Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 137 of 378
Found at i:38962646 original size:26 final size:25
Alignment explanation
Indices: 38962599--38962660 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
38962589 TGAAATTTTC
* * *
38962599 TTGAATCTAGTTGCGTGAAATAAAAT
1 TTGAATCGAGTTGAGTCAAAT-AAAT
*
38962625 TTGAATCGAGTTGAGTCTAATAAAT
1 TTGAATCGAGTTGAGTCAAATAAAT
*
38962650 TT-ATTCGAGTT
1 TTGAATCGAGTT
38962661 AAATTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 8 0.26
25 6 0.19
26 17 0.55
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (25 bp):
TTGAATCGAGTTGAGTCAAATAAAT
Found at i:38962868 original size:20 final size:20
Alignment explanation
Indices: 38962829--38962867 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38962819 TTTGGAAAAA
38962829 GAATATTTTATAATTATTTT
1 GAATATTTTATAATTATTTT
* *
38962849 GAATTTTTTGTAATT-TTTT
1 GAATATTTTATAATTATTTT
38962868 TAGTGTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
GAATATTTTATAATTATTTT
Found at i:38967745 original size:88 final size:88
Alignment explanation
Indices: 38967584--38967759 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 88
38967574 TAATAACAAG
* *
38967584 AATTATATCCGCCACATTTCCATCTATAGTTATGTCCTTGTTTCTTTGAGCTCAGAATGACAAAT
1 AATTATATCCGCCACATTTCCATCTATAGTTATGCCCTGGTTTCTTTGAGCTCAGAATGACAAAT
*
38967649 GCACCGGACATAACGACTTAGCA
66 GCAACGGACATAACGACTTAGCA
* * * *
38967672 AATTATATCCGCCACGTTTCCATCTATAGTTATGCCCTGGTTTGTTTGAGCTCGGAATGATGAAA
1 AATTATATCCGCCACATTTCCATCTATAGTTATGCCCTGGTTTCTTTGAGCTCAGAATGA-CAAA
38967737 -GCAACGGACATAACGACTTAGCA
65 TGCAACGGACATAACGACTTAGCA
38967760 TCGAATAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 77 0.96
89 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (88 bp):
AATTATATCCGCCACATTTCCATCTATAGTTATGCCCTGGTTTCTTTGAGCTCAGAATGACAAAT
GCAACGGACATAACGACTTAGCA
Found at i:38971513 original size:21 final size:20
Alignment explanation
Indices: 38971487--38971539 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
38971477 AAAATAATAT
38971487 ATTAATATTTTTAAAAATAAC
1 ATTAAT-TTTTTAAAAATAAC
* *
38971508 ATTAATTTTAT-CAAATAAC
1 ATTAATTTTTTAAAAATAAC
38971527 ATTCAATTTTTTA
1 ATT-AATTTTTTA
38971540 TTTTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.37
20 11 0.41
21 6 0.22
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAATTTTTTAAAAATAAC
Found at i:38972500 original size:2 final size:2
Alignment explanation
Indices: 38972495--38972533 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
38972485 ATCTCTCCCC
*
38972495 TA TA TA TA CA TA 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 TA TA TA TA TA TA T
38972534 GGGAGGGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38974939 original size:22 final size:21
Alignment explanation
Indices: 38974885--38974939 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
38974875 GTCACCTATA
38974885 TATATATATTTAAAATACAAT
1 TATATATATTTAAAATACAAT
* * * *
38974906 TATTTTTCATTTAAAATTCGCAT
1 TATATAT-ATTTAAAATAC-AAT
38974929 TATATATATTT
1 TATATATATTT
38974940 GCTACCATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
21 5 0.19
22 14 0.54
23 7 0.27
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATATATTTAAAATACAAT
Found at i:38975055 original size:21 final size:22
Alignment explanation
Indices: 38975031--38975072 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
38975021 ACATGATTTA
*
38975031 AATTACATAATATA-TTAAAAT
1 AATTACATAATAAACTTAAAAT
*
38975052 AATTATATAATAAACTTAAAA
1 AATTACATAATAAACTTAAAA
38975073 ACAGGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTACATAATAAACTTAAAAT
Found at i:38975907 original size:28 final size:28
Alignment explanation
Indices: 38975874--38975940 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
38975864 TCAAAATAAT
38975874 TTTTAAGAATTTTA-A-ATATTTATAAAAA
1 TTTTAA-AATTTTATATATATTT-TAAAAA
*
38975902 TTTT-AACTTTTATATATATTTTAAAAA
1 TTTTAAAATTTTATATATATTTTAAAAA
38975929 TTTTAAAATTTT
1 TTTTAAAATTTT
38975941 CTAAAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.18
27 12 0.35
28 16 0.47
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTTAAAATTTTATATATATTTTAAAAA
Found at i:38975915 original size:18 final size:19
Alignment explanation
Indices: 38975867--38975940 Score: 64
Period size: 19 Copynumber: 4.0 Consensus size: 19
38975857 AAAAAATTCA
* *
38975867 AAATAATTTTTAAGAATTTT
1 AAAT-ATTTATAAAAATTTT
38975887 AAATATTTATAAAAATTTT
1 AAATATTTATAAAAATTTT
* * *
38975906 AACT-TTTATATATATTTT
1 AAATATTTATAAAAATTTT
*
38975924 AAAAATTT-T-AAAATTTT
1 AAATATTTATAAAAATTTT
38975941 CTAAAATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
17 6 0.14
18 15 0.34
19 19 0.43
20 4 0.09
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
AAATATTTATAAAAATTTT
Found at i:38976417 original size:15 final size:15
Alignment explanation
Indices: 38976379--38976419 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
38976369 ATTTTCTTAG
38976379 TTATAGAATTTAATTT
1 TTAT-GAATTTAATTT
38976395 TTAT-AATTTAATTT
1 TTATGAATTTAATTT
38976409 TT-TGGAATTTA
1 TTAT-GAATTTA
38976420 TTCTCTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 6 0.26
16 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TTATGAATTTAATTT
Found at i:38978063 original size:13 final size:13
Alignment explanation
Indices: 38978045--38978072 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38978035 CACTAGCCAT
38978045 TAGTAATTAATAA
1 TAGTAATTAATAA
38978058 TAGTAATTAATAA
1 TAGTAATTAATAA
38978071 TA
1 TA
38978073 ACGATGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (13 bp):
TAGTAATTAATAA
Found at i:38978913 original size:18 final size:18
Alignment explanation
Indices: 38978887--38978921 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38978877 TTATTACAAA
38978887 TTTTAATATTTTAATATT
1 TTTTAATATTTTAATATT
* *
38978905 TTTTTATATTTTTATAT
1 TTTTAATATTTTAATAT
38978922 AATTCTAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATATTTTAATATT
Found at i:38984649 original size:40 final size:40
Alignment explanation
Indices: 38984604--38984770 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
38984594 CGGAATATAA
38984604 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38984644 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
38984684 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
38984724 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38984763 CCGGATAT
1 CCGGATAT
38984771 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38984754 original size:80 final size:79
Alignment explanation
Indices: 38984604--38984770 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
38984594 CGGAATATAA
* *
38984604 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
38984669 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
38984684 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
38984746 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
38984763 CCGGATAT
1 CCGGATAT
38984771 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:38985617 original size:17 final size:19
Alignment explanation
Indices: 38985594--38985639 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
38985584 AAGAAGCATG
38985594 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
38985612 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
38985630 AATCATGCTC
1 AATCATGCTC
38985640 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:38992651 original size:40 final size:40
Alignment explanation
Indices: 38992606--38992772 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
38992596 CGGAATATAA
38992606 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
38992646 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
38992686 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
38992726 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
38992765 CCGGATAT
1 CCGGATAT
38992773 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:38992756 original size:80 final size:79
Alignment explanation
Indices: 38992606--38992772 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
38992596 CGGAATATAA
* *
38992606 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
38992671 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
38992686 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
38992748 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
38992765 CCGGATAT
1 CCGGATAT
38992773 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:38993620 original size:17 final size:19
Alignment explanation
Indices: 38993597--38993642 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
38993587 AAGAAGCATG
38993597 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
38993615 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
38993633 AATCATGCTC
1 AATCATGCTC
38993643 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:38997426 original size:40 final size:40
Alignment explanation
Indices: 38997367--38997508 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
38997357 AAATTGAATG
* *
