Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 98 of 131
Found at i:32618327 original size:60 final size:62
Alignment explanation
Indices: 32618203--32618499 Score: 348
Period size: 60 Copynumber: 4.6 Consensus size: 62
32618193 AATTAAATTA
32618203 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCCTAACCC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATT-AAAA--C-AACCCTAACCC
32618268 T
62 T
*
32618269 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATT-AAA-AACCCTAACCCT
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAACAACCCTAACCCT
**
32618329 AAAACCCTAACCTAATTTAATTAAAAACTTTAACCTAATTAAATTAAAACCTCTAA-CCTAATTC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAA---C-AACCCTAA--C
**
32618393 AATT
60 -CCT
* * *
32618397 AAAAACCCTAACCTAATTAAATTAAAAACCCTAACCAAATTTAATTAAAAACCCTAACCCCTAAC
1 -AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATT-AAAA--C-AA-CCCTAAC
32618462 CCT
60 CCT
32618465 AAAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACC
32618500 CCTTACTTAA
Statistics
Matches: 203, Mismatches: 15, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
60 54 0.27
61 3 0.01
64 3 0.01
65 5 0.02
66 46 0.23
67 35 0.17
68 2 0.01
69 46 0.23
70 4 0.02
71 5 0.02
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (62 bp):
AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTAAATTAAAACAACCCTAACCCT
Found at i:32618333 original size:37 final size:37
Alignment explanation
Indices: 32618292--32618500 Score: 139
Period size: 37 Copynumber: 5.0 Consensus size: 37
32618282 AATTTAATTA
32618292 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
***
32618329 AAAACCCTAACCTAATTTAATTAAAAACTTTAACCTAATTAAATT
1 AAAACCCTAACCTAATTTAATTAAAAAC-----CCT-A--ACCCT
* *
32618374 AAAACCTCTAACCTAATTCAATTAAAAACCCTAACCTAATTAAATT
1 AAAACC-CTAACCTAATTTAATTAAAAACCCTAACC--------CT
*
32618420 AAAAACCCTAACCAAATTTAATTAAAAACCCTAACCCCTAACCCT
1 -AAAACCCTAACCTAATTTAATT--AAA----AA-CCCTAACCCT
32618465 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCC
32618501 CTTACTTAAA
Statistics
Matches: 137, Mismatches: 10, Indels: 50
0.70 0.05 0.25
Matches are distributed among these distances:
37 37 0.27
38 3 0.02
40 1 0.01
41 3 0.02
42 6 0.04
43 1 0.01
44 21 0.15
45 9 0.07
46 37 0.27
47 6 0.04
48 3 0.02
52 2 0.01
53 8 0.06
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.26
Consensus pattern (37 bp):
AAAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
Found at i:32618388 original size:172 final size:175
Alignment explanation
Indices: 32617812--32618490 Score: 639
Period size: 172 Copynumber: 3.8 Consensus size: 175
32617802 NNNNNNNNNN
* * *
32617812 TTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACC-CTAAGCTAACTGT-ATTTAAAAC
1 TTAATTAAAAACCCTAACCTAA-TT-A---AATTAAAAACCTCTAACCTAA-TTTAATTAAAAAC
* * * **
32617875 CCTACCCTAACTT-AATTAAAAACCTTAA-CCTAACTTAATTAAAAACCCTAACCTAACTTAATG
60 CCTAACCTAA-TTAAATTAAAAACCCTAACCCTAA--TAACTAAAAACCCTAACC---CTTAACC
* *** *
32617938 TAAAACCCTAACCTAATTGAATT-AAA-AA--CCTAATTTAATTAAAAACCCTAACC---C
119 TAAAACCCTAACCTAATTTAATTAAAACAACCCCTAA---CCCT-AAAACCCTAACCTAAT
* * *
32617992 TTAACCCT-AAAACCCTAACCTAATTGAATTAAAAACCT-TAACATAATTTAATTAAAAACCCTA
1 TTAA--TTAAAAACCCTAACCTAATTAAATTAAAAACCTCTAACCTAATTTAATTAAAAACCCTA
* *
32618055 ACCTAATTAAATTAAAAACCCTAA-CCTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAATC
64 ACCTAATTAAATTAAAAACCCTAACCCTAA--TAACTAAAAACCCTAACCCTTAA-CCTAAAACC
* *
32618119 CTAACCTAATTTAATTAAAAACCCTAACCCCTAACCCTAAAACCCTAATCTGAT
126 CTAACCTAATTTAATT-AAAA--C-AACCCCTAACCCTAAAACCCTAACCTAAT
32618173 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACC-CTAACCTAATTTAATTAAAAACCCTAAC
1 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCTCTAACCTAATTTAATTAAAAACCCTAAC
** * *
32618237 CTAATTAAATTAAAAACCCTAACCCTAA-CCCT-AAAACCCTAACCTAATTTAA-TTAAAAACCC
66 CTAATTAAATTAAAAACCCTAACCCTAATAACTAAAAACCCTAACC---CTTAACCT-AAAACCC
32618299 TAACCTAATTTAATT-AAA-AA-CCCTAACCCTAAAACCCTAACCTAAT
127 TAACCTAATTTAATTAAAACAACCCCTAACCCTAAAACCCTAACCTAAT
** *
32618345 TTAATTAAAAACTTTAACCTAATTAAATT-AAAACCTCTAACCTAATTCAATTAAAAACCCTAAC
1 TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCTCTAACCTAATTTAATTAAAAACCCTAAC
* * *
32618409 CTAATTAAATTAAAAACCCTAA-CCAAATTTAATTAAAAACCCTAACCCCTAACCCTAAAACCCT
66 CTAATTAAATTAAAAACCCTAACCCTAA--TAACTAAAAACCCTAACCCTTAA-CCTAAAACCCT
32618473 AACCTAATTTAATTAAAA
128 AACCTAATTTAATTAAAA
32618491 ACCCTAACCC
Statistics
Matches: 428, Mismatches: 39, Indels: 70
0.80 0.07 0.13
Matches are distributed among these distances:
171 10 0.02
172 103 0.24
173 29 0.07
174 26 0.06
175 16 0.04
176 75 0.18
177 15 0.04
178 13 0.03
179 23 0.05
180 88 0.21
181 24 0.06
182 6 0.01
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.28
Consensus pattern (175 bp):
TTAATTAAAAACCCTAACCTAATTAAATTAAAAACCTCTAACCTAATTTAATTAAAAACCCTAAC
CTAATTAAATTAAAAACCCTAACCCTAATAACTAAAAACCCTAACCCTTAACCTAAAACCCTAAC
CTAATTTAATTAAAACAACCCCTAACCCTAAAACCCTAACCTAAT
Found at i:32618510 original size:21 final size:21
Alignment explanation
Indices: 32618395--32618583 Score: 105
Period size: 21 Copynumber: 8.6 Consensus size: 21
32618385 CCTAATTCAA
* *
32618395 TTAAAAACCCTAACCTAATTAAA
1 TTAAAAACCCTAACC-ACTT-AC
* *
32618418 TTAAAAACCCTAACCAAATTTAA
1 TTAAAAACCCTAACC--ACTTAC
* *
32618441 TTAAAAACCCTAACCCCTAACC
1 TTAAAAACCCTAACCACTTA-C
* * *
32618463 CT-AAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAACC--ACTTAC
*
32618485 TTAAAAACCCTAACCCCTTAC
1 TTAAAAACCCTAACCACTTAC
*
32618506 TTAAAAACCCTAA-CTCTTAAC
1 TTAAAAACCCTAACCACTT-AC
* *
32618527 TTAAAAACCATTACC-CTTAAC
1 TTAAAAACCCTAACCACTT-AC
* * * *
32618548 TTTAAAACCCTAAACTAAGTTAA
1 TTAAAAACCCT-AAC-CACTTAC
32618571 TTAAAAACCCTAA
1 TTAAAAACCCTAA
32618584 ACTAAGTTAA
Statistics
Matches: 131, Mismatches: 25, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.03
21 58 0.44
22 7 0.05
23 57 0.44
24 5 0.04
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.26
Consensus pattern (21 bp):
TTAAAAACCCTAACCACTTAC
Found at i:32618713 original size:54 final size:54
Alignment explanation
Indices: 32618649--32618830 Score: 143
Period size: 54 Copynumber: 3.2 Consensus size: 54
32618639 CTAGTACTAA
32618649 CAATTAATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTAT
1 CAATTAATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTAT
* * * **** ** * ** * *
32618703 CAATTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATATT-TTGACTGGTACTAA
1 CAATTAATAATTTTATA-T-A-AT-TTGATA-ATTTTTCTAACCATTAAT-AC-AAT-TTAT
32618764 CAATTAATAATTTTATATAATTTGA-AATTTTTACTAACCATTAATACAATTTAT
1 CAATTAATAATTTTATATAATTTGATAATTTTT-CTAACCATTAATACAATTTAT
32618818 CAATTAATAATTT
1 CAATTAATAATTT
32618831 GACAAACTTA
Statistics
Matches: 90, Mismatches: 28, Indels: 20
0.65 0.20 0.14
Matches are distributed among these distances:
54 31 0.34
55 6 0.07
56 9 0.10
57 5 0.06
58 7 0.08
59 12 0.13
60 2 0.02
61 18 0.20
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (54 bp):
CAATTAATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTAT
Found at i:32618804 original size:115 final size:116
Alignment explanation
Indices: 32618590--32618830 Score: 414
Period size: 115 Copynumber: 2.1 Consensus size: 116
32618580 CTAAACTAAG
* * **
32618590 TTAATAATTTTACTTTCACATAATGTTAGATTTGGAAAAATGTTTTTTCCTAGTACTAACAATTA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGATTTTGACTAGTACTAACAATTA
32618655 ATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTATCAA
66 ATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTATCAA
*
32618706 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAAT-ATTTTGACTGGTACTAACAATTA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGATTTTGACTAGTACTAACAATTA
32618770 ATAATTTTATATAATTTGA-AATTTTTACTAACCATTAATACAATTTATCAA
66 ATAATTTTATATAATTTGATAATTTTT-CTAACCATTAATACAATTTATCAA
32618821 TTAATAATTT
1 TTAATAATTT
32618831 GACAAACTTA
Statistics
Matches: 119, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
114 7 0.06
115 72 0.61
116 40 0.34
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGATTTTGACTAGTACTAACAATTA
ATAATTTTATATAATTTGATAATTTTTCTAACCATTAATACAATTTATCAA
Found at i:32620578 original size:21 final size:21
Alignment explanation
Indices: 32620552--32620595 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
32620542 TCAATACTAT
32620552 ACCTGCAGTATATGTATGTGG
1 ACCTGCAGTATATGTATGTGG
32620573 ACCTGCAGTATATGTATGTGG
1 ACCTGCAGTATATGTATGTGG
32620594 AC
1 AC
32620596 TTTTGTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (21 bp):
ACCTGCAGTATATGTATGTGG
Found at i:32622057 original size:123 final size:121
Alignment explanation
Indices: 32621837--32622183 Score: 541
Period size: 123 Copynumber: 2.8 Consensus size: 121
32621827 CAAACATGCT
*
32621837 ACTGTAGCAAAAGCGTGTCCACGAGGGCCCGATTTTCACAAATTCTTCTCAAATAGCATCCTGCT
1 ACTGTAGCAAAAGCGCGTCCACGAGGG--CGATTTT-ACAAATTCTTCTCAAATAGCATCCTGCT
* *
32621902 AGAAGCGATTTTATACTGTTTGCTCATAAACGTCAAAAAAAATATTTCTTCCATGACCG
63 AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTCTTCCATGACCG
*
32621961 ACTGTAGCAAAAGCGCGTCCACGAGAGTGCGATTTTACAAATTTTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAG-G-GCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
* * *
32622026 AAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTCCATGACCT
64 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTCTTCCATGACCG
* *
32622084 ACTGTTGCAAAAGCGCGTCCACGAGGGCAAGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
1 ACTGTAGCAAAAGCGCGTCCACGAGGGC--GATTTTACAAATTCTTCTCAAATAGCATCCTGCTA
*
32622149 GAAGCGATTTTATACTATTTGATCAGAAACGTCAA
64 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
32622184 CTCGAAATTA
Statistics
Matches: 207, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
121 2 0.01
122 1 0.00
123 171 0.83
124 31 0.15
125 1 0.00
126 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (121 bp):
ACTGTAGCAAAAGCGCGTCCACGAGGGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGA
AGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTTCTTCCATGACCG
