Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 79 of 210
Found at i:27627179 original size:20 final size:20
Alignment explanation
Indices: 27627149--27627197 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
27627139 TATTTAAAAA
27627149 ATATGAAAAATGTAAATAGAT
1 ATAT-AAAAATGTAAATAGAT
* *
27627170 ATATAAAAATTTAAATATAT
1 ATATAAAAATGTAAATAGAT
27627190 ATATAAAA
1 ATATAAAA
27627198 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
ATATAAAAATGTAAATAGAT
Found at i:27627191 original size:18 final size:18
Alignment explanation
Indices: 27627140--27627198 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
27627130 TGATAGTTTT
*
27627140 ATTTAAA-AAATATGAAAA
1 ATTTAAATATATAT-AAAA
*
27627158 ATGTAAATAGATATATAAAA
1 ATTTAAAT--ATATATAAAA
27627178 ATTTAAATATATATATAAA
1 ATTTAAATATATATA-AAA
27627197 AT
1 AT
27627199 CTAGAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 13 0.38
19 5 0.15
20 11 0.32
21 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
ATTTAAATATATATAAAA
Found at i:27627219 original size:11 final size:11
Alignment explanation
Indices: 27627203--27627232 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
27627193 TAAAATCTAG
27627203 AAAAATAATAT
1 AAAAATAATAT
27627214 AAAAATAATAT
1 AAAAATAATAT
27627225 AAAAATAA
1 AAAAATAA
27627233 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:27632582 original size:8 final size:8
Alignment explanation
Indices: 27632569--27632596 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
27632559 TGCTTGTCTT
27632569 AATTATAA
1 AATTATAA
27632577 AATTATAA
1 AATTATAA
27632585 AATTATAA
1 AATTATAA
27632593 AATT
1 AATT
27632597 TTGGGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATTATAA
Found at i:27634561 original size:26 final size:26
Alignment explanation
Indices: 27634532--27634588 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
27634522 TCCAAAACCC
27634532 CAAACGACATACTTGAGAAACTACTT
1 CAAACGACATACTTGAGAAACTACTT
*
27634558 CAAACGACATACTTGATAAACTACTT
1 CAAACGACATACTTGAGAAACTACTT
27634584 CAAAC
1 CAAAC
27634589 TTCAAGAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.23
Consensus pattern (26 bp):
CAAACGACATACTTGAGAAACTACTT
Found at i:27635615 original size:16 final size:16
Alignment explanation
Indices: 27635590--27635631 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
27635580 GTTAGAAAGT
*
27635590 TATAAATATATTTAAA
1 TATAATTATATTTAAA
*
27635606 TATAATTATAATTAAA
1 TATAATTATATTTAAA
*
27635622 -ATAATAATAT
1 TATAATTATAT
27635632 AAACATGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATTATATTTAAA
Found at i:27642521 original size:46 final size:46
Alignment explanation
Indices: 27642440--27642623 Score: 194
Period size: 46 Copynumber: 4.3 Consensus size: 46
27642430 TACGTATGAT
* * * * *
27642440 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
27642484 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
* *
27642530 CACTTATCATTTTGTCACTTGATCAG----ATA-AG-T---G-TAG
1 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
* * *
27642566 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
27642612 CACTTATCACTT
1 CACTTATCACTT
27642624 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
36 26 0.22
37 1 0.01
40 2 0.02
41 4 0.03
42 4 0.03
44 10 0.09
45 6 0.05
46 63 0.54
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAATATAGCTAAAGCTAA
Found at i:27642570 original size:36 final size:36
Alignment explanation
Indices: 27642530--27642602 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 36
27642520 CTAAAGCTAA
27642530 CACTTATCA-TTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTT-TCACTTGATCAGATAAGTGTAG
27642566 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
27642602 C
1 C
27642603 TAAAGCTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
Found at i:27648840 original size:27 final size:28
Alignment explanation
Indices: 27648791--27648843 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
27648781 CTCATTACAA
**
27648791 TAATTAAAAATACAATATTTATAAAAAC
1 TAATTAAAAATACAATACGTATAAAAAC
*
27648819 TAATTAAAAATTCAA-ACGTATAAAA
1 TAATTAAAAATACAATACGTATAAAA
27648844 TCACATAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (28 bp):
TAATTAAAAATACAATACGTATAAAAAC
Found at i:27650363 original size:43 final size:44
Alignment explanation
Indices: 27650272--27650443 Score: 303
Period size: 44 Copynumber: 3.9 Consensus size: 44
27650262 CAGCATTTAC
27650272 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
27650316 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
*
27650360 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTT--A
1 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
*
27650402 AAAAAAGCACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AAAAAA-AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
27650444 TCATCACGAA
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
42 7 0.06
43 33 0.27
44 84 0.68
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (44 bp):
AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCGA
Found at i:27650499 original size:43 final size:43
Alignment explanation
Indices: 27650267--27650505 Score: 284
Period size: 44 Copynumber: 5.5 Consensus size: 43
27650257 TTTTGCAGCA
27650267 TTTACAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 TTTA-AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
*
27650311 TTCGAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 TT-TAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
* *
27650355 TTCGAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGC
1 TT-TAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
*
27650399 -TTAAAAAAAGCACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
1 TTTAAAAAAA-AACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
* ** ** * * *
27650442 TTTCATCACGAACGCCGCGAAA-AGTAATGTTCTTTAGCGACGC
1 TTTAAAAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGC
* * *
27650485 TTTTATAAAAAACGCCACTAA
1 TTTAAAAAAAAACGCCGCTAA
27650506 TTTTTGGATT
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
42 8 0.05
43 74 0.43
44 88 0.51
45 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (43 bp):
TTTAAAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC
Found at i:27650886 original size:21 final size:22
Alignment explanation
Indices: 27650862--27650934 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
27650852 GCTTCTCTCG
27650862 CTGCTTCT-TATGCTGCAGCCT
1 CTGCTTCTCTATGCTGCAGCCT
* *
27650883 CTGCTTCTCT-CGCTGTAGCCT
1 CTGCTTCTCTATGCTGCAGCCT
*
27650904 CTACTTCTCTCAT--TGCAGCCT
1 CTGCTTCTCT-ATGCTGCAGCCT
27650925 CTGCTTCTCT
1 CTGCTTCTCT
27650935 CGTTGCCGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.08, C:0.37, G:0.15, T:0.40
Consensus pattern (22 bp):
CTGCTTCTCTATGCTGCAGCCT
Found at i:27650935 original size:21 final size:21
Alignment explanation
Indices: 27650875--27650947 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
27650865 CTTCTTATGC
*
27650875 TGCAGCCTCTGCTTCTCTCGC
1 TGCAGCCTCTGCTTCTCTCGT
* * *
27650896 TGTAGCCTCTACTTCTCTCAT
1 TGCAGCCTCTGCTTCTCTCGT
27650917 TGCAGCCTCTGCTTCTCTCGT
1 TGCAGCCTCTGCTTCTCTCGT
*
27650938 TGCCGCCTCT
1 TGCAGCCTCT
27650948 ACTTTAAGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.07, C:0.40, G:0.16, T:0.37
