATCC
*
28706167 GTTGACATGCTAATTCTAT
1 GTTGACAAGCTAATTCTAT
28706186 TCAAATCCAT
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:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTGACAAGCTAATTCTATCC
Found at i:28717155 original size:16 final size:16
Alignment explanation
Indices: 28717130--28717166 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28717120 CTCTACACAG
*
28717130 GTGA-GGTGATGTGAT
1 GTGATGGTGATGTAAT
28717145 GTGATGGTGATGTAAT
1 GTGATGGTGATGTAAT
28717161 GTGATG
1 GTGATG
28717167 TACTCCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (16 bp):
GTGATGGTGATGTAAT
Found at i:28719443 original size:49 final size:49
Alignment explanation
Indices: 28719332--28719503 Score: 197
Period size: 49 Copynumber: 3.6 Consensus size: 49
28719322 GATGCCAATG
* ** * * **
28719332 CCATGTCCTAGACATGGTCTTACACTGGCTCATC--TATCAA-GTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAACT-ATCGAAATCAAGGCCGACA
* *
28719379 CCATGTCCCAAACATGGTATTACACTAACTATCGAAATCAAGGCCGACA
1 CCATGTCCCAGACATGGTCTTACACTAACTATCGAAATCAAGGCCGACA
* ** *
28719428 CCATGTCCCAGACATGGTCTTATACTAACTATCGAAATTGAGGCTGACA
1 CCATGTCCCAGACATGGTCTTACACTAACTATCGAAATCAAGGCCGACA
28719477 CCATGTCCCAGACATGGTCTTACACTA
1 CCATGTCCCAGACATGGTCTTACACTA
28719504 GCCCTCACAT
Statistics
Matches: 106, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
46 3 0.03
47 25 0.24
48 5 0.05
49 73 0.69
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACACTAACTATCGAAATCAAGGCCGACA
Found at i:28719616 original size:46 final size:48
Alignment explanation
Indices: 28719478--28719696 Score: 172
Period size: 46 Copynumber: 4.7 Consensus size: 48
28719468 AGGCTGACAC
* ** *
28719478 CATGTCCCAGACATGGTCTTACACTAGCCCTCACATATCCGT-GCAGATG
1 CATGTCCCAGACATGGTCTTACACTAG--CTCACATCTCAATAGCCGATG
** * *
28719527 CCATGTCCCAGACATGGTCTTGTACT-G-ACACATCTC-GTAGCCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAATAGCCGATG
* *
28719573 CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTCAAT-GCCGATC
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAATAGCCGATG
* * * *
28719619 CAT-TCCCAAACATGGTCTTACACTGGCTCTCA--T-AATGTGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAA--TAGCCGATG
* *
28719665 CATGTCCCAAACAT-GTCTTACACTAGCCCACA
1 CATGTCCCAGACATGGTCTTACACTAGCTCACA
28719697 AATAACCCGA
Statistics
Matches: 143, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
43 2 0.01
44 9 0.06
45 27 0.19
46 70 0.49
47 11 0.08
49 1 0.01
50 23 0.16
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (48 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCACATCTCAATAGCCGATG
Found at i:28723574 original size:78 final size:79
Alignment explanation
Indices: 28723408--28723601 Score: 248
Period size: 78 Copynumber: 2.5 Consensus size: 79
28723398 TCGTTCAAAC
* ** * *
28723408 GCCTTCGGGACATAGCCC-GATTATGGTAACCCGCACAAATGCCTTCGGGACTTAACCCGGGTAT
1 GCCTTCGGG-CTTAGCCCGGA-TATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATAT
28723472 CACAACTCGAACAATT
64 CACAACTCGAACAATT
* *
28723488 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATCA
* * *
28723552 CAATTCGCACATTT
66 CAACTCGAACAATT
* *
28723566 GCCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
28723602 TTCATACACA
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
78 59 0.58
79 31 0.31
80 11 0.11
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (79 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATCA
CAACTCGAACAATT
Found at i:28723603 original size:39 final size:39
Alignment explanation
Indices: 28723439--28723601 Score: 245
Period size: 39 Copynumber: 4.2 Consensus size: 39
28723429 TATGGTAACC
* * *
28723439 CGCACAAATGCCTTCGGGACTTAACCCGGGTATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28723479 CGAACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28723518 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
28723557 CGCACATTTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28723596 CGCACA
1 CGCACA
28723602 TTCATACACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 98 0.86
40 16 0.14
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28733492 original size:29 final size:28
Alignment explanation
Indices: 28733442--28733496 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
28733432 ATAATTTATA
28733442 CGATTTAGTCCAAAATCTTATTCTTTCCC
1 CGATTTAGTCCAAAATCTTATT-TTTCCC
* *
28733471 CGATTTAGTTCCAGACTC-TATTTTTC
1 CGATTTAG-TCCAAAATCTTATTTTTC
28733497 TTGATCTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 12 0.52
