Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 131 of 171
Found at i:40978508 original size:40 final size:41
Alignment explanation
Indices: 40978446--40978692 Score: 110
Period size: 40 Copynumber: 5.6 Consensus size: 41
40978436 CATCTTGCTC
*
40978446 TTACTACAACTT-TAGAGAGATAAAGGTTCGTTATCCAACT
1 TTACTACAACTTCAAGAGAGATAAAGGTTCGTTATCCAACT
* * ***
40978486 TTACTATAACTTCAAGAG-GATAAGAATTGACGTTTGAAGCTTCATCTTGCT
1 TTACTACAACTTCAAGAGAGAT-A-AA--G--G-TT--CG-TT-ATCCAACT
40978537 CTTACTACAACTTC-AGAGAGATAAAGGTTCGTTATCCAACT
1 -TTACTACAACTTCAAGAGAGATAAAGGTTCGTTATCCAACT
* * * ***
40978578 TTACTATAAATTCAAGAG-GATAAGAATTGACGTTTGAAGCTTCATCTTGCT
1 TTACTACAACTTCAAGAGAGAT-A-AA--G--G-TT--CG-TT-ATCCAACT
40978629 CTTACTACAACTTC-AGAGAGATAAAGGTTCGTTATCCAACT
1 -TTACTACAACTTCAAGAGAGATAAAGGTTCGTTATCCAACT
* *
40978670 TTACTATAAATTCAAGAG-GATAA
1 TTACTACAACTTCAAGAGAGATAA
40978693 GAATTGATGT
Statistics
Matches: 153, Mismatches: 25, Indels: 58
0.65 0.11 0.25
Matches are distributed among these distances:
40 44 0.29
41 24 0.16
42 8 0.05
43 2 0.01
44 2 0.01
45 4 0.03
46 4 0.03
47 4 0.03
48 2 0.01
49 2 0.01
50 8 0.05
51 20 0.13
52 29 0.19
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (41 bp):
TTACTACAACTTCAAGAGAGATAAAGGTTCGTTATCCAACT
Found at i:40990582 original size:60 final size:60
Alignment explanation
Indices: 40990444--40990621 Score: 220
Period size: 60 Copynumber: 3.0 Consensus size: 60
40990434 GGTTGAAATT
* * * *
40990444 GGGTCAAAAA-CGAGATTTTGGAAAGTTCAAGGGTAAAATGGTAATTTTTTTGTAAAAAT-AA
1 GGGTCAAAAATAGA-ATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTTTGGT-AAAATCAA
*
40990505 GGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCAA
1 GGGTCAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCAA
* * *
40990565 GGTTTAAAAATAGAATTTTAGAAAGTTT-GAGGGTAAAATGGTAA-TTTTGGTAAAATC
1 GGGTCAAAAATAGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTTGGTAAAATC
40990622 GGAGGCAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
59 19 0.18
60 47 0.44
61 38 0.36
62 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (60 bp):
GGGTCAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTAAAATCAA
Found at i:40990656 original size:28 final size:27
Alignment explanation
Indices: 40990571--40990675 Score: 77
Period size: 29 Copynumber: 3.7 Consensus size: 27
40990561 TCAAGGTTTA
* * * *
40990571 AAAATAGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGAATTTTTGAAA-ATTGAGGGC
* *
40990599 AAAATGGTAATTTTGGTAAAATCG-GAGGC
1 AAAATGG-AATTTTTG-AAAATTGAG-GGC
40990628 AAAATGGAATTTTTGAAAACTTGAGGGC
1 AAAATGGAATTTTTGAAAA-TTGAGGGC
*
40990656 AAAAATGAAATTTTTAGAAA
1 -AAAATGGAATTTTT-GAAA
40990676 GTTTTGAGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
27 4 0.06
28 19 0.31
29 32 0.52
30 7 0.11
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.30
Consensus pattern (27 bp):
AAAATGGAATTTTTGAAAATTGAGGGC
Found at i:40990690 original size:31 final size:31
Alignment explanation
Indices: 40990648--40990810 Score: 112
Period size: 31 Copynumber: 5.4 Consensus size: 31
40990638 TTTTGAAAAC
*
40990648 TTGAGGGCAAAAATGAAATTTTTAGAAAGTT
1 TTGAGGTCAAAAATGAAATTTTTAGAAAGTT
*
40990679 TTGAGGTCAAAAAT-ATAATTTTCA-AAAGGTT
1 TTGAGGTCAAAAATGA-AATTTTTAGAAA-GTT
* *
40990710 TTG-GTGTCAAAAAT-ATAATTTTCAAAAAGTT
1 TTGAG-GTCAAAAATGA-AATTTTTAGAAAGTT
* *
40990741 TT-AGGGT-TAAAATGTAATTTTTAGAAAGTT
1 TTGA-GGTCAAAAATGAAATTTTTAGAAAGTT
* * *
40990771 TAG-GAGT-TAAAATGTAA-TTTTAGAAAGTT
1 TTGAG-GTCAAAAATGAAATTTTTAGAAAGTT
40990800 TT-AGGGTCAAA
1 TTGA-GGTCAAA
40990811 TATAATTTTG
Statistics
Matches: 111, Mismatches: 9, Indels: 25
0.77 0.06 0.17
Matches are distributed among these distances:
29 16 0.14
30 39 0.35
31 52 0.47
32 4 0.04
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (31 bp):
TTGAGGTCAAAAATGAAATTTTTAGAAAGTT
Found at i:40990759 original size:30 final size:30
Alignment explanation
Indices: 40990657--40990870 Score: 152
Period size: 30 Copynumber: 7.2 Consensus size: 30
40990647 CTTGAGGGCA
* * * *
40990657 AAAATGAAATTTTTAGAAAGTTTT-GAGGTCA
1 AAAATGTAATTTTCAAAAAGTTTTAG-GGT-T
* * *
40990688 AAAATATAATTTTCAAAAGGTTTT-GGTGTCA
1 AAAATGTAATTTTCAAAAAGTTTTAGG-GT-T
*
40990719 AAAATATAATTTTCAAAAAGTTTTAGGGTT
1 AAAATGTAATTTTCAAAAAGTTTTAGGGTT
* *
40990749 AAAATGTAATTTTTAGAAAG-TTTAGGAGTT
1 AAAATGTAATTTTCAAAAAGTTTTAGG-GTT
*
40990779 AAAATGTAATTTT-AGAAAGTTTTAGGG-T
1 AAAATGTAATTTTCAAAAAGTTTTAGGGTT
* * **** **
40990807 CAAATATAATTTTGGTGAAGTTCGAGGGTT
1 AAAATGTAATTTTCAAAAAGTTTTAGGGTT
* *
40990837 AAAATGTAATTTTC-AAAAGTTTTGGGGTC
1 AAAATGTAATTTTCAAAAAGTTTTAGGGTT
40990866 AAAAT
1 AAAAT
40990871 ACCATTTTTG
Statistics
Matches: 151, Mismatches: 26, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
28 12 0.08
29 36 0.24
30 52 0.34
31 49 0.32
32 2 0.01
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTCAAAAAGTTTTAGGGTT
Found at i:40990791 original size:29 final size:28
Alignment explanation
Indices: 40990511--40990858 Score: 134
Period size: 30 Copynumber: 11.8 Consensus size: 28
40990501 ATAAGGGTCA
* * *
40990511 AAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGTAATTTTAGAAAGTTTAGGGTT
* * ** *
40990539 AAAATGGTAATTTTTGGTAAAATCAAGGTTT
1 AAAAT-GTAA-TTTTAG-AAAGTTTAGGGTT
40990570 AAAAATAG-AATTTTAGAAAGTTTGAGGG-T
1 -AAAAT-GTAATTTTAGAAAGTTT-AGGGTT
* * * **
40990599 AAAATGGTAATTTTGGTAAA--ATCGGAGGC
1 AAAAT-GTAATTTTAG-AAAGTTTAGG-GTT
* * * * **
40990628 AAAATGGAATTTTTGAAAACTTGAGGGCA
1 AAAATGTAATTTTAG-AAAGTTTAGGGTT
* * *
40990657 AAAATGAAATTTTTAGAAAGTTTTGAGGTCA
1 AAAATGTAA-TTTTAGAAAGTTTAG-GGT-T
* * *
40990688 AAAATATAATTTTCA-AAAGGTTTTGGTGTCA
1 AAAATGTAATTTT-AGAAA-GTTTAGG-GT-T
* *
40990719 AAAATATAATTTTCAAAAAGTTTTAGGGTT
1 AAAATGTAATTTT-AGAAAG-TTTAGGGTT
40990749 AAAATGTAATTTTTAGAAAGTTTAGGAGTT
1 AAAATGTAA-TTTTAGAAAGTTTAGG-GTT
40990779 AAAATGTAATTTTAGAAAGTTTTAGGG-T
1 AAAATGTAATTTTAGAAAG-TTTAGGGTT
* * * * *
40990807 CAAATATAATTTTGGTGAAGTTCGAGGGTT
1 AAAATGTAATTTTAG-AAAGTT-TAGGGTT
40990837 AAAATGTAATTTTCA-AAAGTTT
1 AAAATGTAATTTT-AGAAAGTTT
40990859 TGGGGTCAAA
Statistics
Matches: 247, Mismatches: 47, Indels: 52
0.71 0.14 0.15
Matches are distributed among these distances:
27 2 0.01
28 39 0.16
29 64 0.26
30 77 0.31
31 51 0.21
32 14 0.06
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAAGTTTAGGGTT
Found at i:40990838 original size:58 final size:58
Alignment explanation
Indices: 40990719--40990868 Score: 173
Period size: 58 Copynumber: 2.6 Consensus size: 58
40990709 TTTGGTGTCA
* * * *
40990719 AAAATATAATTTTCAAAAAGTTTTAGGGTTAAAATGTAATTTTTAGAAAGTTTAGGAGTT
1 AAAATGTAATTTTC-AAAAGTTTTAGGG-TCAAATATAATTTTTAGAAAGTTGAGGAGTT
40990779 AAAATGTAATTTT-AGAAAGTTTTAGGGTCAAATATAATTTTGGT-G-AAGTTCGAGG-GTT
1 AAAATGTAATTTTCA-AAAGTTTTAGGGTCAAATATAATTTT--TAGAAAGTT-GAGGAGTT
*
40990837 AAAATGTAATTTTCAAAAGTTTTGGGGTCAAA
1 AAAATGTAATTTTCAAAAGTTTTAGGGTCAAA
40990869 ATACCATTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
58 50 0.62
59 17 0.21
60 13 0.16
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTCAAAAGTTTTAGGGTCAAATATAATTTTTAGAAAGTTGAGGAGTT
Found at i:40993187 original size:89 final size:89
Alignment explanation
Indices: 40993085--40993251 Score: 221
Period size: 90 Copynumber: 1.9 Consensus size: 89
40993075 AAATTTTTTG
* * * * *
40993085 AAAAAAATAATTAAGCCCCTACATTTT-TTTT-CACTCACTTGGGTACTTGCACTTTCAAAATGC
1 AAAAAAACAATTAAGCCACTAC-TTTTATTTTACACTCAATTGAGTACTTGAACTTTCAAAATGC
40993148 ATAAAAAAGACCCTTAAACTATTTC
65 ATAAAAAAGACCCTTAAACTATTTC
* *
40993173 AAAAAAAGCAATTAAGCCATTGCTTTTATTTTACACTCAATTGAGTACTTGAACTTTCAAAATGC
1 AAAAAAA-CAATTAAGCCACTACTTTTATTTTACACTCAATTGAGTACTTGAACTTTCAAAATGC
* *
40993238 ATCAAAAAGGCCCT
65 ATAAAAAAGACCCT
40993252 CAAAGTTTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 11 0.16
89 15 0.22
90 41 0.61
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (89 bp):
AAAAAAACAATTAAGCCACTACTTTTATTTTACACTCAATTGAGTACTTGAACTTTCAAAATGCA
TAAAAAAGACCCTTAAACTATTTC
Found at i:40993504 original size:16 final size:16
Alignment explanation
Indices: 40993483--40993514 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40993473 ATTAAATTTT
*
40993483 AATAAAAATTTTAAAA
1 AATAAAAATTATAAAA
40993499 AATAAAAATTATAAAA
1 AATAAAAATTATAAAA
40993515 TGCATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAATTATAAAA
Found at i:40993512 original size:9 final size:9
Alignment explanation
Indices: 40993441--40993514 Score: 57
Period size: 9 Copynumber: 8.4 Consensus size: 9
40993431 CATGTGGCAA
40993441 AAAAATTAT
1 AAAAATTAT
40993450 AAAAA--AT
1 AAAAATTAT
*
40993457 AGAAATTAT
1 AAAAATTAT
*
40993466 AAAAGTTATT
1 AAAAATTA-T
**
40993476 AAATTTTAAT
1 AAAAATT-AT
*
40993486 AAAAATTTT
1 AAAAATTAT
40993495 AAAAA--AT
1 AAAAATTAT
40993502 AAAAATTAT
1 AAAAATTAT
40993511 AAAA
1 AAAA
40993515 TGCATAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
7 12 0.24
9 25 0.50
10 12 0.24
11 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40993802 original size:43 final size:43
Alignment explanation
Indices: 40993692--40993830 Score: 176
Period size: 42 Copynumber: 3.3 Consensus size: 43
40993682 TTATGATGAA
* * * *
40993692 AAACGCCGCTATAGAACATGTTCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCACTAAAGAACATGTTCTTTAGCGACGCTTTTTCCAC
40993734 AAACGCCACTAAA-AACTATGTTCTTTAGCGACGCTTTTTCCAC
1 AAACGCCACTAAAGAAC-ATGTTCTTTAGCGACGCTTTTTCCAC
* * * *
40993777 AAACGCCACTAAAGAACATGGTCTTTAGCAACACTTTCT-CAC
1 AAACGCCACTAAAGAACATGTTCTTTAGCGACGCTTTTTCCAC
40993819 AAACGCCACTAA
1 AAACGCCACTAA
40993831 TATTAACAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
41 3 0.03
42 42 0.49
43 38 0.44
44 3 0.03
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25
Consensus pattern (43 bp):
AAACGCCACTAAAGAACATGTTCTTTAGCGACGCTTTTTCCAC
Found at i:40998916 original size:41 final size:40
Alignment explanation
Indices: 40998836--40999013 Score: 108
Period size: 41 Copynumber: 4.4 Consensus size: 40
40998826 TTAAAATCCA
* * *
40998836 CTTTTAGCGGCACTTTTCTACAACGCTGCTAATGCTCTGAT
1 CTTTT-GCGGCGCTTTTCTACAACGCCGCTAATGCTCTGAC
* * * *
40998877 CTTTTGCGGCGCTTTTCTATAAGTGCCGCTATTGTTCTGAC
1 CTTTTGCGGCGCTTTTCTACAA-CGCCGCTAATGCTCTGAC
* * * * * *
40998918 CTTTAGTGGCGC-TTTCAAAGCAGCGTCGCTATTGCTCTG-C
1 CTTTTGCGGCGCTTTTC-TA-CAACGCCGCTAATGCTCTGAC
* * * * * *
40998958 CTTTAGCGGTGCTTTCCAAGAAGCGCCGCTATTGCTCTGAC
1 CTTTTGCGGCGCTTTTCTACAA-CGCCGCTAATGCTCTGAC
* *
40998999 CTTTAGCGGTGCTTT
1 CTTTTGCGGCGCTTT
40999014 CCCATAAGCA
Statistics