38997367 ATATCCGGGCTAA-AGCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGA-CCCGAAGACAATTATGCTAGAAACT
* * * ***
38997407 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
38997447 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
38997487 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
38997509 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.03
40 82 0.95
41 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:38997509 original size:40 final size:39
Alignment explanation
Indices: 38997406--38997534 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
38997396 TGCTGGAAAT
* * *
38997406 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
38997446 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
38997486 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
38997526 TATATCCGG
1 TATATCCGG
38997535 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:39005423 original size:40 final size:40
Alignment explanation
Indices: 39005364--39005505 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
39005354 AAATTGAATG
* *
39005364 ATATCCGGGCTAA-ATCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGA-CCCGAAGACAATTATGCTAGAAACT
* * * ***
39005404 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
39005444 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
39005484 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
39005506 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.03
40 82 0.95
41 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:39005506 original size:40 final size:39
Alignment explanation
Indices: 39005403--39005531 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
39005393 TGCTGGAAAT
* * *
39005403 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
39005443 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
39005483 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
39005523 TATATCCGG
1 TATATCCGG
39005532 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:39018937 original size:13 final size:13
Alignment explanation
Indices: 39018919--39018943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39018909 TAAAATTCTA
39018919 TTTTGTTTAATTT
1 TTTTGTTTAATTT
39018932 TTTTGTTTAATT
1 TTTTGTTTAATT
39018944 ATCAATTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTGTTTAATTT
Found at i:39028683 original size:40 final size:41
Alignment explanation
Indices: 39028634--39028838 Score: 138
Period size: 40 Copynumber: 5.1 Consensus size: 41
39028624 CGAAATTTAA
* * * *
39028634 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACATT-GC
1 CCGGTTATAGTGACTCGCACGATTGCCTTCGGGACATTAGC
* *
39028674 CCGGTTATAGTGATTCGCACAATTGCCTTCGGGA-ATTAGC
1 CCGGTTATAGTGACTCGCACGATTGCCTTCGGGACATTAGC
* * *
39028714 CCGGATT-TAGTAACTCGCACGAATGCCTTCGGGAC-TTAAC
1 CCGG-TTATAGTGACTCGCACGATTGCCTTCGGGACATTAGC
* * * * * *
39028754 CCGATTTTGGTAACTCGCACAAATGCCTTCGGGA-ATT-GAC
1 CCGGTTATAGTGACTCGCACGATTGCCTTCGGGACATTAG-C
* * * **
39028794 CCGGATT-TAGTCACTTAGCACAAAAGCCTTCGGGAC-TTAGC
1 CCGG-TTATAGTGAC-TCGCACGATTGCCTTCGGGACATTAGC
39028835 CCGG
1 CCGG
39028839 ACACCATTCG
Statistics
Matches: 135, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
39 5 0.04
40 100 0.74
41 29 0.21
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (41 bp):
CCGGTTATAGTGACTCGCACGATTGCCTTCGGGACATTAGC
Found at i:39028772 original size:80 final size:81
Alignment explanation
Indices: 39028688--39028837 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 81
39028678 TTATAGTGAT
* * * *
39028688 TCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAGTAAC-TCGCACGAATGCCTTCGGGACTT
1 TCGCACAAATGCCTTCGGGAATTGA-CCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTT
39028751 AACCCGATTTTGGTAAC
65 AACCCGATTTTGGTAAC
*
39028768 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTA
1 TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTTA
*
39028833 GCCCG
66 ACCCG
39028838 GACACCATTC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
80 36 0.58
81 26 0.42
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
TCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGTAACTTAGCACAAAAGCCTTCGGGACTTA
ACCCGATTTTGGTAAC
Found at i:39028838 original size:41 final size:40
Alignment explanation
Indices: 39028660--39028839 Score: 188
Period size: 40 Copynumber: 4.5 Consensus size: 40
39028650 GCTCGATTGT
* * *
39028660 CTTCGGGACATT-GCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGAC-TTAGCCCGGATT-TAGTAACTCGCACAAATGC
* *
39028700 CTTCGGGAATTAGCCCGGATTTAGTAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
* *
39028740 CTTCGGGACTTAACCC-GATTTTGGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGA-TTTAGTAACTCGCACAAATGC
* * * *
39028780 CTTCGGGAATT-GACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGC
39028821 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
39028840 CACCATTCGA
Statistics
Matches: 117, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
39 4 0.03
40 82 0.70
41 30 0.26
42 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:39037242 original size:46 final size:47
Alignment explanation
Indices: 39037079--39037248 Score: 172
Period size: 48 Copynumber: 3.7 Consensus size: 47
39037069 TGATATGTGT
* * *
39037079 GCTACTGTAAGACATGTCTGGGACATG-ATCAGCCA-C-A-ACATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCAT-TGGCATCGAGACAT-AGA
* * * *
39037124 GCTAGTGTAAGACATGTCTGGGAAATGCATAGGCCTCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCATCGAGACA--TAGA
* * *
39037172 GCCAGTGTAAGACATGTCTAGGACATGCATTGGCATTGAGACA-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATTGGCATCGAGACATAGA
39037218 GCTAGTGTAAGACATGTCTGGGACATGCATT
1 GCTAGTGTAAGACATGTCTGGGACATGCATT
39037249 AGCCTCGCGG
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
45 29 0.28
46 33 0.32
47 1 0.01
48 39 0.38
49 1 0.01
50 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATTGGCATCGAGACATAGA
Found at i:39037291 original size:94 final size:94
Alignment explanation
Indices: 39037121--39037292 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
39037111 CCACAACATG
***
39037121 AGAGCTAGTGTAAGACATGTCTGGGAAATGCATAGGCCTCGAGATATTTAAGCCAGTGTAAGACA
1 AGAGCTAGTGTAAGACATGTCTGGGAAATGCATAGGCCTCGAGATAGACAAGCCAGTGTAAGACA
*
39037186 TGTCTAGGACATGCATTGGCATTGAGACA
66 TGTATAGGACATGCATTGGCATTGAGACA
* * * *
39037215 AGAGCTAGTGTAAGACATGTCTGGGACATGCATTA-GCCTCGCGGTAGACAAGCTAGTGTAAGAC
1 AGAGCTAGTGTAAGACATGTCTGGGAAATGCA-TAGGCCTCGAGATAGACAAGCCAGTGTAAGAC
*
39037279 CTGTAT-GAGACATG
65 ATGTATAG-GACATG
39037293 GCATCGACAC
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 1 0.01
94 64 0.96
95 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (94 bp):
AGAGCTAGTGTAAGACATGTCTGGGAAATGCATAGGCCTCGAGATAGACAAGCCAGTGTAAGACA
TGTATAGGACATGCATTGGCATTGAGACA
Found at i:39037372 original size:49 final size:49
Alignment explanation
Indices: 39037221--39037392 Score: 172
Period size: 49 Copynumber: 3.5 Consensus size: 49
39037211 GACAAGAGCT
* * ** *
39037221 AGTGTAAGACATGTCTGGGACAT-GCATTAGCCTCGCGGTA-GACAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGA-AAGCC
* * * * *
39037269 AGTGTAAGACCTGTATGAGACATGGCATC-GACAC-CGATAAATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAG-C-CTCGCTATATGAAAGCC
* *
39037318 GGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGAAATCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGAAAGCC
39037367 AGTGTAAGACCATGTCTGGGACATGG
1 AGTGTAAGACC-TGTCTGGGACATGG
39037393 TGTCGGCATC
Statistics
Matches: 99, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
48 22 0.22
49 59 0.60
50 18 0.18
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCGCTATATGAAAGCC
Found at i:39040988 original size:12 final size:12
Alignment explanation
Indices: 39040973--39041060 Score: 54
Period size: 12 Copynumber: 6.9 Consensus size: 12
39040963 TAATTTCTCC
39040973 TTTTTCTTCTTT
1 TTTTTCTTCTTT
39040985 TTTTTCTTC-TT
1 TTTTTCTTCTTT
*
39040996 TCTTTCTTTCTATT
1 TTTTTC-TTCT-TT
*
39041010 TCGTTTCTTCTCTGT
1 T-TTTTCTTCT-T-T
*
39041025 TTCTTT-TTCTTG
1 TT-TTTCTTCTTT
39041037 TTTTTCTTTCTTT
1 TTTTTC-TTCTTT
* *
39041050 TATTTATTCTT
1 TTTTTCTTCTT
39041061 CATTTTATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
11 10 0.17
12 19 0.32
13 10 0.17
14 12 0.20
15 9 0.15
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:39041226 original size:3 final size:3
Alignment explanation
Indices: 39041218--39041269 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
39041208 TTGATAAAAT
39041218 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39041266 ATA A
1 ATA A
39041270 GTAAATATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39044037 original size:28 final size:28
Alignment explanation
Indices: 39044006--39044075 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
39043996 GCCTACTAGA
* *
39044006 CCCAATTATATTCACATGGCCCATTAGG
1 CCCAATCACATTCACATGGCCCATTAGG
* * *
39044034 CCCAAATCACATTTATATGGCCCTTTAGG
1 CCC-AATCACATTCACATGGCCCATTAGG
39044063 CCCAAATCACATT
1 CCC-AATCACATT
39044076 ATATTCATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (28 bp):
CCCAATCACATTCACATGGCCCATTAGG