Found at i:32630497 original size:20 final size:21
Alignment explanation
Indices: 32630472--32630521 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
32630462 GAATAGTCCA
32630472 GGCCGTGTGGCTT-CACACAT
1 GGCCGTGTGGCTTACACACAT
*
32630492 GGCCGTGTGGCTTACCCACAT
1 GGCCGTGTGGCTTACACACAT
*
32630513 GCCCGTGTG
1 GGCCGTGTG
32630522 ATCAGACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (21 bp):
GGCCGTGTGGCTTACACACAT
Found at i:32630618 original size:15 final size:14
Alignment explanation
Indices: 32630585--32630636 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
32630575 TATAAGACAT
*
32630585 ATGGCCGTGTGTCT
1 ATGGCCGTGTGTCC
32630599 A-GGCCGTGTGTCAC
1 ATGGCCGTGTGTC-C
*
32630613 ATGGCCGTGTGGCC
1 ATGGCCGTGTGTCC
*
32630627 A-GACCGTGTG
1 ATGGCCGTGTG
32630637 CACCTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 19 0.58
14 4 0.12
15 10 0.30
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (14 bp):
ATGGCCGTGTGTCC
Found at i:32633465 original size:24 final size:26
Alignment explanation
Indices: 32633421--32633470 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
32633411 CATACATTTC
32633421 AGAAAAAATAAATAAATAAAACCAAT
1 AGAAAAAATAAATAAATAAAACCAAT
32633447 AGAAAACAA-AAA-AAA-AAAACCAAT
1 AGAAAA-AATAAATAAATAAAACCAAT
32633471 GTCCAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 9 0.39
27 2 0.09
ACGTcount: A:0.76, C:0.10, G:0.04, T:0.10
Consensus pattern (26 bp):
AGAAAAAATAAATAAATAAAACCAAT
Found at i:32634935 original size:18 final size:16
Alignment explanation
Indices: 32634903--32634943 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
32634893 TTTCAACTTT
32634903 TATATATTATTATGTA
1 TATATATTATTATGTA
32634919 TATATTATTATTTATGT-
1 TATA-TATTA-TTATGTA
32634936 TAT-TATTA
1 TATATATTA
32634944 AGTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 8 0.35
18 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TATATATTATTATGTA
Found at i:32634938 original size:12 final size:13
Alignment explanation
Indices: 32634902--32634943 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
32634892 ATTTCAACTT
32634902 TTATATATTATTA
1 TTATATATTATTA
32634915 TGTATATATTATTA
1 T-TATATATTATTA
*
32634929 TT-TATGTTATTA
1 TTATATATTATTA
32634941 TTA
1 TTA
32634944 AGTTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 2 0.08
14 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:32639534 original size:12 final size:11
Alignment explanation
Indices: 32639506--32639545 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
32639496 GGTTCAGATT
32639506 AAAA-AAAATC
1 AAAATAAAATC
32639516 -AAA-AAAATC
1 AAAATAAAATC
32639525 AAAATCAAAATC
1 AAAAT-AAAATC
32639537 AAAATAAAA
1 AAAATAAAA
32639546 AACAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 3 0.11
11 4 0.15
12 11 0.41
ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:32639685 original size:18 final size:18
Alignment explanation
Indices: 32639662--32639703 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
32639652 CGAAAACCCT
32639662 CAAAGGGCGCTTTGTGAC
1 CAAAGGGCGCTTTGTGAC
**
32639680 CAAAGGTTGCTTTGTGAC
1 CAAAGGGCGCTTTGTGAC
32639698 CAAAGG
1 CAAAGG
32639704 TGGTTTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (18 bp):
CAAAGGGCGCTTTGTGAC
Found at i:32639704 original size:18 final size:18
Alignment explanation
Indices: 32639670--32639704 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
32639660 CTCAAAGGGC
32639670 GCTTTGTGACCAAAGGTT
1 GCTTTGTGACCAAAGGTT
32639688 GCTTTGTGACCAAAGGT
1 GCTTTGTGACCAAAGGT
32639705 GGTTTTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (18 bp):
GCTTTGTGACCAAAGGTT
Found at i:32639711 original size:18 final size:18
Alignment explanation
Indices: 32639670--32639711 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
32639660 CTCAAAGGGC
*
32639670 GCTTTGTGACCAAAGGTT
1 GCTTTGTGACCAAAGGTG
32639688 GCTTTGTGACCAAAGGTG
1 GCTTTGTGACCAAAGGTG
*
32639706 GTTTTG
1 GCTTTG
32639712 AGATGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (18 bp):
GCTTTGTGACCAAAGGTG
Found at i:32643308 original size:86 final size:86
Alignment explanation
Indices: 32643110--32643726 Score: 838
Period size: 86 Copynumber: 7.1 Consensus size: 86
32643100 AGATCAGTGA
32643110 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGA-AGCAGATCTTGC
* *
32643175 CTTCCTGCGTTAACAGCAAAGT
65 CTTCCTGCGTTAACAGCGAAGC
* * * *
32643197 ATATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGAAGCAGATCTTGCC
* * *
32643262 TTCCTGCATTGACTGCGAAGC
66 TTCCTGCGTTAACAGCGAAGC
32643283 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGA-AGCAGATCTTGC
*
32643348 CTTCCTGTGTTAACAGCGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
* * * * *
32643370 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAAATCTTACC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGAAGCAGATCTTGCC
* * *
32643435 TTCCTGCATTGACAACGAAGC
66 TTCCTGCGTTAACAGCGAAGC
* * * * *
32643456 AGATCGGAAACAAAGTCTTGCCTCCATTGGTTGTTGTAGTGGAGATAGTTGAAGATAGCAGATCT
1 AGATCGAAAACAAAGCCTTGCCTCCA-TCG--GTTGTAGTGGAGCTGGTTGAAGA-AGCAGATCT
*
32643521 TGCCTTCCTGCGTTAACAGTGAAGC
62 TGCCTTCCTGCGTTAACAGCGAAGC
* * * * *
32643546 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTAGTTAAAGAAGCAAATCTTACC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGAAGCAGATCTTGCC
* * * *
32643611 GTCCTGCATTGACAACGAAGC
66 TTCCTGCGTTAACAGCGAAGC
* * *
32643632 AGATCGGAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGCTAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAG-AAGCAGATCTTGC
*
32643697 CTTCCTGCGTTAACAGTGAAGC
65 CTTCCTGCGTTAACAGCGAAGC
32643719 AGATCGAA
1 AGATCGAA
32643727 GATTACAAGT
Statistics
Matches: 459, Mismatches: 65, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
86 202 0.44
87 183 0.40
89 22 0.05
90 52 0.11
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (86 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGAAGCAGATCTTGCC
TTCCTGCGTTAACAGCGAAGC
Found at i:32643399 original size:173 final size:173
Alignment explanation
Indices: 32643110--32643726 Score: 1018
Period size: 173 Copynumber: 3.5 Consensus size: 173
32643100 AGATCAGTGA
32643110 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * * *
32643175 CTTCCTGCGTTAACAGCAAAGTATATTGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
* * * **
32643240 GGTTAAAGAAGCAGATCTTGCCTTCCTGCATTGACTGCGAAGC
131 AGTTAAAGAAGCAAATCTTACCTTCCTGCATTGACAACGAAGC
32643283 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
*
32643348 CTTCCTGTGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
32643413 AGTTAAAGAAGCAAATCTTACCTTCCTGCATTGACAACGAAGC
131 AGTTAAAGAAGCAAATCTTACCTTCCTGCATTGACAACGAAGC
* * * * *
32643456 AGATCGGAAACAAAGTCTTGCCTCCATTGGTTGTTGTAGTGGAGATAGTTGAAGATAGCAGATCT
1 AGATCGAAAACAAAGCCTTGCCTCCA-TCG--GTTGTAGTGGAGCTGGTTGAAGATAGCAGATCT
*
32643521 TGCCTTCCTGCGTTAACAGTGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGA
63 TGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGA
*
32643586 GCTAGTTAAAGAAGCAAATCTTACCGTCCTGCATTGACAACGAAGC
128 GCTAGTTAAAGAAGCAAATCTTACCTTCCTGCATTGACAACGAAGC
* * *
32643632 AGATCGGAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGCTAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
*
32643697 CTTCCTGCGTTAACAGTGAAGCAGATCGAA
66 CTTCCTGCGTTAACAGCGAAGCAGATCGAA
32643727 GATTACAAGT
Statistics
Matches: 419, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
173 250 0.60
174 2 0.00
175 2 0.00
176 165 0.39
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (173 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCT
AGTTAAAGAAGCAAATCTTACCTTCCTGCATTGACAACGAAGC
Found at i:32644373 original size:21 final size:21
Alignment explanation
Indices: 32644343--32644383 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
32644333 ATACATTTCA
32644343 AAAAAAAAAATAAAACCAATAG
1 AAAAAAAAAA-AAAACCAATAG
*
32644365 AAAACAAAAAAAAACCAAT
1 AAAAAAAAAAAAAACCAAT
32644384 GTCCAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.78, C:0.12, G:0.02, T:0.07
Consensus pattern (21 bp):
AAAAAAAAAAAAAACCAATAG
Found at i:32645857 original size:18 final size:16
Alignment explanation
Indices: 32645825--32645865 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
32645815 TTTCAACTTT
32645825 TATATATTATTATGTA
1 TATATATTATTATGTA
32645841 TATATTATTATTTATGT-
1 TATA-TATTA-TTATGTA
32645858 TAT-TATTA
1 TATATATTA
32645866 AGTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.22
16 4 0.17
17 8 0.35
18 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (16 bp):
TATATATTATTATGTA
Found at i:32645860 original size:12 final size:13
Alignment explanation
Indices: 32645824--32645865 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
32645814 ATTTCAACTT
32645824 TTATATATTATTA
1 TTATATATTATTA
32645837 TGTATATATTATTA
1 T-TATATATTATTA
*
32645851 TT-TATGTTATTA
1 TTATATATTATTA
32645863 TTA
1 TTA
32645866 AGTTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 11 0.42
13 2 0.08
14 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:32650547 original size:15 final size:15
Alignment explanation
Indices: 32650527--32650562 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
32650517 AGAAGGAGAA
*
32650527 GAAGAAGACGACGAT
1 GAAGAAGAAGACGAT
*
32650542 GAAGAAGAAGAGGAT
1 GAAGAAGAAGACGAT
32650557 GAAGAA
1 GAAGAA
32650563 AAAAAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.36, T:0.06
Consensus pattern (15 bp):
GAAGAAGAAGACGAT
Found at i:32654514 original size:11 final size:12
Alignment explanation
Indices: 32654492--32654535 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
32654482 AACAAATCCT
32654492 CTCTCAAATTTC
1 CTCTCAAATTTC
32654504 CTCTC-AATTTC
1 CTCTCAAATTTC
32654515 CT-TCCAAATTT-
1 CTCT-CAAATTTC
32654526 CTCTCAAATT
1 CTCTCAAATT
32654536 CATATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 17 0.59
12 11 0.38
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:32656463 original size:18 final size:18
Alignment explanation
Indices: 32656436--32656473 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32656426 CAGATGCGTT
* *