Matches: 110, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.01
40 47 0.43
41 61 0.55
42 1 0.01
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.36
Consensus pattern (40 bp):
CTTTTGCGGCGCTTTTCTACAACGCCGCTAATGCTCTGAC
Found at i:40999014 original size:41 final size:41
Alignment explanation
Indices: 40998863--40999038 Score: 183
Period size: 41 Copynumber: 4.3 Consensus size: 41
40998853 CTACAACGCT
* * * * * * *
40998863 GCTAATGCTCTGATCTTTTGCGGCGCTTTTCTATAAGTGCC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTTCCAAGAAGCGCC
* * * * *
40998904 GCTATTGTTCTGACCTTTAGTGGCGCTTTCAAAGCAGCGTC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTTCCAAGAAGCGCC
*
40998945 GCTATTGCTCTG-CCTTTAGCGGTGCTTTCCAAGAAGCGCC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTTCCAAGAAGCGCC
* * * *
40998985 GCTATTGCTCTGACCTTTAGCGGTGCTTTCCCATAAGCACC
1 GCTATTGCTCTGACCTTTAGCGGCGCTTTCCAAGAAGCGCC
*
40999026 GCTATTACTCTGA
1 GCTATTGCTCTGA
40999039 GAAGCGCCGC
Statistics
Matches: 112, Mismatches: 22, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
40 35 0.31
41 77 0.69
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.34
Consensus pattern (41 bp):
GCTATTGCTCTGACCTTTAGCGGCGCTTTCCAAGAAGCGCC
Found at i:40999048 original size:21 final size:21
Alignment explanation
Indices: 40999019--40999058 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40999009 GCTTTCCCAT
40999019 AAGCACCGCTATTACTCTGAG
1 AAGCACCGCTATTACTCTGAG
* *
40999040 AAGCGCCGCTATTGCTCTG
1 AAGCACCGCTATTACTCTG
40999059 GCCTTTAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (21 bp):
AAGCACCGCTATTACTCTGAG
Found at i:40999091 original size:62 final size:62
Alignment explanation
Indices: 40998976--40999098 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
40998966 GTGCTTTCCA
** * *
40998976 AGAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGCTTTCCCATAAGCACCGCTATTACTCTG
1 AGAAGCGCCGCTATTGCTCTGACCTTTAGCGGCACTTTCCAAGAAGCACCGCTATTACTCTG
* ** *
40999038 AGAAGCGCCGCTATTGCTCTGGCCTTTAGCGGCACTTTCCAAGAAGCGTCGCTATTGCTCT
1 AGAAGCGCCGCTATTGCTCTGACCTTTAGCGGCACTTTCCAAGAAGCACCGCTATTACTCT
40999099 AACTTTTAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (62 bp):
AGAAGCGCCGCTATTGCTCTGACCTTTAGCGGCACTTTCCAAGAAGCACCGCTATTACTCTG
Found at i:40999107 original size:41 final size:42
Alignment explanation
Indices: 40999038--40999150 Score: 119
Period size: 41 Copynumber: 2.8 Consensus size: 42
40999028 TATTACTCTG
** *
40999038 AGAAGCGCCGCTATTGCTCTGGCCTTTAGCGGCACTTTC-CA-
1 AGAAGCG-CGCTATTGCTCTAACTTTTAGCGGCACTTTCTCAT
**
40999079 AGAAGCGTCGCTATTGCTCTAACTTTTAGCGGTGCTTTCTCAT
1 AGAAGCG-CGCTATTGCTCTAACTTTTAGCGGCACTTTCTCAT
*
40999122 A-AA-CGCGCTATTGCTCTACCTTTT-GCGGC
1 AGAAGCGCGCTATTGCTCTAACTTTTAGCGGC
40999151 GTTTATGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
39 4 0.06
40 18 0.29
41 35 0.56
42 4 0.06
43 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.22, T:0.32
Consensus pattern (42 bp):
AGAAGCGCGCTATTGCTCTAACTTTTAGCGGCACTTTCTCAT
Found at i:40999406 original size:32 final size:31
Alignment explanation
Indices: 40999351--40999422 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
40999341 ATAAGAAAAA
40999351 TAAATTCTATTAGAATTTAAAAAGGAGTAATT
1 TAAATT-TATTAGAATTTAAAAAGGAGTAATT
* * * *
40999383 TAAATTTAGTTAGGATTTTAAAAGTATTAATT
1 TAAATTTA-TTAGAATTTAAAAAGGAGTAATT
40999415 TAAATTTA
1 TAAATTTA
40999423 AAATTAAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.43
Consensus pattern (31 bp):
TAAATTTATTAGAATTTAAAAAGGAGTAATT
Found at i:41002894 original size:16 final size:18
Alignment explanation
Indices: 41002869--41002903 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
41002859 TTTTTAAATT
41002869 TTTTATAATTTAT-ATAA
1 TTTTATAATTTATAATAA
41002886 TTTTA-AATTTATAATAA
1 TTTTATAATTTATAATAA
41002903 T
1 T
41002904 AAAATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATAATTTATAATAA
Found at i:41002974 original size:15 final size:16
Alignment explanation
Indices: 41002956--41002991 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
41002946 TAATATTTTA
41002956 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
41002971 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
41002987 AAATT
1 AAATT
41002992 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:41005591 original size:9 final size:9
Alignment explanation
Indices: 41005577--41005646 Score: 53
Period size: 9 Copynumber: 8.4 Consensus size: 9
41005567 CATGTGGAAA
41005577 AAAAATTAT
1 AAAAATTAT
41005586 -AAAA--AT
1 AAAAATTAT
41005592 AAAAATTAT
1 AAAAATTAT
*
41005601 AAAAGTTAT
1 AAAAATTAT
* * *
41005610 TAAATTTTT
1 AAAAATTAT
41005619 AAAAA-TA-
1 AAAAATTAT
41005626 AAAAA-TAT
1 AAAAATTAT
*
41005634 AAAAAATAT
1 AAAAATTAT
41005643 AAAA
1 AAAA
41005647 TGCATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 2 0.04
7 11 0.22
8 10 0.20
9 26 0.53
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:41005653 original size:18 final size:16
Alignment explanation
Indices: 41005619--41005657 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
41005609 TTAAATTTTT
41005619 AAAAATAAAAAATATA
1 AAAAATAAAAAATATA
*
41005635 AAAAATATAAAATGCATA
1 AAAAATAAAAAAT--ATA
41005653 AAAAA
1 AAAAA
41005658 CCCTTTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (16 bp):
AAAAATAAAAAATATA
Found at i:41005655 original size:33 final size:33
Alignment explanation
Indices: 41005584--41005656 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
41005574 AAAAAAAATT
* ** * **
41005584 ATAAAAATAAAAATTATAAAAGTTATTAAATTT
1 ATAAAAATAAAAAATATAAAAAATATAAAATGC
*
41005617 TTAAAAATAAAAAATATAAAAAATATAAAATGC
1 ATAAAAATAAAAAATATAAAAAATATAAAATGC
41005650 ATAAAAA
1 ATAAAAA
41005657 ACCCTTTAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
ATAAAAATAAAAAATATAAAAAATATAAAATGC
Found at i:41006999 original size:17 final size:17
Alignment explanation
Indices: 41006979--41007050 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
41006969 AATAAGTTTG
*
41006979 AATTTATTTTAAATTCA
1 AATTTATTTTAAATTTA
* * * *
41006996 AATTCATTTTGAGTTTG
1 AATTTATTTTAAATTTA
**
41007013 AATTTCCTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
41007030 AATTTATTTTGAATTAA
1 AATTTATTTTAAATTTA
41007047 AATT
1 AATT
41007051 AAAATTAAAG
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:41007016 original size:34 final size:34
Alignment explanation
Indices: 41006973--41007041 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
41006963 TTTTAAAATA
*
41006973 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
* * *
41007007 AGTTTGAATTTCCTTTAAATTTAAATTTATTTTG
1 AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
41007041 A
1 A
41007042 ATTAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.54
Consensus pattern (34 bp):
AGTTTGAATTTACTTTAAATTCAAATTCATTTTG
Found at i:41008973 original size:30 final size:30
Alignment explanation
Indices: 41008902--41008975 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
41008892 AAACTGTCCA
41008902 AAAATTACATTTTTAACTCTGAACTTTTCG
1 AAAATTACATTTTTAACTCTGAACTTTTCG
* **
41008932 -AAATTCCATTTTTGAAC-CTGATTTTTTCG
1 AAAATTACATTTTT-AACTCTGAACTTTTCG
*
41008961 AAAATTATATTTTTA
1 AAAATTACATTTTTA
41008976 CCCGAACTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (30 bp):
AAAATTACATTTTTAACTCTGAACTTTTCG
Found at i:41009073 original size:59 final size:59
Alignment explanation
Indices: 41008901--41009151 Score: 151
Period size: 59 Copynumber: 4.3 Consensus size: 59
41008891 TAAACTGTCC
* * ** * * * * *
41008901 AAAAATTACATTTTTAACTCTGAACTTTTCGAAATTCCATTTTTGAACCTG-ATTTTTT
1 AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAATTTTCT
* * * * * * ** *
41008959 CGAAAATTATATTTTTA--CCCGAAC-TCCCAAAAATTTC-GTTTTGACCTTGATTTTTCT
1 -AAAAATTACATTTTTACCCCCAAACTTTCC-AAAATTCCATTTTTGACCCCGAATTTTCT
*
41009016 AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAATTTTCC
1 AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAATTTTCT
* * * * * * *
41009075 AAAAATTACCA-TTTTATCCTCAGA-TGTCTAAAAATTCCATTTTTGACCTCGAA-CTTCT
1 AAAAATTA-CATTTTTACCCCCAAACTTTC-CAAAATTCCATTTTTGACCCCGAATTTTCT
*
41009133 GAAAATTATCA-TTTTACCC
1 AAAAATTA-CATTTTTACCC
41009152 TCGGATGTCT
Statistics
Matches: 150, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
56 25 0.17
57 16 0.11
58 35 0.23
59 72 0.48
60 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.40
Consensus pattern (59 bp):
AAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCCCGAATTTTCT
Found at i:41009159 original size:58 final size:60
Alignment explanation
Indices: 41009046--41009324 Score: 311
Period size: 59 Copynumber: 4.8 Consensus size: 60
41009036 CAAACTTTCC
* ** * * *
41009046 AAAATTCCATTTTTGA-CCCCGAATTTTCCAAAAATTACCATTTTATCCTCAGATGTCTA
1 AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
** * *
41009105 AAAATTCCATTTTTGA-CCTCGAA-CTTCTGAAAATTATCATTTTACCCTCGGATGTCTA
1 AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* * * * *
41009163 AAAATTTCATTTTTGATCC-CAAACCTTTCGAAAATTATCATTTTACCCCCGGATGTCTA
1 AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* *
41009222 AAAACTCCATTTTTGATCCT-GAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCTA
1 AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
* * * * *
41009281 AAAATTTCATTTTT-AACCCCAAACCTTCC-AAAATTACCGTTTTA
1 AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTA
41009325 TTCCCGGGTA
Statistics
Matches: 191, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
58 64 0.34
59 127 0.66
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (60 bp):
AAAATTCCATTTTTGATCCTCGAACCTTCCAAAAATTACCATTTTACCCCCGGATGTCTA
Found at i:41009167 original size:117 final size:117
Alignment explanation
Indices: 41009016--41009325 Score: 358
Period size: 117 Copynumber: 2.6 Consensus size: 117
41009006 TGATTTTTCT
* * * * * *
41009016 AAAAATTA-CATTTTTACCCCCAAACTTTC-CAAAATTCCATTTTTGACCCCGAATTTTCCAAAA
1 AAAAATTACCA-TTTTACCCCCGAA-TGTCTAAAAATTTCATTTTTGACCCCAAACTTTCC-AAA
* * *
41009079 ATTACCATTTTATCCTCAGATGTCTAAAAATTCCATTTTTGA-CCTCGAA-CTTCT
63 ATTACCATTTTATCCCCAGATGTCTAAAAACTCCATTTTTGATCCT-GAACCTTCC
* * * * * *
41009133 GAAAATTATCATTTTACCCTCGGATGTCTAAAAATTTCATTTTTGATCCCAAACCTTTCGAAAAT
1 AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTTCATTTTTGACCCCAAA-CTTTCCAAAAT
* * *
41009198 TATCATTTTACCCCCGGATGTCTAAAAACTCCATTTTTGATCCTGAACCTTCC
65 TACCATTTTATCCCCAGATGTCTAAAAACTCCATTTTTGATCCTGAACCTTCC
* *
41009251 AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTTCATTTTTAACCCCAAACCTTCCAAAATT