Found at i:39044054 original size:29 final size:28
Alignment explanation
Indices: 39044021--39044079 Score: 100
Period size: 29 Copynumber: 2.1 Consensus size: 28
39044011 TTATATTCAC
39044021 ATGGCCCATTAGGCCCAAATCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACA-TTAT
*
39044050 ATGGCCCTTTAGGCCCAAATCACATTAT
1 ATGGCCCATTAGGCCCAAATCACATTAT
39044078 AT
1 AT
39044080 TCATGCTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.29
Consensus pattern (28 bp):
ATGGCCCATTAGGCCCAAATCACATTAT
Found at i:39044311 original size:16 final size:16
Alignment explanation
Indices: 39044292--39044334 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
39044282 AAACTTTCAG
39044292 CTTTTTGACATTTCGA
1 CTTTTTGACATTTCGA
* *
39044308 CTTTTCGACAATTCGA
1 CTTTTTGACATTTCGA
*
39044324 -TTTTTGCCATT
1 CTTTTTGACATT
39044335 CTACTTGTGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.49
Consensus pattern (16 bp):
CTTTTTGACATTTCGA
Found at i:39045548 original size:16 final size:16
Alignment explanation
Indices: 39045527--39045559 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39045517 AAAAATTCAA
39045527 GATTTCAGGATTTTTG
1 GATTTCAGGATTTTTG
*
39045543 GATTTCGGGATTTTTG
1 GATTTCAGGATTTTTG
39045559 G
1 G
39045560 GGCGTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.30, T:0.48
Consensus pattern (16 bp):
GATTTCAGGATTTTTG
Found at i:39046896 original size:55 final size:53
Alignment explanation
Indices: 39046799--39046975 Score: 169
Period size: 55 Copynumber: 3.3 Consensus size: 53
39046789 AGGATACCAC
* * *
39046799 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAATCAT
1 GTAAGACCATGTCAAGACATGGC-ATTGATAA-G-TTCATAAGGCAAGGAAATCAT
* ***
39046854 GTAAAACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCT-AT
1 GTAAGACCATGTCAAGACATGGCATTGATAAGTT-C-ATAAGGC-AAGGAAATCAT
* * * * * *
39046909 GTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCAT
1 GTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGCAAGGAAATCAT
39046962 GTAAGACCATGTCA
1 GTAAGACCATGTCA
39046976 CCTGTGTATC
Statistics
Matches: 100, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
52 6 0.06
53 24 0.24
54 8 0.08
55 57 0.57
56 5 0.05
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.23
Consensus pattern (53 bp):
GTAAGACCATGTCAAGACATGGCATTGATAAGTTCATAAGGCAAGGAAATCAT
Found at i:39047067 original size:23 final size:24
Alignment explanation
Indices: 39047041--39047085 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
39047031 AAGGTAAGGT
*
39047041 AAGGTAAGACAAGTT-ATGCTAAA
1 AAGGTAAAACAAGTTCATGCTAAA
39047064 AAGGTAAAACAAGTTCATGCTA
1 AAGGTAAAACAAGTTCATGCTA
39047086 GAAGAGCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (24 bp):
AAGGTAAAACAAGTTCATGCTAAA
Found at i:39047185 original size:16 final size:16
Alignment explanation
Indices: 39047164--39047194 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39047154 ATAAATTTGA
39047164 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
39047180 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
39047195 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:39051377 original size:29 final size:29
Alignment explanation
Indices: 39051306--39051395 Score: 103
Period size: 29 Copynumber: 3.2 Consensus size: 29
39051296 CACATACCTG
* * *
39051306 TATATGGCCCACTAGACCC-AATTATATT
1 TATATGGCCCATTAGACCCAAATCACATT
* *
39051334 CACATGGCCCATTAGACCCAAATCACATT
1 TATATGGCCCATTAGACCCAAATCACATT
* *
39051363 TATATGGCCCTTTAGGCCCAAATCACA-T
1 TATATGGCCCATTAGACCCAAATCACATT
39051391 TATAT
1 TATAT
39051396 TCATGCTCAC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 22 0.42
29 30 0.58
ACGTcount: A:0.32, C:0.28, G:0.11, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGACCCAAATCACATT
Found at i:39051633 original size:8 final size:8
Alignment explanation
Indices: 39051606--39051649 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
39051596 AGCAGCAAAA
39051606 ATTTCAGC
1 ATTTCAGC
* *
39051614 ATTTCGGT
1 ATTTCAGC
39051622 ATTTCAGC
1 ATTTCAGC
*
39051630 ATTTTAGC
1 ATTTCAGC
39051638 ATTTCAGC
1 ATTTCAGC
39051646 ATTT
1 ATTT
39051650 TGGCTTTTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (8 bp):
ATTTCAGC
Found at i:39053920 original size:45 final size:45
Alignment explanation
Indices: 39053853--39053945 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
39053843 AGATATGATT
*
39053853 CATGAGATCCATAAAAGCAGCTGGAGCATTTGTCAACCTGAATGG
1 CATGAGATCCATAAAAGCAGCTGGAGCATTTGTCAACCCGAATGG
* *
39053898 CATGAGATCCATAAAGGTAGCTGGAGCATTTGTCAACCCGAATGG
1 CATGAGATCCATAAAAGCAGCTGGAGCATTTGTCAACCCGAATGG
39053943 CAT
1 CAT
39053946 TACTAAGAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (45 bp):
CATGAGATCCATAAAAGCAGCTGGAGCATTTGTCAACCCGAATGG
Found at i:39057333 original size:26 final size:26
Alignment explanation
Indices: 39057261--39057325 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
39057251 TCAAATTGTA
39057261 TTTCTCATTTCATCTTATAATATCAC
1 TTTCTCATTTCATCTTATAATATCAC
39057287 TTTCTCATTTCATCTTATAATATCAC
1 TTTCTCATTTCATCTTATAATATCAC
39057313 TTTCTCATTTCAT
1 TTTCTCATTTCAT
39057326 TCAATAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTCTCATTTCATCTTATAATATCAC
Found at i:39058491 original size:11 final size:11
Alignment explanation
Indices: 39058475--39058504 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
39058465 TAATTTCTCA
39058475 TTTTTCTTCTT
1 TTTTTCTTCTT
39058486 TTTTTCTTCTT
1 TTTTTCTTCTT
*
39058497 TCTTTCTT
1 TTTTTCTT
39058505 TCTATTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTCTT
Found at i:39058728 original size:3 final size:3
Alignment explanation
Indices: 39058720--39058759 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
39058710 TTGATAAAAT
39058720 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39058760 GTAAATATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39060064 original size:28 final size:28
Alignment explanation
Indices: 39060032--39060091 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
39060022 ATTAGCCAAA
*
39060032 GAGAAGAGAAAAACTAATATTGAGTCTC
1 GAGAAAAGAAAAACTAATATTGAGTCTC
* *
39060060 GAGAAAAGAAAAGCTGATATTGAGTCTC
1 GAGAAAAGAAAAACTAATATTGAGTCTC
39060088 GAGA
1 GAGA
39060092 CTCAAGGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.25, T:0.20
Consensus pattern (28 bp):
GAGAAAAGAAAAACTAATATTGAGTCTC
Found at i:39061216 original size:74 final size:74
Alignment explanation
Indices: 39061095--39061234 Score: 253
Period size: 74 Copynumber: 1.9 Consensus size: 74
39061085 AGAAAGACAA
*
39061095 GTCGATGAGGTTATGTATAGACTACAGGCAACTCAACAAGGTGACTGTGAAGAATAAGTATCCCT
1 GTCGATGAGGTTATGTATAGACTACAGGCAACTCAACAAGGTGACTGTGAAGAAAAAGTATCCCT
39061160 TGCCAACGG
66 TGCCAACGG
* *
39061169 GTCGATGAGGTTATGTATAGACTATAGGCAGCTCAACAAGGTGACTGTGAAGAAAAAGTATCCCT
1 GTCGATGAGGTTATGTATAGACTACAGGCAACTCAACAAGGTGACTGTGAAGAAAAAGTATCCCT
39061234 T
66 T
39061235 TCTAAGGATC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (74 bp):
GTCGATGAGGTTATGTATAGACTACAGGCAACTCAACAAGGTGACTGTGAAGAAAAAGTATCCCT
TGCCAACGG
Found at i:39066546 original size:13 final size:13
Alignment explanation
Indices: 39066528--39066554 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39066518 CCACTTTAAG
39066528 GAGTTTAAACAGA
1 GAGTTTAAACAGA
39066541 GAGTTTAAACAGA
1 GAGTTTAAACAGA
39066554 G
1 G
39066555 TTCGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GAGTTTAAACAGA
Found at i:39071728 original size:40 final size:40
Alignment explanation
Indices: 39071673--39071753 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
39071663 ATTGGTACGA
39071673 TGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTTGATGC
1 TGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTTGATGC
39071713 TGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTTGATGC
1 TGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTTGATGC
39071753 T
1 T
39071754 TACTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.48
Consensus pattern (40 bp):
TGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTTGATGC
Found at i:39071759 original size:34 final size:36
Alignment explanation
Indices: 39071671--39071764 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 36
39071661 GGATTGGTAC
*
39071671 GATGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTT
1 GATGCGTT-AACTATTTTTGTGTTTGTAACGCCTCTT
39071708 GATGCTGTGTTAAACTATTTTTGTGTTTGTAACGCCTCTT
1 GATGC---GTT-AACTATTTTTGTGTTTGTAACGCCTCTT
39071748 GATGC-TT-ACTATTTTTG
1 GATGCGTTAACTATTTTTG
39071765 AATTTGATAC
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
34 10 0.19
36 2 0.04
37 4 0.08
40 37 0.70
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (36 bp):
GATGCGTTAACTATTTTTGTGTTTGTAACGCCTCTT
Found at i:39076633 original size:12 final size:12
Alignment explanation
Indices: 39076609--39076640 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
39076599 TTAATTTTTG
39076609 GGCATGT-ACTA
1 GGCATGTGACTA
39076620 GGCATGTGACTA
1 GGCATGTGACTA
39076632 GGCATGTGA
1 GGCATGTGA
39076641 TCACACAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.25
Consensus pattern (12 bp):