30 7 0.30
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.44
Consensus pattern (28 bp):
CGATTTAGTCCAAAATCTTATTTTTCCC
Found at i:28742890 original size:21 final size:21
Alignment explanation
Indices: 28742841--28742893 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
28742831 ACCTGTCATG
* *
28742841 GAGTATTGATATATTTACCCC
1 GAGTATTGATACACTTACCCC
*
28742862 -AATATTGATACACTTACCCC
1 GAGTATTGATACACTTACCCC
28742882 GAGTATTGATAC
1 GAGTATTGATAC
28742894 TTGAGTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (21 bp):
GAGTATTGATACACTTACCCC
Found at i:28746023 original size:27 final size:27
Alignment explanation
Indices: 28745970--28746024 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
28745960 TTAATGAATA
*
28745970 ATTATGTTAGTTATATCTTAAGTGATT
1 ATTATGTTAGTTATATCTTAAGAGATT
28745997 ATTATG-T-GTTATATGCTTAAAGAGATT
1 ATTATGTTAGTTATAT-CTT-AAGAGATT
28746024 A
1 A
28746025 AATAGTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 14 0.56
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (27 bp):
ATTATGTTAGTTATATCTTAAGAGATT
Found at i:28747963 original size:45 final size:45
Alignment explanation
Indices: 28747898--28748119 Score: 372
Period size: 45 Copynumber: 4.9 Consensus size: 45
28747888 TATATCATTG
* * *
28747898 CACCGGCATTATAGCCTGCTAGGCTCGAAGGCCTGAATAGTATCT
1 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* *
28747943 CACTGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
28747988 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
*
28748033 CACTGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
1 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
* *
28748078 CACCGGTATCATAACCTGCTAGGCTCAAAGGCCCGAATAGTA
1 CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTA
28748120 CCGTATGATA
Statistics
Matches: 168, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 168 1.00
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (45 bp):
CACCGGCATCATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATCT
Found at i:28751702 original size:46 final size:47
Alignment explanation
Indices: 28751600--28751771 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 47
28751590 ACATTATGAG
* *
28751600 AGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACATTGAGACGAGT
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAG-CATCGAGACGAGT
* *
28751649 -GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGAC-A-T
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGACGAGT
* *
28751693 AAGCCAGTGTAAGACATGTTTGGGACATGCATCAGC-TACTAGA--AGT
1 -AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCAT-CGAGACGAGT
* *
28751739 -GTCAGTGTGAGACCATGTCTGGGACATGGCATC
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
28751772 GGCACCGATA
Statistics
Matches: 106, Mismatches: 10, Indels: 17
0.80 0.08 0.13
Matches are distributed among these distances:
44 11 0.10
45 16 0.15
46 54 0.51
47 14 0.13
48 11 0.10
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (47 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGACGAGT
Found at i:28762654 original size:40 final size:40
Alignment explanation
Indices: 28762617--28762799 Score: 209
Period size: 40 Copynumber: 4.6 Consensus size: 40
28762607 GCTACTCGTT
*
28762617 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28762657 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
*
28762697 CAAATGCCTTC-GG-CTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * *
28762735 CAAATGCCTTC-GGATCTTAGTCTGGATT-TAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TTATAGTAAC-TCGCA
28762776 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28762800 ACATCATTCG
Statistics
Matches: 123, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
38 34 0.28
39 2 0.02
40 74 0.60
41 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28762738 original size:78 final size:82
Alignment explanation
Indices: 28762617--28762800 Score: 247
Period size: 78 Copynumber: 2.3 Consensus size: 82
28762607 GCTACTCGTT
* *
28762617 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
*
28762680 GGATTTAGTAAC-TCGCA
65 GGATTTAGTAACTTAGCA
** *
28762697 CAAATGCCTTC-GG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCTG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
*
28762759 GATTTAGTCACTTAGCA
66 GATTTAGTAACTTAGCA
28762776 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28762801 CATCATTCGA
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
77 3 0.03
78 54 0.59
79 13 0.14
80 22 0.24