32656436 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
32656454 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
32656472 TC
1 TC
32656474 TTTTTTCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:32657076 original size:66 final size:66
Alignment explanation
Indices: 32657000--32657132 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
32656990 TTATAATTAA
32657000 ATGCATAATTTAATTGACAAACTATAAACCCTTAAACTAAAAACCCTAACCCTAATATTAACCAT
1 ATGCATAATTTAATTGACAAACTATAAACCCTTAAACTAAAAACCCTAACCCTAATATTAACCAT
32657065 T
66 T
32657066 ATGCATAATTTAATTGACAAACTATAAACCCTTAAACTAAAAACCCTAACCCTAATATTAACCAT
1 ATGCATAATTTAATTGACAAACTATAAACCCTTAAACTAAAAACCCTAACCCTAATATTAACCAT
32657131 T
66 T
32657132 A
1 A
32657133 ACTTAAAAAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (66 bp):
ATGCATAATTTAATTGACAAACTATAAACCCTTAAACTAAAAACCCTAACCCTAATATTAACCAT
T
Found at i:32657148 original size:21 final size:21
Alignment explanation
Indices: 32657124--32657206 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
32657114 ACCCTAATAT
*
32657124 TAACCATTAACTTAAAAACCC
1 TAACCCTTAACTTAAAAACCC
* * ***
32657145 TAACCCTTAAATCAAAAAGGG
1 TAACCCTTAACTTAAAAACCC
32657166 TAACCCTTAACTTAAAAACCAC
1 TAACCCTTAACTTAAAAACC-C
* * *
32657188 AAACCCTAAACCTAAAAAC
1 TAACCCTTAACTTAAAAAC
32657207 ATCAAACCTT
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
21 31 0.66
22 16 0.34
ACGTcount: A:0.49, C:0.28, G:0.04, T:0.19
Consensus pattern (21 bp):
TAACCCTTAACTTAAAAACCC
Found at i:32657192 original size:22 final size:22
Alignment explanation
Indices: 32657167--32657368 Score: 144
Period size: 22 Copynumber: 8.9 Consensus size: 22
32657157 CAAAAAGGGT
*
32657167 AACCCTTAACTTAAAAACCACA
1 AACCCTAAACTTAAAAACCACA
*
32657189 AACCCTAAACCTAAAAA-CATCA
1 AACCCTAAACTTAAAAACCA-CA
*
32657211 AACCTTAAACTTTAAAAACCTAAAAACCA
1 AACCCTAAAC-TTAAAAACC-----A-CA
* * *
32657240 TAAACCTTAAACTTAAAAATCATA
1 -AACCC-TAAACTTAAAAACCACA
* * *
32657264 AACCCTAAACCTAGAAA-CACT
1 AACCCTAAACTTAAAAACCACA
*
32657285 AACCCTTAACTTAAAAACCACA
1 AACCCTAAACTTAAAAACCACA
*
32657307 AACCCTAAACTTAAAAACTACA
1 AACCCTAAACTTAAAAACCACA
*
32657329 AACCCTAAACCTT--AAACTTA-A
1 AACCCTAAA-CTTAAAAAC-CACA
*
32657350 AACCCTAAACTTTAAAACC
1 AACCCTAAACTTAAAAACC
32657369 CTAAACCTTA
Statistics
Matches: 144, Mismatches: 21, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.02
21 32 0.22
22 74 0.51
23 13 0.09
24 2 0.01
25 1 0.01
29 3 0.02
30 11 0.08
31 5 0.03
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.20
Consensus pattern (22 bp):
AACCCTAAACTTAAAAACCACA
Found at i:32657233 original size:31 final size:30
Alignment explanation
Indices: 32657195--32657358 Score: 127
Period size: 29 Copynumber: 5.3 Consensus size: 30
32657185 CACAAACCCT
32657195 AAACCTAAAAA-CATCAAACCTTAAACTTTAA
1 AAACCTAAAAACCAT-AAACCTTAAAC-TTAA
32657226 AAACCTAAAAACCATAAACCTTAAACTTAA
1 AAACCTAAAAACCATAAACCTTAAACTTAA
* * * * *
32657256 AAATC-ATAAACCCTAAACCTAGAAACACTAA
1 AAACCTAAAAACCATAAACCT-TAAAC-TTAA
* * * *
32657287 CCCTTAACTTAAAAACCACAAACCCTAAACTTAA
1 ----AAACCTAAAAACCATAAACCTTAAACTTAA
* *
32657321 AAA-CTACAAACCCTAAACCTTAAACTTAA
1 AAACCTAAAAACCATAAACCTTAAACTTAA
*
32657350 AACCCTAAA
1 AAACCTAAA
32657359 CTTTAAAACC
Statistics
Matches: 102, Mismatches: 22, Indels: 19
0.71 0.15 0.13
Matches are distributed among these distances:
29 36 0.35
30 18 0.18
31 25 0.25
32 3 0.03
34 3 0.03
35 6 0.06
36 11 0.11
ACGTcount: A:0.53, C:0.27, G:0.01, T:0.20
Consensus pattern (30 bp):
AAACCTAAAAACCATAAACCTTAAACTTAA
Found at i:32657353 original size:43 final size:44
Alignment explanation
Indices: 32657306--32657401 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
32657296 TAAAAACCAC
32657306 AAACCCTAAACTTAAAAACTAC-AAACCCT-AAACCTTAAAC-TTA
1 AAACCCTAAACTTAAAAAC-ACTAAACCCTAAAACCTT-AACTTTA
* * * *
32657349 AAACCCTAAACTTTAAAACCCTAAACCTTAAAATCTTAACTTTA
1 AAACCCTAAACTTAAAAACACTAAACCCTAAAACCTTAACTTTA
32657393 AAACCCTAA
1 AAACCCTAA
32657402 CCCTTAAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.59
44 18 0.39
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (44 bp):
AAACCCTAAACTTAAAAACACTAAACCCTAAAACCTTAACTTTA
Found at i:32657366 original size:15 final size:15
Alignment explanation
Indices: 32657335--32657401 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
32657325 TACAAACCCT
*
32657335 AAACCTTAAAC-TTA
1 AAACCCTAAACTTTA
32657349 AAACCCTAAACTTTA
1 AAACCCTAAACTTTA
*
32657364 AAACCCTAAACCTTA
1 AAACCCTAAACTTTA
* *
32657379 AAA-TCTTAACTTTA
1 AAACCCTAAACTTTA
32657393 AAACCCTAA
1 AAACCCTAA
32657402 CCCTTAAGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 21 0.48
15 23 0.52
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACCCTAAACTTTA
Found at i:32657367 original size:29 final size:29
Alignment explanation
Indices: 32657335--32657408 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
32657325 TACAAACCCT
*
32657335 AAACCTTAAA-CTTAAAACCCTAAACTTTA
1 AAACCCTAAACCTTAAAA-CCTAAACTTTA
* *
32657364 AAACCCTAAACCTTAAAATCTTAACTTTA
1 AAACCCTAAACCTTAAAACCTAAACTTTA
*
32657393 AAACCCTAACCCTTAA
1 AAACCCTAAACCTTAA
32657409 GTTAAATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 33 0.82
30 7 0.17
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (29 bp):
AAACCCTAAACCTTAAAACCTAAACTTTA
Found at i:32657375 original size:65 final size:65
Alignment explanation
Indices: 32657226--32657380 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 65
32657216 TAAACTTTAA
* * * *
32657226 AAACCTAAAAACCATAAACCTTAAACTTAAAAATCATAAACCCTAAACCTAGAAACACTAACCCT
1 AAACTTAAAAACCCTAAACCTTAAACTTAAAAATCACAAACCCTAAACCTAGAAACACAAACCCT
* * *
32657291 TAACTTAAAAACCAC-AAACCCTAAACTTAAAAA-CTACAAACCCTAAACCT-TAAACTTA-AAA
1 AAACTTAAAAACC-CTAAACCTTAAACTTAAAAATC-ACAAACCCTAAACCTAGAAAC--ACAAA
32657352 CCCT
62 CCCT
*
32657356 AAACTTTAAAACCCTAAACCTTAAA
1 AAACTTAAAAACCCTAAACCTTAAA
32657381 ATCTTAACTT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
64 6 0.08
65 68 0.91
66 1 0.01
ACGTcount: A:0.52, C:0.28, G:0.01, T:0.20
Consensus pattern (65 bp):
AAACTTAAAAACCCTAAACCTTAAACTTAAAAATCACAAACCCTAAACCTAGAAACACAAACCCT
Found at i:32660910 original size:125 final size:126
Alignment explanation
Indices: 32660619--32660910 Score: 378
Period size: 125 Copynumber: 2.3 Consensus size: 126
32660609 NNNNNNNNNN
*
32660619 AGGGCGCAATTTCACAAATTCTTCTCATAAAGCATCCTGC-TAGAAGCGATTTTATACAATTTGC
1 AGGGCGCAATTTCACAAATTCTTCTGATAAAGCATCCTGCTTAGAAGCGATTTTATACAATTTGC
* * *
32660683 TCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTGTAGCAAAAGCGCGTCCACG
66 TCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTATAGCAAAAACGCGTACACG
* * **
32660744 AGGGCGCAATTTCACAAATTCTTC-GCATATAGCATCCTGCTTA-AAGCGTTTTTTATAGTATTT
1 AGGGCGCAATTTCACAAATTCTTCTG-ATAAAGCATCCTGCTTAGAAGCG-ATTTTATACAATTT
* * *
32660807 GCTCAGAAACGTTAACTCGAAATTATTT-TTCCAGGACCTACTATAGCAAAAACGCGTACAC-
64 GCTCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTATAGCAAAAACGCGTACACG
* * * * *
32660868 ATGGGCGCGATTGCAAAAATCCTTCTGATAAATCATCCTGCTT
1 A-GGGCGCAATTTCACAAATTCTTCTGATAAAGCATCCTGCTT
32660911 TGATTTTATC
Statistics
Matches: 145, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
124 1 0.01
125 104 0.72
126 40 0.28
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (126 bp):
AGGGCGCAATTTCACAAATTCTTCTGATAAAGCATCCTGCTTAGAAGCGATTTTATACAATTTGC
TCAGAAACGTCAACTCAAAATTATTTCTTCCAGGACCAACTATAGCAAAAACGCGTACACG
Found at i:32663141 original size:3 final size:3
Alignment explanation
Indices: 32663133--32663163 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
32663123 AATTTATTTT
*
32663133 TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
32663164 TTTTTGTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:32663974 original size:6 final size:6
Alignment explanation
Indices: 32663963--32664010 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
32663953 GTCTCCCTGC
* *
32663963 AAAATA AAAATA AAAATA AATAATA AGAAA-A AAAATT AAAATT AAAAT
1 AAAATA AAAATA AAAATA AA-AATA A-AAATA AAAATA AAAATA AAAAT
32664011 GTGTATTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
5 3 0.08
6 27 0.71
7 7 0.18
8 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:32663985 original size:16 final size:16
Alignment explanation
Indices: 32663964--32664010 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
32663954 TCTCCCTGCA
32663964 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
* *
32663980 AAATAATAAGAAAAA-
1 AAATAAAAATAAAAAT
* *
32663995 AAATTAAAATTAAAAT
1 AAATAAAAATAAAAAT
32664011 GTGTATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:32666398 original size:15 final size:14
Alignment explanation
Indices: 32666373--32666407 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
32666363 AATTACTTAT
32666373 TTAACTTAATTAAACC
1 TTAA-TTAATTAAA-C
32666389 TTAATTAATTAAAC
1 TTAATTAATTAAAC
32666403 TTAAT
1 TTAAT
32666408 CACCATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 9 0.47
16 4 0.21
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAATTAAAC
Found at i:32670603 original size:86 final size:86
Alignment explanation
Indices: 32670535--32670787 Score: 346
Period size: 87 Copynumber: 2.9 Consensus size: 86
32670525 TTTTTTTCTC
* *
32670535 AAACGCCGGAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAAT
1 AAACGCCGTAATAGACCCTGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAAT
32670600 CTTTAGCGGCGCTTTCCCCTA
66 CTTTAGCGGCGCTTTCCCCTA
* *
32670621 AAAAGCCGTAATAGACCCTGATCTATAGCGGCGCTTCAACCACAAAACGCCACTAAAGAACCTAA
1 AAACGCCGTAATAGACCCTGATCTATAGCGGCGCTTTAACCAC-AAACGCCACTAAAGAACCTAA
*
32670686 TCTTTAGCGGCGCTTTCCCCAA
65 TCTTTAGCGGCGCTTTCCCCTA
* * * *** * * *
32670708 AAACGCCGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTTCACAAACGCCGCTAAAGACCCTTA
1 AAACGCCG-TAATAGACCCTGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAA
*
32670772 TCTTTAGCGGCACTTT
65 TCTTTAGCGGCGCTTT
32670788 TACCAAAAAC
Statistics
Matches: 148, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
86 72 0.49
87 73 0.49
88 3 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (86 bp):
AAACGCCGTAATAGACCCTGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAAT
CTTTAGCGGCGCTTTCCCCTA
Found at i:32670788 original size:43 final size:43
Alignment explanation
Indices: 32670389--32670807 Score: 283
Period size: 43 Copynumber: 9.7 Consensus size: 43
32670379 TGTTGGTCTA
* * * ***
32670389 TAGCGGCGCTTCTAGCACAAACGCCGCTGAAGACTAAGA-CATT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATC-TT
**** *
32670432 TAGCGGCGC-TTTAATGGAAGCGCCGCTAAAGACCCTGATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTT
* * * * * * * ** *
32670474 TAGCAGCG-TTTGTGCTAGAAGCGCCGCTATAGATCAGGGTCTT
1 TAGCGGCGCTTT-TACCACAAACGCCGCTAAAGACCCTGATCTT
* ** * * *
32670517 TAGCGGCGTTTTTTTCTCAAACGCCG-GAATAGACCCTGATCTA
1 TAGCGGCGCTTTTACCACAAACGCCGCTAA-AGACCCTGATCTT
* * * *
32670560 TAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTT
** * *
32670603 TAGCGGCGCTTTCCCCTA-AAAAGCCG-TAATAGACCCTGATCTA
1 TAGCGGCGCTTTTACC-ACAAACGCCGCTAA-AGACCCTGATCTT
** * * *
32670646 TAGCGGCGCTTCAACCACAAAACGCCACTAAAGAACCTAATCTT
1 TAGCGGCGCTTTTACCAC-AAACGCCGCTAAAGACCCTGATCTT
** * *
32670690 TAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGACCATGATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTT
* ** *
32670733 TAGTGGCGCTTTTTTCACAAACGCCGCTAAAGACCCTTATCTT
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTT
* * *
32670776 TAGCGGCACTTTTACCAAAAACGCCACTAAAG
1 TAGCGGCGCTTTTACCACAAACGCCGCTAAAG
32670808 GCCAACACCT
Statistics
Matches: 286, Mismatches: 79, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
42 35 0.12
43 212 0.74
44 36 0.13
45 3 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (43 bp):
TAGCGGCGCTTTTACCACAAACGCCGCTAAAGACCCTGATCTT
Found at i:32670794 original size:86 final size:86
Alignment explanation
Indices: 32670547--32670807 Score: 337
Period size: 86 Copynumber: 3.0 Consensus size: 86
32670537 ACGCCGGAAT
* *
32670547 AGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGC
1 AGACCATGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGC
32670612 TTTCCCCTAAAAA-GCCG-TAA
66 TTTCCCC-AAAAACGCCGCTAA
* *
32670632 TAGACCCTGATCTATAGCGGCGCTTCAACCACAAAACGCCACTAAAGAACCTAATCTTTAGCGGC
1 -AGACCATGATCTATAGCGGCGCTTTAACCAC-AAACGCCACTAAAGAACCTAATCTTTAGCGGC
32670697 GCTTTCCCCAAAAACGCCGCTAA
64 GCTTTCCCCAAAAACGCCGCTAA
* * *** * * * *
32670720 AGACCATGATCTTTAGTGGCGCTTTTTTCACAAACGCCGCTAAAGACCCTTATCTTTAGCGGCAC
1 AGACCATGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGC
** *
32670785 TTTTACCAAAAACGCCACTAA
66 TTTCCCCAAAAACGCCGCTAA
32670806 AG
1 AG
32670808 GCCAACACCT
Statistics
Matches: 156, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
86 84 0.54
87 69 0.44
88 3 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (86 bp):
AGACCATGATCTATAGCGGCGCTTTAACCACAAACGCCACTAAAGAACCTAATCTTTAGCGGCGC
TTTCCCCAAAAACGCCGCTAA
Found at i:32671183 original size:21 final size:21
Alignment explanation
Indices: 32671157--32671268 Score: 134
Period size: 21 Copynumber: 5.3 Consensus size: 21
32671147 TTTGACGCTG
32671157 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
32671178 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
32671199 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
32671220 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
32671241 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
32671262 ATCTGCT
1 CTCTGCT
32671269 CTAAGCTGTT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:32671330 original size:66 final size:66
Alignment explanation
Indices: 32671240--32671386 Score: 215
Period size: 66 Copynumber: 2.2 Consensus size: 66
32671230 CTCGCTGCCG
* * *
32671240 CCTCTGCTTCTCTTGCTGCCGCATCTGCTCTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTTG
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTT-GTTG
32671304 AA
65 AA
* * * *
32671306 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
32671371 A
66 A
32671372 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
32671387 ATGTTGCCTC
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
66 69 0.95
67 4 0.05
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTCTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:32678314 original size:40 final size:40
Alignment explanation
Indices: 32678209--32678324 Score: 121
Period size: 40 Copynumber: 3.0 Consensus size: 40
32678199 CGATTTTCAG
*
32678209 AAAA-CGCCGCTAATGCT-AATTTTTAGCGGCGTTTTCTGT
1 AAAAGCGCCGCTAATGCTCAATTTTTAGCGGCGTTTT-TAT
* * **
32678248 -TAAGCGCCGCTAATGCTCTACCTTTAGCGGCGTTTTTAT
1 AAAAGCGCCGCTAATGCTCAATTTTTAGCGGCGTTTTTAT
* * * *
32678287 AAAAGCGCCGCTAATTCTCGATTTTTAGTGGTGTTTTT
1 AAAAGCGCCGCTAATGCTCAATTTTTAGCGGCGTTTTT
32678325 TGTCCAAACG
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
38 2 0.03
39 15 0.24
40 45 0.73
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTCAATTTTTAGCGGCGTTTTTAT
Found at i:32678739 original size:140 final size:142
Alignment explanation
Indices: 32678482--32678764 Score: 462
Period size: 140 Copynumber: 2.0 Consensus size: 142
32678472 TTCATGTGTC
** *
32678482 GAAAATTTGTGAAACTTGAGTTTTTTTTTTTTTAAGTTTTTAATAGATTAGACCGAAAGAAATTT
1 GAAAATTTGTGAAACTTGAG-TTTTTTTAATTT-A-TTTTTAACAGATTAGACCGAAAGAAATTT
*
32678547 ATTTAGACAATATTAAAATGACCAAAAGCTTCCTTATATTATCACATAATTTCAAGTGTTTCCTT
63 ATTTAGACAATATTAAAATGACCAAAAGCTTCCCTATATTATCACATAATTTCAAGTGTTTCCTT
32678612 TTTTTAATTCATTCT
128 TTTTTAATTCATTCT
* *
32678627 GAAAATTTGTGAAACTTGAG-TTTTTTAATTT-TTTTTAACAGGTTAGACCGAAATAAATTTATT
1 GAAAATTTGTGAAACTTGAGTTTTTTTAATTTATTTTTAACAGATTAGACCGAAAGAAATTTATT
*
32678690 TAGACAATATTAAAATGACCAAAAGCTTCCCTGTATTATCACATAATTTCAAGTGTTTCCTTTTT
66 TAGACAATATTAAAATGACCAAAAGCTTCCCTATATTATCACATAATTTCAAGTGTTTCCTTTTT
32678755 TTAATTCATT
131 TTAATTCATT
32678765 AGATAATTTA
Statistics
Matches: 131, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
140 102 0.78
143 9 0.07
145 20 0.15
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (142 bp):
GAAAATTTGTGAAACTTGAGTTTTTTTAATTTATTTTTAACAGATTAGACCGAAAGAAATTTATT
TAGACAATATTAAAATGACCAAAAGCTTCCCTATATTATCACATAATTTCAAGTGTTTCCTTTTT
TTAATTCATTCT
Found at i:32678836 original size:16 final size:17
Alignment explanation
Indices: 32678815--32678847 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32678805 TTGAATATAA
*
32678815 TTTAAA-TATATTATTT
1 TTTAAAGTAAATTATTT
32678831 TTTAAAGTAAATTATTT
1 TTTAAAGTAAATTATTT
32678848 AACAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTAAAGTAAATTATTT
Found at i:32680376 original size:14 final size:14
Alignment explanation
Indices: 32680352--32680385 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
32680342 AATTACTTAT
32680352 TTAACTTAATTAAAC
1 TTAA-TTAATTAAAC
32680367 TTAATTAATTAAAC
1 TTAATTAATTAAAC
32680381 TTAAT
1 TTAAT
32680386 CACCATTAAT
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:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATTAATTAAAC
Found at i:32684336 original size:21 final size:19
Alignment explanation
Indices: 32684290--32684345 Score: 94
Period size: 19 Copynumber: 2.8 Consensus size: 19
32684280 AATCTTCAAG
32684290 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
32684309 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
32684328 GATATATGCAATCTTAGA
1 G--ATATGCAATCTTAGA
32684346 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 20 0.57
21 15 0.43
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:32684367 original size:23 final size:24
Alignment explanation
Indices: 32684291--32684368 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 24
32684281 ATCTTCAAGG
32684291 ATATGCAATCTT---AGATATG--
1 ATATGCAATCTTAGAAGATATGAT
32684310 ATATGCAATCTTAG---ATATGAT
1 ATATGCAATCTTAGAAGATATGAT
32684331 ATATGCAATCTTAGAAGATATGAT
1 ATATGCAATCTTAGAAGATATGAT
* *
32684355 -TTTGTAATCTTAGA
1 ATATGCAATCTTAGA
32684369 GATTTAATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
19 17 0.34
21 14 0.28
23 12 0.24
24 7 0.14
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.38
Consensus pattern (24 bp):
ATATGCAATCTTAGAAGATATGAT
Found at i:32684615 original size:23 final size:23
Alignment explanation
Indices: 32684571--32684615 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
32684561 TCTTATTTTG
* *
32684571 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
32684594 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
32684616 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:32685232 original size:20 final size:20
Alignment explanation
Indices: 32685178--32685233 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
32685168 TTTATGTTTT
*
32685178 CATATAGTTTTTATATACATA
1 CATATA-TTTTTATACACATA
*
32685199 CATAT-TCTTATATACACATA
1 CATATAT-TTTTATACACATA
32685219 CATATATTTTTATAC
1 CATATATTTTTATAC
32685234 TTTATAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 23 0.77
21 6 0.20
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (20 bp):
CATATATTTTTATACACATA
Found at i:32686778 original size:24 final size:25
Alignment explanation
Indices: 32686716--32686801 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 25
32686706 GCTTATCCGG
* *
32686716 GCAATATAACGAGAAGCTCACAAAGA
1 GCAATATAACGGGTAGCTC-CAAAGA
* *
32686742 GC-CTATAAAGGGTAGCTCCAAAGA
1 GCAATATAACGGGTAGCTCCAAAGA
*
32686766 GCAAT-TAACGGGTAGCTCCGAAGA
1 GCAATATAACGGGTAGCTCCAAAGA
*
32686790 GCACT-TAACGGG
1 GCAATATAACGGG
32686802 AAGCACCGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
24 36 0.71
25 13 0.25
26 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (25 bp):
GCAATATAACGGGTAGCTCCAAAGA
Found at i:32686810 original size:24 final size:24
Alignment explanation
Indices: 32686762--32686829 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
32686752 GGTAGCTCCA
* *
32686762 AAGAGCAATTAACGGGTAGCTCCG
1 AAGAGCAATTAACGGGAAGCACCG
*
32686786 AAGAGCACTTAACGGGAAGCACCG
1 AAGAGCAATTAACGGGAAGCACCG
* * *
32686810 AATAGCCATATAACTGGAAG
1 AAGAGCAAT-TAACGGGAAG
32686830 TTCAAGAGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 27 0.75
25 9 0.25
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (24 bp):