GGCATGTGACTA
Found at i:39077971 original size:28 final size:28
Alignment explanation
Indices: 39077938--39078006 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
39077928 GCGTAGATCA
39077938 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39077966 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39077994 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39078007 GGTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:39082015 original size:28 final size:28
Alignment explanation
Indices: 39081982--39082050 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
39081972 GCGTAGATCA
39081982 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39082010 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39082038 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39082051 GGTTTTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:39086056 original size:28 final size:28
Alignment explanation
Indices: 39086024--39086092 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
39086014 GCATAGATCA
39086024 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39086052 TGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
39086080 CGATA-TACCCCTA
1 CGAAATTACCCCTA
39086093 GAGTTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 8 0.21
28 30 0.79
ACGTcount: A:0.43, C:0.26, G:0.10, T:0.20
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:39094488 original size:20 final size:21
Alignment explanation
Indices: 39094447--39094490 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39094437 ATTAATACTC
*
39094447 AATAATTACTAAAGTTTCAAA
1 AATAATTACTAAAGTTCCAAA
39094468 AATAATTACT-AAG-TCCAAA
1 AATAATTACTAAAGTTCCAAA
39094487 AATA
1 AATA
39094491 TTTTTTTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 3 0.14
21 10 0.45
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.30
Consensus pattern (21 bp):
AATAATTACTAAAGTTCCAAA
Found at i:39096934 original size:40 final size:40
Alignment explanation
Indices: 39096875--39097082 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
39096865 CAAATGAATG
* * * *
39096875 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
39096915 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * **
39096955 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
39096995 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
39097035 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
39097075 ATATCCGG
1 ATATCCGG
39097083 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
39 2 0.01
40 136 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:39097013 original size:80 final size:80
Alignment explanation
Indices: 39096877--39097082 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 80
39096867 AATGAATGAT
* * ** * * *
39096877 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCCA-
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CAT
*
39096941 TTGTGCTAGT-GACCAC
65 TTGTGCAAGTCGACC-C
* * *
39096957 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
** *
39097022 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGACCC
* *
39097037 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
39097083 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 103 0.96
81 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGACCC
Found at i:39100816 original size:26 final size:25
Alignment explanation
Indices: 39100778--39100849 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 25
39100768 ATTTTTTATT
39100778 TTTATTAAATTATATTTAATAATAA
1 TTTATTAAATTATATTTAATAATAA
*
39100803 TTATATTAAATTATGA-TT-A-AATTA
1 TT-TATTAAATTAT-ATTTAATAATAA
*
39100827 TTTATTAAATTATTTTTAATAAT
1 TTTATTAAATTATATTTAATAAT
39100850 TCTCCTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 13 0.32
24 7 0.17
25 6 0.15
26 13 0.32
27 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTATTAAATTATATTTAATAATAA
Found at i:39100840 original size:63 final size:64
Alignment explanation
Indices: 39100712--39100851 Score: 169
Period size: 63 Copynumber: 2.2 Consensus size: 64
39100702 AATATTATAT
* * **
39100712 TTTTTATTAATTCATACTTTAATAATAAATATATTAAGAATGTTATTAAATTATATATTTTTTA
1 TTTTTATTAATTCATACTTTAATAATAAATATATTAAGAATATGATTAAATTATATATTAATTA
* * *
39100776 TTTTTATTAAATT-ATA-TTTAATAATAATTATATTAA-ATTATGATTAAATTATTTATTAAATT
1 TTTTTATT-AATTCATACTTTAATAATAAATATATTAAGAATATGATTAAATTATATATT-AATT
39100838 A
64 A
*
39100839 TTTTTAATAATTC
1 TTTTTATTAATTC
39100852 TCCTATTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 21 0.32
63 29 0.45
64 11 0.17
65 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (64 bp):
TTTTTATTAATTCATACTTTAATAATAAATATATTAAGAATATGATTAAATTATATATTAATTA
Found at i:39101437 original size:16 final size:16
Alignment explanation
Indices: 39101416--39101446 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39101406 GTATTTAGTC
39101416 ATATAATAAATTATTA
1 ATATAATAAATTATTA
*
39101432 ATATAATTAATTATT
1 ATATAATAAATTATT
39101447 TTAATAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:39101514 original size:16 final size:17
Alignment explanation
Indices: 39101478--39101514 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
39101468 AATTTTATTT
39101478 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
39101495 -AATAA-AAATTTTAAA
1 TAATAATAAATTTTAAA
39101510 TAATA
1 TAATA
39101515 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:39104710 original size:18 final size:19
Alignment explanation
Indices: 39104687--39104725 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
39104677 ATTATAATAG
39104687 TATTTAACA-TTT-AAATTA
1 TATTTAA-ATTTTAAAATTA
39104705 TATTTAAATTTTAAAATTA
1 TATTTAAATTTTAAAATTA
39104724 TA
1 TA
39104726 ATATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTAAATTTTAAAATTA
Found at i:39105606 original size:19 final size:20
Alignment explanation
Indices: 39105566--39105607 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
39105556 AAAATTATTA
*
39105566 TTTTTATATATTCTTTAGAT
1 TTTTTATATATTCTTTAAAT
39105586 TTTTTA-ATATT-TTTATAAT
1 TTTTTATATATTCTTTA-AAT
39105605 TTT
1 TTT
39105608 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATATATTCTTTAAAT
Found at i:39106796 original size:24 final size:25
Alignment explanation
Indices: 39106768--39106817 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
39106758 TATACTTAAA
39106768 AGCCCCTTAG-TTTTCCTTATAATT
1 AGCCCCTTAGTTTTTCCTTATAATT
39106792 AGCCCCTTAGTTTTTCCTTATAATT
1 AGCCCCTTAGTTTTTCCTTATAATT
39106817 A
1 A
39106818 TAGTCTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (25 bp):
AGCCCCTTAGTTTTTCCTTATAATT
Found at i:39109767 original size:6 final size:6
Alignment explanation
Indices: 39109756--39109783 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39109746 TTTTTGTTCC
39109756 GAATGA GAATGA GAATGA GAATGA GAAT
1 GAATGA GAATGA GAATGA GAATGA GAAT
39109784 TAAGCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
GAATGA
Found at i:39110168 original size:5 final size:5
Alignment explanation
Indices: 39110158--39110201 Score: 72
Period size: 5 Copynumber: 8.8 Consensus size: 5
39110148 ATCTGTATGT
39110158 TTTTA TTTTA TTTTA TTTTTA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39110202 CACAAATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:39114490 original size:28 final size:28
Alignment explanation
Indices: 39114458--39114511 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
39114448 ATATATAGAT
39114458 ATAGTCTATTCCTCTTATAATTATTCTC
1 ATAGTCTATTCCTCTTATAATTATTCTC
*
39114486 ATAGTCTATTCCTCTTCTAATTATTC
1 ATAGTCTATTCCTCTTATAATTATTC
39114512 GAATTTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.50
Consensus pattern (28 bp):
ATAGTCTATTCCTCTTATAATTATTCTC
Found at i:39117253 original size:50 final size:53
Alignment explanation
Indices: 39117175--39117273 Score: 159
Period size: 50 Copynumber: 1.9 Consensus size: 53
39117165 GATTCAGGCG
*
39117175 TGTTTCTGGGAGAGGATGTGTAGCCTTCGGGCTTGACACTTAGTGCCCAGACA
1 TGTTTCTGGGAGAGGATGTGTAGCCTTCGGGCTTGACACTCAGTGCCCAGACA
*
39117228 TGTTTCT-GGAG-GGATGT-TAGCCTTCGGGCTTGGCACTCAGTGCCCA
1 TGTTTCTGGGAGAGGATGTGTAGCCTTCGGGCTTGACACTCAGTGCCCA
39117274 AGTGTGTTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 27 0.61
51 6 0.14
52 4 0.09
53 7 0.16
ACGTcount: A:0.16, C:0.22, G:0.32, T:0.29
Consensus pattern (53 bp):
TGTTTCTGGGAGAGGATGTGTAGCCTTCGGGCTTGACACTCAGTGCCCAGACA
Found at i:39119375 original size:46 final size:46
Alignment explanation
Indices: 39119322--39119493 Score: 290
Period size: 46 Copynumber: 3.7 Consensus size: 46
39119312 TTTGGCATCT
* *
39119322 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
*
39119368 GAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
*
39119414 GAACTCCTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
* *
39119460 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39119494 GCGGGTTACA
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
Found at i:39123608 original size:35 final size:35
Alignment explanation
Indices: 39123562--39123639 Score: 131
Period size: 35 Copynumber: 2.2 Consensus size: 35