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATTTAGTAACTTAGCA
Found at i:28783885 original size:15 final size:16
Alignment explanation
Indices: 28783857--28783886 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28783847 GTTGGAATAA
28783857 ATTGAATGTGAGTTAT
1 ATTGAATGTGAGTTAT
28783873 ATTGAAT-TGAGTTA
1 ATTGAATGTGAGTTA
28783887 AATCCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (16 bp):
ATTGAATGTGAGTTAT
Found at i:28784224 original size:25 final size:25
Alignment explanation
Indices: 28784171--28784250 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
28784161 TATTGATTTT
* **
28784171 AGCTCTTATGAGCTTACCAATACTT-
1 AGCTCCTATGAGCTTACCGTTA-TTC
28784196 AGCTCCTATGAGCTTACCGTTATTC
1 AGCTCCTATGAGCTTACCGTTATTC
*** * *
28784221 AGCTTGGAGGAGCTTATCGTTATTC
1 AGCTCCTATGAGCTTACCGTTATTC
28784246 AGCTC
1 AGCTC
28784251 GGAGGTGTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 2 0.04
25 43 0.96
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (25 bp):
AGCTCCTATGAGCTTACCGTTATTC
Found at i:28784254 original size:25 final size:25
Alignment explanation
Indices: 28784205--28784255 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
28784195 TAGCTCCTAT
*
28784205 GAGCTTACCGTTATTCAGCTTGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
*
28784230 GAGCTTATCGTTATTCAGCTCGGAG
1 GAGCTTACCGTTATTCAGCTCGGAG
28784255 G
1 G
28784256 TGTAACATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCGGAG
Found at i:28794613 original size:93 final size:93
Alignment explanation
Indices: 28794485--28794656 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
28794475 GCCCATAAGT
* *
28794485 GAACTCGGACTCAACTCAACAAACTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
28794550 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * ** *
28794578 GAACTCGGACTCAACTCTACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
28794643 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
28794657 CAAATATCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAACTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28794652 original size:46 final size:46
Alignment explanation
Indices: 28794477--28794652 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
28794467 TGTAACCCGC
* * * *
28794477 CCATAAGTGAACTCGGACTCAACTCAACAAACTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
28794523 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
28794569 ACATCTCTCGAACTCGGACTCAACTCTACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28794616 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
28794653 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 66 0.63
47 30 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:28794671 original size:46 final size:44
Alignment explanation
Indices: 28794528--28794671 Score: 98
Period size: 46 Copynumber: 3.1 Consensus size: 44
28794518 CGCATCCATA
* * *
28794528 AGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * * *
28794577 --CGAACTCGGACTCAACTCTACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
28794620 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
28794667 AGTGA
1 AGTGA
28794672 CATGTCACTT
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 32 0.43
47 26 0.35
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:28798952 original size:40 final size:40
Alignment explanation
Indices: 28798897--28799117 Score: 347
Period size: 40 Copynumber: 5.5 Consensus size: 40
28798887 CATTTGAATG
*
28798897 ATATCCGGGCTAAGACCCGAAGGCATTTGTGTGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
28798937 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
28798977 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
*
28799017 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
* * * * * *
28799057 ATGTCCGGGTTAAGACCCGAAGGCAATTGGGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
28799097 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
28799118 AAGCTTGGGT
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.07
40 156 0.92
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTT
Found at i:28806057 original size:78 final size:80
Alignment explanation
Indices: 28805937--28806117 Score: 246
Period size: 78 Copynumber: 2.3 Consensus size: 80
28805927 TACTCGTTCA
* *
28805937 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTT-ACCCGG
*
28806000 ATTTAGTAAC-TCGCAC
64 ATTTAGTAACTTAGCAC
**
28806016 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTACCCGGAT
*
28806079 TTAGTCACTTAGCAC