Consensus pattern (21 bp):
TGCAGCCTCTGCTTCTCTCGT
Found at i:27651753 original size:13 final size:13
Alignment explanation
Indices: 27651744--27651780 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27651734 AATAGTAAAT
*
27651744 TATTTAAGTAATA
1 TATTAAAGTAATA
*
27651757 TATTCAAGTAATA
1 TATTAAAGTAATA
27651770 TATTAAAGTAA
1 TATTAAAGTAA
27651781 ATTTTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TATTAAAGTAATA
Found at i:27655724 original size:9 final size:9
Alignment explanation
Indices: 27655708--27655785 Score: 65
Period size: 9 Copynumber: 9.1 Consensus size: 9
27655698 CTAACAGCGT
27655708 TGTAAGTTA
1 TGTAAGTTA
*
27655717 TTTAAGTTA
1 TGTAAGTTA
**
27655726 TGTAAGTGG
1 TGTAAGTTA
27655735 TGT-A-TTA
1 TGTAAGTTA
27655742 TGTAAGTTA
1 TGTAAGTTA
*
27655751 AGTAAGTTA
1 TGTAAGTTA
* *
27655760 TGTAGGCTA
1 TGTAAGTTA
27655769 TGT-A-TTA
1 TGTAAGTTA
*
27655776 TGCAAGTTA
1 TGTAAGTTA
27655785 T
1 T
27655786 TTAACCTATG
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
7 8 0.15
8 3 0.06
9 41 0.79
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.44
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:27655763 original size:25 final size:25
Alignment explanation
Indices: 27655714--27655763 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27655704 GCGTTGTAAG
* * *
27655714 TTATTTAAGTTATGTAAGTGGTGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
*
27655739 TTATGTAAGTTAAGTAAGTTATGTA
1 TTATGTAAGTTAAGTAAGTGATGTA
27655764 GGCTATGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTAAGTAAGTGATGTA
Found at i:27655773 original size:34 final size:34
Alignment explanation
Indices: 27655708--27655784 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
27655698 CTAACAGCGT
** *
27655708 TGTAAGTTATTTAAGTTATGTAAGTGGTGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
*
27655742 TGTAAGTTAAGTAAGTTATGTAGGCT-ATGTATTA
1 TGTAAGTTAAGTAAGTTATGTAAG-TGATGTATTA
*
27655776 TGCAAGTTA
1 TGTAAGTTA
27655785 TTTAACCTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 36 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (34 bp):
TGTAAGTTAAGTAAGTTATGTAAGTGATGTATTA
Found at i:27658260 original size:15 final size:15
Alignment explanation
Indices: 27658240--27658271 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27658230 TCTAACATCT
27658240 AACCCCTAAACCCTA
1 AACCCCTAAACCCTA
*
27658255 AACCCCTAAACCTTA
1 AACCCCTAAACCCTA
27658270 AA
1 AA
27658272 TCTTGGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.16
Consensus pattern (15 bp):
AACCCCTAAACCCTA
Found at i:27658556 original size:15 final size:15
Alignment explanation
Indices: 27658536--27658569 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27658526 CCTAGCACGT
27658536 CTAA-CCTCTAAACCC
1 CTAACCCTCT-AACCC
27658551 CTAACCCTCTAACCC
1 CTAACCCTCTAACCC
27658566 CTAA
1 CTAA
27658570 ACATAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (15 bp):
CTAACCCTCTAACCC
Found at i:27659141 original size:114 final size:114
Alignment explanation
Indices: 27658905--27659669 Score: 964
Period size: 114 Copynumber: 6.7 Consensus size: 114
27658895 ATTTTTGGCT
* ** *
27658905 GCTAAATGCCCTGAAAGCT-AAGAAAACGGCGTCGTTATGCTTAGGTTTTTTTGCGGCGCTTCCT
1 GCTAAAT-CCCCGAAAGCTCAA-AAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCT
* * * *
27658969 CAAAAATGCCGCTAAAGCCCTGAGCGTTAGCGGCACTTTCTTAGAAACGCC
64 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * *
27659020 GCTAAATCCCCCGAAAGCTCAAAAAACGACATCGTTGTGCTTAGGTTTTTTTGCGACGCTTTCTC
1 GCTAAAT-CCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTC
* * *
27659085 -AAAATGCCGTTAAATCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
65 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * * *
27659134 GCTAAATCCCCGAAAGCTCACAAAACGACGTCGCTGGGCTTAGGTTTTCTTGCGGCGCTTCCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* * *
27659199 AAAACGTCGCTAAAGCCCTGAGCTTTAGCGGCGCTTTCTTAGAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * *
27659248 GCTAAATCTCCCGAAAGCTCAGAAAATGGCGTCGTTGTGTTTAGGTTTTTTT-CTGGCGCTTTCT
1 GCTAAATC-CCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGC-GGCGCTTTCT
* * *
27659312 CAGAAACGCCACTAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCC
64 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * *
27659363 GCTAGATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* *
27659428 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGC-ATTTACCTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAAACGCC
* * * * *
27659477 GCTAAATCCCTGAAAGCTCACAAAATGGCGTCGTTGGGCATATG-TTTTTTGCGGCGCTTTCTCA
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
* ** *
27659541 GAATTGCCGCTAAAGCCCTGAGAATTAGCGGCGCTTTCTTAAAAACGCC
66 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
* * * * * * *
27659590 GCAAAATCCCCAAAAGCTCAAAAAACAGTGTCGTTGGGCTTATGTTTTTTTTGCGGCTCTTTCTT
1 GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTA-GGTTTTTTTGCGGCGCTTTCTC
*
27659655 AAAAACGTCGCTAAA
65 AAAAACGCCGCTAAA
27659670 TCCCCAAAAG
Statistics
Matches: 563, Mismatches: 78, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
113 146 0.26
114 234 0.42
115 181 0.32
116 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (114 bp):
GCTAAATCCCCGAAAGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCA
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCC
Found at i:27659689 original size:74 final size:74
Alignment explanation
Indices: 27659568--27659733 Score: 221
Period size: 74 Copynumber: 2.3 Consensus size: 74
27659558 CTGAGAATTA
* *
27659568 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
27659633 GTTTTTTTT
66 GTTTTTTTT
* * * ** *
27659642 GCGGCTCTTTCTTAAAAACGTCGCTAAATCCCCAAAAGCTCGTAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
27659707 G---TTTTT
66 GTTTTTTTT
**
27659713 GCGGCGCTTTCTGGAAAACGC
1 GCGGCGCTTTCTTAAAAACGC
27659734 TGCTAATGCT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
71 22 0.28
74 58 0.73
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (74 bp):
GCGGCGCTTTCTTAAAAACGCCGCAAAATCCCCAAAAGCTCAAAAAACAGCGTCGTTGGGCTTAG
GTTTTTTTT
Found at i:27661408 original size:9 final size:9
Alignment explanation
Indices: 27661323--27661407 Score: 109
Period size: 9 Copynumber: 9.4 Consensus size: 9
27661313 GTAGTGATTC
*
27661323 AATTTGGTT
1 AATTCGGTT
*
27661332 AATTCGATT
1 AATTCGGTT
*
27661341 AATTCGGGT
1 AATTCGGTT
27661350 AATTCGGTT
1 AATTCGGTT
27661359 AATTCGAG-T
1 AATTCG-GTT
*
27661368 AATTCGGAT
1 AATTCGGTT
27661377 AATTCGGTT
1 AATTCGGTT
27661386 AATTCGGTT
1 AATTCGGTT
*
27661395 AATTTGGTT
1 AATTCGGTT
27661404 AATT
1 AATT
27661408 TTTAACCAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
8 1 0.01
9 65 0.97
10 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:27662722 original size:16 final size:16
Alignment explanation
Indices: 27662703--27662733 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27662693 TTGAAAAAGT
27662703 TTTCAAATCTATATGG
1 TTTCAAATCTATATGG
*
27662719 TTTCAAATTTATATG
1 TTTCAAATCTATATG
27662734 CTCTGACATG
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:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATCTATATGG
Found at i:27684426 original size:20 final size:19
Alignment explanation