1 AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTTCATTTTTGACCCCAAACTTTCCAAAATT
*
41009316 ACCGTTTTAT
66 ACCATTTTAT
41009326 TCCCGGGTAT
Statistics
Matches: 160, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
116 3 0.02
117 97 0.61
118 60 0.38
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.36
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCCCGAATGTCTAAAAATTTCATTTTTGACCCCAAACTTTCCAAAATT
ACCATTTTATCCCCAGATGTCTAAAAACTCCATTTTTGATCCTGAACCTTCC
Found at i:41009286 original size:29 final size:30
Alignment explanation
Indices: 41009013--41009300 Score: 119
Period size: 29 Copynumber: 9.8 Consensus size: 30
41009003 CCTTGATTTT
* *
41009013 TCTAAAAATTA-CATTTTTACCCCCAAACTT
1 TCTAAAAATTACCATTTTTA-CCCCGAACTG
* * *
41009043 TC-CAAAATT-CCATTTTTGACCCCGAATTT
1 TCTAAAAATTACCATTTTT-ACCCCGAACTG
* *
41009072 TCCAAAAATTACCA-TTTTATCCTC-AGA-TG
1 TCTAAAAATTACCATTTTTA-CCCCGA-ACTG
*
41009101 TCTAAAAATT-CCATTTTTGACCTCGAACT-
1 TCTAAAAATTACCATTTTT-ACCCCGAACTG
* * *
41009130 TCTGAAAATTATCA-TTTTACCCTCGGA-TG
1 TCTAAAAATTACCATTTTTACCC-CGAACTG
* * * *
41009159 TCTAAAAATT-TCATTTTTGATCCCAAACCTT
1 TCTAAAAATTACCATTTTT-ACCCCGAA-CTG
* * *
41009190 TC-GAAAATTATCA-TTTTACCCCCGGA-TG
1 TCTAAAAATTACCATTTTTA-CCCCGAACTG
* * *
41009218 TCTAAAAACT-CCATTTTTGATCCTGAACCT-
1 TCTAAAAATTACCATTTTT-ACCCCGAA-CTG
*
41009248 TCCAAAAATTACCA-TTTTACCCCCGAA-TG
1 TCTAAAAATTACCATTTTTA-CCCCGAACTG
*
41009277 TCTAAAAATT-TCATTTTTAACCCC
1 TCTAAAAATTACCATTTTT-ACCCC
41009301 AAACCTTCCA
Statistics
Matches: 196, Mismatches: 33, Indels: 59
0.68 0.11 0.20
Matches are distributed among these distances:
28 18 0.09
29 107 0.55
30 58 0.30
31 13 0.07
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (30 bp):
TCTAAAAATTACCATTTTTACCCCGAACTG
Found at i:41025482 original size:20 final size:21
Alignment explanation
Indices: 41025454--41025492 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41025444 AGTCAATGGG
41025454 TCAAAGTCAACGG-TCAACGC
1 TCAAAGTCAACGGTTCAACGC
*
41025474 TCAAGGTCAACGGTTCAAC
1 TCAAAGTCAACGGTTCAAC
41025493 ATCAACAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
TCAAAGTCAACGGTTCAACGC
Found at i:41025497 original size:20 final size:20
Alignment explanation
Indices: 41025454--41025497 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41025444 AGTCAATGGG
*
41025454 TCAAAGTCAACGGTCAACGC
1 TCAAAGTCAACGGTCAACGA
*
41025474 TCAAGGTCAACGGTTCAAC-A
1 TCAAAGTCAACGG-TCAACGA
41025494 TCAA
1 TCAA
41025498 CAGATCGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
TCAAAGTCAACGGTCAACGA
Found at i:41026574 original size:5 final size:5
Alignment explanation
Indices: 41026564--41026596 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
41026554 TGCAATAAGA
*
41026564 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
41026597 ACGCTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:41026582 original size:14 final size:14
Alignment explanation
Indices: 41026563--41026596 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
41026553 TTGCAATAAG
41026563 ATTTATTTTATTTT
1 ATTTATTTTATTTT
41026577 ATTTATTTTATTTT
1 ATTTATTTTATTTT
41026591 AGTTTA
1 A-TTTA
41026597 ACGCTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
ATTTATTTTATTTT
Found at i:41034828 original size:6 final size:6
Alignment explanation
Indices: 41034803--41034841 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
41034793 ACAATTTATA
* * *
41034803 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
41034842 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:41036625 original size:22 final size:22
Alignment explanation
Indices: 41036597--41036642 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
41036587 TAATGTTGCA
*
41036597 ACTTCAACTGAGGTGAATCACG
1 ACTTCAACCGAGGTGAATCACG
*
41036619 ACTTCAACCGAGGTGAGTCACG
1 ACTTCAACCGAGGTGAATCACG
41036641 AC
1 AC
41036643 CTTGAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (22 bp):
ACTTCAACCGAGGTGAATCACG
Found at i:41048249 original size:22 final size:22
Alignment explanation
Indices: 41048221--41048273 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
41048211 ACAAATGAAT
**
41048221 AGAGAGCACCGAGGTGCTAAAC
1 AGAGAGCACAAAGGTGCTAAAC
*
41048243 AGAGAGCACAAATGTGCTAAAC
1 AGAGAGCACAAAGGTGCTAAAC
*
41048265 GGAGAGCAC
1 AGAGAGCAC
41048274 TTTACGTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.30, T:0.09
Consensus pattern (22 bp):
AGAGAGCACAAAGGTGCTAAAC
Found at i:41052812 original size:25 final size:25
Alignment explanation
Indices: 41052781--41052830 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
41052771 ACTATGACTC
* *
41052781 AATCGACAATTAATTCTATATTTAT
1 AATCGACAATCAATTCTAAATTTAT
41052806 AATCGACAATCAATTCTAAATTTAT
1 AATCGACAATCAATTCTAAATTTAT
41052831 TGATGAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (25 bp):
AATCGACAATCAATTCTAAATTTAT
Found at i:41053051 original size:15 final size:17
Alignment explanation
Indices: 41053017--41053054 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
41053007 ATTTTTAATG
41053017 TAATTTCATCATTTTAA
1 TAATTTCATCATTTTAA
*
41053034 TAATTT-AT-ATTTTTA
1 TAATTTCATCATTTTAA
41053049 TAATTT
1 TAATTT
41053055 TAAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTCATCATTTTAA
Found at i:41055401 original size:29 final size:30
Alignment explanation
Indices: 41055369--41055429 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
41055359 GAGTTTCAAA
* *
41055369 TGTATAATTG-CATCAAATTAAAATTCATG
1 TGTACAATTGACATCAAATCAAAATTCATG
*
41055398 TGTACAATTGCACATTAAATCAAAATTCATG
1 TGTACAATTG-ACATCAAATCAAAATTCATG
41055429 T
1 T
41055430 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
31 18 0.67
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (30 bp):
TGTACAATTGACATCAAATCAAAATTCATG
Found at i:41063951 original size:30 final size:30
Alignment explanation
Indices: 41063906--41064075 Score: 234
Period size: 30 Copynumber: 5.7 Consensus size: 30
41063896 TTCAGATACA
* * * *
41063906 ACAAGTTGACTTTATAATA-AGGTTGCTCAT
1 ACAAGCTGACATTATAATAGA-ATTGCTCAC
41063936 ACAAGCTGACATTATAATAGAATTGCTCAC
1 ACAAGCTGACATTATAATAGAATTGCTCAC
*
41063966 ACAAGCTAACATTATAATAGAATTGCTCAC
1 ACAAGCTGACATTATAATAGAATTGCTCAC
* *
41063996 ACAAGCTGACATTATAGTAGATTTGCTCAC
1 ACAAGCTGACATTATAATAGAATTGCTCAC
* *
41064026 ACAAGCTGACATTATAATAGATTTGCTCAT
1 ACAAGCTGACATTATAATAGAATTGCTCAC
*
41064056 ACAAGCTAACATTATAATAG
1 ACAAGCTGACATTATAATAG
41064076 GATTACCCGG
Statistics
Matches: 128, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
30 127 0.99
31 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (30 bp):
ACAAGCTGACATTATAATAGAATTGCTCAC
Found at i:41064419 original size:2 final size:2
Alignment explanation
Indices: 41064412--41064436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41064402 TCCAATTCTA
41064412 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41064437 AATTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41067354 original size:19 final size:20
Alignment explanation
Indices: 41067327--41067369 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41067317 TATGGTACAC
* *
41067327 TTAATACAT-TTTTTCATAT
1 TTAAAACATCTTTCTCATAT
41067346 TTAAAACATCGTTTCTCATAT
1 TTAAAACATC-TTTCTCATAT
41067367 TTA
1 TTA
41067370 TAAGACATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (20 bp):
TTAAAACATCTTTCTCATAT
Found at i:41071980 original size:31 final size:29
Alignment explanation
Indices: 41071944--41072005 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
41071934 AATTATATAA
41071944 ATGAAA-TTTGAATTATGATTCATATGTGTAC
1 ATGAAACTTTG-ATTATGATTCAT-T-TGTAC
*
41071975 ATGAAACTTTGATTTTGATTCATTTGTAC
1 ATGAAACTTTGATTATGATTCATTTGTAC
41072004 AT
1 AT
41072006 ATATAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 1 0.03
31 17 0.59
32 4 0.14
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (29 bp):
ATGAAACTTTGATTATGATTCATTTGTAC
Found at i:41072269 original size:2 final size:2
Alignment explanation
Indices: 41072264--41072290 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41072254 AATTTTTTAC
41072264 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
41072291 TGGATTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41074109 original size:13 final size:12
Alignment explanation
Indices: 41074093--41074152 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 12
41074083 GGCTTCTAAG
41074093 TTGGTTTGGGTAT
1 TTGGTTTGGGT-T
41074106 TTGGTTTGGGTT
1 TTGGTTTGGGTT
41074118 TTGGTTTTAGGGTAT
1 TTGG-TTT-GGGT-T
* *
41074133 TAGTTTTGGGCTT
1 TTGGTTTGGG-TT
41074146 TTGGTTT
1 TTGGTTT
41074153 TGAGTTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 5 0.13
13 23 0.59
14 8 0.21
15 3 0.08
ACGTcount: A:0.07, C:0.02, G:0.35, T:0.57
Consensus pattern (12 bp):
TTGGTTTGGGTT
Found at i:41074133 original size:27 final size:27
Alignment explanation
Indices: 41074093--41074154 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
41074083 GGCTTCTAAG
*
41074093 TTGG-TTTGGGTATTTGGTTTGGG-TT
1 TTGGTTTTGGGTATTAGGTTTGGGCTT
*
41074118 TTGGTTTTAGGGTATTAGTTTTGGGCTT
1 TTGGTTTT-GGGTATTAGGTTTGGGCTT
41074146 TTGGTTTTG
1 TTGGTTTTG
41074155 AGTTATAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 15 0.47
28 10 0.31
ACGTcount: A:0.06, C:0.02, G:0.35, T:0.56
Consensus pattern (27 bp):
TTGGTTTTGGGTATTAGGTTTGGGCTT
Found at i:41074152 original size:14 final size:13
Alignment explanation
Indices: 41074093--41074154 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 13
41074083 GGCTTCTAAG
41074093 TTGG-TTTGGGTAT
1 TTGGTTTTGGGT-T
41074106 TTGG-TTTGGGTT
1 TTGGTTTTGGGTT
*
41074118 TTGGTTTTAGGGTA
1 TTGGTTTT-GGGTT
*
41074132 TTAGTTTTGGGCTT
1 TTGGTTTTGGG-TT
41074146 TTGGTTTTG
1 TTGGTTTTG
41074155 AGTTATAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
12 5 0.12
13 17 0.40
14 20 0.48
ACGTcount: A:0.06, C:0.02, G:0.35, T:0.56
Consensus pattern (13 bp):
TTGGTTTTGGGTT
Found at i:41077414 original size:32 final size:32
Alignment explanation
Indices: 41077370--41077441 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
41077360 TTTAAAATGA
*
41077370 AAAAATTTTCATTTAAGTTTTTTATAATTTAT
1 AAAATTTTTCATTTAAGTTTTTTATAATTTAT
*
41077402 AAAATTTTTCATTTAAGTTTTTTGTAATTTAT
1 AAAATTTTTCATTTAAGTTTTTTATAATTTAT
41077434 AAAATTTT
1 AAAATTTT
41077442 AAATTAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (32 bp):
AAAATTTTTCATTTAAGTTTTTTATAATTTAT
Found at i:41080272 original size:75 final size:75