66 TTAGTAACTTAGCAC
*
28806094 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28806118 CATCATTCGA
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
77 16 0.18
78 51 0.56
79 24 0.26
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTACCCGGAT
TTAGTAACTTAGCAC
Found at i:28806059 original size:39 final size:40
Alignment explanation
Indices: 28805935--28806117 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
28805925 GCTACTCGTT
*
28805935 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28805975 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28806015 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28806053 CAAATGCCTTC-GGATCTTAG-TCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28806093 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28806118 CATCATTCGA
Statistics
Matches: 127, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
38 26 0.20
39 43 0.34
40 56 0.44
41 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28814078 original size:78 final size:81
Alignment explanation
Indices: 28813958--28814139 Score: 257
Period size: 78 Copynumber: 2.3 Consensus size: 81
28813948 TACTCGTTCA
* *
28813958 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
28814021 ATTTAGTAAC-TCGCAC
65 ATTTAGTAACTTAGCAC
**
28814037 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
28814100 TTTAGTCACTTAGCAC
66 TTTAGTAACTTAGCAC
*
28814116 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28814140 CATCATTCGA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
77 3 0.03
78 49 0.53
79 29 0.32
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TTTAGTAACTTAGCAC
Found at i:28814139 original size:40 final size:40
Alignment explanation
Indices: 28813956--28814139 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
28813946 GCTACTCGTT
*
28813956 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28813996 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28814036 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28814074 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28814115 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28814140 CATCATTCGA
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
38 26 0.20
39 21 0.16
40 69 0.53
41 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28817341 original size:30 final size:30
Alignment explanation
Indices: 28817306--28817367 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
28817296 TGAAAGTAAG
28817306 TATAATTATGATGATTTAAATGTTCAATAT
1 TATAATTATGATGATTTAAATGTTCAATAT
28817336 TATAATTATGATGATTTAAATGTTCAATAT
1 TATAATTATGATGATTTAAATGTTCAATAT
28817366 TA
1 TA
28817368 ATTCGACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (30 bp):
TATAATTATGATGATTTAAATGTTCAATAT
Found at i:28825292 original size:47 final size:46
Alignment explanation
Indices: 28825235--28825468 Score: 281
Period size: 47 Copynumber: 5.0 Consensus size: 46
28825225 ACACGTTTCG
* ** * * *
28825235 CATTAGCCATTCGGCTTCGCCACATATATAC-TCTTCCACGTTCATCA
1 CATTGGCCATTCGGCTT-ATCACATATATGCATGTT-CACATTCATCA
** *
28825282 CATTGGCCATTCTACCTTATCACATATATGCATGTTCGCATTCATCA
1 CATTGGCCATTC-GGCTTATCACATATATGCATGTTCACATTCATCA
28825329 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGG-CTTATCACATATATGCATGTTCACATTCATCA
28825376 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGG-CTTATCACATATATGCATGTTCACATTCATCA
* * * **
28825423 CATTGGCCATTCGGCCTTATCTCAAATATACACATTCACATTCATC
1 CATTGGCCATTCGG-CTTATCACATATATGCATGTTCACATTCATC
28825469 TCATAAAATC
Statistics
Matches: 167, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
47 161 0.96
48 6 0.04
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (46 bp):
CATTGGCCATTCGGCTTATCACATATATGCATGTTCACATTCATCA
Found at i:28825350 original size:22 final size:22
Alignment explanation
Indices: 28825325--28825443 Score: 66
Period size: 22 Copynumber: 5.1 Consensus size: 22
28825315 GTTCGCATTC
28825325 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
28825347 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
28825371 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
* * *
28825394 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
28825418 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28825441 ATC
1 ATC
28825444 TCAAATATAC
Statistics
Matches: 71, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
22 23 0.32
23 14 0.20
24 14 0.20
25 20 0.28
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28829037 original size:12 final size:12