Indices: 27684387--27684428 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27684377 GTTCAATTAA
* *
27684387 ATAAAAAAATTTATTTTTT
1 ATAAAAAAATTTACTATTT
27684406 ATAAAAAAATGTTACTATTT
1 ATAAAAAAAT-TTACTATTT
27684426 ATA
1 ATA
27684429 TTTTGTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAAAAAAATTTACTATTT
Found at i:27684480 original size:17 final size:17
Alignment explanation
Indices: 27684458--27684491 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27684448 TATTTTTATT
*
27684458 AGTGAATAATATTCAAA
1 AGTGAATAAAATTCAAA
27684475 AGTGAATAAAATTCAAA
1 AGTGAATAAAATTCAAA
27684492 CCACTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (17 bp):
AGTGAATAAAATTCAAA
Found at i:27685372 original size:7 final size:7
Alignment explanation
Indices: 27685360--27685384 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27685350 TGAGAAAAAG
27685360 TAAATTT
1 TAAATTT
27685367 TAAATTT
1 TAAATTT
27685374 TAAATTT
1 TAAATTT
27685381 TAAA
1 TAAA
27685385 AAGTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:27685391 original size:14 final size:14
Alignment explanation
Indices: 27685354--27685392 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27685344 GGTTGATGAG
27685354 AAAAAGTAAATTTT
1 AAAAAGTAAATTTT
***
27685368 AAATTTTAAATTTT
1 AAAAAGTAAATTTT
27685382 AAAAAGTAAAT
1 AAAAAGTAAAT
27685393 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
AAAAAGTAAATTTT
Found at i:27693840 original size:16 final size:18
Alignment explanation
Indices: 27693819--27693856 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27693809 TTCTATATGG
27693819 ATTTTACT-TT-TATTTT
1 ATTTTACTATTGTATTTT
27693835 ATTTTACTATTGTATTTT
1 ATTTTACTATTGTATTTT
27693853 ATTT
1 ATTT
27693857 AAATAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTGTATTTT
Found at i:27694080 original size:27 final size:27
Alignment explanation
Indices: 27694050--27694106 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
27694040 GAAGCGACTT
27694050 AGTCATCAAATCTATAGGATTTTCATG
1 AGTCATCAAATCTATAGGATTTTCATG
27694077 AGTCATCAAATCTATAGGATTTTCATG
1 AGTCATCAAATCTATAGGATTTTCATG
27694104 AGT
1 AGT
27694107 ACTAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (27 bp):
AGTCATCAAATCTATAGGATTTTCATG
Found at i:27698565 original size:17 final size:18
Alignment explanation
Indices: 27698543--27698580 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
27698533 GATTTGACAA
27698543 AAAAAAGTT-TAAAACTT
1 AAAAAAGTTGTAAAACTT
27698560 AAAAAAGTTGTAAAACTT
1 AAAAAAGTTGTAAAACTT
27698578 AAA
1 AAA
27698581 GGCCTCTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAAAGTTGTAAAACTT
Found at i:27698565 original size:18 final size:19
Alignment explanation
Indices: 27698542--27698580 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
27698532 TGATTTGACA
27698542 AAAAAAAGTT-TAAAACTT
1 AAAAAAAGTTGTAAAACTT
27698560 -AAAAAAGTTGTAAAACTT
1 AAAAAAAGTTGTAAAACTT
27698578 AAA
1 AAA
27698581 GGCCTCTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 8 0.42
19 2 0.11
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AAAAAAAGTTGTAAAACTT
Found at i:27700466 original size:145 final size:143
Alignment explanation
Indices: 27700205--27700495 Score: 564
Period size: 145 Copynumber: 2.0 Consensus size: 143
27700195 GTCAATAGTT
27700205 TATGCTTGTCAAAAAAAAAAAAAAATCAGAGGTAATATTTTGCTGATATAAGAGGAAAGAGAATT
1 TATGCTTGTCAAAAAAAAAAAAAAATCAGAGGTAATATTTTGCTGATATAAGAGGAAAGAGAATT
27700270 GAGCATCGACCAGTGAATCTATACAATGTGACAAAGAGTAAATGAAGCTGTGTCATAGACAAGCA
66 GAGCATCGACCAGTGAATCTATACAATGTGACAAAGAGTAAATGAAGCTGTGTCATAGACAAGCA
27700335 AATCTGTTATATA
131 AATCTGTTATATA
27700348 TATGCTTGTCAAAAAAAAAAAAAAAAATCAGAGGTAATATTTTGCTGATATAAGAGGAAAGAGAA
1 TATGCTTGTC--AAAAAAAAAAAAAAATCAGAGGTAATATTTTGCTGATATAAGAGGAAAGAGAA
27700413 TTGAGCATCGACCAGTGAATCTATACAATGTGACAAAGAGTAAATGAAGCTGTGTCATAGACAAG
64 TTGAGCATCGACCAGTGAATCTATACAATGTGACAAAGAGTAAATGAAGCTGTGTCATAGACAAG
27700478 CAAATCTGTTATATA
129 CAAATCTGTTATATA
27700493 TAT
1 TAT
27700496 AAAAAAAATA
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
143 10 0.07
145 136 0.93
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (143 bp):
TATGCTTGTCAAAAAAAAAAAAAAATCAGAGGTAATATTTTGCTGATATAAGAGGAAAGAGAATT
GAGCATCGACCAGTGAATCTATACAATGTGACAAAGAGTAAATGAAGCTGTGTCATAGACAAGCA
AATCTGTTATATA
Found at i:27704390 original size:9 final size:9
Alignment explanation
Indices: 27704373--27704411 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
27704363 GTTAAATTTT
27704373 ATAATTCGA
1 ATAATTCGA
*
27704382 ATAACTCGA
1 ATAATTCGA
*
27704391 ATAATTTGA
1 ATAATTCGA
27704400 ATAATTCGA
1 ATAATTCGA
27704409 ATA
1 ATA
27704412 GCAGATTGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (9 bp):
ATAATTCGA
Found at i:27706393 original size:25 final size:25
Alignment explanation
Indices: 27706356--27706406 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
27706346 TCACTTAATT
27706356 GCCAACTCATTTGGGTTCGATCCTC
1 GCCAACTCATTTGGGTTCGATCCTC
27706381 GCCAACTTC-TTTGGGTTCGATCCTC
1 GCCAAC-TCATTTGGGTTCGATCCTC
27706406 G
1 G
27706407 GAGTACTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (25 bp):
GCCAACTCATTTGGGTTCGATCCTC
Found at i:27707140 original size:13 final size:15
Alignment explanation
Indices: 27707111--27707142 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
27707101 TATGTTATTG
27707111 TTAATATAATATTTA
1 TTAATATAATATTTA
27707126 TTAAT-TAAT-TTTA
1 TTAATATAATATTTA
27707139 TTAA
1 TTAA
27707143 AGGCAATCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATATAATATTTA
Found at i:27721746 original size:21 final size:21
Alignment explanation
Indices: 27721708--27721751 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27721698 ATTTATCATA
*
27721708 TTTATTAAATTTAGAAATTAT
1 TTTATTAAATTTAGAAATGAT
*
27721729 TTTATTATAATTT-TAAATGAT
1 TTTATTA-AATTTAGAAATGAT
27721750 TT
1 TT
27721752 ATTTACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTATTAAATTTAGAAATGAT
Found at i:27722204 original size:19 final size:19
Alignment explanation
Indices: 27722182--27722219 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
27722172 AGCCATTGTC
*
27722182 ACCCACTGTAATCAAATTT
1 ACCCACCGTAATCAAATTT
27722201 ACCCACCGTAATCAAATTT
1 ACCCACCGTAATCAAATTT
27722220 GTTATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (19 bp):
ACCCACCGTAATCAAATTT
Found at i:27724925 original size:122 final size:123
Alignment explanation
Indices: 27724769--27725013 Score: 483
Period size: 122 Copynumber: 2.0 Consensus size: 123
27724759 ACAGAGTATG
27724769 AGGTATTACTAAATTTTTAAAAAATTTCGACAGCATTTCTACTTATTTTTGCTTAAACCTCCTGC
1 AGGTATTACTAAATTTTTAAAAAATTTCGACAGCATTTCTACTTATTTTTGCTTAAACCTCCTGC
27724834 AAATTTTCAAACACAATTCAATATTCCAACCAAGTTCAGTTGTATAAACATACACAAT
66 AAATTTTCAAACACAATTCAATATTCCAACCAAGTTCAGTTGTATAAACATACACAAT
27724892 AGGTA-TACTAAATTTTTAAAAAATTTCGACAGCATTTCTACTTATTTTTGCTTAAACCTCCTGC
1 AGGTATTACTAAATTTTTAAAAAATTTCGACAGCATTTCTACTTATTTTTGCTTAAACCTCCTGC
27724956 AAATTTTCAAACACAATTCAATATTCCAACCAAGTTCAGTTGTATAAACATACACAAT
66 AAATTTTCAAACACAATTCAATATTCCAACCAAGTTCAGTTGTATAAACATACACAAT
27725014 TTTACCATTA
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 117 0.96
123 5 0.04
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (123 bp):
AGGTATTACTAAATTTTTAAAAAATTTCGACAGCATTTCTACTTATTTTTGCTTAAACCTCCTGC