Alignment explanation
Indices: 41080148--41080297 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
41080138 TAGCTAAGGG
*
41080148 TAACATTGTTGCCACGTTTCTTTGAAAATGTAAACGCACATAGTCCGAAGTTTTAGACAAAGGAA
1 TAACATTGTTGCCACGTTTCTTTGAAAATGTAAACCCACATAGTCCGAAGTTTTAGACAAAGGAA
41080213 TCATCTGAGA
66 TCATCTGAGA
*
41080223 TAACATTGTTGCCACGTTTCTTTGAAAATGTAAACCCACATAGTTCGAAGTTTTAGACAAAGGAA
1 TAACATTGTTGCCACGTTTCTTTGAAAATGTAAACCCACATAGTCCGAAGTTTTAGACAAAGGAA
41080288 TCATCTGAGA
66 TCATCTGAGA
41080298 AAGTATCGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (75 bp):
TAACATTGTTGCCACGTTTCTTTGAAAATGTAAACCCACATAGTCCGAAGTTTTAGACAAAGGAA
TCATCTGAGA
Found at i:41080610 original size:41 final size:41
Alignment explanation
Indices: 41080551--41080629 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
41080541 ACTTAAAAAC
*
41080551 ATTAAAACAAATATTAAAACAACAAACAAATTAAAAACGAT
1 ATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACGAT
* * * *
41080592 ATTAAAACAATTCGTAAAACAATAAACAAATTGAAAAC
1 ATTAAAACAAATAGTAAAACAACAAACAAATTAAAAAC
41080630 ACAATAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.63, C:0.13, G:0.04, T:0.20
Consensus pattern (41 bp):
ATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACGAT
Found at i:41085860 original size:23 final size:24
Alignment explanation
Indices: 41085812--41085863 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
41085802 ATTGTTTATA
41085812 AACATGTTCAATTATATGTTCATG
1 AACATGTTCAATTATATGTTCATG
** *
41085836 AACATGTTCGTTTA-ATGTTCGTG
1 AACATGTTCAATTATATGTTCATG
41085859 AACAT
1 AACAT
41085864 ACTCGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (24 bp):
AACATGTTCAATTATATGTTCATG
Found at i:41087858 original size:8 final size:8
Alignment explanation
Indices: 41087841--41087879 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
41087831 ACTTTAAAAA
41087841 TTAA-TTT
1 TTAATTTT
41087848 TTAATTTT
1 TTAATTTT
41087856 TTAATTCTT
1 TTAATT-TT
41087865 TTAATTTT
1 TTAATTTT
41087873 TT-ATTTT
1 TTAATTTT
41087880 CTTTTACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 9 0.30
8 13 0.43
9 8 0.27
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTAATTTT
Found at i:41087881 original size:18 final size:18
Alignment explanation
Indices: 41087846--41087903 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
41087836 AAAAATTAAT
*
41087846 TTTTAATTTTTTA-ATTC
1 TTTTAATTTTTTATTTTC
41087863 TTTTAATTTTTTATTTTC
1 TTTTAATTTTTTATTTTC
*
41087881 TTTTACATTATTTATCTTTC
1 TTTTA-ATTTTTTAT-TTTC
41087901 TTT
1 TTT
41087904 ATTTTTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 13 0.36
18 8 0.22
19 8 0.22
20 7 0.19
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAATTTTTTATTTTC
Found at i:41090072 original size:21 final size:21
Alignment explanation
Indices: 41089993--41090085 Score: 98
Period size: 21 Copynumber: 4.3 Consensus size: 21
41089983 TTGGGGAAAT
* * *
41089993 AGTAAGCACACAGTTCAAATC
1 AGTAAGCACACAATGCGAATC
*
41090014 AGTAAGCACATACAGTGCGAATC
1 AGTAAGCAC--ACAATGCGAATC
* *
41090037 AGTAAACACATAATGCGAATC
1 AGTAAGCACACAATGCGAATC
41090058 AGTAAGCACACAATGCTGAA-C
1 AGTAAGCACACAATGC-GAATC
41090079 AGTAAGC
1 AGTAAGC
41090086 GCGCTAATGT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
21 41 0.66
22 3 0.05
23 18 0.29
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (21 bp):
AGTAAGCACACAATGCGAATC
Found at i:41096782 original size:20 final size:20
Alignment explanation
Indices: 41096757--41096794 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41096747 GTATCGATCT
41096757 AGTATCGATACTTTTTATCA
1 AGTATCGATACTTTTTATCA
* *
41096777 AGTATCGGTAGTTTTTAT
1 AGTATCGATACTTTTTAT
41096795 TGAATACCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (20 bp):
AGTATCGATACTTTTTATCA
Found at i:41112147 original size:86 final size:86
Alignment explanation
Indices: 41112002--41112173 Score: 308
Period size: 86 Copynumber: 2.0 Consensus size: 86
41111992 TGTTTGGAAG
* *
41112002 TTAGAATCGATATAACCATTAGGAGTAAGATCTCCTCTAGAATGTACAAGTACATAATCTTTCAT
1 TTAGAATCGATATAACCATTAGGAGTAAGATCTCCTCCAAAATGTACAAGTACATAATCTTTCAT
41112067 TCTCTGTAAATACTTAAGTAT
66 TCTCTGTAAATACTTAAGTAT
* *
41112088 TTAGAATTGATATAACCATTAGGAGTAAGATCTCCTCCAAAATGTACAAGTATATAATCTTTCAT
1 TTAGAATCGATATAACCATTAGGAGTAAGATCTCCTCCAAAATGTACAAGTACATAATCTTTCAT
41112153 TCTCTGTAAATACTTAAGTAT
66 TCTCTGTAAATACTTAAGTAT
41112174 CTGCTTAATT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (86 bp):
TTAGAATCGATATAACCATTAGGAGTAAGATCTCCTCCAAAATGTACAAGTACATAATCTTTCAT
TCTCTGTAAATACTTAAGTAT
Found at i:41118358 original size:22 final size:22
Alignment explanation
Indices: 41118326--41118371 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
41118316 ATAATAGAAC
*
41118326 AAAATTGTATAAAATATATTAA
1 AAAATTATATAAAATATATTAA
41118348 AAAATTATATAAAATATATTAA
1 AAAATTATATAAAATATATTAA
41118370 AA
1 AA
41118372 TGAAATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATTATATAAAATATATTAA
Found at i:41135035 original size:27 final size:29
Alignment explanation
Indices: 41134987--41135046 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
41134977 AACTTTAATT
* *
41134987 TAAATATCACATTCAACA-TTTTAAAATA
1 TAAATATCACATTAAACATTTTTAAAAAA
*
41135015 TAAATATC-TATTAAACATTTTTAAAAAA
1 TAAATATCACATTAAACATTTTTAAAAAA
41135043 TAAA
1 TAAA
41135047 AATAGTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAATATCACATTAAACATTTTTAAAAAA
Found at i:41138639 original size:17 final size:18
Alignment explanation
Indices: 41138617--41138658 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
41138607 CCCAATGAGA
*
41138617 TAAATTTGGTTTTAAA-T
1 TAAATTTGATTTTAAATT
41138634 TAAATTT-ATTTTAAATT
1 TAAATTTGATTTTAAATT
41138651 TAAATTTG
1 TAAATTTG
41138659 CACAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTGATTTTAAATT
Found at i:41138692 original size:17 final size:17
Alignment explanation
Indices: 41138629--41138692 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
41138619 AATTTGGTTT
*
41138629 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTATTA
*
41138645 TAAATTTAAATTTGCA-CA
1 TAAATTTAAATTT--ATTA
*
41138663 -AAATTTAAGTTTATTA
1 TAAATTTAAATTTATTA
*
41138679 TAAATATAAATTTA
1 TAAATTTAAATTTA
41138693 AAATTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 30 0.81
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:41139160 original size:26 final size:26
Alignment explanation
Indices: 41139101--41139176 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
41139091 TTGTAAAGGT
* *
41139101 TACGACCCCTATTCTTGAAATTAAAA
1 TACGAACCCTATTCTTGAAATCAAAA
* * * *
41139127 CACAAACCCTATTCTTGATATCCAAA
1 TACGAACCCTATTCTTGAAATCAAAA
*
41139153 TACGAACCC-AGTTCTGGAAATCAA
1 TACGAACCCTA-TTCTTGAAATCAA
41139177 TAGACAAACC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (26 bp):
TACGAACCCTATTCTTGAAATCAAAA
Found at i:41139488 original size:10 final size:9
Alignment explanation
Indices: 41139447--41139579 Score: 54
Period size: 9 Copynumber: 13.8 Consensus size: 9
41139437 TAAATGACCT
*
41139447 TAATAATAA
1 TAATATTAA
*
41139456 TATTATTAA
1 TAATATTAA
41139465 TAATATT-A
1 TAATATTAA
41139473 -AATATTAA
1 TAATATTAA
*
41139481 TAACTATTTTGA
1 TAA-TA--TTAA
*
41139493 TAATAGTAA
1 TAATATTAA
* *
41139502 TTAATGTTTAG
1 -TAAT-ATTAA
*
41139513 TAATAATAA
1 TAATATTAA
*
41139522 TAAATGCTTTAA
1 T-AAT--ATTAA
41139534 TAATATTAA
1 TAATATTAA
*
41139543 TAAATATTTTA
1 T-AATA-TTAA
* *
41139554 TAATAATGA
1 TAATATTAA
41139563 TAATCATTAA
1 TAAT-ATTAA
41139573 TAATATT
1 TAATATT
41139580 TTTAATAATA
Statistics
Matches: 91, Mismatches: 20, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
7 6 0.07
8 2 0.02
9 34 0.37
10 28 0.31
11 11 0.12
12 10 0.11
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (9 bp):
TAATATTAA
Found at i:41139502 original size:21 final size:21
Alignment explanation
Indices: 41139473--41139558 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 21
41139463 AATAATATTA
*
41139473 AATATTAATAACTATTTTGAT
1 AATATTAATAAATATTTTGAT
* * * *
41139494 AATAGTAATTAATGTTTAG-T
1 AATATTAATAAATATTTTGAT
* ** *
41139514 AATAATAATAAATGCTTTAAT
1 AATATTAATAAATATTTTGAT
41139535 AATATTAATAAATATTTT-AT
1 AATATTAATAAATATTTTGAT
41139555 AATA
1 AATA
41139559 ATGATAATCA
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
20 21 0.41
21 30 0.59
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (21 bp):
AATATTAATAAATATTTTGAT
Found at i:41139522 original size:20 final size:21
Alignment explanation
Indices: 41139492--41139577 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 21
41139482 AACTATTTTG
* *
41139492 ATAATAGTAATTAATG-TTTA
1 ATAATAATAATAAATGCTTTA
*
41139512 GTAATAATAATAAATGCTTTA
1 ATAATAATAATAAATGCTTTA
* * *
41139533 ATAATATTAATAAAT-ATTTT
1 ATAATAATAATAAATGCTTTA
* *
41139553 ATAATAATGAT-AAT-CATTA
1 ATAATAATAATAAATGCTTTA
41139572 ATAATA
1 ATAATA
41139578 TTTTTAATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 11 0.21
20 25 0.47
21 17 0.32
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (21 bp):
ATAATAATAATAAATGCTTTA
Found at i:41139537 original size:41 final size:39
Alignment explanation
Indices: 41139492--41139577 Score: 93
Period size: 41 Copynumber: 2.2 Consensus size: 39
41139482 AACTATTTTG
* *
41139492 ATAATAGTAATTAAT-GTTTAGTAATAATAATAAATGCTTTA
1 ATAATAGTAATAAATAGTTTA-TAATAATAAT-AAT-CATTA
* * *
41139533 ATAATATTAATAAATATTTTATAATAATGATAATCATTA
1 ATAATAGTAATAAATAGTTTATAATAATAATAATCATTA
41139572 ATAATA
1 ATAATA
41139578 TTTTTAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
39 10 0.26
40 3 0.08
41 22 0.56
42 4 0.10
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (39 bp):
ATAATAGTAATAAATAGTTTATAATAATAATAATCATTA
Found at i:41141112 original size:59 final size:59
Alignment explanation
Indices: 41141045--41141181 Score: 188
Period size: 59 Copynumber: 2.3 Consensus size: 59
41141035 TGGATACCCG
* * *
41141045 AGGGTAAAATGGTAATTTT-GGTGTAATCGGGGTTAAAAAATGGAATTTTAAAAGATTC-A
1 AGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTT--AAAACGGAATTTTAAAAGATTCGA
* *
41141104 AGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAACGGAATTTTAGAAGATTCGG
1 AGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAACGGAATTTTAAAAGATTCGA
*
41141163 GGGGTAAAATGGTAATTTT
1 AGGGTAAAATGGTAATTTT
41141182 TGAAAGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
58 20 0.29
59 37 0.53
60 13 0.19
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.31
Consensus pattern (59 bp):
AGGGTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAACGGAATTTTAAAAGATTCGA
Found at i:41141202 original size:30 final size:30
Alignment explanation
Indices: 41141163--41141479 Score: 496
Period size: 30 Copynumber: 10.6 Consensus size: 30
41141153 GAAGATTCGG
*
41141163 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
41141192 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
41141222 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41141252 GGGGTCAAAATATAATTTTGGAGAAA-TTTT
1 GGGGTCAAAATGTAATTTTGGA-AAAGTTTT
41141282 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
41141312 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41141342 GGGGTAAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
41141372 AGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
41141402 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41141432 GGGGTTAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* * *
41141462 TGGTTCAAAATATAATTT
1 GGGGTCAAAATGTAATTT
41141480 CTAGATTGTT
Statistics
Matches: 268, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
29 17 0.06
30 248 0.93
31 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:41141300 original size:19 final size:19
Alignment explanation
Indices: 41141276--41141332 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
41141266 ATTTTGGAGA
41141276 AATTTTGGGGTCAAAATGT
1 AATTTTGGGGTCAAAATGT
41141295 AATTTT--GG--AAAA-G-
1 AATTTTGGGGTCAAAATGT
41141308 --TTTTGGGGTCAAAATGT
1 AATTTTGGGGTCAAAATGT
41141325 AATTTTGG
1 AATTTTGG
41141333 AAAAGTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
11 4 0.13
13 2 0.07
14 1 0.03
15 8 0.27
16 1 0.03
17 2 0.07
19 12 0.40
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.39
Consensus pattern (19 bp):
AATTTTGGGGTCAAAATGT
Found at i:41143233 original size:38 final size:37
Alignment explanation
Indices: 41143191--41143825 Score: 429
Period size: 38 Copynumber: 17.6 Consensus size: 37
41143181 ACGTTGCTCT
* *
41143191 TACTTCAATTTCAGAGATTAAGACTTGTTATCTAACTC
1 TACTTCAATTTCAGAGATGAAGACTTGTTATC-CACTC
* * * *
41143229 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
* * *
41143260 TACTTCAATTTCAGAGACGAGGA-TGAGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGACT-TGTTATCCACTC
* * *
41143297 TACTTCAATTTCAAGGGGATGACG-TTATGTTATCCACTC
1 TACTTCAATTTC-A-GAGATGAAGACT-TGTTATCCACTC
* * *
41143336 TACTTCAATTTCAAGGGATGAAGACGTATTATCCACTC
1 TACTTCAATTTC-AGAGATGAAGACTTGTTATCCACTC
* *
41143374 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTC-AGAGATGAAGACTTGTTATCCACTC
* * * *
41143412 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
41143443 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTC
* * * *
41143481 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
* * *
41143512 TACTTCAATTTCAGAGATCAAGACGTATTATCCACTC
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
* ** * * *
41143549 TACTTCAGTTTCA-AGGGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
* *
41143580 TACTTGAATTTCAGAGATCAAGACTTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTC
* * * *
41143618 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT-
1 TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
* * *
41143649 TACTTCAATTTCAGAGACGAGGA-TGAGTTATCCACTC
1 TACTTCAATTTCAGAGATGAAGACT-TGTTATCCACTC
* * *
41143686 TACTTCAATTTCAAGGGGATGACG-TTGTGTTATCCACTC
1 TACTTCAATTTC-A-GAGATGAAGACT-TGTTATCCACTC
* *
41143725 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTC-AGAGATGAAGACTTGTTATCCACTC
* *
41143763 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTC
1 TACTTCAATTTC-AGAGATGAAGACTTGTTATCCACTC
*
41143801 TACTTCAATTTCAAGGGATGAAGAC
1 TACTTCAATTTC-AGAGATGAAGAC
41143826 GTGGTGTGCA
Statistics
Matches: 483, Mismatches: 72, Indels: 84
0.76 0.11 0.13
Matches are distributed among these distances:
31 63 0.13
32 49 0.10
33 7 0.01
34 8 0.02
35 8 0.02
36 29 0.06
37 63 0.13
38 191 0.40
39 65 0.13
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (37 bp):
TACTTCAATTTCAGAGATGAAGACTTGTTATCCACTC
Found at i:41143290 original size:69 final size:68
Alignment explanation
Indices: 41143115--41143394 Score: 237
Period size: 69 Copynumber: 4.0 Consensus size: 68
41143105 GGAAATGATC
** * * * *
41143115 TTGCTCTTACTTCAATTTCAGA-AATAAAAGCGT-GTTATCCAACTCTATTTCGATTTAAAGGGG
1 TTGCTCTTACTTCAATTTCAGAGACGAAGA-C-TAGTTAT-CAACTCTACTTCAATTTCAAGGGG
*
41143178 ACGACG
63 ATGACG
** * *
41143184 TTGCTCTTACTTCAATTTCAGAGATTAAGACTTGTTATCTAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGACGAAGACTAGTTATC-AACTCTACTTCAATTTCAAGGGGAT
41143249 GACG
65 GACG
* *
41143253 TTGCTCTTACTTCAATTTCAGAGACGAGGA-TGAGTTATCCACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGACGAAGACT-AGTTATCAACTCTACTTCAATTTCAAGGGGAT
41143317 GACG
65 GACG
* * * *
41143321 TTATGTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTA-TTATCCACTCTACTTCAATTT
1 -T-TG-----CTCT-TACTTCAATTTC-AGAGACGAAGAC-TAGTTATCAACTCTACTTCAATTT
41143385 CAA-GGGATGA
56 CAAGGGGATGA
41143395 AGACGTGTTA
Statistics
Matches: 179, Mismatches: 17, Indels: 23
0.82 0.08 0.11
Matches are distributed among these distances:
68 30 0.17
69 86 0.48
70 7 0.04
75 3 0.02
76 19 0.11
77 32 0.18
78 1 0.01
79 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.35
Consensus pattern (68 bp):
TTGCTCTTACTTCAATTTCAGAGACGAAGACTAGTTATCAACTCTACTTCAATTTCAAGGGGATG
ACG
Found at i:41143472 original size:68 final size:68
Alignment explanation
Indices: 41143374--41143783 Score: 561
Period size: 69 Copynumber: 5.9 Consensus size: 68
41143364 TTATCCACTC
*
41143374 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
41143439 CTCT
65 CTCT
*
41143443 TACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTG
41143508 CTCT
65 CTCT
* * * *
41143512 TACTTCAATTTCAGAGATCAAGACGTATTATCCACTCTACTTCAGTTTCAAGGGGATGACGTTGC
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
41143577 TCT
66 TCT
* * *
41143580 TACTTGAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATGACGTTG
41143645 CTCT
65 CTCT
* * * * *
41143649 TACTTCAATTTCAGAGACGAGGATGAGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGT
1 TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACG-T-T
*
41143714 GTTATCCACT
64 G-----CTCT
*
41143724 CTACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAG-GGATGA
1 -TACTTCAATTTC-AGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGA
41143784 AGACGTGTTA
Statistics
Matches: 304, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
68 109 0.36
69 137 0.45
70 2 0.01
75 3 0.01
76 18 0.06
77 35 0.12
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (68 bp):
TACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTGC
TCT
Found at i:41143569 original size:137 final size:137
Alignment explanation
Indices: 41143374--41143783 Score: 576
Period size: 137 Copynumber: 2.9 Consensus size: 137
41143364 TTATCCACTC
* * * *
41143374 TACTTCAATTTCAAGGGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATGACGTTG
1 TACTTCAATTTC-AGAGATCAAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
41143439 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
65 CTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGAC
41143504 GTTGCTCT
130 GTTGCTCT
*
41143512 TACTTCAATTTCAGAGATCAAGACGTATTATCCACTCTACTTCAGTTTCAAGGGGATGACGTTGC
1 TACTTCAATTTCAGAGATCAAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC
* *
41143577 TCTTACTTGAATTTCAGAGATCAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
66 TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
41143642 TTGCTCT
131 TTGCTCT
* *
41143649 TACTTCAATTTCAGAGA-CGAGGATG-AGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTT
1 TACTTCAATTTCAGAGATC-AAGACGTA-TTATCCACTCTACTTCAATTTCAAGGGGATGACG-T
* * *
41143712 GTGTTATCCACTCTACTTCAATTTCAAGGGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCA
63 -TG-----CTCT-TACTTCAATTTC-AGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCA
41143776 AG-GGATGA
120 AGAGGATGA
41143784 AGACGTGTTA
Statistics
Matches: 246, Mismatches: 15, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
136 2 0.01
137 172 0.70
138 13 0.05
139 2 0.01
144 9 0.04
145 30 0.12
146 18 0.07
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (137 bp):
TACTTCAATTTCAGAGATCAAGACGTATTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGC
TCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACG
TTGCTCT
Found at i:41152945 original size:23 final size:23
Alignment explanation
Indices: 41152861--41153074 Score: 144
Period size: 23 Copynumber: 9.5 Consensus size: 23
41152851 TAAATGGAAC
* * *
41152861 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
41152883 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
41152905 GGGCAAA-AGAGAGCACACAAAGTGCT
1 ----AAACAGAGAGCACACAAAGTGCT
*
41152931 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
41152951 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
41152970 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
41152993 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
41153016 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
41153041 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
41153064 AATCAGAGAGC
1 AAACAGAGAGC
41153075 GCGCTAGTGT
Statistics
Matches: 150, Mismatches: 24, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 21 0.14
23 75 0.50
24 2 0.01
25 25 0.17
26 10 0.07
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:41152969 original size:39 final size:39
Alignment explanation
Indices: 41152915--41152989 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
41152905 GGGCAAAAGA
*
41152915 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
41152954 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
41152990 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:41153028 original size:48 final size:46
Alignment explanation
Indices: 41152954--41153074 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
41152944 ACAAAGTACT
* * *
41152954 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
41153000 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
41153048 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
41153075 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:41159392 original size:23 final size:23
Alignment explanation
Indices: 41159308--41159521 Score: 144
Period size: 23 Copynumber: 9.5 Consensus size: 23
41159298 TAAATGGAAC
* * *
41159308 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