Alignment explanation
Indices: 28829020--28829044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28829010 TTATTAAATG
28829020 AATTAAAAGCCA
1 AATTAAAAGCCA
28829032 AATTAAAAGCCA
1 AATTAAAAGCCA
28829044 A
1 A
28829045 TTTTTGTCCA
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:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AATTAAAAGCCA
Found at i:28829976 original size:43 final size:42
Alignment explanation
Indices: 28829854--28830005 Score: 196
Period size: 42 Copynumber: 3.6 Consensus size: 42
28829844 TAAGACTATG
* * *
28829854 TGTAAGACCATATCTGGGATATGGCATCTATATGAGACTTCG
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
* *
28829896 TGTAGGACCATATCTGGGATATGGCATCGATATGAGATTTCT
1 TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
* * * *
28829938 TGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTACA
1 TGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATTTCA
* *
28829981 TGTAAGCCCATTTCTGGGATATGGC
1 TGTAAGACCATATCTGGGATATGGC
28830006 GTTGGTATGG
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
42 60 0.63
43 35 0.37
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCA
Found at i:28830851 original size:28 final size:29
Alignment explanation
Indices: 28830820--28830879 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
28830810 GATTTTTTAC
*
28830820 AAAAATGTCAATT-AGGGATTAAATTGAG
1 AAAAATGTAAATTGAGGGATTAAATTGAG
* *
28830848 AAAAATGTAAATTGAGGGGTTAAATTGTG
1 AAAAATGTAAATTGAGGGATTAAATTGAG
28830877 AAA
1 AAA
28830880 TAAATGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.28
Consensus pattern (29 bp):
AAAAATGTAAATTGAGGGATTAAATTGAG
Found at i:28831416 original size:43 final size:42
Alignment explanation
Indices: 28831364--28831526 Score: 141
Period size: 43 Copynumber: 3.8 Consensus size: 42
28831354 ATCGAGATGT
* * *
28831364 GATTCCATGTAATACCATGTCTGGGACATCGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACAT-GGCATCGTATTGA
* * * *
28831407 GATTACATGTAAGAACATGTCTGGCACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACA-TGGCATCG-TATTGA
* * * *
28831450 GATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACA-TGGCATCGTAT-TGA
* * *
28831493 GATAACATGTAAGACCATATCTGGGATATGGCAT
1 GATTACATGTAAGACCATGTCTGGGACATGGCAT
28831527 TGTACTAACT
Statistics
Matches: 95, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 83 0.87
44 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (42 bp):
GATTACATGTAAGACCATGTCTGGGACATGGCATCGTATTGA
Found at i:28834146 original size:40 final size:39
Alignment explanation
Indices: 28834082--28834241 Score: 176
Period size: 39 Copynumber: 4.1 Consensus size: 39
28834072 GCTACTCGTT
* * * ** *
28834082 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* * *
28834122 CAAATGCCTTCGGGACTTAACCCGGGTATCACAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* *
28834162 CAATTGCCTTCGGGCTTAGCCCAGATATCATAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * *
28834201 CAATTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
28834240 CA
1 CA
28834242 TTCATACACA
Statistics
Matches: 104, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 59 0.57
40 45 0.43
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.22
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
Found at i:28834182 original size:79 final size:79
Alignment explanation
Indices: 28834087--28834241 Score: 204
Period size: 79 Copynumber: 2.0 Consensus size: 79
28834077 TCGTTCAAAC
* * ** *
28834087 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATGCCTTCGGGACTTAACCCGGGTATC
1 GCCTTCGGGACATAGCCCAGATATCATAACCCGCACAAATGCCTTCGGG-CTTAACCCGGATATC
28834152 ACAACTCGCACAATT
65 ACAACTCGCACAATT
* * * *
28834167 GCCTTCGGG-CTTAGCCCAGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGACATAGCCCAGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCA
*
28834231 CAATTCGCACA
66 CAACTCGCACA
28834242 TTCATACACA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 24 0.37
79 32 0.49
80 9 0.14
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (79 bp):
GCCTTCGGGACATAGCCCAGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCA
CAACTCGCACAATT
Found at i:28834202 original size:39 final size:39
Alignment explanation
Indices: 28834118--28834241 Score: 185
Period size: 39 Copynumber: 3.2 Consensus size: 39
28834108 TATGGTAACC
* * *
28834118 CGCACAAATGCCTTCGGGACTTAACCCGGGTATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28834158 CGCACAATTGCCTTCGGGCTTAGCCCAGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28834197 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28834236 CGCACA