AAATTTTCAAACACAATTCAATATTCCAACCAAGTTCAGTTGTATAAACATACACAAT
Found at i:27726226 original size:33 final size:33
Alignment explanation
Indices: 27726178--27726366 Score: 133
Period size: 33 Copynumber: 5.6 Consensus size: 33
27726168 AAGATATGGT
27726178 GGAATCAGCACTTAGCAACCACCAATGAATAGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* * * *
27726211 GGAATTAGCATTTAGCAACCCCCTTTCACATTAAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A-T--GAATA-GG
* *
27726253 TGGGATCAGCACTTAGCAACCACCAAT-AGGTAGG
1 -GGAATCAGCACTTAGCAACCACCAATGA-ATAGG
*
27726287 GGAATTAGCACTTAGCAACC-CC--TCG----GG
1 GGAATCAGCACTTAGCAACCACCAAT-GAATAGG
27726314 GGAATCAGCACTTAGCAACCACCAATGAATAGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* *
27726347 GGAATTAGCATTTAGCAACC
1 GGAATCAGCACTTAGCAACC
27726367 CTACATTAAG
Statistics
Matches: 122, Mismatches: 14, Indels: 40
0.69 0.08 0.23
Matches are distributed among these distances:
27 21 0.17
28 2 0.02
29 1 0.01
30 2 0.02
32 2 0.02
33 54 0.44
34 6 0.05
35 2 0.02
37 3 0.02
38 2 0.02
39 3 0.02
41 4 0.03
42 5 0.04
43 15 0.12
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:27726272 original size:76 final size:77
Alignment explanation
Indices: 27726132--27726308 Score: 252
Period size: 76 Copynumber: 2.3 Consensus size: 77
27726122 CAACCCCTTG
* * * *
27726132 GGGGAATCAGTACTTAGCAACCCCCTTCACATTTCAAAGATATGGTGGAATCAGCACTTAGCAAC
1 GGGGAATTAGCACTTAGCAACCCCCTTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAAC
27726197 CACCAAT-GAATA
66 CACCAATAG-ATA
* *
27726209 GGGGAATTAGCATTTAGCAACCCCCTTTCACA-TT-AAAAATACGGTGGGATCAGCACTTAGCAA
1 GGGGAATTAGCACTTAGCAACCCCC-TTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAA
*
27726272 CCACCAATAGGTA
65 CCACCAATAGATA
27726285 GGGGAATTAGCACTTAGCAACCCC
1 GGGGAATTAGCACTTAGCAACCCC
27726309 TCGGGGGAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
76 59 0.66
77 25 0.28
78 6 0.07
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (77 bp):
GGGGAATTAGCACTTAGCAACCCCCTTCACATTTCAAAAATACGGTGGAATCAGCACTTAGCAAC
CACCAATAGATA
Found at i:27726425 original size:136 final size:133
Alignment explanation
Indices: 27726178--27726445 Score: 301
Period size: 136 Copynumber: 2.0 Consensus size: 133
27726168 AAGATATGGT
*
27726178 GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCCCCTTTCACATT
1 GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCCCATTTCACATT
* * * * **
27726243 AAAAATACGGTGGGATCAGCACTTAGCAACCACCAATAGGTAGGGGAATTAGCACTTAGCAACCC
66 AAAAATACGCTCGGAT---CACTTAGCAACCACCAATAGATAGGGGAATCAGCACACAGCAACCC
27726308 CTCGGG
128 CTCGGG
27726314 GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCCTACATTAAGTC
1 GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCC--CATT---TC
** ** * *
27726379 ACATGTTTACTTAC-CTCGG-T-ACTTAGCAACCACC-ATTGAATCGGGGAATCAGCACACAGCA
61 ACAT-TAAAAATACGCTCGGATCACTTAGCAACCACCAATAG-ATAGGGGAATCAGCACACAGCA
27726440 ACCCCT
124 ACCCCT
27726446 TTATATGCAA
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
135 3 0.03
136 91 0.81
138 3 0.03
140 1 0.01
141 9 0.08
142 5 0.04
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (133 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATTAGCATTTAGCAACCCCATTTCACATT
AAAAATACGCTCGGATCACTTAGCAACCACCAATAGATAGGGGAATCAGCACACAGCAACCCCTC
GGG
Found at i:27729749 original size:23 final size:26
Alignment explanation
Indices: 27729709--27729755 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
27729699 ATATTTATGT
*
27729709 TCAATATAGGAAGTAATT-CTAATAA
1 TCAATATAGGAAGAAATTACTAATAA
27729734 TCAAT-TA-GAAGAAATTACTAAT
1 TCAATATAGGAAGAAATTACTAAT
27729756 TCTAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
TCAATATAGGAAGAAATTACTAATAA
Found at i:27741006 original size:210 final size:211
Alignment explanation
Indices: 27740643--27741066 Score: 683
Period size: 210 Copynumber: 2.0 Consensus size: 211
27740633 CAAGAAGTTT
* * *
27740643 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTTGGGGTCAAGAAATAACATTTTGAGAGA
1 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
* *
27740708 TGAGGGTGGTGCATATGATTCTTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
66 CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* * *
27740773 CGATATTGGAACTAACGAATTTTCATATGATGTCCTAGTTTACTAAATACAGAAGAGTAGGTTTA
131 CGATATTGGAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
27740838 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
* *
27740854 ATAGTCTTGATTGCTGGTTCAGTTTTCC-GATATTGGTAGGGCTCAAGAAATAACATTGT-AGAG
1 ATAGTCTTGATTGCTGGTTCAG-TTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAG
* *
27740917 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGGTGAAATT
65 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAAT
* *
27740982 TTGATATTGTG-ACTAAAGAATTTTCATATGATGCCCTCGTTTACTAAAGACAGAAGAGTAGGTT
130 TCGATATTG-GAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTT
27741046 TAATATGGTTCAACTTCC
194 TAATATGGTTCAACTTCC
27741064 ATA
1 ATA
27741067 AAGAAGCCTG
Statistics
Matches: 197, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
210 143 0.73
211 49 0.25
212 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (211 bp):
ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
CGATATTGGAACTAAAGAATTTTCATATGATGCCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
ATATGGTTCAACTTCC
Found at i:27744300 original size:18 final size:18
Alignment explanation
Indices: 27744274--27744309 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27744264 ATTGAATCGA
*
27744274 TTGTTATGTTGAAATATT
1 TTGTCATGTTGAAATATT
*
27744292 TTGTCATGTTGGAATATT
1 TTGTCATGTTGAAATATT
27744310 ACTTCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (18 bp):
TTGTCATGTTGAAATATT
Found at i:27744459 original size:55 final size:54
Alignment explanation
Indices: 27744303--27744631 Score: 164
Period size: 55 Copynumber: 5.9 Consensus size: 54
27744293 TGTCATGTTG
* ** * * *
27744303 GAATATTACTTCTTTTGAATCGGTTGTTTATATGTTTAAAAT-AATTGTTATGTAG
1 GAATACTACTTCTTTTGAAT-AATTGTTTATATGGTT-AAATCGATTGTTATGTAA
* * * * *
27744358 GAATACTA-TT-TTTTTAATTGACTGTTTACAT-GTGTAAATGGATTGTTATGTAA
1 GAATACTACTTCTTTTGAA-TAATTGTTTATATGGT-TAAATCGATTGTTATGTAA
* * *
27744411 TAATACTACTTCTTTTGAATCAATTGTTTATACGGTTAAATCGATTGTTCTGGTGAA
1 GAATACTACTTCTTTTGAAT-AATTGTTTATATGGTTAAATCGATTGTTAT-GT-AA
* * * * **
27744468 -ATATTGCTTCTTCTTCTTTGGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTG
1 GA-A-TACTACTTC-T-TTT-GAATA-ATTGTTTATATGGTTAAATCGATTGTTATGTAA
* * ** ** * **
27744527 GAATATTGCTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCG
1 GAATACTACTTCTTTTGAATA-ATTGTTTATATGGTTAAATCGATTGTTATGTAA
* * * * * **
27744582 GAATATTACTTCTTTTGAGTTCATCGTTTATATGTTTAAATTAATTGTTA
1 GAATACTACTTCTTTTGA-ATAATTGTTTATATGGTTAAATCGATTGTTA
27744632 AAAAACACGT
Statistics
Matches: 219, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
52 5 0.02
53 34 0.16
54 6 0.03
55 110 0.50
56 9 0.04
57 4 0.02
58 13 0.06
59 2 0.01
60 7 0.03
61 29 0.13
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (54 bp):
GAATACTACTTCTTTTGAATAATTGTTTATATGGTTAAATCGATTGTTATGTAA
Found at i:27744514 original size:61 final size:57
Alignment explanation
Indices: 27744419--27744567 Score: 160
Period size: 61 Copynumber: 2.6 Consensus size: 57
27744409 AATAATACTA
* * * *