39123552 CTTCTTCATT
39123562 TCTTCTTCTCTCTAGTTC-TTTTTATTTTCCTTCCA
1 TCTTCTTCTCTCTA-TTCTTTTTTATTTTCCTTCCA
39123597 TCTTCTTCTCTCTATTCTTTTTTATTTTCCTTCCA
1 TCTTCTTCTCTCTATTCTTTTTTATTTTCCTTCCA
*
39123632 TTTTCTTC
1 TCTTCTTC
39123640 AAGATCTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 3 0.07
35 38 0.93
ACGTcount: A:0.08, C:0.28, G:0.01, T:0.63
Consensus pattern (35 bp):
TCTTCTTCTCTCTATTCTTTTTTATTTTCCTTCCA
Found at i:39127585 original size:31 final size:31
Alignment explanation
Indices: 39127550--39127611 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39127540 ACCCGAAGTA
39127550 AAAATATTTATTTTTTATTATTTCTTTAAGG
1 AAAATATTTATTTTTTATTATTTCTTTAAGG
39127581 AAAATATTTATTTTTTATTATTTCTTTAAGG
1 AAAATATTTATTTTTTATTATTTCTTTAAGG
39127612 TTTACAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (31 bp):
AAAATATTTATTTTTTATTATTTCTTTAAGG
Found at i:39131248 original size:84 final size:88
Alignment explanation
Indices: 39131146--39131310 Score: 266
Period size: 91 Copynumber: 1.9 Consensus size: 88
39131136 ACAACTCCCC
39131146 AACCCTTACTTTTGCTCTTGCCAAC-T-T-AA-TCCCAACTTTCACTTTCTTGCTTCTTGTTATC
1 AACCCTTACTTTTGCTCTTGCCAACTTATCAACTCCCAACTTTCACTTTCTTGCTTCTTGTTATC
*
39131207 TTCAAGTTCGTCTACAGCTCTCG
66 TTCAAGCTCGTCTACAGCTCTCG
39131230 AACCCTTACTTTTGCTCTTGCCAACTTAATCCCAACTCCCAACTTTCACTTTCTTGCTTCTTGTT
1 AACCCTTACTTTTGCTCTTGCCAACTT-AT--CAACTCCCAACTTTCACTTTCTTGCTTCTTGTT
39131295 ATCTTCAAGCTCGTCT
63 ATCTTCAAGCTCGTCT
39131311 GCTGCTATGC
Statistics
Matches: 73, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
84 25 0.34
85 1 0.01
87 1 0.01
90 2 0.03
91 44 0.60
ACGTcount: A:0.18, C:0.32, G:0.08, T:0.41
Consensus pattern (88 bp):
AACCCTTACTTTTGCTCTTGCCAACTTATCAACTCCCAACTTTCACTTTCTTGCTTCTTGTTATC
TTCAAGCTCGTCTACAGCTCTCG
Found at i:39133370 original size:21 final size:19
Alignment explanation
Indices: 39133346--39133402 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
39133336 TATAATTGTG
39133346 TTAATATCTAATTATAAATAT
1 TTAATAT-TAATT-TAAATAT
39133367 TTAATGATTATATTTAAATAT
1 TTAAT-ATTA-ATTTAAATAT
*
39133388 TTAAAATATAATTTA
1 TTAATAT-TAATTTA
39133403 TCTATTCTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.22
21 20 0.62
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATATTAATTTAAATAT
Found at i:39134322 original size:2 final size:2
Alignment explanation
Indices: 39134315--39134353 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
39134305 AACTCATGCT
39134315 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39134354 AATAATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39134694 original size:18 final size:19
Alignment explanation
Indices: 39134666--39134702 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
39134656 GGAAAAAAGA
39134666 ATTTCATAATAAGGAAAAT
1 ATTTCATAATAAGGAAAAT
*
39134685 ATTT-ATAATAGGGAAAAT
1 ATTTCATAATAAGGAAAAT
39134703 GAGTAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
ATTTCATAATAAGGAAAAT
Found at i:39136555 original size:13 final size:13
Alignment explanation
Indices: 39136537--39136562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39136527 CACCCCATGT
39136537 ACAGATACAGATA
1 ACAGATACAGATA
39136550 ACAGATACAGATA
1 ACAGATACAGATA
39136563 TACAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
ACAGATACAGATA
Found at i:39140691 original size:54 final size:55
Alignment explanation
Indices: 39140610--39140720 Score: 215
Period size: 54 Copynumber: 2.0 Consensus size: 55
39140600 ACCTTTTAGG
39140610 CTATATAAAAAATTAAAAAATAAATAAATAAATAATTTTAATTTTATTAATCATA
1 CTATATAAAAAATTAAAAAATAAATAAATAAATAATTTTAATTTTATTAATCATA
39140665 CTATAT-AAAAATTAAAAAATAAATAAATAAATAATTTTAATTTTATTAATCATA
1 CTATATAAAAAATTAAAAAATAAATAAATAAATAATTTTAATTTTATTAATCATA
39140719 CT
1 CT
39140721 TGTAAAGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 50 0.89
55 6 0.11
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (55 bp):
CTATATAAAAAATTAAAAAATAAATAAATAAATAATTTTAATTTTATTAATCATA
Found at i:39150222 original size:42 final size:42
Alignment explanation
Indices: 39150175--39150254 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
39150165 GGTAGTAAAC
*
39150175 ACACGGGC-ACAGACACGGCCGTGTGTCTCAACCGTGTGTAGG
1 ACACGGGCTA-AGACACGGCCGTGTGCCTCAACCGTGTGTAGG
* * * *
39150217 ACACGGTCTAATACACGGGCGTGTGCCTCAGCCGTGTG
1 ACACGGGCTAAGACACGGCCGTGTGCCTCAACCGTGTG
39150255 CCCCTAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.20, C:0.29, G:0.33, T:0.19
Consensus pattern (42 bp):
ACACGGGCTAAGACACGGCCGTGTGCCTCAACCGTGTGTAGG
Found at i:39150467 original size:20 final size:20
Alignment explanation
Indices: 39150444--39150482 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
39150434 AGGGACACGG
39150444 GCGTGCCCCAATGCACACAA
1 GCGTGCCCCAATGCACACAA
*
39150464 GCGTGTCCCAATGCACACA
1 GCGTGCCCCAATGCACACA
39150483 GGCATGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.38, G:0.21, T:0.13
Consensus pattern (20 bp):
GCGTGCCCCAATGCACACAA
Found at i:39153171 original size:101 final size:101
Alignment explanation
Indices: 39152965--39153178 Score: 250
Period size: 101 Copynumber: 2.1 Consensus size: 101
39152955 AATTGATGGA
* * * * * * * *
39152965 TAAGACCATGGTTGGACCATGGAAAATGTTTATATGTAAGACCATAGCTGGGCTATGTCATTTTA
1 TAAGACCATGGTTGGACTATTG-CAGTATTTATATGTAACACCATAGCTGGGCTATGGCATTCTA
* * * * *
39153030 ATGAAAAGACCATAATTGGGTTATGGCACCTTGAACG
65 ATGAAAAGACCATAACTGAGATATGACACCTGGAACG
* *
39153067 TAAGCCCATGGTTGGACTATTGCAGTATTTATATGTAACACCATAGCTGGGCTATGGCATTCTGA
1 TAAGACCATGGTTGGACTATTGCAGTATTTATATGTAACACCATAGCTGGGCTATGGCATTCTAA
* *
39153132 TGATAAGACCATAACTGAGATATGACA-CTAGGAATG
66 TGAAAAGACCATAACTGAGATATGACACCT-GGAACG
39153168 TAAGACCATGG
1 TAAGACCATGG
39153179 CATGGCCATG
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
100 2 0.02
101 72 0.77
102 19 0.20
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTGGACTATTGCAGTATTTATATGTAACACCATAGCTGGGCTATGGCATTCTAA
TGAAAAGACCATAACTGAGATATGACACCTGGAACG
Found at i:39165901 original size:64 final size:64
Alignment explanation
Indices: 39165800--39165928 Score: 240
Period size: 64 Copynumber: 2.0 Consensus size: 64
39165790 GGATGCCAAG
*
39165800 TTATTGGGGGAAAACATAAGGACTGTTGGTCTTGAAATAAGTAAGAACATTACCTCCAAAGTGC
1 TTATTGGGGGAAAACATAAGGACTGATGGTCTTGAAATAAGTAAGAACATTACCTCCAAAGTGC
*
39165864 TTATTGGGGGAAAACATAAGGACTGATGGTCTTGAAATAAGTAAGAGCATTACCTCCAAAGTGC
1 TTATTGGGGGAAAACATAAGGACTGATGGTCTTGAAATAAGTAAGAACATTACCTCCAAAGTGC
39165928 T
1 T
39165929 GATTCAACAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (64 bp):
TTATTGGGGGAAAACATAAGGACTGATGGTCTTGAAATAAGTAAGAACATTACCTCCAAAGTGC
Found at i:39168426 original size:16 final size:15
Alignment explanation
Indices: 39168401--39168431 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39168391 GAAGTTTCAA
39168401 GTTATTAATTATTTT
1 GTTATTAATTATTTT
39168416 GTTATTTAATTATTTT
1 GTTA-TTAATTATTTT
39168432 TTTTATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
GTTATTAATTATTTT
Found at i:39174461 original size:19 final size:19
Alignment explanation
Indices: 39174437--39174473 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39174427 GTCTCAGTTG
*
39174437 CAAGAATGTCAGAGAAGAT
1 CAAGAATGTCAGAAAAGAT
39174456 CAAGAATGTCAGAAAAGA
1 CAAGAATGTCAGAAAAGA
39174474 AAGTTGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.24, T:0.14
Consensus pattern (19 bp):
CAAGAATGTCAGAAAAGAT
Found at i:39174512 original size:216 final size:216
Alignment explanation
Indices: 39174239--39174659 Score: 770
Period size: 216 Copynumber: 1.9 Consensus size: 216
39174229 TGTAATTGAT
*
39174239 TCAAGAATGTCAGAAAAGAAAGTTGAATCTGTGCCTGTTGTCTGTGAGTTCCCTGATGTGTTTCT
1 TCAAGAATGTCAGAAAAGAAAGTTGAATCTATGCCTGTTGTCTGTGAGTTCCCTGATGTGTTTCT
* *
39174304 TGAAGAACTTCTGGGATTACCTCCGGCTAGAGAAGTTAAATTTGGCATTGAATTGGTACTTGGTA
66 TGAAGAACTTCCGGGATTACCTCCGGCTAGAGAAGTTAAATTTGGCATTGAATTGGTACCTGGTA
* *
39174369 CTACTCCGATTTTGATAGCTCCGTATAGAATGGCTCCGACCAAACTTAAAAAACTGAAGTCTCAG
131 CTACTCCGATTTTGATAGCTCCATATAGAATGGATCCGACCAAACTTAAAAAACTGAAGTCTCAG
39174434 TTGCAAGAATGTCAGAGAAGA
196 TTGCAAGAATGTCAGAGAAGA
39174455 TCAAGAATGTCAGAAAAGAAAGTTGAATCTATGCCTGTTGTCTGTGAGTTCCCTGATGTGTTTCT
1 TCAAGAATGTCAGAAAAGAAAGTTGAATCTATGCCTGTTGTCTGTGAGTTCCCTGATGTGTTTCT
* * *
39174520 TGAAGAACTTCCGGGATTACCTTCGGTTAGAGAAGTTGAATTTGGCATTGAATTGGTACCTGGTA
66 TGAAGAACTTCCGGGATTACCTCCGGCTAGAGAAGTTAAATTTGGCATTGAATTGGTACCTGGTA
39174585 CTACTCCGATTTTGATAGCTCCATATAGAATGGATCCGACCAAACTTAAAAAACTGAAGTCTCAG
131 CTACTCCGATTTTGATAGCTCCATATAGAATGGATCCGACCAAACTTAAAAAACTGAAGTCTCAG
39174650 TTGCAAGAAT
196 TTGCAAGAAT
39174660 TGACCGATAG
Statistics
Matches: 197, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 197 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (216 bp):
TCAAGAATGTCAGAAAAGAAAGTTGAATCTATGCCTGTTGTCTGTGAGTTCCCTGATGTGTTTCT
TGAAGAACTTCCGGGATTACCTCCGGCTAGAGAAGTTAAATTTGGCATTGAATTGGTACCTGGTA
CTACTCCGATTTTGATAGCTCCATATAGAATGGATCCGACCAAACTTAAAAAACTGAAGTCTCAG
TTGCAAGAATGTCAGAGAAGA
Found at i:39183526 original size:40 final size:40
Alignment explanation