AAGAGCAATTAACGGGAAGCACCG
Found at i:32695243 original size:21 final size:21
Alignment explanation
Indices: 32695218--32695273 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
32695208 CACCGTTGTT
32695218 TCTAATCTCACCGCTATAGTA
1 TCTAATCTCACCGCTATAGTA
*
32695239 TCTAATCTCACCGTTATAGTA
1 TCTAATCTCACCGCTATAGTA
*
32695260 ACTAATCTCACCGC
1 TCTAATCTCACCGC
32695274 CGCCGCTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (21 bp):
TCTAATCTCACCGCTATAGTA
Found at i:32696866 original size:30 final size:30
Alignment explanation
Indices: 32696824--32696880 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
32696814 AAAAAAAAAT
*
32696824 CAAACGATTTTCTT-TCTCCACAAGAAACTA
1 CAAACGATTTTCTTCTCT-AACAAGAAACTA
32696854 CAAACTGA-TTTCTTCTCTAACAAGAAA
1 CAAAC-GATTTTCTTCTCTAACAAGAAA
32696881 TTGTATACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (30 bp):
CAAACGATTTTCTTCTCTAACAAGAAACTA
Found at i:32711846 original size:12 final size:12
Alignment explanation
Indices: 32711829--32711853 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32711819 TTTGCCCCTA
32711829 ATAATACATATT
1 ATAATACATATT
32711841 ATAATACATATT
1 ATAATACATATT
32711853 A
1 A
32711854 ATGTATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATACATATT
Found at i:32718221 original size:50 final size:50
Alignment explanation
Indices: 32718128--32718370 Score: 252
Period size: 50 Copynumber: 4.7 Consensus size: 50
32718118 TTTCTTGTAC
* * ** * ** *
32718128 TGCCAATACCATATCCCAGATGTGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
32718178 TGCCCATGCCATGTCCCAGACATGATCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
32718228 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * ** *
32718278 TGCCAATGCCATGTCCTAGACATGGTCTTACATGACACCTCTCATAAACTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCAT---CTC---GG
* *
32718334 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
32718371 TCTCATTCCC
Statistics
Matches: 162, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
50 125 0.77
53 3 0.02
56 34 0.21
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:32720177 original size:30 final size:30
Alignment explanation
Indices: 32720143--32720233 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
32720133 CACTATTTTG
*
32720143 TATGAGTCATAAAAGTAAGTTTATTTGTTA
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
32720173 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
* *
32720203 TATAAGTCATAAAAATAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
32720233 T
1 T
32720234 GTAAAGGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.44
Consensus pattern (30 bp):
TATGAGTCATAAAAGTAAGTTTGTTTGTTA
Found at i:32722782 original size:25 final size:26
Alignment explanation
Indices: 32722732--32722781 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
32722722 TTTTCTTAAT
32722732 ATTTAATATTTTTTATAATTTTTTTG
1 ATTTAATATTTTTTATAATTTTTTTG
32722758 ATTT-ATACTTTTTTATAATTTTTT
1 ATTTAATA-TTTTTTATAATTTTTT
32722782 GCCATATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
ATTTAATATTTTTTATAATTTTTTTG
Found at i:32724160 original size:33 final size:33
Alignment explanation
Indices: 32724114--32724435 Score: 637
Period size: 33 Copynumber: 9.8 Consensus size: 33
32724104 TTTAGTTCGC
32724114 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724146 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724179 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724212 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724245 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724278 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724311 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724344 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724377 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
32724410 TGTATTGGGATTAGAGGTGTATTGGA
1 TGTATTGGGATTAGAGGTGTATTGGA
32724436 GGGATTCACT
Statistics
Matches: 289, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
32 6 0.02
33 283 0.98
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (33 bp):
TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
Found at i:32737198 original size:26 final size:25
Alignment explanation
Indices: 32737165--32737218 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
32737155 TCTTTTCTTC
*
32737165 TTTTATAAATT-TTAATTATTTTATT
1 TTTTATAAATTAAT-ATTATTTTATT
*
32737190 TTTTCATAAATTAATATTTTTTTATT
1 TTTT-ATAAATTAATATTATTTTATT
32737216 TTT
1 TTT
32737219 GTGCAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 20 0.80
27 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATAAATTAATATTATTTTATT
Found at i:32737312 original size:142 final size:143
Alignment explanation
Indices: 32737147--32737431 Score: 563
Period size: 142 Copynumber: 2.0 Consensus size: 143
32737137 TAAAATTATA
32737147 AACAAACATCTTTTCTTCTTTTATAAATTTTAATTATTTTATTTTTTCATAAATTAATATTTTTT
1 AACAAACATCTTTTCTTCTTTTATAAATTTTAATTATTTTATTTTTTCATAAATTAATATTTTTT
32737212 TATTTTTGTGCAACCAATTTTAAAAAATAGTATTTTTTATGCAATTTTTCCATGTCATTGATATA
66 TATTTTTGTGCAACCAATTTTAAAAAATAGTATTTTTTATGCAATTTTTCCATGTCATTGATATA
32737277 TAATTTTGGTAAT
131 TAATTTTGGTAAT
32737290 AACAAACATC-TTTCTTCTTTTATAAATTTTAATTATTTTATTTTTTCATAAATTAATATTTTTT
1 AACAAACATCTTTTCTTCTTTTATAAATTTTAATTATTTTATTTTTTCATAAATTAATATTTTTT
32737354 TATTTTTGTGCAACCAATTTTAAAAAATAGTATTTTTTATGCAATTTTTCCATGTCATTGATATA
66 TATTTTTGTGCAACCAATTTTAAAAAATAGTATTTTTTATGCAATTTTTCCATGTCATTGATATA
32737419 TAATTTTGGTAAT
131 TAATTTTGGTAAT
32737432 TATTTTACTT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 132 0.93
143 10 0.07
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (143 bp):
AACAAACATCTTTTCTTCTTTTATAAATTTTAATTATTTTATTTTTTCATAAATTAATATTTTTT
TATTTTTGTGCAACCAATTTTAAAAAATAGTATTTTTTATGCAATTTTTCCATGTCATTGATATA
TAATTTTGGTAAT
Found at i:32737340 original size:26 final size:25
Alignment explanation
Indices: 32737307--32737360 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
32737297 ATCTTTCTTC
*
32737307 TTTTATAAATT-TTAATTATTTTATT
1 TTTTATAAATTAAT-ATTATTTTATT
*
32737332 TTTTCATAAATTAATATTTTTTTATT
1 TTTT-ATAAATTAATATTATTTTATT
32737358 TTT
1 TTT
32737361 GTGCAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 20 0.80
27 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTATAAATTAATATTATTTTATT
Found at i:32737503 original size:6 final size:6
Alignment explanation
Indices: 32737492--32737525 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
32737482 TTAGGGTTGA
32737492 GGGTTT GGGTTT GGCGTTT CGGGTTT GGGTTT GG
1 GGGTTT GGGTTT GG-GTTT -GGGTTT GGGTTT GG
32737526 CTTCAAGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.62
7 8 0.31
8 2 0.08
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (6 bp):
GGGTTT
Found at i:32737517 original size:14 final size:12
Alignment explanation
Indices: 32737492--32737525 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
32737482 TTAGGGTTGA
32737492 GGGTTTGGGTTT
1 GGGTTTGGGTTT
32737504 GGCGTTTCGGGTTT
1 GG-GTTT-GGGTTT
32737518 GGGTTTGG
1 GGGTTTGG
32737526 CTTCAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.20
13 8 0.40
14 8 0.40
ACGTcount: A:0.00, C:0.06, G:0.50, T:0.44
Consensus pattern (12 bp):
GGGTTTGGGTTT
Found at i:32741097 original size:28 final size:28
Alignment explanation
Indices: 32741066--32741133 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
32741056 GACAATAGCT
* *
32741066 TGCTGCTGCATTCTAGTGGACATGTGCA
1 TGCTGCTGCATTCTAGTGAACATGTACA
* * *
32741094 TGCTGCTCCATTCTTGTGAACATTTACA
1 TGCTGCTGCATTCTAGTGAACATGTACA
*
32741122 CGCTGCTGCATT
1 TGCTGCTGCATT
32741134 GTTGACAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (28 bp):
TGCTGCTGCATTCTAGTGAACATGTACA
Found at i:32756432 original size:25 final size:25
Alignment explanation
Indices: 32756394--32756471 Score: 86
Period size: 25 Copynumber: 3.1 Consensus size: 25
32756384 CAGTTCGCAA
* *
32756394 GAGCATTCCATTATTTAGCTCTTAT
1 GAGCATTCCGTTATTTAGCTCTCAT
* * *
32756419 GAGCATTCCGTTATATGGCTCTCAC
1 GAGCATTCCGTTATTTAGCTCTCAT
*
32756444 GAGC-TTCCCGATATTTAGCTCTCAT
1 GAGCATT-CCGTTATTTAGCTCTCAT
32756469 GAG
1 GAG
32756472 TTTTTTGATT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (25 bp):
GAGCATTCCGTTATTTAGCTCTCAT
Found at i:32758551 original size:9 final size:9
Alignment explanation
Indices: 32758537--32758567 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
32758527 GTTAAACGAA
32758537 TCGAGTTAT
1 TCGAGTTAT
*
32758546 TCGAGTTAA
1 TCGAGTTAT
32758555 TCGAGTTAT
1 TCGAGTTAT
32758564 TCGA
1 TCGA
32758568 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:32758633 original size:9 final size:9
Alignment explanation
Indices: 32758616--32758652 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
32758606 TAAATTTTCA
32758616 AATTCGAAT
1 AATTCGAAT
*
32758625 AACTCGAAT
1 AATTCGAAT
32758634 AATTCGAAT
1 AATTCGAAT
32758643 AATTCGAAT
1 AATTCGAAT
32758652 A
1 A
32758653 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:32764862 original size:32 final size:34
Alignment explanation
Indices: 32764794--32764866 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
32764784 AATAGCAACT
*
32764794 GAAAAAGTGAGTGAATGTTGAGAGAAAAAAAGAA
1 GAAAAAGTAAGTGAATGTTGAGAGAAAAAAAGAA
* *
32764828 GAAAAAGTAAGTGAGTGTTGAGA-AAAAAGA-AA
1 GAAAAAGTAAGTGAATGTTGAGAGAAAAAAAGAA
32764860 GAAAAAG
1 GAAAAAG
32764867 AGTGAGAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 9 0.25
33 6 0.17
34 21 0.58
ACGTcount: A:0.58, C:0.00, G:0.29, T:0.14
Consensus pattern (34 bp):
GAAAAAGTAAGTGAATGTTGAGAGAAAAAAAGAA
Found at i:32764871 original size:30 final size:32
Alignment explanation
Indices: 32764802--32764877 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 32
32764792 CTGAAAAAGT
*
32764802 GAGTGAATGTTGAGAGAAAAAAAGAAGAAAAA
1 GAGTGAGTGTTGAGAGAAAAAAAGAAGAAAAA
*
32764834 GTAAGTGAGTGTTGAGA-AAAAAGA-AAGAAAAA
1 G--AGTGAGTGTTGAGAGAAAAAAAGAAGAAAAA
*
32764866 GAGTGAGAGTTG
1 GAGTGAGTGTTG
32764878 TAAACTAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
30 10 0.26
32 10 0.26