27744419 CTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAAATATTGCTTCTT
1 CTTC-TTTGAAT-AGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTG---CTT
* *
27744480 CTTCTTTGGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATATTGCTT
1 CTTCTTT-GAATAGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTGCTT
*
27744538 C-T-TTTGAATAGATTGTTTATATATTTAAAT
1 CTTCTTTGAATAGATTGTTTATATGTTTAAAT
27744568 TAATTGTTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
55 24 0.30
56 3 0.04
57 1 0.01
58 4 0.05
60 4 0.05
61 43 0.54
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (57 bp):
CTTCTTTGAATAGATTGTTTATATGTTTAAATCGATTATTATGGTGAAATATTGCTT
Found at i:27749927 original size:10 final size:10
Alignment explanation
Indices: 27749878--27749925 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
27749868 TAAACTCTCA
27749878 AAAGATAAAT
1 AAAGATAAAT
* ** *
27749888 ACATTTAATT
1 AAAGATAAAT
27749898 AAAGATAAAT
1 AAAGATAAAT
27749908 AAAGATAAAT
1 AAAGATAAAT
27749918 AAA-ATAAA
1 AAAGATAAA
27749926 ATCCTAAAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:27750903 original size:27 final size:26
Alignment explanation
Indices: 27750873--27750939 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
27750863 GCACATAATT
*
27750873 GGGAAGCCTTCTCTCAAGCCATATAAC
1 GGGAAGCCTTATCT-AAGCCATATAAC
* * *
27750900 GGGAAG-CTTATGTGAGCCATGTAAC
1 GGGAAGCCTTATCTAAGCCATATAAC
*
27750925 GGGAAGCTTTATCTA
1 GGGAAGCCTTATCTA
27750940 GGCTGTAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
25 16 0.50
26 10 0.31
27 6 0.19
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (26 bp):
GGGAAGCCTTATCTAAGCCATATAAC
Found at i:27751120 original size:26 final size:26
Alignment explanation
Indices: 27751091--27751141 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
27751081 CGGAGAGTTA
27751091 TTAATC-AGGAAGCTCAAAAAGAGCCT
1 TTAATCGA-GAAGCTCAAAAAGAGCCT
**
27751117 TTAATCGAGAAGCTCACGAAGAGCC
1 TTAATCGAGAAGCTCAAAAAGAGCC
27751142 ATATAACGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
TTAATCGAGAAGCTCAAAAAGAGCCT
Found at i:27755905 original size:24 final size:24
Alignment explanation
Indices: 27755872--27755950 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
27755862 AAAAAATATA
*
27755872 TTTAATTTTAAATCTAATATTATT
1 TTTAAATTTAAATCTAATATTATT
** *
27755896 TTTATGTTT-AAGCTTAATATTATT
1 TTTAAATTTAAATC-TAATATTATT
*
27755920 TTTAAATTTATCATC-AATATTA-T
1 TTTAAATTTA-AATCTAATATTATT
27755943 TTTAAATT
1 TTTAAATT
27755951 ACAATGTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
23 12 0.27
24 31 0.69
26 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (24 bp):
TTTAAATTTAAATCTAATATTATT
Found at i:27758003 original size:21 final size:21
Alignment explanation
Indices: 27757979--27758020 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
27757969 GCCTAGACAA
27757979 AACTTAAGTTTATATGCTACT
1 AACTTAAGTTTATATGCTACT
27758000 AACTTAAGTTTATATGCTACT
1 AACTTAAGTTTATATGCTACT
27758021 TAAGTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
AACTTAAGTTTATATGCTACT
Found at i:27758023 original size:17 final size:19
Alignment explanation
Indices: 27757979--27758027 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 19
27757969 GCCTAGACAA
27757979 AACTTAAGTTTATATGCTACT
1 AACTTAAGTTTATATG--ACT
27758000 AACTTAAGTTTATATG-CT
1 AACTTAAGTTTATATGACT
27758018 -ACTTAAGTTT
1 AACTTAAGTTT
27758028 TTCTTACATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.36
18 2 0.07
21 16 0.57
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
AACTTAAGTTTATATGACT
Found at i:27759045 original size:24 final size:24
Alignment explanation
Indices: 27759017--27759071 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
27759007 GATTGGCTCA
*
27759017 TTTAATA-ATATATGCTGATTTTTT
1 TTTAATATATATATGCTG-TTGTTT
*
27759041 TTTAAATATATATATGTTGTTGTTT
1 TTT-AATATATATATGCTGTTGTTT
27759066 TTTAAT
1 TTTAAT
27759072 TTACCGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 12 0.44
26 9 0.33
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTAATATATATATGCTGTTGTTT
Found at i:27759951 original size:36 final size:36
Alignment explanation
Indices: 27759904--27759977 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
27759894 TACTAGGGAA
27759904 GGTGCCGAACAAGTTTAGGGGTAGCCGGATTGAGAT
1 GGTGCCGAACAAGTTTAGGGGTAGCCGGATTGAGAT
27759940 GGTGCCGAACAAGTTTAGGGGTAGCCGGATTGAGAT
1 GGTGCCGAACAAGTTTAGGGGTAGCCGGATTGAGAT
27759976 GG
1 GG
27759978 GATGGTTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (36 bp):
GGTGCCGAACAAGTTTAGGGGTAGCCGGATTGAGAT
Found at i:27767351 original size:19 final size:21
Alignment explanation
Indices: 27767322--27767364 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
27767312 TACAATATAA
27767322 AAATACAAATAATA-CAGCCC
1 AAATACAAATAATATCAGCCC
*
27767342 AAAT-CAAATAATATCAGTCC
1 AAATACAAATAATATCAGCCC
27767362 AAA
1 AAA
27767365 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.19
Consensus pattern (21 bp):
AAATACAAATAATATCAGCCC
Found at i:27767367 original size:22 final size:21
Alignment explanation
Indices: 27767320--27767368 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 21
27767310 ACTACAATAT
27767320 AAAAATACAAATAATACAGCC
1 AAAAATACAAATAATACAGCC
*
27767341 -CAAAT-CAAATAATATCAGTCC
1 AAAAATACAAATAATA-CAG-CC
27767362 AAAAATA
1 AAAAATA
27767369 AAAAAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
19 9 0.41
20 7 0.32
21 2 0.09
22 4 0.18
ACGTcount: A:0.59, C:0.18, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAATACAAATAATACAGCC
Found at i:27767421 original size:15 final size:16
Alignment explanation
Indices: 27767401--27767439 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
27767391 AGTTCAGTCC
27767401 AAAACCCAAA-TAAAT
1 AAAACCCAAACTAAAT
*
27767416 AAAACCCAAACTCAAT
1 AAAACCCAAACTAAAT
27767432 -AAACCCAA
1 AAAACCCAA
27767440 CAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAACCCAAACTAAAT
Found at i:27768563 original size:3 final size:3
Alignment explanation
Indices: 27768555--27768585 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
27768545 GTTAATCTGT
27768555 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27768586 ATCCGTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27771174 original size:27 final size:27
Alignment explanation
Indices: 27771144--27771210 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
27771134 CCTATCAGGT
27771144 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
27771171 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
27771198 AGGCGCCAATGAA
1 AGGCGCCAATGAA
27771211 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:27771233 original size:19 final size:19
Alignment explanation
Indices: 27771209--27771355 Score: 95
Period size: 19 Copynumber: 7.4 Consensus size: 19
27771199 GGCGCCAATG
27771209 AATATTGTAATTTTGTATT
1 AATATTGTAATTTTGTATT
*
27771228 AATATTGTAATTAT-T-TT
1 AATATTGTAATTTTGTATT
* *
27771245 -ATAAT-TAAATTTGTATTT
1 AATATTGTAATTTTGTA-TT
* *
27771263 ATAGTTTTGGATTAGTATTTTGTATG
1 A-A-TATT-G--TA--ATTTTGTATT
*
27771289 AATATTGTAATTTTTTATAT
1 AATATTGTAATTTTGTAT-T
*
27771309 GAATATTGTAATTTTGTATG
1 -AATATTGTAATTTTGTATT
* *
27771329 AATATTCTAATTTTGTATG
1 AATATTGTAATTTTGTATT
27771348 AATATTGT
1 AATATTGT
27771356 TGTAATACCC
Statistics