41159330 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
41159352 GGGCAAA-AGAGAGCACACAAAGTGCT
1 ----AAACAGAGAGCACACAAAGTGCT
*
41159378 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
41159398 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
41159417 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
41159440 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
41159463 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
41159488 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
41159511 AATCAGAGAGC
1 AAACAGAGAGC
41159522 GCGCTAGTGT
Statistics
Matches: 150, Mismatches: 24, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.07
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 21 0.14
23 75 0.50
24 2 0.01
25 25 0.17
26 10 0.07
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:41159416 original size:39 final size:39
Alignment explanation
Indices: 41159362--41159436 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
41159352 GGGCAAAAGA
*
41159362 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
41159401 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
41159437 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:41159475 original size:48 final size:46
Alignment explanation
Indices: 41159401--41159521 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
41159391 ACAAAGTACT
* * *
41159401 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
41159447 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
41159495 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
41159522 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:41165140 original size:29 final size:29
Alignment explanation
Indices: 41165051--41165151 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 29
41165041 TCGGGGTTAA
*
41165051 AAAATGG-AATTTTAAAAGATTCGGGGGT
1 AAAATGGTAATTTTAGAAGATTCGGGGGT
* ** * * *
41165079 AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGGTAATTTTAGAAG-ATTCGGGGGT
*
41165109 AAAACGG-AATTTTAGAAGATTCAGGGGGT
1 AAAATGGTAATTTTAGAAGATTC-GGGGGT
41165138 AAAATGGTAATTTT
1 AAAATGGTAATTTT
41165152 TGAAAGTTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 10 0.19
29 25 0.46
30 19 0.35
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTAGAAGATTCGGGGGT
Found at i:41165152 original size:59 final size:59
Alignment explanation
Indices: 41165013--41165153 Score: 205
Period size: 59 Copynumber: 2.4 Consensus size: 59
41165003 TATGGATACC
* * * *
41165013 CGGGGGAAAAATGGTAA-TTTTGGTGTAATCGGGGTTAAAAAATGGAATTTTAAAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAAACGGAATTTTAAAAGATT
*
41165072 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAACGGAATTTTAGAAGATT
1 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAACGGAATTTTAAAAGATT
41165130 CAGGGGGTAAAATGGTAATTTTTG
1 C-GGGGGTAAAATGGTAATTTTTG
41165154 AAAGTTTTGG
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
58 20 0.27
59 38 0.51
60 17 0.23
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAACGGAATTTTAAAAGATT
Found at i:41165172 original size:30 final size:30
Alignment explanation
Indices: 41165133--41165626 Score: 739
Period size: 30 Copynumber: 16.6 Consensus size: 30
41165123 GAAGATTCAG
*
41165133 GGGGT-AAAATGGTAATTTTTG-AAAGTTTT
1 GGGGTCAAAAT-GTAATTTTGGAAAAGTTTT
41165162 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165192 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165222 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* * *
41165252 GGGCTTAAAATATAATTTTGGAGAAA-TTTT
1 GGGGTCAAAATGTAATTTTGGA-AAAGTTTT
* *
41165282 AGGGT-TAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165311 GGGGTCAAAATGTAATTTTAGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
41165341 GGGGTCAAAATATAATTTTGGTAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165371 -GGGTCAGAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165400 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
41165430 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165460 GGGGTAAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165490 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
*
41165520 GGGGTCAAAATATAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
** *
41165550 CAGGTTAAAATGTAATTTTGGAAAAG-TTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
41165579 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
1 GGGGTCAAAATGTAATTTTGGAAAAGTTTT
* *
41165609 GGGGTTAAAATATAATTT
1 GGGGTCAAAATGTAATTT
41165627 CTAGATTGTT
Statistics
Matches: 426, Mismatches: 32, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
28 3 0.01
29 88 0.21
30 332 0.78
31 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGGAAAAGTTTT
Found at i:41165226 original size:89 final size:90
Alignment explanation
Indices: 41165145--41165626 Score: 758
Period size: 89 Copynumber: 5.4 Consensus size: 90
41165135 GGTAAAATGG
* * *
41165145 TAATTTTTG-AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
41165209 TTGGAAAAGTTTTGGGGTCAAAATA
66 TTGGAAAAGTTTTGGGGTCAAAATA
* * * *
41165234 TAATTTTGGAAAAGTTTTGGGCTTAAAATATAATTTTGGAGAAA-TTTTAGGGT-TAAATGTAAT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGA-AAAGTTTTGGGGTCAAAATGTAAT
*
41165297 TTTGGAAAAGTTTTGGGGTCAAAATG
65 TTTGGAAAAGTTTTGGGGTCAAAATA
* * *
41165323 TAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGGTAAAGTTTT-GGGTCAGAATGTAATT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
41165387 TTGGAAAAGTTTTGGGGTCAAAATA
66 TTGGAAAAGTTTTGGGGTCAAAATA
* *
41165412 TAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTAAAAATGTAATT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
41165477 TTGGAAAAGTTTTGGGGTCAAAATA
66 TTGGAAAAGTTTTGGGGTCAAAATA
** *
41165502 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTCAGGTTAAAATGTAATT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
*
41165567 TTGGAAAAG-TTTGGGGTCAAAATG
66 TTGGAAAAGTTTTGGGGTCAAAATA
*
41165591 TAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTT
1 TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTT
41165627 CTAGATTGTT
Statistics
Matches: 362, Mismatches: 26, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
88 7 0.02
89 208 0.57
90 144 0.40
91 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (90 bp):
TAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATT
TTGGAAAAGTTTTGGGGTCAAAATA
Found at i:41167171 original size:20 final size:21
Alignment explanation
Indices: 41167139--41167178 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41167129 CAGGGCATGG
*
41167139 TGGAGCTTGGTGGTCAGCAGA
1 TGGAGCTTGGTGGCCAGCAGA
41167160 TGGAGC-TGGTGGCCAGCAG
1 TGGAGCTTGGTGGCCAGCAG
41167179 CAGTAGGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.20
Consensus pattern (21 bp):
TGGAGCTTGGTGGCCAGCAGA
Found at i:41167377 original size:6 final size:6
Alignment explanation
Indices: 41167337--41167438 Score: 77
Period size: 6 Copynumber: 17.0 Consensus size: 6
41167327 ACTTTGGACT
* * ** *
41167337 TTTAAA TTTTTAA TTTAATA TTTTAA TTTTTA TTTAAA TTTAAA TTCAAA
1 TTTAAA -TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
41167387 -TTAAA TTTAAATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA --TAAA
1 TTTAAA TTT-AA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41167433 TTTAAA
1 TTTAAA
41167439 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 47 0.61
7 14 0.18
8 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:41167402 original size:25 final size:25
Alignment explanation
Indices: 41167374--41167423 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41167364 TTTTATTTAA
* *
41167374 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
41167399 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
41167424 TTAAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:41167404 original size:42 final size:42
Alignment explanation
Indices: 41167348--41167438 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
41167338 TTAAATTTTT
* * ** *
41167348 AATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAATTA
1 AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA-TA
*
41167390 AATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAATA
1 AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAATA
41167431 AATTTAAA
1 AATTTAAA
41167439 ATCAATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 10 0.24
42 28 0.67
43 4 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (42 bp):
AATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAATA
Found at i:41167405 original size:31 final size:31
Alignment explanation
Indices: 41167367--41167430 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41167357 TTTTAATTTT
*
41167367 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
41167398 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
41167429 TA
1 TA
41167431 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:41167440 original size:17 final size:16
Alignment explanation
Indices: 41167368--41167438 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 16
41167358 TTTAATTTTT
41167368 ATTTAAATTTAAATTCAA
1 ATTTAAATTTAAA-T-AA
41167386 A-TTAAATTTAAAT--
1 ATTTAAATTTAAATAA
41167399 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
*
41167416 ATCTAAATTTAAATAA
1 ATTTAAATTTAAATAA
41167432 ATTTAAA
1 ATTTAAA
41167439 ATCAATTTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.02
14 8 0.17
15 4 0.09
16 13 0.28
17 20 0.43
18 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:41169350 original size:23 final size:22
Alignment explanation
Indices: 41169320--41169446 Score: 128
Period size: 23 Copynumber: 5.5 Consensus size: 22
41169310 ACACTAGCGC
*
41169320 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTGT-GT
41169343 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCAC-GTGTGT
* *
41169368 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
* * *
41169391 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
*
41169414 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCAC-GTGTGT
41169437 GCTCTCTGTT
1 GCTCTCTGTT
41169447 GCCCAGCACT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 71 0.77
24 1 0.01
25 17 0.18
26 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACGTGTGT
Found at i:41169420 original size:46 final size:47
Alignment explanation
Indices: 41169321--41169445 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 47
41169311 CACTAGCGCG