33 6 0.15
34 13 0.33
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.16
Consensus pattern (32 bp):
GAGTGAGTGTTGAGAGAAAAAAAGAAGAAAAA
Found at i:32772185 original size:31 final size:30
Alignment explanation
Indices: 32772143--32772208 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
32772133 CTGAAAAAGT
32772143 GAGTGAATGTTGTGAGAAAAAAA-AGAAGAAAA
1 GAGTGAATG-T-TGAGAAAAAAAGA-AAGAAAA
*
32772175 -AGTGAGTGTTGAGAAAAAAAGAAAGAAAA
1 GAGTGAATGTTGAGAAAAAAAGAAAGAAAA
32772204 GAGTG
1 GAGTG
32772209 GGAGTTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 18 0.58
30 6 0.19
31 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (30 bp):
GAGTGAATGTTGAGAAAAAAAGAAAGAAAA
Found at i:32774537 original size:43 final size:43
Alignment explanation
Indices: 32774412--32774720 Score: 367
Period size: 42 Copynumber: 7.2 Consensus size: 43
32774402 ACGTCGTAAA
* * *
32774412 CTTTTGCGGCGCTTACAGAAAA-AAATGCCACTAAAGATCATGTT
1 CTTTAGCGGCGC-TA-AAAAAATAAACGCCACTAAAGATCATGTT
* * * *
32774456 CTTTAGCGGCGCT-TAGAAAGAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
32774498 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
* * *
32774541 ATTTAACGGCGCT-AAAAAATAAACGCCACTAAAGAGCATGTT
1 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
* * * *
32774583 CTTTAGCGGCGCT-TAGAAATAAATGCCACTAAAGATCTTGTT
1 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
** *
32774625 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
** * *
32774668 CTTTAGCGGCGCTTAGGACAA-AAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGC-TAAAAAAATAAACGCCACTAAAGATCATGTT
32774711 CTTTAGCGGC
1 CTTTAGCGGC
32774721 ACTTTGAAAG
Statistics
Matches: 233, Mismatches: 28, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
41 3 0.01
42 109 0.47
43 105 0.45
44 16 0.07
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
Found at i:32774538 original size:85 final size:84
Alignment explanation
Indices: 32774412--32774766 Score: 406
Period size: 85 Copynumber: 4.2 Consensus size: 84
32774402 ACGTCGTAAA
* * * *
32774412 CTTTTGCGGCGCTTACAGAAAAAAATGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAGA
1 CTTTAGCGGCGC-TA-AAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAGA
32774477 AACGCCGCTAAAGATCATGTT
64 AACGCCGCTAAAGATCATGTT
* * * *
32774498 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTATTTAACGGCGCTAAAAAATAA
1 CTTTAGCGGCGCTAAAAAAA-AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAGAA
* *
32774563 ACGCCACTAAAGAGCATGTT
65 ACGCCGCTAAAGATCATGTT
* * * * * *
32774583 CTTTAGCGGCGCTTAGAAATAAATGCCACTAAAGATCTTGTTCTTTAGCGGCGCTAAGGAAATAA
1 CTTTAGCGGCGCTAAAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAA-GAAAGAA
32774648 ACGCCGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTT
** * * * **
32774668 CTTTAGCGGCGCTTAGGACAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTGAAAGAA
1 CTTTAGCGGCGC-TAAAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAG-A
* *
32774733 AACGCCTCTAAA-AGTAATGTT
64 AACGCCGCTAAAGA-TCATGTT
*
32774754 CTATAGCGGCGCT
1 CTTTAGCGGCGCT
32774767 TGTTTAAAAA
Statistics
Matches: 230, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
84 38 0.17
85 117 0.51
86 75 0.33
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (84 bp):
CTTTAGCGGCGCTAAAAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAGAAA
CGCCGCTAAAGATCATGTT
Found at i:32774735 original size:43 final size:42
Alignment explanation
Indices: 32774412--32774767 Score: 419
Period size: 43 Copynumber: 8.3 Consensus size: 42
32774402 ACGTCGTAAA
* *
32774412 CTTTTGCGGCGCTTACAGAAAAAAATGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTT
* *
32774456 CTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* *
32774498 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCACTAAAGATCATGTT
* * * *
32774541 ATTTAACGGCGC-TAAAAAATAAACGCCACTAAAGAGCATGTT
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCACTAAAGATCATGTT
* * *
32774583 CTTTAGCGGCGCTTAGAAATAAATGCCACTAAAGATCTTGTT
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
* * *
32774625 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCACTAAAGATCATGTT
* *
32774668 CTTTAGCGGCGCTTAGGACAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAAAAAACGCCACTAAAGATCATGTT
* * * *
32774711 CTTTAGCGGCACTTTGAAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGAAA-AAAACGCCACTAAAGA-TCATGTT
*
32774754 CTATAGCGGCGCTT
1 CTTTAGCGGCGCTT
32774768 GTTTAAAAAC
Statistics
Matches: 274, Mismatches: 33, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
42 117 0.43
43 144 0.53
44 13 0.05
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTT
Found at i:32775290 original size:15 final size:12
Alignment explanation
Indices: 32775232--32775304 Score: 89
Period size: 12 Copynumber: 6.3 Consensus size: 12
32775222 TTTTGAACCT
*
32775232 CTGCTTCTATCG
1 CTGCTTCTCTCG
*
32775244 CTGCTTCTATCG
1 CTGCTTCTCTCG
32775256 CTGCTTCTCTCG
1 CTGCTTCTCTCG
32775268 CTGCTTCTCTCG
1 CTGCTTCTCTCG
**
32775280 CTGCAGCT-T--
1 CTGCTTCTCTCG
32775289 CTGCTTCTCTCG
1 CTGCTTCTCTCG
32775301 CTGC
1 CTGC
32775305 GGCCTCTGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
9 6 0.11
10 1 0.02
11 1 0.02
12 45 0.85
ACGTcount: A:0.04, C:0.38, G:0.18, T:0.40
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:32775294 original size:21 final size:21
Alignment explanation
Indices: 32775268--32775336 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
32775258 GCTTCTCTCG
*
32775268 CTGCTTCTCTCGCTGCAGCTT
1 CTGCTTCTCTCGCTGCAGCCT
*
32775289 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
32775310 CTGTTTCTCTCGTTGCTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
32775331 CTGCTT
1 CTGCTT
32775337 TAAGTTGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.01, C:0.38, G:0.20, T:0.41
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:32785495 original size:35 final size:35
Alignment explanation
Indices: 32785385--32785495 Score: 89
Period size: 35 Copynumber: 3.1 Consensus size: 35
32785375 CCCCAGCACT
* * * *
32785385 TAAACCCTAAACCGTAAAACATAATCAC-TAAACCC
1 TAAACCATAAACCTTAAAGCATAA-CCCTTAAACCC
* *** * * *
32785420 ATAATCCATAAACCTTAAATTGTAACTCTTAAATCT
1 -TAAACCATAAACCTTAAAGCATAACCCTTAAACCC
*
32785456 TAAACCATAAACCTTAGAGCATAACCCTTAAACCC
1 TAAACCATAAACCTTAAAGCATAACCCTTAAACCC
32785491 TAAAC
1 TAAAC
32785496 TGTAAAACCA
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
35 34 0.60
36 23 0.40
ACGTcount: A:0.45, C:0.27, G:0.04, T:0.24
Consensus pattern (35 bp):
TAAACCATAAACCTTAAAGCATAACCCTTAAACCC
Found at i:32785580 original size:31 final size:32
Alignment explanation
Indices: 32785518--32785580 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
32785508 CCCTAAATAT
*
32785518 ATCCCCATAACCCCTTAAAGCATAACCCCTAA
1 ATCCCCATAACCCCTTAAAGCATAACACCTAA
* *
32785550 ATCCCCCTAACCCC-TAAATCATAACACCTAA
1 ATCCCCATAACCCCTTAAAGCATAACACCTAA
32785581 CGCTTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.38, C:0.41, G:0.02, T:0.19
Consensus pattern (32 bp):
ATCCCCATAACCCCTTAAAGCATAACACCTAA
Found at i:32785822 original size:112 final size:110
Alignment explanation
Indices: 32785591--32785826 Score: 260
Period size: 112 Copynumber: 2.1 Consensus size: 110
32785581 CGCTTTTATG
* *
32785591 AAAGCGCCGCTAAAAACCCAGCATTAGCGACGCTTTACTAAAAACGCCGTTAAACCCCCGAAAGC
1 AAAGCGCCGCT-AAAACCCAGCATTAGCGACGCATTACTAAAAACGCCGCTAAACCCCCGAAAGC
* ** *
32785656 AAAGAAAACGGTGTCGTTGGGTTTAATTTTTTTCGGCGCTTCCATA
65 AAAGAAAACGGCGTCGTTGGACTTAATTTTTTTCGGCGCTTCCACA
* * * * * *
32785702 AAAACGCCGCTAAAGCCCTGCATTAGCGGCGCATTATTAAAAACGCCGCTAAACCCCCCCGGAAG
1 AAAGCGCCGCTAAAACCCAGCATTAGCGACGCATTACTAAAAACGCCGCTAAA--CCCCCGAAAG
** * * *
32785767 CTTAGAAAACGGCGTCGTTGGACTTAGTTTTTTGT-GGTGCTT-TAGCA
64 CAAAGAAAACGGCGTCGTTGGACTTAATTTTTT-TCGGCGCTTCCA-CA
32785814 AAAGCGCCGCTAA
1 AAAGCGCCGCTAA
32785827 TTCTTATTTT
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
110 36 0.35
111 11 0.11
112 55 0.53
113 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (110 bp):
AAAGCGCCGCTAAAACCCAGCATTAGCGACGCATTACTAAAAACGCCGCTAAACCCCCGAAAGCA
AAGAAAACGGCGTCGTTGGACTTAATTTTTTTCGGCGCTTCCACA
Found at i:32786069 original size:13 final size:13
Alignment explanation
Indices: 32786051--32786083 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
32786041 TCACTACACG
32786051 CTGGGGCGATGGC
1 CTGGGGCGATGGC
32786064 CTGGGGCGATGGC
1 CTGGGGCGATGGC
*
32786077 TTGGGGC
1 CTGGGGC
32786084 AAAGGTACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.21, G:0.55, T:0.18
Consensus pattern (13 bp):
CTGGGGCGATGGC
Found at i:32791451 original size:8 final size:8
Alignment explanation
Indices: 32791438--32791468 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
32791428 TTGATGAGAT
32791438 AATTTGAG
1 AATTTGAG
32791446 AATTTGAG
1 AATTTGAG
32791454 AATTTGAG
1 AATTTGAG
32791462 AATTTGA
1 AATTTGA
32791469 AGATGAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (8 bp):
AATTTGAG
Found at i:32796240 original size:42 final size:42
Alignment explanation
Indices: 32796181--32796265 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
32796171 ATCTCAGGCC
32796181 TTAGGTGCAAACCCTGCTTTGAGCTTCTGAATTGTGTAAACA
1 TTAGGTGCAAACCCTGCTTTGAGCTTCTGAATTGTGTAAACA
32796223 TTAGGTGCAAACCCTGCTTTGAGCTTCTGAATTGTGTAAACA
1 TTAGGTGCAAACCCTGCTTTGAGCTTCTGAATTGTGTAAACA
32796265 T
1 T
32796266 CTGTTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (42 bp):
TTAGGTGCAAACCCTGCTTTGAGCTTCTGAATTGTGTAAACA
Found at i:32800109 original size:67 final size:67
Alignment explanation
Indices: 32800001--32800132 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 67
32799991 TTTTATATTA
* *
32800001 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTATGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGAAGTATGCTCTCT
32800066 TG
66 TG
*
32800068 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGAAGTGTGCTCTCT
1 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGAAGTATGCTCTCT
32800133 GAATTGGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGAAGTATGCTCTCT
TG