Indices: 39183471--39183680 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
39183461 AACATTGGAA
39183471 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
39183511 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
39183551 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
39183591 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
39183630 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
39183671 CTATATCCGG
1 ATATATCCGG
39183681 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:39191662 original size:40 final size:40
Alignment explanation
Indices: 39191607--39191776 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
39191597 AACATTGGAA
39191607 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
39191647 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
39191687 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
39191726 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
39191767 CTATATCCGG
1 ATATATCCGG
39191777 TTAAATCCCG
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 109 0.98
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:39196131 original size:10 final size:9
Alignment explanation
Indices: 39196101--39196185 Score: 62
Period size: 9 Copynumber: 8.7 Consensus size: 9
39196091 AAAATTTATC
39196101 TATAATTTTT
1 TATAA-TTTT
*
39196111 TATTATTTT
1 TATAATTTT
39196120 TATAATTCTT
1 TATAATT-TT
39196130 TATAAAATTTT
1 TAT--AATTTT
* *
39196141 AATAATTTA
1 TATAATTTT
39196150 TATAATTTT
1 TATAATTTT
*
39196159 ACTATAGTTTT
1 --TATAATTTT
*
39196170 CTAAAATTTT
1 -TATAATTTT
39196180 TATAAT
1 TATAAT
39196186 ACCGTGTAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 27 0.45
10 17 0.28
11 12 0.20
12 4 0.07
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (9 bp):
TATAATTTT
Found at i:39196928 original size:8 final size:8
Alignment explanation
Indices: 39196915--39196940 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39196905 AATAAATATT
39196915 TTGGTTAA
1 TTGGTTAA
39196923 TTGGTTAA
1 TTGGTTAA
39196931 TTGGTTAA
1 TTGGTTAA
39196939 TT
1 TT
39196941 CGATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (8 bp):
TTGGTTAA
Found at i:39204635 original size:131 final size:130
Alignment explanation
Indices: 39204487--39204949 Score: 357
Period size: 130 Copynumber: 3.5 Consensus size: 130
39204477 TAAGAAATCA
* * * * * *
39204487 CAACCCAGCACGATAGGGCATGATCCC-CGACTCGTCAAACA-C-CGAGTATTGCCTTCGTTTTA
1 CAACCCAACACGTTAGGGCACGATCCCGCGAATCGCCAAACATCAC-A-TATCGCCTTCGTTTTA
* ** ** * *
39204549 AAGGATTTTTAGAAGAGTCGAGTGAAATTTTGAAAG-GATATTTGATTATTTTAAAC-AATCGGG
64 AA-GA-TTTTAAAAGACACGAGCAAAATTTT-AAAGTGATATTCGATTATTTTAAACAAAT-GCG
39204612 AAATTG
125 AAATTG
* * * * *
39204618 CTACCCAACACGTTAGGGTACGATCCCGCGAATTGCCAAATATCACATATCGCCTTCGTTTTAGA
1 CAACCCAACACGTTAGGGCACGATCCCGCGAATCGCCAAACATCACATATCGCCTTCGTTTTAAA
*
39204683 GATTTTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTGAACAAATGCGAAATTG
66 GATTTTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTAAACAAATGCGAAATTG
* * * * *** *
39204748 CAACCCAACACGTTAGGGCTA-GATTCCGCGAATTGCCAAACATCAAATCTCATTTTC-ATTTAA
1 CAACCCAACACGTTAGGGC-ACGATCCCGCGAATCGCCAAACATCACATATCGCCTTCGTTTTAA
* * * ** ** * * *
39204811 GGGATTTTAAAAGATATGAATAAAATTTCGAAGGGA-AGTTCGATTATTTTGAGCAAATGCGAAA
65 -AGATTTTAAAAGACACGAGCAAAATTTTAAAGTGATA-TTCGATTATTTTAAACAAATGCGAAA
39204875 TTG
128 TTG
* ** * * * * * * *
39204878 TAACCCAACACGTTAGGGCACGATTTCGTGAATCGCCGAACATGAAATTTCGTCTTCGTTTTGAA
1 CAACCCAACACGTTAGGGCACGATCCCGCGAATCGCCAAACATCACATATCGCCTTCGTTTTAAA
39204943 GAATTTT
66 G-ATTTT
39204950 TGGATGAATA
Statistics
Matches: 270, Mismatches: 51, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
129 10 0.04
130 194 0.72
131 37 0.14
132 26 0.10
133 2 0.01
134 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (130 bp):
CAACCCAACACGTTAGGGCACGATCCCGCGAATCGCCAAACATCACATATCGCCTTCGTTTTAAA
GATTTTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTAAACAAATGCGAAATTG
Found at i:39204730 original size:130 final size:132
Alignment explanation
Indices: 39204537--39204896 Score: 376
Period size: 130 Copynumber: 2.8 Consensus size: 132
39204527 ACCGAGTATT
* ** ** *
39204537 GCCTTCGTTTTAAAGGATTTTTAGAAGAGTCGAGTGAAATTTTGAAAGGATATTTGATTATTTTA
1 GCCTTCGTTTTAAAGGATTTTTAAAAGACACGAGCAAAATTTTGAAAGGATATTCGATTATTTTA
* * *
39204602 AAC-AATCGGGAAATTGCTACCCAACACGTTAGGG-TACGATCCCGCGAATTGCCAAATATCACA
66 AACAAAT-GCGAAATTGCAACCCAACACGTTAGGGCTA-GATCCCGCGAATTGCCAAACATCACA
39204665 TATC
129 TATC
*
39204669 GCCTTCGTTTTAGA-GA-TTTTAAAAGACACGAGCAAAATTTT-AAAGTGATATTCGATTATTTT
1 GCCTTCGTTTTAAAGGATTTTTAAAAGACACGAGCAAAATTTTGAAAG-GATATTCGATTATTTT
* * *
39204731 GAACAAATGCGAAATTGCAACCCAACACGTTAGGGCTAGATTCCGCGAATTGCCAAACATCAAAT
65 AAACAAATGCGAAATTGCAACCCAACACGTTAGGGCTAGATCCCGCGAATTGCCAAACATCACAT
*
39204796 CTC
130 ATC
*** * * * * ** * *
39204799 ATTTTC-ATTTAAGGGA-TTTTAAAAGATATGAATAAAATTTCGAAGGGA-AGTTCGATTATTTT
1 GCCTTCGTTTTAAAGGATTTTTAAAAGACACGAGCAAAATTTTGAAAGGATA-TTCGATTATTTT
* * *
39204861 GAGCAAATGCGAAATTGTAACCCAACACGTTAGGGC
65 AAACAAATGCGAAATTGCAACCCAACACGTTAGGGC
39204897 ACGATTTCGT
Statistics
Matches: 194, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
129 9 0.05
130 162 0.84
131 10 0.05
132 13 0.07
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (132 bp):
GCCTTCGTTTTAAAGGATTTTTAAAAGACACGAGCAAAATTTTGAAAGGATATTCGATTATTTTA
AACAAATGCGAAATTGCAACCCAACACGTTAGGGCTAGATCCCGCGAATTGCCAAACATCACATA
TC
Found at i:39205870 original size:2 final size:2
Alignment explanation
Indices: 39205865--39205897 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39205855 ACACACACAC
39205865 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39205898 CACCATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39206041 original size:2 final size:2
Alignment explanation
Indices: 39206034--39206067 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
39206024 TTATAACGTG
39206034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39206068 GGAGTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39207895 original size:44 final size:44
Alignment explanation
Indices: 39207819--39208110 Score: 460
Period size: 44 Copynumber: 6.6 Consensus size: 44
39207809 CGGGAACACC
* * * *
39207819 AATCTGTTATTTTCGATCTGCTCTCTGTCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
* *
39207863 AATATG-TCGTCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCT-ATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
* *
39207907 AATCTGTTATTTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
39207951 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
*
39207995 AATCTGCTATCTTCGATCTGCTCTCCGTCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
*
39208039 AATCTGCTATCCTCGATCTGCTCTCCGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
* *
39208083 AATCTACTATCCTCGATCTGCTCTCCGC
1 AATCTGCTATCTTCGATCTGCTCTCCGC
39208111 GATCTGCGGG
Statistics
Matches: 232, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
43 1 0.00
44 230 0.99
45 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (44 bp):
AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATGCCA
Found at i:39216530 original size:60 final size:60
Alignment explanation
Indices: 39216437--39216557 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
39216427 TACATAAAGT
*
39216437 CGAGTTACAAATAAAATTTCGCTCTAATACTCAAAGTCCTAATTTTTCTAAGCAATGAGG
1 CGAGTTACAAATAAAATTTCGCTCTAATACTCAAAGTCCTAATTTTTCTAAGCAATAAGG
39216497 CGAGTTACAAATAAAATTTCGCTCTAATACTCAAAGTCCTAATTTTTCTAAGCAATAAGG
1 CGAGTTACAAATAAAATTTCGCTCTAATACTCAAAGTCCTAATTTTTCTAAGCAATAAGG
39216557 C
1 C
39216558 CAGCTCCTGC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.31
Consensus pattern (60 bp):
CGAGTTACAAATAAAATTTCGCTCTAATACTCAAAGTCCTAATTTTTCTAAGCAATAAGG
Found at i:39220029 original size:130 final size:130
Alignment explanation
Indices: 39219760--39220249 Score: 468
Period size: 130 Copynumber: 3.8 Consensus size: 130
39219750 TGAAAACCTA
* * * * ** * * *
39219760 AAGGAATATTCGATTGTTTTG-ACTAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCC
1 AAGGGATATTCGATTATTTTGAAC-AAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * * * * * * *
39219824 -CGAATCGTCAAACACCAAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAGAGC-CGAGTGAAAT
65 GCGAATTGCCAAACATCAAATATCGCCTTCGTTTTAGA-GA-TTTTAAAAGA-CACAAGTGAAAT
39219887 TTTG
127 TTTG
* * * * * *
39219891 AAGGGATATTTGATTATTTTAAAC-AATCGGGAAATTGCTACCCAACACGTTAAGGCACGATCCC
1 AAGGGATATTCGATTATTTTGAACAAAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* ** *
39219955 GCGAATTGCCAAATATCACCTATCGCCTTCGTTTTAGAGATTTTAAAAGACACAAGTAAAATTTT
65 GCGAATTGCCAAACATCAAATATCGCCTTCGTTTTAGAGATTTTAAAAGACACAAGTGAAATTTT
*
39220020 A
130 G
* *
39220021 AAGTGATATTCGATTATTTTGAACAAATGCAAAATTGCAACCCAACACGTTAGGGCACGATTCCG
1 AAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
* ** * * * * * *
39220086 CGAATTGCCAAACATCAAATCTCATCTTCATTTAAGGGATTTTAAAAGATATGAA-TGAAATTTC
66 CGAATTGCCAAACATCAAATATCGCCTTCGTTTTAGAGATTTTAAAAGACA-CAAGTGAAATTTT
39220150 G
130 G
* *
39220151 AAGGGAAATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