* * *
41169321 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTG-TATTAGCACTGTGTGTA
* * *
41169369 CTCTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTA
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
*
41169415 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGT
41169446 TGCCCAGCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 41 0.61
48 24 0.36
49 2 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (47 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTA
Found at i:41169485 original size:69 final size:69
Alignment explanation
Indices: 41169344--41169493 Score: 209
Period size: 69 Copynumber: 2.1 Consensus size: 69
41169334 ACGTCTCGTG
*
41169344 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
41169409 TGTGTA
64 TGTGTA
41169415 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGTAC
41169477 TTTG-GTA
62 TTTGTGTA
41169484 CTCTCTGTTT
1 CTCTCTGTTT
41169494 GTTCCGCATA
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
68 2 0.03
69 35 0.47
70 12 0.16
71 20 0.27
72 5 0.07
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:41169492 original size:21 final size:23
Alignment explanation
Indices: 41169341--41169490 Score: 146
Period size: 23 Copynumber: 6.4 Consensus size: 23
41169331 AGCACGTCTC
*
41169341 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTTTGT
41169366 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
41169389 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
41169412 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
*
41169435 GTGCTCTCTG-TTGCCCAGCAC-TTAT
1 GTGCTCTCTGATT----AGCACTTTGT
*
41169460 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
41169481 GTACTCTCTG
1 GTGCTCTCTG
41169491 TTTGTTCCGC
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
21 13 0.12
22 4 0.04
23 62 0.57
25 24 0.22
26 5 0.05
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:41170293 original size:29 final size:28
Alignment explanation
Indices: 41170250--41170337 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 28
41170240 ATAGGTCCCT
*
41170250 AAACTATCCAAAAATTACATTTTAACCTCA
1 AAACT-TCCAAAAATTACATTTT-ACCCCA
* *
41170280 AAACTTCTAAAAATTACCATTTTACCCCT
1 AAACTTCCAAAAATTA-CATTTTACCCCA
*
41170309 AAACTTTCCAAAAATTCCATTTTGACCCC
1 AAAC-TTCCAAAAATTACATTTT-ACCCC
41170338 GATTTTACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 24 0.48
30 26 0.52
ACGTcount: A:0.40, C:0.27, G:0.01, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTACCCCA
Found at i:41170301 original size:30 final size:29
Alignment explanation
Indices: 41170250--41170364 Score: 103
Period size: 29 Copynumber: 3.9 Consensus size: 29
41170240 ATAGGTCCCT
*
41170250 AAACTATCCAAAAATTA-CATTTTAACCTCA
1 AAACT-TCCAAAAATTACCATTTT-ACCCCA
* *
41170280 AAACTTCTAAAAATTACCATTTTACCCCT
1 AAACTTCCAAAAATTACCATTTTACCCCA
41170309 AAACTTTCCAAAAATT-CCATTTTGACCCC-
1 AAAC-TTCCAAAAATTACCATTTT-ACCCCA
* **
41170338 GATTTTACC-AAAATTACCATTTTACCC
1 AAACTT-CCAAAAATTACCATTTTACCC
41170365 TCGAACCTTC
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
28 12 0.16
29 35 0.48
30 26 0.36
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCA
Found at i:41170379 original size:29 final size:29
Alignment explanation
Indices: 41170260--41170380 Score: 72
Period size: 29 Copynumber: 4.2 Consensus size: 29
41170250 AAACTATCCA
* *
41170260 AAAATTA-CATTTTAACCTCAAAACTT-CT
1 AAAATTACCATTTT-ACCCCAAACCTTACT
* * *
41170288 AAAAATTACCATTTTACCCCTAAACTTTCCA
1 -AAAATTACCATTTTACCCC-AAACCTTACT
* ** *
41170319 AAAATT-CCATTTTGACCCC-GATTTTACC
1 AAAATTACCATTTT-ACCCCAAACCTTACT
*
41170347 AAAATTACCATTTTACCCTCGAACCTT-CT
1 AAAATTACCATTTTACCC-CAAACCTTACT
41170376 AAAAT
1 AAAAT
41170381 CCTATTTTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
28 15 0.21
29 32 0.44
30 25 0.34
31 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCAAACCTTACT
Found at i:41170529 original size:59 final size:59
Alignment explanation
Indices: 41170288--41170519 Score: 269
Period size: 59 Copynumber: 3.9 Consensus size: 59
41170278 CAAAACTTCT
* * *
41170288 AAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCC-A-TTTTGACCCCGATTTTACC
1 AAAAATTACCATTTTACCCCTAAACCTTCC-AAAA-TCCTATTTTTAACCCCGAATTTACC
* * * *
41170347 -AAAATTACCATTTTA-CCCTCGAACCTTCTAAAATCCTATTTTTAACCTCG-ATTTCACT
1 AAAAATTACCATTTTACCCCT-AAACCTTCCAAAATCCTATTTTTAACCCCGAATTT-ACC
* * *
41170405 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTC-AATTCTACC
1 AAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCTATTTTTAACCCCGAATT-TACC
* *
41170464 AAAAATTACCATTTTACCCTTGAACCTTCCAAAATCCTATTTTTAACCCCGAATTT
1 AAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCTATTTTTAACCCCGAATTT
41170520 CCTTGAAATT
Statistics
Matches: 147, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
56 3 0.02
57 12 0.08
58 32 0.22
59 91 0.62
60 9 0.06
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTAAACCTTCCAAAATCCTATTTTTAACCCCGAATTTACC
Found at i:41170543 original size:118 final size:117
Alignment explanation
Indices: 41170286--41170520 Score: 364
Period size: 117 Copynumber: 2.0 Consensus size: 117
41170276 CTCAAAACTT
* * * *
41170286 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTGACCCCGATTTTACCAAAA
1 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATCCCATTTTAACCCCAATTCTACCAAAA
* *
41170351 TTACCATTTTACCCTCGAACCTTCTAAAATCCTATTTTTAACCTCGATTTCA
66 TTACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCGATTTCA
*
41170403 CTAAAAATTACCATTTTACCCCTAAACTTTCC-AAAATCCCATTTTTAACCTCAATTCTACCAAA
1 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATCCCA-TTTTAACCCCAATTCTACC-AA
*
41170467 AATTACCATTTTACCCTTGAACCTTCCAAAATCCTATTTTTAACCCCGAATTTC
64 AATTACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCG-ATTTC
41170521 CTTGAAATTT
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
116 8 0.07
117 47 0.44
118 47 0.44
119 5 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (117 bp):
CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATCCCATTTTAACCCCAATTCTACCAAAA
TTACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCGATTTCA
Found at i:41170567 original size:118 final size:116
Alignment explanation
Indices: 41170286--41170571 Score: 317
Period size: 118 Copynumber: 2.4 Consensus size: 116
41170276 CTCAAAACTT
** * * *
41170286 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTGACCCCGATTTTACCAAAA
1 CTAAAAATTACCATTTTACCCCTAAACAGT-CAAAAATTCCATTTTAACCCCAATTCTACCAAAA
* *
41170351 TTACCATTTTACCCTCGAACCTTCTAAAATCCTATTTTTAACCTCGATTTCA
65 TTACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCGATTTCA
** * * *
41170403 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCTCAATTCTACCAAAA
1 CTAAAAATTACCATTTTACCCCTAAACAGTCAAAAATTCCA-TTTTAACCCCAATTCTACC-AAA
*
41170468 ATTACCATTTTACCCTTGAACCTTCCAAAATCCTATTTTTAACCCCGAATTTC-
64 ATTACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCG-ATTTCA
** * * ** *
41170521 CTTGAAATT-TCATTTTTGCCCCTCGAGAGTCAAAAATTACCATTTT-ACCCC
1 CTAAAAATTACCA-TTTTACCCCTAAACAGTCAAAAATT-CCATTTTAACCCC
41170572 TGGGTATCCA
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
116 9 0.06
117 51 0.36
118 75 0.52
119 8 0.06
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (116 bp):
CTAAAAATTACCATTTTACCCCTAAACAGTCAAAAATTCCATTTTAACCCCAATTCTACCAAAAT
TACCATTTTACCCTCGAACCTTCCAAAATCCTATTTTTAACCCCGATTTCA
Found at i:41172966 original size:14 final size:14
Alignment explanation
Indices: 41172947--41172974 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41172937 TATTGTTATA
41172947 TTAAAAAAATATTT
1 TTAAAAAAATATTT
41172961 TTAAAAAAATATTT
1 TTAAAAAAATATTT
41172975 GTTAGCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAAAATATTT
Found at i:41173068 original size:7 final size:7
Alignment explanation
Indices: 41173056--41173096 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
41173046 CCCTTTTTAA
41173056 AAAATAT
1 AAAATAT
41173063 AAAATAT
1 AAAATAT
41173070 AATACA-AT
1 AA-A-ATAT
41173078 AAAATA-
1 AAAATAT
41173084 AAAATAT
1 AAAATAT
41173091 AAAATA
1 AAAATA
41173097 ACATAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.23
7 17 0.57
8 5 0.17
9 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:41173096 original size:23 final size:22
Alignment explanation
Indices: 41173056--41173105 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
41173046 CCCTTTTTAA
41173056 AAAATATAAAATATAAT-ACAAT
1 AAAATATAAAATATAATAAC-AT
41173078 AAAATA-AAAATATAAAATAACAT
1 AAAATATAAAATAT--AATAACAT
41173101 AAAAT
1 AAAAT
41173106 TAGAATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 10 0.40
24 2 0.08
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAATATAAAATATAATAACAT
Found at i:41174783 original size:16 final size:15
Alignment explanation
Indices: 41174749--41174781 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
41174739 GTAGAAAAAG
41174749 AAAGAAAAAAATTTC
1 AAAGAAAAAAATTTC
41174764 AAAGAAAAAAATTTC
1 AAAGAAAAAAATTTC
41174779 AAA
1 AAA
41174782 AGTAAGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAGAAAAAAATTTC
Found at i:41178626 original size:2 final size:2
Alignment explanation
Indices: 41178619--41178643 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41178609 ACCACATTAA
41178619 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41178644 ATTAAATCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41180527 original size:16 final size:16
Alignment explanation
Indices: 41180508--41180541 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41180498 TTCCTCTCCC
41180508 CACATTTTATTCGGCA
1 CACATTTTATTCGGCA
41180524 CACATTTTATTCGGCA
1 CACATTTTATTCGGCA
41180540 CA
1 CA
41180542 TTATCCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (16 bp):
CACATTTTATTCGGCA
Found at i:41187966 original size:15 final size:16
Alignment explanation
Indices: 41187946--41187975 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41187936 TATTTAAAAT
41187946 TTAAAA-TTATTATTG
1 TTAAAATTTATTATTG
41187961 TTAAAATTTATTATT
1 TTAAAATTTATTATT
41187976 AAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTAAAATTTATTATTG
Found at i:41188689 original size:37 final size:34
Alignment explanation
Indices: 41188633--41188702 Score: 88
Period size: 37 Copynumber: 2.0 Consensus size: 34
41188623 AATATTCTTA
41188633 AAATATTATTAAAATTTTATATTAATATTTTAATAAT
1 AAATATTATTAAAATTTTATA--AATA-TTTAATAAT
*
41188670 AAATATATATTACAA-TTTATAAATATTTAATAA
1 AAATAT-TATTAAAATTTTATAAATATTTAATAA