Found at i:32810581 original size:15 final size:16
Alignment explanation
Indices: 32810560--32810595 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
32810550 GGCAGCCAGG
*
32810560 GCAGGGATGATTTTGA
1 GCAGGGATGATGTTGA
32810576 -CAGGGATGATGTTGA
1 GCAGGGATGATGTTGA
32810591 GCAGG
1 GCAGG
32810596 TTGTTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (16 bp):
GCAGGGATGATGTTGA
Found at i:32813180 original size:16 final size:16
Alignment explanation
Indices: 32813161--32813198 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32813151 ATCTTTCTAT
32813161 TTTTCTACCCCTT-CAA
1 TTTTCTA-CCCTTCCAA
*
32813177 TTTTCTATCCTTCCAA
1 TTTTCTACCCTTCCAA
32813193 TTTTCT
1 TTTTCT
32813199 TTCCACTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCTACCCTTCCAA
Found at i:32823132 original size:125 final size:126
Alignment explanation
Indices: 32822902--32823251 Score: 535
Period size: 125 Copynumber: 2.8 Consensus size: 126
32822892 ACGTAGACGC
* *
32822902 GAAGAATTTGTGAAATCGCGCCCTCCTGGATGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* * *
32822967 TTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTCTACCAGGATGCTT-TATGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATG-TTATATGA
* * * * * *
32823027 GAAGAATTTGTTAAATCGCGCCCACGTGGACGCGTTTTTGCTACAGTAGGTCCT-GAAAAAATTA
1 GAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
* * *
32823091 TTTCAAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAAGATGTTATTTGA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATGTTATATGA
*
32823152 GAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
1 GAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
32823217 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA
66 TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAA
32823252 NNNNNNNNNN
Statistics
Matches: 200, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
124 40 0.20
125 118 0.59
126 42 0.21
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (126 bp):
GAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGAAATAA
TTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAACCAAGATGTTATATGA
Found at i:32825804 original size:2 final size:2
Alignment explanation
Indices: 32825797--32825821 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32825787 AACTTAGTTT
32825797 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 T
32825822 GTACATTTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32829463 original size:18 final size:18
Alignment explanation
Indices: 32829440--32829479 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
32829430 GACTCAGAAA
* *
32829440 AGGATACATATAAGGGTT
1 AGGATACATAGAAGGGCT
32829458 AGGATACATAGAAGGGCT
1 AGGATACATAGAAGGGCT
32829476 AGGA
1 AGGA
32829480 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
AGGATACATAGAAGGGCT
Found at i:32829950 original size:111 final size:112
Alignment explanation
Indices: 32829779--32830002 Score: 423
Period size: 111 Copynumber: 2.0 Consensus size: 112
32829769 ACGCTAACTC
32829779 TGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCGATATTTCTATGTACT
1 TGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCGATATTTCTATGTACT
32829844 CGAACTAGTATCTCGGCCAATCCGTATTCAATTGCCGAAGGTCGACT
66 CGAACTAGTATCTCGGCCAATCCGTATTCAATTGCCGAAGGTCGACT
*
32829891 TGGAACGATGA-TGGTTCCCAAGTAGGTATATATTCATCCCGATCTTCCGATATTTCTATGTACT
1 TGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCGATATTTCTATGTACT
*
32829955 CGAACTAGTATCTCGGCCAATCCGTATTCCATTGCCGAAGGTCGACT
66 CGAACTAGTATCTCGGCCAATCCGTATTCAATTGCCGAAGGTCGACT
32830002 T
1 T
32830003 TGTGTTGATC
Statistics
Matches: 110, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 99 0.90
112 11 0.10
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (112 bp):
TGGAACGATGATTGGTTCCCAAGTAGGTATATATTCATACCGATCTTCCGATATTTCTATGTACT
CGAACTAGTATCTCGGCCAATCCGTATTCAATTGCCGAAGGTCGACT
Found at i:32831448 original size:18 final size:18
Alignment explanation
Indices: 32831425--32831464 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
32831415 GACTCGAAAA
*
32831425 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
32831443 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
32831461 AGGA
1 AGGA
32831465 AACGCACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:32833329 original size:51 final size:51
Alignment explanation
Indices: 32833274--32833371 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
32833264 AATTATTTAA
32833274 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * * *
32833325 AAATATGGATTTGAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
32833372 GAGGAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 3 0.07
51 39 0.93
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:32833369 original size:12 final size:11
Alignment explanation
Indices: 32833333--32833392 Score: 61
Period size: 11 Copynumber: 5.3 Consensus size: 11
32833323 TTAAATATGG
32833333 ATTTGAGAGAA
1 ATTTGAGAGAA
*
32833344 ATTTTGA-AGGA
1 A-TTTGAGAGAA
32833355 ATTTGAGAGCAA
1 ATTTGAGAG-AA
32833367 A-TTGAGAGGAA
1 ATTTGAGA-GAA
32833378 ATTTGAGAGAGA
1 ATTTGAGAGA-A
32833390 ATT
1 ATT
32833393 AGTTTGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.12
11 18 0.44
12 18 0.44
ACGTcount: A:0.42, C:0.02, G:0.28, T:0.28
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:32833380 original size:23 final size:21
Alignment explanation
Indices: 32833333--32833392 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 21
32833323 TTAAATATGG
32833333 ATTTGAGAGAAATTTTGAAGGA
1 ATTTGAGAGAAA-TTTGAAGGA
32833355 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGG-A
32833378 ATTTGAGAGAGAATT
1 ATTTGAGAGA-AATT
32833393 AGTTTGTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.12
22 13 0.39
23 15 0.45
24 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.28, T:0.28
Consensus pattern (21 bp):
ATTTGAGAGAAATTTGAAGGA
Found at i:32839798 original size:23 final size:22
Alignment explanation
Indices: 32839762--32839807 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
32839752 ATAATTTTTT
32839762 AAAATAATTTAATAACTTAAATA
1 AAAATAATTTAATAA-TTAAATA
*
32839785 AAAAT-ATTTGAATAATTCAATA
1 AAAATAATTT-AATAATTAAATA
32839807 A
1 A
32839808 CCATATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATAATTTAATAATTAAATA
Found at i:32843504 original size:37 final size:36
Alignment explanation
Indices: 32843410--32843504 Score: 88
Period size: 37 Copynumber: 2.6 Consensus size: 36
32843400 TGTATTTATG
* *
32843410 TTAATAATA-ATTTTATTAATAATTAATTAATTTTTGA
1 TTAATAATATA-TTTATT-ATAATTAATAAATTTTTCA
*
32843447 TTAATTAATATAAATT-TTATAA-TAATAAATTTTTACA
1 TTAA-TAATAT-ATTTATTATAATTAATAAATTTTT-CA
32843484 TTGAATAATATATTTATTATA
1 TT-AATAATATATTTATTATA
32843505 TCATTATATG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
36 14 0.29
37 22 0.46
38 9 0.19
39 2 0.04
40 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (36 bp):
TTAATAATATATTTATTATAATTAATAAATTTTTCA
Found at i:32848056 original size:21 final size:21
Alignment explanation
Indices: 32848010--32848057 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
32848000 TTTTAATTAC
*
32848010 ACTAATGTGAAAAAAATATTG
1 ACTAATATGAAAAAAATATTG
32848031 A--AATATGAAATAAAATATT-
1 ACTAATATGAAA-AAAATATTG
32848050 ACTAATAT
1 ACTAATAT
32848058 ATAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (21 bp):
ACTAATATGAAAAAAATATTG
Found at i:32851004 original size:19 final size:20
Alignment explanation
Indices: 32850976--32851026 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
32850966 TGACTATTGC
*
32850976 TATTAGTATTATGA-ATTAA
1 TATTATTATTATGATATTAA
*
32850995 TATTATTATTATGATATTTA
1 TATTATTATTATGATATTAA
32851015 T-TTATTTATTAT
1 TATTA-TTATTAT
32851027 TTATCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
TATTATTATTATGATATTAA
Found at i:32854555 original size:17 final size:17
Alignment explanation
Indices: 32854514--32854555 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
32854504 GATTCATTTA
*
32854514 TCTTTTATATGAAATAAT
1 TCTTTT-TATAAAATAAT
32854532 T-TATTTTATAAAATAAT
1 TCT-TTTTATAAAATAAT
32854549 TCTTTTT
1 TCTTTTT
32854556 TTGAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
TCTTTTTATAAAATAAT
Found at i:32854562 original size:17 final size:17
Alignment explanation
Indices: 32854521--32854562 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
32854511 TTATCTTTTA
32854521 TATGAAATAATTTATTT
1 TATGAAATAATTTATTT
*
32854538 TATAAAATAATTCT-TTT
1 TATGAAATAATT-TATTT
*
32854555 TTTGAAAT
1 TATGAAAT
32854563 TTTGATGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
TATGAAATAATTTATTT
Found at i:32868019 original size:73 final size:72
Alignment explanation
Indices: 32867942--32868136 Score: 201
Period size: 73 Copynumber: 2.6 Consensus size: 72
32867932 GGCTGTATAA
* * * * *
32867942 CAGGAAGCTCATAAGAGCCATAATTAGGAAGCTCATGCGGGCCAATAACGGGTAGCTCCGAAGAG
1 CAGGAAGCTCAAAAGAGCCATAATTGGGAAGCTCATGCGAGCC-ATAACAGGTAGCACCGAAGAG
32868007 CCATTAAT
65 CCATTAAT
*** * * * * * *
32868015 CAGGAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGCGAGCCATATCAGGTAGCACCGGAGAG
1 CAGGAAGCTCAAAAGAGCCATA-ATTGGGAAGCTCATGCGAGCCATAACAGGTAGCACCGAAGAG
32868080 CCATTAAT
65 CCATTAAT
* *
32868088 CAGGAAGCTCACAAAGAGCCTTTAATTGGGAAGCTCATGAAGAGCCATA
1 CAGGAAGCTCA-AAAGAGCC-ATAATTGGGAAGCTCATG-CGAGCCATA
32868137 TAACGGAAAG
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
73 53 0.55
74 33 0.34
75 10 0.10
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (72 bp):
CAGGAAGCTCAAAAGAGCCATAATTGGGAAGCTCATGCGAGCCATAACAGGTAGCACCGAAGAGC
CATTAAT
Found at i:32868023 original size:25 final size:25
Alignment explanation
Indices: 32867995--32868135 Score: 94
Period size: 25 Copynumber: 5.6 Consensus size: 25
32867985 AATAACGGGT
32867995 AGCTCCGAAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * *
32868020 AGCTCCGGATAGCCA-TATATCGGGA
1 AGCTCCGAAGAGCCATTA-ATCAGGA
* *
32868045 AG-TTC-AAGCGAGCCA-T-ATCAGGT
1 AGCTCCGAA--GAGCCATTAATCAGGA
* *
32868068 AGCACCGGAGAGCCATTAATCAGGA
1 AGCTCCGAAGAGCCATTAATCAGGA
* * **