1 AAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
* * * * **
39220216 CGAATTTCCGAACAACAAATTTCATCTTCGTTTT
66 CGAATTGCCAAACATCAAATATCGCCTTCGTTTT
39220250 GAAGAATTTT
Statistics
Matches: 295, Mismatches: 58, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
129 1 0.00
130 212 0.72
131 51 0.17
132 31 0.11
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (130 bp):
AAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
CGAATTGCCAAACATCAAATATCGCCTTCGTTTTAGAGATTTTAAAAGACACAAGTGAAATTTTG
Found at i:39221190 original size:2 final size:2
Alignment explanation
Indices: 39221185--39221229 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39221175 AAACACACAC
39221185 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39221227 AT A
1 AT A
39221230 CATCATAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39221451 original size:18 final size:18
Alignment explanation
Indices: 39221430--39221464 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39221420 TATATATGCA
*
39221430 TATATATGTAGTTACATG
1 TATAGATGTAGTTACATG
*
39221448 TATAGATGTATTTACAT
1 TATAGATGTAGTTACAT
39221465 ATAAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (18 bp):
TATAGATGTAGTTACATG
Found at i:39234233 original size:21 final size:22
Alignment explanation
Indices: 39234207--39234247 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
39234197 AAACAACGTA
*
39234207 GTTTTGCCTTTTAA-TTTAATG
1 GTTTTGACTTTTAACTTTAATG
39234228 GTTTTGACTTTTAACTTTAA
1 GTTTTGACTTTTAACTTTAA
39234248 AAAAGGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (22 bp):
GTTTTGACTTTTAACTTTAATG
Found at i:39234281 original size:70 final size:66
Alignment explanation
Indices: 39234157--39234288 Score: 165
Period size: 70 Copynumber: 1.9 Consensus size: 66
39234147 ATAGACAATA
**
39234157 TAATGTTTTGACTTTTAACTTAATGAGTAAACATTTATAAAAACAACGTAGTTTTGCCTTTTAAT
1 TAATGTTTTGACTTTTAACTTAAAAAGTAAACATTTATAAAAACAACGTAGTTTTGCCTTTTAAT
39234222 T
66 T
* * ** *
39234223 TAATGGTTTTGACTTTTAACTTTAAAAAAGGTAAACGTTTATCAAAACGGCGTTGTTTTGCCTTT
1 TAAT-GTTTTGACTTTTAAC-TT-AAAAA-GTAAACATTTATAAAAACAACGTAGTTTTGCCTTT
39234288 T
62 T
39234289 CTTATTCAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 4 0.07
67 15 0.27
68 2 0.04
69 3 0.05
70 31 0.56
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (66 bp):
TAATGTTTTGACTTTTAACTTAAAAAGTAAACATTTATAAAAACAACGTAGTTTTGCCTTTTAAT
T
Found at i:39235901 original size:42 final size:42
Alignment explanation
Indices: 39235830--39235944 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
39235820 TGTTTCAATA
* * * *
39235830 CCATATTCCCGATATGGTCTTACATGAAAT-ATCATATCGACG
1 CCATATCCCCGATATGGTCTTATACGAAATCA-CATACCGACG
* * * *
39235872 CTATATCCCCGACATAGTCTTATACGAAATCACATACCGAGG
1 CCATATCCCCGATATGGTCTTATACGAAATCACATACCGACG
* *
39235914 CCATATCTCAGATATGGTCTTATACGAAATC
1 CCATATCCCCGATATGGTCTTATACGAAATC
39235945 TTAATAACCT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
42 58 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (42 bp):
CCATATCCCCGATATGGTCTTATACGAAATCACATACCGACG
Found at i:39238616 original size:16 final size:16
Alignment explanation
Indices: 39238597--39238628 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39238587 AGTTGTGATT
39238597 GTAAATCAGTTAACTC
1 GTAAATCAGTTAACTC
39238613 GTAAATCAGTTAACTC
1 GTAAATCAGTTAACTC
39238629 AAAATGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
GTAAATCAGTTAACTC
Found at i:39238638 original size:15 final size:16
Alignment explanation
Indices: 39238599--39238638 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39238589 TTGTGATTGT
*
39238599 AAATCAGTTAACTCGT
1 AAATCAGTTAACTCGA
39238615 AAATCAGTTAACTC-A
1 AAATCAGTTAACTCGA
*
39238630 AAATGAGTT
1 AAATCAGTT
39238639 GTTCATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (16 bp):
AAATCAGTTAACTCGA
Found at i:39238976 original size:134 final size:135
Alignment explanation
Indices: 39238639--39239298 Score: 693
Period size: 134 Copynumber: 4.9 Consensus size: 135
39238629 AAAATGAGTT
* * * * * * *
39238639 GTTCATAATCATAAATCAATGAAC-TAAGTTGTGATCATAAATCAACGAGTTTTAAGAATATCAG
1 GTTCATGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACGAGCTTTAACAATATCAA
* * * * *
39238703 TTGTGATCATAAATTAGTGAAA-TGTTTGAATGTAGTTGCGATTATAAATC-GATGAACTTTAAG
66 TTGTGATCGTAAATTAGTGAAACTGTTTGAATGGAGTTGCAATCATAAATCAG-TGAACTCTAAG
39238766 TGAA-A
130 TGAACA
* ** * * * * * *
39238771 GTTTATGATTATAAATTAATAAACTTAATCTATGATCGTAAATCAACGAGTTTTAACAATATCAG
1 GTTCATGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACGAGCTTTAACAATATCAA
* * * *
39238836 TTGTGATCGTAAATTAAT-AAACTATTTGAATGGAGTTGTGAA-CGTAAATCAGTGAACTCTAAG
66 TTGTGATCGTAAATTAGTGAAACTGTTTGAATGGAGTTG-CAATCATAAATCAGTGAACTCTAAG
*
39238899 TGAACC
130 TGAACA
* * *
39238905 GTTCATGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACAAGCTTTAATATTATCAA
1 GTTCATGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACGAGCTTTAACAATATCAA
* * ** *
39238970 TTGTGATCGTAAA-TAATCG-AACTATTCAAATGGAGTTGCAATCGTAAATCAGT-AACCTCTAA
66 TTGTGATCGTAAATTAGT-GAAACTGTTTGAATGGAGTTGCAATCATAAATCAGTGAA-CTCTAA
39239032 GTGAACTA
129 GTGAAC-A
* *
39239040 -TTCATGATCGTAAATCAATGAACCTAA-CATGTGAACGTAAATCAACGAGCTTTAACAATATCA
1 GTTCATGATCGTAAATCAATGAACTTAAGC-TGTGATCGTAAATCAACGAGCTTTAACAATATCA
* **
39239103 ATTGTGATCGTAAATTAGTGAAA-TGTTTGAATAGAGTTGCAATCATAAATTGGTGAACTCTAAG
65 ATTGTGATCGTAAATTAGTGAAACTGTTTGAATGGAGTTGCAATCATAAATCAGTGAACTCTAAG
*
39239167 TGAATA
130 TGAACA
* * * * * *
39239173 GTTCATGATCGTAAATCAATGAACGTAAGCTATGAAT-ATAAATC-ACTGAGCTTTGATAGTATC
1 GTTCATGATCGTAAATCAATGAACTTAAGCTGTG-ATCGTAAATCAAC-GAGCTTTAACAATATC
* * * *
39239236 AATTGTGATCATAAATCAGTG-AACTGTTTGAATGTAGTTGCAATCATAAATCAATGAACTCTA
64 AATTGTGATCGTAAATTAGTGAAACTGTTTGAATGGAGTTGCAATCATAAATCAGTGAACTCTA
39239299 TAACTTATCC
Statistics
Matches: 445, Mismatches: 64, Indels: 36
0.82 0.12 0.07
Matches are distributed among these distances:
132 22 0.05
133 99 0.22
134 315 0.71
135 9 0.02
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (135 bp):
GTTCATGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACGAGCTTTAACAATATCAA
TTGTGATCGTAAATTAGTGAAACTGTTTGAATGGAGTTGCAATCATAAATCAGTGAACTCTAAGT
GAACA
Found at i:39238979 original size:63 final size:62
Alignment explanation
Indices: 39238910--39239117 Score: 150
Period size: 63 Copynumber: 3.2 Consensus size: 62
39238900 GAACCGTTCA
39238910 TGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACAAGCTTTAATATTATCAATTG
1 TGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACAAGCTTTAA-ATTATCAATTG
** ** * * * * *
39238973 TGATCGTAAAT-AATCGAACTATTCAAATGGAGTTGCAATCGTAAATCAGTAACCTCTAAGTGAA
1 TGATCGTAAATCAAT-GAAC--TT--AA-GCTG-TG--ATCGTAAATCAACAAGCTTTAAATTAT
* *
39239037 CTATTCA
57 CAATT-G
* * * *
39239044 TGATCGTAAATCAATGAACCTAA-CATGTGAACGTAAATCAACGAGCTTTAACAATATCAATTG
1 TGATCGTAAATCAATGAACTTAAGC-TGTGATCGTAAATCAACAAGCTTTAA-ATTATCAATTG
39239107 TGATCGTAAAT
1 TGATCGTAAAT
39239118 TAGTGAAATG
Statistics
Matches: 106, Mismatches: 26, Indels: 26
0.67 0.16 0.16
Matches are distributed among these distances:
62 3 0.03
63 42 0.40
64 5 0.05
65 4 0.04
66 1 0.01
67 4 0.04
68 2 0.02
69 3 0.03
70 6 0.06
71 33 0.31
72 3 0.03
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (62 bp):
TGATCGTAAATCAATGAACTTAAGCTGTGATCGTAAATCAACAAGCTTTAAATTATCAATTG
Found at i:39241778 original size:27 final size:27
Alignment explanation
Indices: 39241695--39241766 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
39241685 ACACGCTAAA
* * * *
39241695 AAATGGAAACTTTTATGGCAATCTATG
1 AAATGGAAGCCTTTGTGGCAATCTGTG
39241722 AAATGGAAGCCTTTGTGGCAATCTGTG
1 AAATGGAAGCCTTTGTGGCAATCTGTG
*
39241749 AAATGGGAGCCTTTGTGG
1 AAATGGAAGCCTTTGTGG
39241767 TGATCATGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAATCTGTG
Found at i:39241912 original size:27 final size:27
Alignment explanation
Indices: 39241881--39241970 Score: 126
Period size: 27 Copynumber: 3.3 Consensus size: 27
39241871 TAAGTATCGT
*
39241881 GAACACAGAAGGAATAGTACATATGGC
1 GAACACTGAAGGAATAGTACATATGGC
* *
39241908 AAACACTGAAGGAATAGTACATATGAC
1 GAACACTGAAGGAATAGTACATATGGC
** *
39241935 GAACTTTGAAGGAATAGAACATATGGC
1 GAACACTGAAGGAATAGTACATATGGC
39241962 GAACACTGA
1 GAACACTGA
39241971 GAGAAAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.18
Consensus pattern (27 bp):
GAACACTGAAGGAATAGTACATATGGC
Found at i:39242542 original size:211 final size:211
Alignment explanation
Indices: 39242178--39242597 Score: 741
Period size: 211 Copynumber: 2.0 Consensus size: 211
39242168 TAAATAATGT
*
39242178 AAGTAATGAATTAGTGAAGAGAAGGGTAAAACATGATTTCAAGGTTAGGTGTGATGTCTATGGTA
1 AAGTAATGAATCAGTGAAGAGAAGGGTAAAACATGATTTCAAGGTTAGGTGTGATGTCTATGGTA
* * * *
39242243 TGAAGAAGAAAAATACTCGCCAAAGTTAAGATGAAGAACGAAGAACAATGACATGACAATAAAAT
66 TAAAGAAGAAAAATACTCGCCAAAGTCAAGATGAAAAACGAAGAACAATCACATGACAATAAAAT
39242308 TCCTAGATACATTGTATGGAGACAATACAAGTAAATTGAATCTAACTCACGAAGCTCTCATGAAC
131 TCCTAGATACATTGTATGGAGACAATACAAGTAAATTGAATCTAACTCACGAAGCTCTCATGAAC
39242373 TTACCTTTGTGTATAC
196 TTACCTTTGTGTATAC