1 CGCACA
28834242 TTCATACACA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 59 0.78
40 17 0.22
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28838094 original size:29 final size:29
Alignment explanation
Indices: 28838061--28838192 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
28838051 GTGACGAGAT
28838061 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28838090 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
28838119 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
28838148 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
28838177 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28838193 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28845560 original size:29 final size:29
Alignment explanation
Indices: 28845527--28845658 Score: 149
Period size: 29 Copynumber: 4.6 Consensus size: 29
28845517 GTGACGAGAT
28845527 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28845556 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * ***
28845585 TGGCACTAAGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
28845614 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
28845643 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
28845659 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28852929 original size:40 final size:39
Alignment explanation
Indices: 28852865--28853102 Score: 242
Period size: 39 Copynumber: 6.1 Consensus size: 39
28852855 GCTACTCGTT
* * * ** *
28852865 CAAACGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
* * * *
28852905 CAAATGCCTTCGGGACTTAACCCGGGTATCACAACTCACA
1 CAAATGCCTTCGGG-CTTAGCCCGGATATCATAACTCGCA
*
28852945 CAATTGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
* * * *
28852984 CAATTGCCTTCAGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
** * * *
28853023 CATTTGCCTTCGGGCTTAGCCTGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
** * *
28853062 CATTTGCCTTCGGGCTTAGCCCGGATATCACAATTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
28853101 CA
1 CA
28853103 TTCATACACA
Statistics
Matches: 177, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
39 133 0.75
40 44 0.25
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATCATAACTCGCA
Found at i:28853034 original size:78 final size:78
Alignment explanation
Indices: 28852870--28853104 Score: 308
Period size: 78 Copynumber: 3.0 Consensus size: 78
28852860 TCGTTCAAAC
* * ** * * * *
28852870 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATGCCTTCGGGACTTAACCCGGGTATC
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGG-CTTAGCCCGGATATC
* * *
28852935 ACAACTCACACAATT
64 ACAATTCGCACATTT
*
28852950 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCAGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28853015 AATTCGCACATTT
66 AATTCGCACATTT
* * * *
28853028 GCCTTCGGGCTTAGCCTGGATATCACAATTCGCACATTTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28853093 AATTCGCACATT
66 AATTCGCACATT
28853105 CATACACATC
Statistics
Matches: 138, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
78 97 0.70
79 32 0.23
80 9 0.07
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
AATTCGCACATTT
Found at i:28853103 original size:39 final size:39
Alignment explanation
Indices: 28852909--28853104 Score: 293
Period size: 39 Copynumber: 5.0 Consensus size: 39
28852899 CCCGCACAAA
* * * * *
28852909 TGCCTTCGGGACTTAACCCGGGTATCACAACTCACACAAT
1 TGCCTTCGGG-CTTAGCCCGGATATCACAATTCGCACATT
* * *
28852949 TGCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAAT
1 TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
*
28852988 TGCCTTCAGGCTTAGCCCGGATATCACAATTCGCACATT
1 TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
*
28853027 TGCCTTCGGGCTTAGCCTGGATATCACAATTCGCACATT
1 TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
28853066 TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
1 TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
28853105 CATACACATC
Statistics
Matches: 145, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 135 0.93
40 10 0.07
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (39 bp):
TGCCTTCGGGCTTAGCCCGGATATCACAATTCGCACATT
Found at i:28858122 original size:39 final size:39
Alignment explanation
Indices: 28857948--28858106 Score: 264
Period size: 39 Copynumber: 4.1 Consensus size: 39
28857938 TGTGAATATA
*