Matches: 99, Mismatches: 15, Indels: 28
0.70 0.11 0.20
Matches are distributed among these distances:
15 5 0.05
16 5 0.05
17 2 0.02
18 3 0.03
19 46 0.46
20 1 0.01
21 21 0.21
23 1 0.01
24 3 0.03
25 3 0.03
26 2 0.02
27 7 0.07
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (19 bp):
AATATTGTAATTTTGTATT
Found at i:27771309 original size:21 final size:19
Alignment explanation
Indices: 27771279--27771355 Score: 118
Period size: 19 Copynumber: 3.9 Consensus size: 19
27771269 TTGGATTAGT
27771279 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
27771298 ATTTTTTATATGAATATTGTA
1 A--TTTTGTATGAATATTGTA
*
27771319 ATTTTGTATGAATATTCTA
1 ATTTTGTATGAATATTGTA
27771338 ATTTTGTATGAATATTGT
1 ATTTTGTATGAATATTGT
27771356 TGTAATACCC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:27771324 original size:40 final size:38
Alignment explanation
Indices: 27771279--27771355 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
27771269 TTGGATTAGT
*
27771279 ATTTTGTATGAATATTGTAATTTTTTATATGAATATTGTA
1 ATTTTGTATGAATATTCTAA--TTTTATATGAATATTGTA
*
27771319 ATTTTGTATGAATATTCTAATTTTGTATGAATATTGT
1 ATTTTGTATGAATATTCTAATTTTATATGAATATTGT
27771356 TGTAATACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 16 0.46
40 19 0.54
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (38 bp):
ATTTTGTATGAATATTCTAATTTTATATGAATATTGTA
Found at i:27771693 original size:27 final size:27
Alignment explanation
Indices: 27771655--27771718 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
27771645 TACAATATTT
27771655 ATTGGCGCCTCTCTATGAGGCACCTTC
1 ATTGGCGCCTCTCTATGAGGCACCTTC
*
27771682 ATTGGCGCCTCTCTGTGAGGCACCTTC
1 ATTGGCGCCTCTCTATGAGGCACCTTC
27771709 ATTGGCGCCT
1 ATTGGCGCCT
27771719 ACCTGATAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.12, C:0.33, G:0.25, T:0.30
Consensus pattern (27 bp):
ATTGGCGCCTCTCTATGAGGCACCTTC
Found at i:27772820 original size:23 final size:19
Alignment explanation
Indices: 27772771--27772807 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27772761 CACTGTTTTA
*
27772771 CCCTCTGCCTCTTCTGTTC
1 CCCTTTGCCTCTTCTGTTC
27772790 CCCTTTGCCTCTTCTGTT
1 CCCTTTGCCTCTTCTGTT
27772808 TCGCCCGATT
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:0.00, C:0.43, G:0.11, T:0.46
Consensus pattern (19 bp):
CCCTTTGCCTCTTCTGTTC
Found at i:27775645 original size:16 final size:16
Alignment explanation
Indices: 27775624--27775658 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27775614 CAAGAATACT
27775624 ATTACGCCTCAATTCC
1 ATTACGCCTCAATTCC
*
27775640 ATTACGCCTCTATTCC
1 ATTACGCCTCAATTCC
27775656 ATT
1 ATT
27775659 CAACCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCAATTCC
Found at i:27775701 original size:16 final size:16
Alignment explanation
Indices: 27775680--27775712 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27775670 TTGATTTGCT
27775680 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
27775696 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
27775712 A
1 A
27775713 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:27775701 original size:56 final size:55
Alignment explanation
Indices: 27775585--27775712 Score: 186
Period size: 56 Copynumber: 2.3 Consensus size: 55
27775575 CCATTATGCT
*
27775585 ATTACACCTCTATTCCATTCAACCAAACACAAGAATACTATTACGCCTCAATTCC
1 ATTACGCCTCTATTCCATTCAACCAAACACAAGAATACTATTACGCCTCAATTCC
* * * *
27775640 ATTACGCCTCTATTCCATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCC
1 ATTACGCCTCTATTCCATTCAACCAAACACA-AGA-ATACTATTACGCCTCAATTCC
27775696 ATTACGCCTCTATTCCA
1 ATTACGCCTCTATTCCA
27775713 ATACAGCGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.02
55 30 0.45
56 35 0.53
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.32
Consensus pattern (55 bp):
ATTACGCCTCTATTCCATTCAACCAAACACAAGAATACTATTACGCCTCAATTCC
Found at i:27776731 original size:13 final size:13
Alignment explanation
Indices: 27776713--27776737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27776703 TTTTATTTGT
27776713 TTATTCCCACCGA
1 TTATTCCCACCGA
27776726 TTATTCCCACCG
1 TTATTCCCACCG
27776738 GTCGAATGTT
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:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:27778786 original size:32 final size:32
Alignment explanation
Indices: 27778745--27778819 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
27778735 TTGTACAATG
27778745 CATTAATTAAATGTGTATATTCATATACAACT
1 CATTAATTAAATGTGTATATTCATATACAACT
* *
27778777 CATTGATTAAATGTGTATATTCATATACTACT
1 CATTAATTAAATGTGTATATTCATATACAACT
27778809 CATTAATTAAA
1 CATTAATTAAA
27778820 AATATTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (32 bp):
CATTAATTAAATGTGTATATTCATATACAACT
Found at i:27780604 original size:44 final size:41
Alignment explanation
Indices: 27780556--27780654 Score: 92
Period size: 44 Copynumber: 2.3 Consensus size: 41
27780546 GGTATTATAT
27780556 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
27780600 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
27780644 ATTATATTTTA
1 ATTATATTTTA
27780655 TAGTGTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
41 3 0.06
42 6 0.13
43 1 0.02
44 15 0.32
45 10 0.21
46 12 0.26
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:27780643 original size:26 final size:28
Alignment explanation
Indices: 27780589--27780652 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
27780579 TAAGAATAAG
* * *
27780589 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
27780617 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
27780643 AATTATATTT
1 AATTATATTT
27780653 TATAGTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:27780720 original size:110 final size:105
Alignment explanation
Indices: 27780502--27780709 Score: 301
Period size: 110 Copynumber: 1.9 Consensus size: 105
27780492 AATAAAGTAG
*
27780502 ATTATAAATTATATTTAATAATAATTATTTAAATTATATTTTATGGTATTATATATTATGATTTT
1 ATTATAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTT
27780567 AGTAAATTCATATAAGAATAAGAATTTTATTAAATTATATATT
66 AGTAAATTCATAT---AATAAGAATTTTATTAAATTATATATT
*
27780610 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTGTTATATATTATGATT
1 ATTA-TAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA--
*
27780675 TTATTAGTAAATTCATAT-TTAAGAATATTTATTAA
62 TT-TTAGTAAATTCATATAATAAGAAT-TTTATTAA
27780710 TCATTTTATT
Statistics
Matches: 91, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
108 4 0.04
109 30 0.33
110 40 0.44
112 2 0.02
113 15 0.16
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (105 bp):
ATTATAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTTT
AGTAAATTCATATAATAAGAATTTTATTAAATTATATATT
Found at i:27780939 original size:39 final size:41
Alignment explanation
Indices: 27780894--27780999 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
27780884 TTTCCTTATG
*
27780894 CTATTACACCTTTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACACCTTTATTCCATTCAACCAAACAAAAGAATTAC
* *
27780934 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTAC-AC-CT-TT--ATTCCATTCAACCAAACAAAAGAATTAC
* *
27780979 CTATTACGCCTCTATTCCATT
1 CTATTACACCTTTATTCCATT
27781000 ACGCCTCTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 5 0.09
40 2 0.04
41 9 0.17
42 2 0.04
43 1 0.02
44 24 0.45
45 5 0.09
46 5 0.09