39242389 AAGTAATGAATCAGTGAAGAGAAGGGTAAAACATGATTTCAAGGTTAGGTGTGATGTCTATGGTA
1 AAGTAATGAATCAGTGAAGAGAAGGGTAAAACATGATTTCAAGGTTAGGTGTGATGTCTATGGTA
* * * *
39242454 TAAAGAAGAAAGATACTCGCCAAAGTCAAGTTGAAAAACGAAGAACAATCACATGATAATGAAAT
66 TAAAGAAGAAAAATACTCGCCAAAGTCAAGATGAAAAACGAAGAACAATCACATGACAATAAAAT
* *
39242519 TCCTAGATACGTTGTATGGAGACAATACAAGTAAATTGAGTCTAACTCACGAAGCTCTCATGAAC
131 TCCTAGATACATTGTATGGAGACAATACAAGTAAATTGAATCTAACTCACGAAGCTCTCATGAAC
39242584 TTACCTTTGTGTAT
196 TTACCTTTGTGTAT
39242598 TGTGTTACAG
Statistics
Matches: 198, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
211 198 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (211 bp):
AAGTAATGAATCAGTGAAGAGAAGGGTAAAACATGATTTCAAGGTTAGGTGTGATGTCTATGGTA
TAAAGAAGAAAAATACTCGCCAAAGTCAAGATGAAAAACGAAGAACAATCACATGACAATAAAAT
TCCTAGATACATTGTATGGAGACAATACAAGTAAATTGAATCTAACTCACGAAGCTCTCATGAAC
TTACCTTTGTGTATAC
Found at i:39243311 original size:199 final size:199
Alignment explanation
Indices: 39242913--39243309 Score: 573
Period size: 199 Copynumber: 2.0 Consensus size: 199
39242903 AGTAAGTATG
* * * *
39242913 TAATTGAGTTGTAACACCCAAGATTCAGATTTGGCGAATAGGATCGGGTTAAGGGCGTTACAAAA
1 TAATCGAGTTGTAACACCCAAGATTCAGATCTAGCGAATAGGATCGGGTTAAGGGCATTACAAAA
* * ** * *
39242978 TTAATATGTGTCACCATGCTAATTGGTCGTCAGCTCCATATCAATGTTTTTTAATTGTGTTAGTC
66 TTAACATGTGTAACCATGCTAATTGGTCGTCAGCTCCATATCAACATATTTTAATAGTGTTAGTC
* * *
39243043 ATGTACTTAAAAAAAGTATCAAGTTAACTTACGATTTTTAAGTTTAAGTACTAGTTATGTCCCAA
131 AGGTACTTAAAAAAAGTATCAAGTTAACTTACAATTTTTAAGTTTAAGTACTAGTTAAGTCCCAA
39243108 AAAA
196 AAAA
* * *
39243112 TAATCGAGTTGTAACACCTAAGATTCGGATCTAGCGAATTGGATCGGGTTGAA-GGCATTACAAA
1 TAATCGAGTTGTAACACCCAAGATTCAGATCTAGCGAATAGGATCGGGTT-AAGGGCATTACAAA
* * * *
39243176 CTTAACATGTGTAACCATGTTAATTGGTCGTTAGTTCCATATCAACATATTTTAATAGTGTTAGT
65 ATTAACATGTGTAACCATGCTAATTGGTCGTCAGCTCCATATCAACATATTTTAATAGTGTTAGT
* *
39243241 TAGGTACTT-AAAAAAGTATCAAGTTAACTTACAATTTTTAAGTTTAGGTACTAGTTAAGTCCCA
130 CAGGTACTTAAAAAAAGTATCAAGTTAACTTACAATTTTTAAGTTTAAGTACTAGTTAAGTCCCA
39243305 AAAAA
195 AAAAA
39243310 ATTAAATACA
Statistics
Matches: 175, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
198 57 0.33
199 116 0.66
200 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (199 bp):
TAATCGAGTTGTAACACCCAAGATTCAGATCTAGCGAATAGGATCGGGTTAAGGGCATTACAAAA
TTAACATGTGTAACCATGCTAATTGGTCGTCAGCTCCATATCAACATATTTTAATAGTGTTAGTC
AGGTACTTAAAAAAAGTATCAAGTTAACTTACAATTTTTAAGTTTAAGTACTAGTTAAGTCCCAA
AAAA
Found at i:39253051 original size:2 final size:2
Alignment explanation
Indices: 39253044--39253073 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39253034 AGTATTTCAA
39253044 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39253074 TTAACACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39260971 original size:46 final size:45
Alignment explanation
Indices: 39260921--39261008 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
39260911 GGGAGAGATG
*
39260921 AGTTTG-GGGTAGATGGGGAGTAAAAATTTTGAGGGAAAATAAAAAA
1 AGTTTGAGGGT-GATGGGAAGT-AAAATTTTGAGGGAAAATAAAAAA
** * *
39260967 AGTTTGAGGGTTTTTGGAAGTAAAATTTTGAGGGAAAGTAAA
1 AGTTTGAGGGTGATGGGAAGTAAAATTTTGAGGGAAAATAAA
39261009 TGGGACAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
45 20 0.56
46 12 0.33
47 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (45 bp):
AGTTTGAGGGTGATGGGAAGTAAAATTTTGAGGGAAAATAAAAAA
Found at i:39264943 original size:34 final size:34
Alignment explanation
Indices: 39264898--39265050 Score: 121
Period size: 34 Copynumber: 4.5 Consensus size: 34
39264888 AATATTCACC
* * *
39264898 AAAATGGAACAAAAATGACAAGGCTTAAAACTAA
1 AAAATGAAACAAAAATAATAAGGCTTAAAACTAA
* *
39264932 AAAATGAAACAAATATAATAAGAG-TTAAAACTAC
1 AAAATGAAACAAAAATAATAAG-GCTTAAAACTAA
* * *
39264966 AAAATGAAACAAAAGTAATAAGACTTAAAACTCTA
1 AAAATGAAACAAAAATAATAAGGCTTAAAACT-AA
* * **** * *
39265001 ATAGTAGAAACACTGCTAATAAGACTTAAAATTAA
1 AAAAT-GAAACAAAAATAATAAGGCTTAAAACTAA
39265036 AAAATGAAA-AAAAAT
1 AAAATGAAACAAAAAT
39265051 TTATAAGACC
Statistics
Matches: 91, Mismatches: 24, Indels: 9
0.73 0.19 0.07
Matches are distributed among these distances:
33 2 0.02
34 59 0.65
35 8 0.09
36 22 0.24
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (34 bp):
AAAATGAAACAAAAATAATAAGGCTTAAAACTAA
Found at i:39265105 original size:40 final size:40
Alignment explanation
Indices: 39265052--39265132 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
39265042 AAAAAAAATT
* *
39265052 TATAAGACCTATAATTAATAATACAAAAGATTCACAAAAA
1 TATAAAACCTATAATTAACAATACAAAAGATTCACAAAAA
* * * *
39265092 TATAAAACTTATAATTAACACTACAAAATATTTACAAAAA
1 TATAAAACCTATAATTAACAATACAAAAGATTCACAAAAA
39265132 T
1 T
39265133 TCAGATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.28
Consensus pattern (40 bp):
TATAAAACCTATAATTAACAATACAAAAGATTCACAAAAA
Found at i:39267754 original size:43 final size:43
Alignment explanation
Indices: 39267701--39267785 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
39267691 CACACGACCG
*
39267701 TGTGACCAGGCCGTCTGACTCACATGTCCAAAAGACACACCCA
1 TGTGACCAGGCCGTCTGACTCACACGTCCAAAAGACACACCCA
* * * *
39267744 TGTGACCAGGCTGTGTGACTTACACGTCCAAGAGACACACCC
1 TGTGACCAGGCCGTCTGACTCACACGTCCAAAAGACACACCC
39267786 GTGTCTTAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (43 bp):
TGTGACCAGGCCGTCTGACTCACACGTCCAAAAGACACACCCA
Found at i:39269378 original size:21 final size:21
Alignment explanation
Indices: 39269352--39269392 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39269342 TTTTCCCTGA
39269352 ATTTAGACTCATATATCCATG
1 ATTTAGACTCATATATCCATG
39269373 ATTTAGACTCATATATCCAT
1 ATTTAGACTCATATATCCAT
39269393 CCATGGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (21 bp):
ATTTAGACTCATATATCCATG
Found at i:39270710 original size:80 final size:80
Alignment explanation
Indices: 39270626--39270774 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39270616 TATGGTAACC
* * * *
39270626 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39270690 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39270706 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39270771 CCGG
66 CCGG
39270775 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39270716 original size:40 final size:38
Alignment explanation
Indices: 39270667--39270774 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39270657 ATCACGATTT
*
39270667 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39270707 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39270747 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39270775 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39278829 original size:80 final size:80
Alignment explanation
Indices: 39278745--39278893 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
39278735 TATGGTAACC
* * * *
39278745 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
39278809 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
39278825 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
39278890 CCGG
66 CCGG
39278894 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:39278835 original size:40 final size:38
Alignment explanation
Indices: 39278786--39278893 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
39278776 ATCACGATTT
*
39278786 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
39278826 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
39278866 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
39278894 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:39284418 original size:18 final size:17
Alignment explanation
Indices: 39284395--39284430 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
39284385 TGTCACCTGG
39284395 CCGTGTGTCACAACACGA
1 CCGTGTGTCAC-ACACGA
39284413 CCGTGTGTCACACACGA
1 CCGTGTGTCACACACGA
39284430 C
1 C
39284431 TAAGGCACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.25, C:0.36, G:0.22, T:0.17
Consensus pattern (17 bp):
CCGTGTGTCACACACGA
Found at i:39287090 original size:43 final size:42
Alignment explanation
Indices: 39286971--39287086 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
39286961 CACATAGTAC
* *
39286971 CATACCAATGCCATATCCCAGATATGGTCTTACATGGGACCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACATGAGACCT
* * * * *
39287013 TATATCAATGCCAATAGCTCAGCTATGGTCTTACATGA-AGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACATGAGA-CCT
39287056 CATATCAATGCCATATCCCAGATATGGTCTT
1 CATATCAATGCCATATCCCAGATATGGTCTT
39287087 TACACGTAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
42 27 0.44
43 34 0.56
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACATGAGACCT
Found at i:39288354 original size:25 final size:25
Alignment explanation
Indices: 39288290--39288357 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 25
39288280 GCTATTACAA
*
39288290 GTAAGCTCATACGAACTGAGAATCG
1 GTAAGCTCATACGAGCTGAGAATCG
39288315 GTAAGCTC-TCACGAGCTGCA-AATCG
1 GTAAGCTCAT-ACGAGCTG-AGAATCG
39288340 GTAAGCTCATACGAGCTG
1 GTAAGCTCATACGAGCTG
39288358 TGGTATGTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.21
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAGAATCG
Done.