28857948 TATATGCGAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTTATGTCCGCAGGC
*
28857987 TATATGCAAGAATTATATCCGGACTTTATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTTATGTCCGCAGGC
* *
28858026 TATATGCGAGAATTATATTCTGACTTTATGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTTATGTCCGCAGGC
* *
28858065 TATATGCGAGAATTATATCCAGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTTATGTCCGCAGGC
28858104 TAT
1 TAT
28858107 GTGCTGGACA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTTATGTCCGCAGGC
Found at i:28864832 original size:15 final size:14
Alignment explanation
Indices: 28864806--28864839 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
28864796 GACTTCTTTA
28864806 AATTTAAATTTTTT
1 AATTTAAATTTTTT
*
28864820 TATTTATAATTTTTT
1 AATTTA-AATTTTTT
28864835 AATTT
1 AATTT
28864840 TTTTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
AATTTAAATTTTTT
Found at i:28864863 original size:19 final size:19
Alignment explanation
Indices: 28864822--28864869 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28864812 AATTTTTTTA
* *
28864822 TTTATAATTTTTTAATTTT
1 TTTATATTTTTTTAATTAT
28864841 TTTATATTTTTATTAA-TAT
1 TTTATATTTTT-TTAATTAT
28864860 TTTATATTTT
1 TTTATATTTT
28864870 AAAATATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATATTTTTTTAATTAT
Found at i:28864877 original size:17 final size:19
Alignment explanation
Indices: 28864822--28864877 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
28864812 AATTTTTTTA
* *
28864822 TTTATAATTTTT-TAATTTT
1 TTTAT-ATTTTTATAAATAT
*
28864841 TTTATATTTTTATTAATAT
1 TTTATATTTTTATAAATAT
28864860 TTTATA-TTTTA-AAATAT
1 TTTATATTTTTATAAATAT
28864877 T
1 T
28864878 ACTAAATGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.19
18 11 0.34
19 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATTTTTATAAATAT
Found at i:28865150 original size:2 final size:2
Alignment explanation
Indices: 28865145--28865178 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28865135 TATATATGTA
*
28865145 AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28865179 CATATTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28868260 original size:14 final size:16
Alignment explanation
Indices: 28868233--28868264 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
28868223 TCTAAAGACT
28868233 AAAAATGATCAAATTA
1 AAAAATGATCAAATTA
28868249 AAAAAT-AT-AAATTA
1 AAAAATGATCAAATTA
28868263 AA
1 AA
28868265 TTTACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAAATGATCAAATTA
Found at i:28868275 original size:7 final size:7
Alignment explanation
Indices: 28868263--28868290 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28868253 ATATAAATTA
28868263 AATTTAC
1 AATTTAC
28868270 AATTTAC
1 AATTTAC
28868277 AATTTAC
1 AATTTAC
28868284 AATTTAC
1 AATTTAC
28868291 GAGATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTTAC
Found at i:28886426 original size:28 final size:29
Alignment explanation
Indices: 28886368--28886437 Score: 133
Period size: 28 Copynumber: 2.4 Consensus size: 29
28886358 GACGAGATTA
28886368 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
28886397 GCACTAAGTGTGCATGC-GGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
28886425 GCACTAAGTGTGC
1 GCACTAAGTGTGC
28886438 GAGCTCGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (29 bp):
GCACTAAGTGTGCATGCTGGAAATATATG
Found at i:28893497 original size:29 final size:29
Alignment explanation
Indices: 28893455--28893525 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
28893445 GACGAGATTA
28893455 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
28893484 GCACTAAGTGTGCATGCTGGAAATATATG
1 GCACTAAGTGTGCATGCTGGAAATATATG
28893513 GCACTAAGTGTGC
1 GCACTAAGTGTGC
28893526 GAGCTCGAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (29 bp):
GCACTAAGTGTGCATGCTGGAAATATATG
Found at i:28893541 original size:29 final size:29
Alignment explanation
Indices: 28893455--28893585 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 29
28893445 GACGAGATTA
* **
28893455 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGA-GCTCGAAACGTATG
* **
28893484 GCACTAAGTGTGC-ATGCTGGAAATATATG
1 GCACTAAGTGTGCGA-GCTCGAAACGTATG
**
28893513 GCACTAAGTGTGCGAGCTCGAAGGGTATG
1 GCACTAAGTGTGCGAGCTCGAAACGTATG
* * * *
28893542 GCACTATGTGTGCGGGCT-TAAATCGCATG
1 GCACTAAGTGTGCGAGCTCGAAA-CGTATG
28893571 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
28893586 AATCGAGTGT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
28 2 0.02
29 85 0.97
30 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTCGAAACGTATG
Found at i:28905863 original size:39 final size:39
Alignment explanation
Indices: 28905809--28905957 Score: 246
Period size: 39 Copynumber: 3.8 Consensus size: 39
28905799 TGTTCGGGTA
*
28905809 ATATCCGGGCTAAGCCTGAAGGCAATTGTGCGAGTTGTG
1 ATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTG
*
28905848 ATATCCGGGCTAAGCCCGAAGGCAATTGTGTGAGTTGTG
1 ATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTG
*
28905887 ATATCCGGGCTAAGCCCGAAGACAATTGTGCGAGTTGTG
1 ATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTG
*
28905926 ATATCCGGGTTAAGTCCCGAAGGC-ATTGTGCG
1 ATATCCGGGCTAAG-CCCGAAGGCAATTGTGCG
28905958 GGCTACCATA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
39 95 0.92
40 8 0.08
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.25
Consensus pattern (39 bp):
ATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTG
Found at i:28905973 original size:78 final size:78
Alignment explanation
Indices: 28905813--28905986 Score: 224
Period size: 78 Copynumber: 2.2 Consensus size: 78
28905803 CGGGTAATAT
* *
28905813 CCGGGCTAAGCCTGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
1 CCGGGCTAAGCCCGAAGACAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
* * *** *
28905878 TGAGTTGTGATAT
66 CGAGCTACCATAA
*
28905891 CCGGGCTAAGCCCGAAGACAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC-ATTGT
1 CCGGGCTAAGCCCGAAGACAATTGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGT
*
28905955 GCGGGCTACCATAA
65 GCGAGCTACCATAA
*
28905969 CCGGGCTATGTCCCGAAG
1 CCGGGCTAAG-CCCGAAG
28905987 GTGTTTGAAC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
78 67 0.81
79 16 0.19
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGACAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTG
CGAGCTACCATAA
Found at i:28911820 original size:80 final size:81
Alignment explanation
Indices: 28911682--28911901 Score: 221
Period size: 80 Copynumber: 2.7 Consensus size: 81
28911672 GAATCACGTA
* * ** * * *
28911682 CCTTC-GGAATTTAACCGGATATAGCGACTAGCTCGATTGTCTTCGGGACATT-GCCCGGTTATA
1 CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGAC-TTAGCCCGGTTATA
* * *
28911745 GTGATTCGCAC-AATTG
65 GTAACTCGCACAAAATG
* * * *
28911761 CCTTCGGGAATTTACCCGGATTTAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGTTTTGG
1 CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
28911826 TAACTCGCACAAAATG
66 TAACTCGCACAAAATG
* * * * * *
28911842 CCTTCGGGACTTAACCCGGTTTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 CCTTCGGGAATTTACCCGGATTTAGTAAC-TAGCACGAATGCCTTCGGGACTTAGCCCGG
28911902 ATACCATTCG
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
79 7 0.06
80 53 0.46
81 29 0.25
82 26 0.23
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (81 bp):
CCTTCGGGAATTTACCCGGATTTAGTAACTAGCACGAATGCCTTCGGGACTTAGCCCGGTTATAG
TAACTCGCACAAAATG
Found at i:28911854 original size:41 final size:40
Alignment explanation
Indices: 28911722--28911901 Score: 200
Period size: 40 Copynumber: 4.5 Consensus size: 40
28911712 GCTCGATTGT
* * * * *
28911722 CTTCGGGACATT-GCCCGGTTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAACCCGGTTTTAGTAACTCGCACAAATGC
* * * *
28911762 CTTCGGGAATTTACCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
*
28911802 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAAATGC
1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCAC-AAATGC
* * *
28911843 CTTCGGGACTTAACCCGGTTTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAACCCGGTTTTAGTAAC-TCGCACAAATGC
*
28911884 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAACCCGG
28911902 ATACCATTCG
Statistics
Matches: 119, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
39 2 0.02
40 59 0.50
41 53 0.45
42 5 0.04
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGC
Found at i:28921591 original size:47 final size:49
Alignment explanation
Indices: 28921475--28921652 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 49
28921465 TGTAACCCGC
* * * *
28921475 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGG--G-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
28921521 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
28921570 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
28921613 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
28921653 TCAACCATCC
Statistics
Matches: 112, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 31 0.28
46 33 0.29
47 31 0.28
48 3 0.03
49 4 0.04
50 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Done.