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (41 bp):
CTATTACACCTTTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:27780974 original size:44 final size:46
Alignment explanation
Indices: 27780911--27781001 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
27780901 ACCTTTATTC
*
27780911 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
27780955 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
27781001 C
1 C
27781002 GCCTCTATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.43
45 4 0.09
46 21 0.48
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:27781002 original size:16 final size:16
Alignment explanation
Indices: 27780981--27781017 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27780971 AGAATTACCT
27780981 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
27780997 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
27781013 TTTAC
1 ATTAC
27781018 AGTGAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:27781757 original size:15 final size:15
Alignment explanation
Indices: 27781733--27781775 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27781723 ATGAGAAATT
27781733 ATTAAGTATTGAAAA
1 ATTAAGTATTGAAAA
*
27781748 ATTAAATATT-AGAAA
1 ATTAAGTATTGA-AAA
*
27781763 TTTAAGTATTGAA
1 ATTAAGTATTGAA
27781776 TTTAGGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 1 0.04
15 21 0.91
16 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (15 bp):
ATTAAGTATTGAAAA
Found at i:27781843 original size:18 final size:19
Alignment explanation
Indices: 27781820--27781857 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
27781810 GGAATATAAT
27781820 TAAATTTTT-TTATAAATA
1 TAAATTTTTATTATAAATA
27781838 TAAATTTTTAATTATAAATA
1 TAAATTTTT-ATTATAAATA
27781858 ATATATTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTTTTATTATAAATA
Found at i:27782108 original size:122 final size:121
Alignment explanation
Indices: 27781960--27782216 Score: 482
Period size: 122 Copynumber: 2.1 Consensus size: 121
27781950 TAATATAATA
27781960 TTAAAATAAATAAAATAAAATAGAATTAATTAAAAATAATCTCCATTAAATGATAAATAACTCTT
1 TTAAAATAAAT-AAATAAAATAGAATTAATTAAAAATAATCTCCATTAAATGATAAATAACTCTT
27782025 ATTTATGTATATTTTTCATATTTTTTATAGAAATTTTCTTATTGAAATTGTTTTTATT
65 ATTTATGTATATTTTTCATATTTTTTATAGAAATTTTCTTATTGAAATTGTTTTTA-T
27782083 TTAAAATAAATAAATAAAATAGAATTAATTAAAAATAATCTCCATTAAATGATAAATAACTCTTA
1 TTAAAATAAATAAATAAAATAGAATTAATTAAAAATAATCTCCATTAAATGATAAATAACTCTTA
27782148 TTTATGTATATTTTTCATATTTTTTATAGAAATTTTCTTATTGAAATTGTTTTTAT
66 TTTATGTATATTTTTCATATTTTTTATAGAAATTTTCTTATTGAAATTGTTTTTAT
27782204 TTAAAA-AAA-AAAT
1 TTAAAATAAATAAAT
27782217 TTAAAGGCCC
Statistics
Matches: 134, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
119 4 0.03
120 3 0.02
121 7 0.05
122 109 0.81
123 11 0.08
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (121 bp):
TTAAAATAAATAAATAAAATAGAATTAATTAAAAATAATCTCCATTAAATGATAAATAACTCTTA
TTTATGTATATTTTTCATATTTTTTATAGAAATTTTCTTATTGAAATTGTTTTTAT
Found at i:27786326 original size:16 final size:17
Alignment explanation
Indices: 27786296--27786328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27786286 TATACAAAAG
*
27786296 AAAATTATTACTTCAAA
1 AAAATTAATACTTCAAA
27786313 AAAATTAATA-TTCAAA
1 AAAATTAATACTTCAAA
27786329 TATCATAATT
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:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATACTTCAAA
Found at i:27789285 original size:22 final size:22
Alignment explanation
Indices: 27789260--27789308 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
27789250 CGATATTTTA
27789260 ACTACAATGCCTACTAATTTGC
1 ACTACAATGCCTACTAATTTGC
*** * *
27789282 ACTATTGTGCCTATTGATTTGC
1 ACTACAATGCCTACTAATTTGC
27789304 ACTAC
1 ACTAC
27789309 GGTGCCTAGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (22 bp):
ACTACAATGCCTACTAATTTGC
Found at i:27789313 original size:22 final size:22
Alignment explanation
Indices: 27789267--27789328 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
27789257 TTAACTACAA
* **
27789267 TGCCTACTAATTTGCACTATTG
1 TGCCTACTGATTTGCACTACGG
*
27789289 TGCCTATTGATTTGCACTACGG
1 TGCCTACTGATTTGCACTACGG
* *
27789311 TGCCTAGTGATTCGCACT
1 TGCCTACTGATTTGCACT
27789329 TTGATGCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.37
Consensus pattern (22 bp):
TGCCTACTGATTTGCACTACGG
Found at i:27790704 original size:41 final size:41
Alignment explanation
Indices: 27790647--27790832 Score: 291
Period size: 41 Copynumber: 4.5 Consensus size: 41
27790637 TTTAACATAT
* * *
27790647 TCACCGGCACTTAGCCTGCTAGGCTTATAGCTTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
27790688 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGG
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
27790729 TCACCGGCACTCAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
* ** *
27790770 TCACCGGCACTTAGCTTGAGAGGTTTATAACCTGATTCAGC
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
27790811 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
27790833 ACTTAAAGTC
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 131 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:27809419 original size:30 final size:30
Alignment explanation
Indices: 27809353--27809424 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
27809343 AAGTTTAAAT
** * *
27809353 TTTAATATGAAAATAATTGTCAAGTTGATGA
1 TTTAATATG-AAATAATTAACAAATTGAGGA
27809384 TTTAATATGAAATAATTAACAAATTGGAGGA
1 TTTAATATGAAATAATTAACAAATT-GAGGA
27809415 -TTAATATGAA
1 TTTAATATGAA
27809425 TAAATAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 23 0.64
31 13 0.36
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTAATATGAAATAATTAACAAATTGAGGA
Found at i:27823004 original size:16 final size:16
Alignment explanation
Indices: 27822983--27823018 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
27822973 TTTGGTTCGC
27822983 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27822999 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
27823015 TGTA
1 TGTA
27823019 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:27823275 original size:18 final size:17
Alignment explanation
Indices: 27823254--27823288 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27823244 TTATTATTAA
*
27823254 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
27823272 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
27823289 TCTNNNNNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:27829609 original size:29 final size:29
Alignment explanation
Indices: 27829573--27829678 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
27829563 TCAGGTTACA
27829573 TTTTAGTCACTTATGTTTGAAATGTTATG
1 TTTTAGTCACTTATGTTTGAAATGTTATG
* * ** * **
27829602 TTTTAGTCTCTTATGTTATCACGTTGTAACA
1 TTTTAGTCACTTATGTT-TGA-AATGTTATG
27829633 TTTTAGTCACTTATGTTTGAAATGTTATG
1 TTTTAGTCACTTATGTTTGAAATGTTATG
*
27829662 TTTTAGTCTCTTATGTT
1 TTTTAGTCACTTATGTT
27829679 ATCACGTTGT
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 36 0.60
30 4 0.07
31 20 0.33
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (29 bp):
TTTTAGTCACTTATGTTTGAAATGTTATG
Found at i:27829640 original size:31 final size:31
Alignment explanation
Indices: 27829602--27829700 Score: 121
Period size: 31 Copynumber: 3.3 Consensus size: 31