32868093 AGCTCACAAAGAGCCTTTAATTGGGA
1 AGCTC-CGAAGAGCCATTAATCAGGA
*
32868119 AGCTCATGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
32868136 ATAACGGAAA
Statistics
Matches: 87, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
23 14 0.16
24 6 0.07
25 38 0.44
26 29 0.33
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCAGGA
Found at i:32868107 original size:26 final size:26
Alignment explanation
Indices: 32868076--32868135 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
32868066 GTAGCACCGG
32868076 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* ** **
32868102 AGAGCCTTTAATTGGGAAGCTCATGA
1 AGAGCCATTAATCAGGAAGCTCACAA
32868128 AGAGCCAT
1 AGAGCCAT
32868136 ATAACGGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:32868624 original size:21 final size:21
Alignment explanation
Indices: 32868591--32868641 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
32868581 TATACGAATG
*
32868591 AATTTGACA-TCAATTTAATAC
1 AATTT-ACATTCAATTCAATAC
*
32868612 AATTTACATTCAATTCAATCC
1 AATTTACATTCAATTCAATAC
*
32868633 AATTCACAT
1 AATTTACAT
32868642 CTTAGGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTTACATTCAATTCAATAC
Found at i:32869976 original size:14 final size:15
Alignment explanation
Indices: 32869957--32869985 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
32869947 CCATTCTCCC
32869957 TTTCTTTTC-TTCTT
1 TTTCTTTTCGTTCTT
32869971 TTTCTTTTCGTTCTT
1 TTTCTTTTCGTTCTT
32869986 AATTCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTCTTTTCGTTCTT
Found at i:32872527 original size:102 final size:102
Alignment explanation
Indices: 32872351--32872562 Score: 372
Period size: 102 Copynumber: 2.1 Consensus size: 102
32872341 TTTAATGTGG
*
32872351 AAAAACCCCTCCAAAGAGGATAAAAAACCATGGGCAAAAATGATTTTACTATAATGGAAAAAGAA
1 AAAAACCCCTCCAAAGAGGATAAAAAACCATGGGCAAAAATAATTTTACTATAATGGAAAAAGAA
32872416 CGAAGAGTACAAAAGATGGAGATAAAAACTAAACCCC
66 CGAAGAGTACAAAAGATGGAGATAAAAACTAAACCCC
* *
32872453 AAAAACCCCTCCAAAGAGGATAAAAAACCAAT-GGCAAAAATAATTTTATTATAATGGCAAAAGA
1 AAAAACCCCTCCAAAGAGGATAAAAAACC-ATGGGCAAAAATAATTTTACTATAATGGAAAAAGA
*
32872517 ACGAAGAGTACAAAAGATGGAGATAAAAACTAAACCCT
65 ACGAAGAGTACAAAAGATGGAGATAAAAACTAAACCCC
32872555 AAAAACCC
1 AAAAACCC
32872563 GAAAATAAAG
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
102 103 0.98
103 2 0.02
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (102 bp):
AAAAACCCCTCCAAAGAGGATAAAAAACCATGGGCAAAAATAATTTTACTATAATGGAAAAAGAA
CGAAGAGTACAAAAGATGGAGATAAAAACTAAACCCC
Found at i:32872714 original size:24 final size:24
Alignment explanation
Indices: 32872686--32872737 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
32872676 TTAGTAGGTC
* *
32872686 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
32872710 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
32872734 AAAT
1 AAAT
32872738 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:32874459 original size:18 final size:19
Alignment explanation
Indices: 32874430--32874465 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32874420 GTAAAAATTA
*
32874430 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
32874449 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
32874466 ATCTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:32875106 original size:40 final size:40
Alignment explanation
Indices: 32874985--32875122 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
32874975 CTTCGAGTCA
*
32874985 ATGAGACACTGGGTGTCAAATTATTACTTCGGATTAAT-TCG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATT-ATCT-G
* * * * * *
32875026 ATGAGGCACTGGGTG-CCAA--TTTACTTTGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
*
32875063 ATGAGACACTGGGTGTCAAATTTTTACTTCGAATTATCTG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
*
32875103 ATGAGGCACTGGGTGTCAAA
1 ATGAGACACTGGGTGTCAAA
32875123 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 16 0.21
38 13 0.17
40 35 0.45
41 14 0.18
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
Found at i:32875885 original size:8 final size:8
Alignment explanation
Indices: 32875872--32875942 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
32875862 TAAAAAATAT
32875872 ATATTATA
1 ATATTATA
32875880 ATATTATA
1 ATATTATA
32875888 ATATTAT-
1 ATATTATA
*
32875895 ATCTTA-A
1 ATATTATA
*
32875902 TTATTA-A
1 ATATTATA
* *
32875909 GTATATATT
1 ATAT-TATA
32875918 ATATTATA
1 ATATTATA
* *
32875926 TTA-TATT
1 ATATTATA
32875933 ATATTATA
1 ATATTATA
32875941 AT
1 AT
32875943 GATAAAATAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
7 18 0.38
8 27 0.56
9 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (8 bp):
ATATTATA
Found at i:32875927 original size:10 final size:10
Alignment explanation
Indices: 32875912--32875940 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
32875902 TTATTAAGTA
32875912 TATATTATAT
1 TATATTATAT
32875922 TATATTATAT
1 TATATTATAT
32875932 TATATTATA
1 TATATTATA
32875941 ATGATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTATAT
Found at i:32875932 original size:15 final size:15
Alignment explanation
Indices: 32875912--32875940 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32875902 TTATTAAGTA
32875912 TATATTATATTATAT
1 TATATTATATTATAT
32875927 TATATTATATTATA
1 TATATTATATTATA
32875941 ATGATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTATATTATAT
Found at i:32875967 original size:4 final size:4
Alignment explanation
Indices: 32875958--32876022 Score: 71
Period size: 4 Copynumber: 15.8 Consensus size: 4
32875948 AATAAAAAAT
*
32875958 AAAG AAAG AAAG AAAG ATAG AAACG AAACAG AAAG -AA- AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG
32876007 AAAG AAAG AAAAG AAA
1 AAAG AAAG -AAAG AAA
32876023 AAGGAAAGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
3 4 0.08
4 38 0.72
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.22, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:32876001 original size:33 final size:31
Alignment explanation
Indices: 32875962--32876022 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
32875952 AAAAATAAAG
*
32875962 AAAGAAAGAAAGATAGAAACGAAACAGAAAGAA
1 AAAGAAAGAAAGAAAGAAA-GAAA-AGAAAGAA
32875995 AAAGAAAGAAAGAAAGAAAGAAAAGAAA
1 AAAGAAAGAAAGAAAGAAAGAAAAGAAA
32876023 AAGGAAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 5 0.19
32 4 0.15
33 18 0.67
ACGTcount: A:0.74, C:0.03, G:0.21, T:0.02
Consensus pattern (31 bp):
AAAGAAAGAAAGAAAGAAAGAAAAGAAAGAA
Found at i:32876044 original size:27 final size:27
Alignment explanation
Indices: 32875967--32876030 Score: 55
Period size: 29 Copynumber: 2.4 Consensus size: 27
32875957 TAAAGAAAGA
*
32875967 AAGAAAGATAGAAACGAAACAGAAAGAA-A
1 AAGAAAGAAAGAAA-GAAA-AGAAA-AAGA
32875996 AAGAAAGAAAGAAAG-AAAG-AAAAGA
1 AAGAAAGAAAGAAAGAAAAGAAAAAGA
*
32876021 AA-AAGGAAAG
1 AAGAAAGAAAG
32876031 GAAGGAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
24 9 0.28
25 5 0.16
26 2 0.06
27 2 0.06
28 1 0.03
29 13 0.41
ACGTcount: A:0.72, C:0.03, G:0.23, T:0.02
Consensus pattern (27 bp):
AAGAAAGAAAGAAAGAAAAGAAAAAGA
Found at i:32876349 original size:18 final size:19
Alignment explanation
Indices: 32876320--32876355 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32876310 GTAAAAATTA
*
32876320 TGAAATTTAGGGATTTAAG
1 TGAAATTTAGGGAGTTAAG
32876339 TGAAA-TTAGGGAGTTAA
1 TGAAATTTAGGGAGTTAA
32876356 ATCTAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (19 bp):
TGAAATTTAGGGAGTTAAG
Found at i:32877052 original size:40 final size:40
Alignment explanation
Indices: 32876931--32877068 Score: 149
Period size: 40 Copynumber: 3.5 Consensus size: 40
32876921 CTTCGAGTCA
*
32876931 ATGAGACACTGGGTGTCAAATTATTACTTCGGATTAAT-TCG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATT-ATCT-G
* * * * * *
32876972 ATGAGGCACTGGGTG-CCAA--TTTACTTTGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
*
32877009 ATGAGACACTGGGTGTCAAATTTTTACTTCGAATTATCTG
1 ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
*
32877049 ATGAGGCACTGGGTGTCAAA
1 ATGAGACACTGGGTGTCAAA
32877069 CTGGTGTGTT
Statistics
Matches: 78, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 16 0.21
38 13 0.17
40 35 0.45
41 14 0.18
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTTTTACTTCGGATTATCTG
Found at i:32883914 original size:35 final size:35
Alignment explanation
Indices: 32883875--32883945 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
32883865 TTTAGCCTGG
32883875 TAAGTTCATATGAACTATATTCTGTATAATTTTAA
1 TAAGTTCATATGAACTATATTCTGTATAATTTTAA
*
32883910 TAAGTTCGTATGAACTATATTCTGTATAATTTTAA
1 TAAGTTCATATGAACTATATTCTGTATAATTTTAA
32883945 T
1 T
32883946 TAAAGTGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (35 bp):
TAAGTTCATATGAACTATATTCTGTATAATTTTAA
Found at i:32888891 original size:46 final size:46
Alignment explanation
Indices: 32888841--32888935 Score: 174
Period size: 46 Copynumber: 2.1 Consensus size: 46
32888831 TCACTTTGGG
32888841 CTGCTGCTGGACGGGCTGATTGGATTGGGCTG-TGGCTGGAGTGAGT
1 CTGCTGCTGGACGGGCTGATTGGATTGGGCTGCT-GCTGGAGTGAGT
32888887 CTGCTGCTGGACGGGCTGATTGGATTGGGCTGCTGCTGGAGTGAGT
1 CTGCTGCTGGACGGGCTGATTGGATTGGGCTGCTGCTGGAGTGAGT
32888933 CTG
1 CTG
32888936 TTGGGTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 47 0.98
47 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.44, T:0.28
Consensus pattern (46 bp):
CTGCTGCTGGACGGGCTGATTGGATTGGGCTGCTGCTGGAGTGAGT
Found at i:32888918 original size:26 final size:26
Alignment explanation
Indices: 32888843--32888921 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 26
32888833 ACTTTGGGCT
32888843 GCTGCTGGACGGGCTGATTGGATTGG
1 GCTGCTGGACGGGCTGATTGGATTGG
* * * **
32888869 GCTG-TGG-C-TG--GAGT-GAGTCT
1 GCTGCTGGACGGGCTGATTGGATTGG
32888889 GCTGCTGGACGGGCTGATTGGATTGG
1 GCTGCTGGACGGGCTGATTGGATTGG
32888915 GCTGCTG
1 GCTGCTG
32888922 CTGGAGTGAG
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
20 7 0.19
21 6 0.16
22 1 0.03
23 2 0.05
24 1 0.03
25 6 0.16
26 14 0.38
ACGTcount: A:0.10, C:0.16, G:0.46, T:0.28
Consensus pattern (26 bp):
GCTGCTGGACGGGCTGATTGGATTGG
Done.