41188703 CATATAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 8 0.26
35 4 0.13
37 12 0.39
38 7 0.23
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
AAATATTATTAAAATTTTATAAATATTTAATAAT
Found at i:41189048 original size:11 final size:11
Alignment explanation
Indices: 41189034--41189067 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
41189024 GAACATTCAA
*
41189034 TGAACTGTTCG
1 TGAACCGTTCG
41189045 TGAACCGTTCG
1 TGAACCGTTCG
41189056 TGAACCGTTCG
1 TGAACCGTTCG
41189067 T
1 T
41189068 TTAATATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (11 bp):
TGAACCGTTCG
Found at i:41189449 original size:23 final size:22
Alignment explanation
Indices: 41189409--41189457 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
41189399 TAACATTCGT
*
41189409 GAACATAAACGAATATGTCCGC
1 GAACATAAACGAACATGTCCGC
* *
41189431 GAACATTAAATGAACATGTTCGC
1 GAACA-TAAACGAACATGTCCGC
41189454 GAAC
1 GAAC
41189458 GCTGAACGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (22 bp):
GAACATAAACGAACATGTCCGC
Found at i:41197933 original size:11 final size:11
Alignment explanation
Indices: 41197913--41197941 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41197903 TTTACTATTT
41197913 AAAA-ATTAAA
1 AAAATATTAAA
41197923 AAAATATTAAA
1 AAAATATTAAA
41197934 AAAATATT
1 AAAATATT
41197942 TTTTTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:41200690 original size:60 final size:59
Alignment explanation
Indices: 41200540--41200938 Score: 281
Period size: 60 Copynumber: 6.7 Consensus size: 59
41200530 ATTGTCAGAT
* * * * **
41200540 AAAAAATTTAATTTTTTTG-TGTTGGCCATGCAATGGTCGA-A-ACCCTTAATTATCTGAT-
1 AAAAAATTCAAATTTTTTGATGTTGGTCATGCAATGGTCGACACTCCCTT--TT-TCAAATA
* * * ** *
41200598 AAAAAA-TCAAATTTTTGGATATTGGCCATGCAATGACCGACACTTCCTTTTTCAAATA
1 AAAAAATTCAAATTTTTTGATGTTGGTCATGCAATGGTCGACACTCCCTTTTTCAAATA
* *
41200656 AAAAAATTCAAAATTTTTTGATGTTGGTCATGCAATGGTTGACAC-CCC-TTTTCAGATA
1 AAAAAATTC-AAATTTTTTGATGTTGGTCATGCAATGGTCGACACTCCCTTTTTCAAATA
*** *
41200714 AAAAAATTTCAAAATTTTTTGATGTTAAACATGGAATGGTCGACAC-CCCTTTTT-ATTTGAAT-
1 AAAAAA-TTC-AAATTTTTTGATGTTGGTCATGCAATGGTCGACACTCCCTTTTTCA----AATA
* *
41200776 AAAAAATT-AAA-TTTTTGAGTGTTGGTCATGCCATGATCGACACTCCCTTTTTGTCAAATA
1 AAAAAATTCAAATTTTTTGA-TGTTGGTCATGCAATGGTCGACACTCCC-TTTT-TCAAATA
* * * * * *
41200836 AAAAATTTAAAATTTTTTG-TGTTAGTCATGCCATGGTCGACA-TCCCCTTTTTTATCTAGTA
1 AAAAAATTCAAATTTTTTGATGTTGGTCATGCAATGGTCGACACT-CCC--TTTT-TCAAATA
* *
41200897 AAAAAA-TCAATTTTTTTG-TGTTGGTCATGCAATGGCCGACAC
1 AAAAAATTCAAATTTTTTGATGTTGGTCATGCAATGGTCGACAC
41200939 CAACTTCCCC
Statistics
Matches: 276, Mismatches: 42, Indels: 43
0.76 0.12 0.12
Matches are distributed among these distances:
57 13 0.05
58 54 0.20
59 68 0.25
60 101 0.37
61 24 0.09
62 13 0.05
63 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (59 bp):
AAAAAATTCAAATTTTTTGATGTTGGTCATGCAATGGTCGACACTCCCTTTTTCAAATA
Found at i:41204761 original size:31 final size:29
Alignment explanation
Indices: 41204716--41204778 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
41204706 ATTATATAAG
* *
41204716 TTTGAATTTAAAATTCTACTTTAAATTTGAA
1 TTTGAATTTAAAATTATA-TTTAAAATT-AA
41204747 TTTGAAATTT-AAATTATATTTAAAATTAA
1 TTTG-AATTTAAAATTATATTTAAAATTAA
41204776 TTT
1 TTT
41204779 AATATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 8 0.28
31 11 0.38
32 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (29 bp):
TTTGAATTTAAAATTATATTTAAAATTAA
Found at i:41204956 original size:84 final size:84
Alignment explanation
Indices: 41204774--41205244 Score: 706
Period size: 83 Copynumber: 5.6 Consensus size: 84
41204764 ATTTAAAATT
* *
41204774 AATTTAATATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTT-
1 AATTTAA-A-TATTTAAAT-AAAAA-ATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
*
41204838 -TGTTCACAATACATTATTTA-TCA
62 AT-TTGACAATACATTATTTACT-A
**
41204861 AATTTTCATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
*
41204926 GACAATACATTATTTAGTA
66 GACAATACATTATTTACTA
*
41204945 AATTTAAATATTTAAATAAAAAATTATTA-TAT-TATA-ATTTTTTATCAAATAATGTGTTGATT
1 AATTTAAATATTTAAATAAAAAATTATTATTATAT-TACAATTTTTATCAAATAATGTGTTGATT
*
41205007 TAACAATACATTATTTACTA
65 TGACAATACATTATTTACTA
* *
41205027 TATTTAAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATTAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
41205091 GACAATACATTATTTACTA
66 GACAATACATTATTTACTA
*
41205110 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATATGTTGATTT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
* *
41205175 GATAATATATTATTTACTA
66 GACAATACATTATTTACTA
41205194 AATTTAAATATTTAAAT-AAAAATTATTATTATATTACAATTTTTATCAAAT
1 AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT
41205245 TTTAAATTTA
Statistics
Matches: 357, Mismatches: 19, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
81 11 0.03
82 65 0.18
83 135 0.38
84 129 0.36
85 11 0.03
86 1 0.00
87 5 0.01
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (84 bp):
AATTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
GACAATACATTATTTACTA
Found at i:41205365 original size:22 final size:22
Alignment explanation
Indices: 41205337--41205397 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
41205327 TGGACCACCC
*
41205337 AAATTTCAGCTCACCTAAACCG
1 AAATTTCAGCTCACCAAAACCG
* *
41205359 AAATTTCAGCTCAGCAAAACTG
1 AAATTTCAGCTCACCAAAACCG
* *
41205381 AAATTCCAACTCACCAA
1 AAATTTCAGCTCACCAA
41205398 CACCTCAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.30, G:0.08, T:0.21
Consensus pattern (22 bp):
AAATTTCAGCTCACCAAAACCG
Found at i:41206558 original size:22 final size:22
Alignment explanation
Indices: 41206533--41206592 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
41206523 TATTTTTTAC
41206533 AAATATTTTTTTTACATTTTCG
1 AAATATTTTTTTTACATTTTCG
******
41206555 AAATATAAAAAATACATTTTCG
1 AAATATTTTTTTTACATTTTCG
41206577 AAATATTTTTTTTACA
1 AAATATTTTTTTTACA
41206593 AAAAAATATG
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (22 bp):
AAATATTTTTTTTACATTTTCG
Found at i:41206609 original size:22 final size:22
Alignment explanation
Indices: 41206584--41206634 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
41206574 TCGAAATATT
41206584 TTTTTTACAAAAAAATATGATA
1 TTTTTTACAAAAAAATATGATA
41206606 TTTTTTACAAAAAAATATGATA
1 TTTTTTACAAAAAAATATGATA
41206628 TTTTTTA
1 TTTTTTA
41206635 GATTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTTTACAAAAAAATATGATA
Found at i:41207206 original size:24 final size:24
Alignment explanation
Indices: 41207179--41207225 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41207169 CCGAGCCTGA
41207179 GGATGAGCCCAAT-GACAAGCCCGT
1 GGATGAGCCC-ATGGACAAGCCCGT
*
41207203 GGATGAGCCCGTGGACAAGCCCG
1 GGATGAGCCCATGGACAAGCCCG
41207226 ATTACGAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.30, G:0.34, T:0.11
Consensus pattern (24 bp):
GGATGAGCCCATGGACAAGCCCGT
Found at i:41207223 original size:12 final size:12
Alignment explanation
Indices: 41207192--41207225 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41207182 TGAGCCCAAT
41207192 GACAAGCCCGTG
1 GACAAGCCCGTG
**
41207204 GATGAGCCCGTG
1 GACAAGCCCGTG
41207216 GACAAGCCCG
1 GACAAGCCCG
41207226 ATTACGAGGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.35, T:0.09
Consensus pattern (12 bp):
GACAAGCCCGTG
Found at i:41207780 original size:17 final size:18
Alignment explanation
Indices: 41207753--41207809 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
41207743 TTTAAATTTA
41207753 ATTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
41207771 ATTT-TAA-TT--T-TAT
1 ATTTCTAATTTCCTGTAT
41207784 -TTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
41207801 A-TTCTAATT
1 ATTTCTAATT
41207810 ATTATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.09
13 6 0.18
14 3 0.09
16 3 0.09
17 14 0.42
18 4 0.12
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.60
Consensus pattern (18 bp):
ATTTCTAATTTCCTGTAT
Found at i:41207809 original size:30 final size:30
Alignment explanation
Indices: 41207712--41207817 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
41207702 TCTGTTTAAC
* * * * * *
41207712 TTTTAAATTTAATTTGTAATTTCATTTTTA
1 TTTTAATTTTATTTTCTAATTTCCTGTATA
* *
41207742 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTATTTTCTAATTTCCTGTATA
41207772 TTTTAATTTTATTTTCTAATTTCCTGTATA
1 TTTTAATTTTATTTTCTAATTTCCTGTATA
*
41207802 TTCTAATTATTATTTT
1 TTTTAATT-TTATTTT
41207818 TTGAAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
30 61 0.90
31 7 0.10
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAATTTTATTTTCTAATTTCCTGTATA
Found at i:41208771 original size:59 final size:58
Alignment explanation
Indices: 41208643--41209134 Score: 436
Period size: 59 Copynumber: 8.2 Consensus size: 58
41208633 TTACATAGAT
* * * *
41208643 AACACCAAAAAAATTTAATTTTTTATC-AATAAAAAGGGGTGTCGGCCATGGCATGGCC
1 AACACCAAAAAAATTAAATTTTTTATCTGA-AAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
41208701 AACACAAAAAAAAATCAAATTTTTTATCTGACAAAAAGGGGTGTCGGCCATAGCATGGCC
1 AACAC-CAAAAAAATTAAATTTTTTATCTGA-AAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
41208761 AACACCAAAAAATTTTAAAATTTTTTTATCTGAAAAAAGGGGTATCGGCCATTGCATGGCT
1 AACACCAAAAAA-ATT-AAA-TTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGACC
* * * *
41208822 AACACTAAAAAATTTTAAAATTTTTTTATCTGAAAAAAAGGGATGTCGACCA-TGACATGACC
1 AACACCAAAAAA-ATT-AAA-TTTTTTATCTG-AAAAAAGGGGTGTCGGCCATTG-CATGACC
* * * * *
41208884 AACA-CAAAAAAATTTGAATTTTTTATCTGATAAAAAGAGGTGTCAGTCATGGCATGACC
1 AACACCAAAAAAA-TTAAATTTTTTATCTGA-AAAAAGGGGTGTCGGCCATTGCATGACC
** * * *
41208943 AACA-CAAAAAAATTTTATTTTTTATTCGGATAAAAAGGGGGTGTCGACCATTGCATAACC
1 AACACCAAAAAAATTAAATTTTTTA-TCTGA-AAAAA-GGGGTGTCGGCCATTGCATGACC
* * * *
41209003 AATACAAAAAAAATTTGAAATTTTTTATCTG-GAAAAGGGGTGTCGGCCATTGCATGACT
1 AACACCAAAAAAA-TT-AAATTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGACC
* * * * *
41209062 AACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGAGGTGTCGACCATTTCATGGCC
1 AACACCAAAAAA-ATT-AAA-TTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGACC
41209123 AACATCCAAAAA
1 AACA-CCAAAAA
41209135 TTTGATTTTT
Statistics
Matches: 361, Mismatches: 54, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
58 16 0.04
59 114 0.32
60 72 0.20
61 102 0.28
62 49 0.14
63 8 0.02
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.28
Consensus pattern (58 bp):
AACACCAAAAAAATTAAATTTTTTATCTGAAAAAAGGGGTGTCGGCCATTGCATGACC
Done.