27829592 AAATGTTATG
27829602 TTTTAGTCTCTTATGTTATCACGTTGTAACA
1 TTTTAGTCTCTTATGTTATCACGTTGTAACA
* * ** * **
27829633 TTTTAGTCACTTATGTT-TGA-AATGTTATG
1 TTTTAGTCTCTTATGTTATCACGTTGTAACA
27829662 TTTTAGTCTCTTATGTTATCACGTTGTAACA
1 TTTTAGTCTCTTATGTTATCACGTTGTAACA
27829693 TTTTAGTC
1 TTTTAGTC
27829701 ACTGAGCCGT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 20 0.38
30 4 0.08
31 28 0.54
ACGTcount: A:0.22, C:0.13, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTTAGTCTCTTATGTTATCACGTTGTAACA
Found at i:27829643 original size:60 final size:60
Alignment explanation
Indices: 27829570--27829703 Score: 268
Period size: 60 Copynumber: 2.2 Consensus size: 60
27829560 GGCTCAGGTT
27829570 ACATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCTCTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCTCTTATGTTATCACGTTGTA
27829630 ACATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCTCTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCTCTTATGTTATCACGTTGTA
27829690 ACATTTTAGTCACT
1 ACATTTTAGTCACT
27829704 GAGCCGTTAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.49
Consensus pattern (60 bp):
ACATTTTAGTCACTTATGTTTGAAATGTTATGTTTTAGTCTCTTATGTTATCACGTTGTA
Found at i:27832540 original size:21 final size:21
Alignment explanation
Indices: 27832516--27832556 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
27832506 ATAAGAGATA
*
27832516 AACGAAAAACCATAATGGTTG
1 AACGAAAAACCATAAGGGTTG
* *
27832537 AACGGAAACCCATAAGGGTT
1 AACGAAAAACCATAAGGGTT
27832557 AAACTGAAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
AACGAAAAACCATAAGGGTTG
Found at i:27832581 original size:42 final size:42
Alignment explanation
Indices: 27832535--27832641 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
27832525 CCATAATGGT
27832535 TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
1 TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
27832577 TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
1 TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
* *
27832619 TAAACGGAAACCCCATTAGGGTT
1 TGAACGGAAA-CCCATAAGGGTT
27832642 GAACGGAAAC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 51 0.82
43 11 0.18
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (42 bp):
TGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGC
Found at i:27832623 original size:63 final size:63
Alignment explanation
Indices: 27832491--27832623 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 63
27832481 AATCCCGAAG
* * * * *
27832491 GCTAAACAGAAGCTCATAAGAGATAAACGAAAAACCATAATGGTTGAACGGAAACCCATAAGG
1 GCTAAACAGAAGCTCAAAAGAGATAAACGAAAAACCATAAGGGTTAAACGGAAACCCAAAAGA
* * * * * * * * *
27832554 GTTAAACTGAAGCTCAAAAGAGCTGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGA
1 GCTAAACAGAAGCTCAAAAGAGATAAACGAAAAACCATAAGGGTTAAACGGAAACCCAAAAGA
27832617 GCTAAAC
1 GCTAAAC
27832624 GGAAACCCCA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (63 bp):
GCTAAACAGAAGCTCAAAAGAGATAAACGAAAAACCATAAGGGTTAAACGGAAACCCAAAAGA
Found at i:27844926 original size:26 final size:27
Alignment explanation
Indices: 27844872--27844928 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27844862 AATTTTAAAA
** * *
27844872 TATTTTTAAAATACTTTTTTATTTTTT
1 TATTTTTAAAATAAATTTTTATGTGTT
27844899 TATTTTTAAAATAAATTTTT-TGTGTT
1 TATTTTTAAAATAAATTTTTATGTGTT
27844925 TATT
1 TATT
27844929 AGAAAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTATGTGTT
Found at i:27847033 original size:23 final size:23
Alignment explanation
Indices: 27846987--27847039 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27846977 TTTATGCATA
* *
27846987 CAAGTGTTAGTGGCACTACGGTG
1 CAAGTGATAGTGGCACTACAGTG
**
27847010 CAAGTGATAGTGGCACTTTAGTG
1 CAAGTGATAGTGGCACTACAGTG
27847033 CAAGTGA
1 CAAGTGA
27847040 CAGAAGCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (23 bp):
CAAGTGATAGTGGCACTACAGTG
Found at i:27854978 original size:26 final size:27
Alignment explanation
Indices: 27854924--27854980 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27854914 AATTTTAAAA
** * *
27854924 TATTTTTAAAATACTTTTTTATTTTTT
1 TATTTTTAAAATAAATTTTTATGTGTT
27854951 TATTTTTAAAATAAATTTTT-TGTGTT
1 TATTTTTAAAATAAATTTTTATGTGTT
27854977 TATT
1 TATT
27854981 AGAAAAATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTAAAATAAATTTTTATGTGTT
Found at i:27857085 original size:23 final size:23
Alignment explanation
Indices: 27857039--27857091 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27857029 TTTATGCATA
* *
27857039 CAAGTGTTAGTGGCACTACGGTG
1 CAAGTGATAGTGGCACTACAGTG
**
27857062 CAAGTGATAGTGGCACTTTAGTG
1 CAAGTGATAGTGGCACTACAGTG
27857085 CAAGTGA
1 CAAGTGA
27857092 CAGAAGCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (23 bp):
CAAGTGATAGTGGCACTACAGTG
Found at i:27872474 original size:439 final size:439
Alignment explanation
Indices: 27871656--27872533 Score: 1756
Period size: 439 Copynumber: 2.0 Consensus size: 439
27871646 GAGCTTGTAT
27871656 GATGACCATTAGTTGGATGGCCATTGCGGGATATATGAGCAGCAACTCCAGCAACTGGTGTCAAA
1 GATGACCATTAGTTGGATGGCCATTGCGGGATATATGAGCAGCAACTCCAGCAACTGGTGTCAAA
27871721 TTGTAGGCCAAATAGCGCCTAAGAACAAAAATGATGACTGTTAAAGAACATCAAGAACACTGCTG
66 TTGTAGGCCAAATAGCGCCTAAGAACAAAAATGATGACTGTTAAAGAACATCAAGAACACTGCTG
27871786 ATATTTCTTAGGTAGAAGAGGCAAAGAAAAAGAGGATGCATGTAGAGAAAATGCCAACTTCTCTT
131 ATATTTCTTAGGTAGAAGAGGCAAAGAAAAAGAGGATGCATGTAGAGAAAATGCCAACTTCTCTT
27871851 ATTCTGAATCAAGAGAAAACATTTTGAACTATTGCAAACCAACAAATAGAGCACAACATATTTAT
196 ATTCTGAATCAAGAGAAAACATTTTGAACTATTGCAAACCAACAAATAGAGCACAACATATTTAT
27871916 ATGGATTTAAAGTAGTCAACAAAGTTTGGGGAAGAAGGGGAAGCAGGGTGTTGCATGCCATTCAC
261 ATGGATTTAAAGTAGTCAACAAAGTTTGGGGAAGAAGGGGAAGCAGGGTGTTGCATGCCATTCAC
27871981 TAATCAGAGAATAAAACCCTTCAGCATACCTATCAAGGGCCATGTTTCTGGTCTGCCCGGATCCC
326 TAATCAGAGAATAAAACCCTTCAGCATACCTATCAAGGGCCATGTTTCTGGTCTGCCCGGATCCC
27872046 AGGCTGAGCACAACGAGCCATCTATCCACAAATCTTGTTCCTTTTTGGA
391 AGGCTGAGCACAACGAGCCATCTATCCACAAATCTTGTTCCTTTTTGGA
27872095 GATGACCATTAGTTGGATGGCCATTGCGGGATATATGAGCAGCAACTCCAGCAACTGGTGTCAAA
1 GATGACCATTAGTTGGATGGCCATTGCGGGATATATGAGCAGCAACTCCAGCAACTGGTGTCAAA
27872160 TTGTAGGCCAAATAGCGCCTAAGAACAAAAATGATGACTGTTAAAGAACATCAAGAACACTGCTG
66 TTGTAGGCCAAATAGCGCCTAAGAACAAAAATGATGACTGTTAAAGAACATCAAGAACACTGCTG
27872225 ATATTTCTTAGGTAGAAGAGGCAAAGAAAAAGAGGATGCATGTAGAGAAAATGCCAACTTCTCTT
131 ATATTTCTTAGGTAGAAGAGGCAAAGAAAAAGAGGATGCATGTAGAGAAAATGCCAACTTCTCTT
27872290 ATTCTGAATCAAGAGAAAACATTTTGAACTATTGCAAACCAACAAATAGAGCACAACATATTTAT
196 ATTCTGAATCAAGAGAAAACATTTTGAACTATTGCAAACCAACAAATAGAGCACAACATATTTAT
27872355 ATGGATTTAAAGTAGTCAACAAAGTTTGGGGAAGAAGGGGAAGCAGGGTGTTGCATGCCATTCAC
261 ATGGATTTAAAGTAGTCAACAAAGTTTGGGGAAGAAGGGGAAGCAGGGTGTTGCATGCCATTCAC
27872420 TAATCAGAGAATAAAACCCTTCAGCATACCTATCAAGGGCCATGTTTCTGGTCTGCCCGGATCCC
326 TAATCAGAGAATAAAACCCTTCAGCATACCTATCAAGGGCCATGTTTCTGGTCTGCCCGGATCCC
27872485 AGGCTGAGCACAACGAGCCATCTATCCACAAATCTTGTTCCTTTTTGGA
391 AGGCTGAGCACAACGAGCCATCTATCCACAAATCTTGTTCCTTTTTGGA
27872534 ATAAGTTCAC
Statistics
Matches: 439, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
439 439 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (439 bp):
GATGACCATTAGTTGGATGGCCATTGCGGGATATATGAGCAGCAACTCCAGCAACTGGTGTCAAA
TTGTAGGCCAAATAGCGCCTAAGAACAAAAATGATGACTGTTAAAGAACATCAAGAACACTGCTG
ATATTTCTTAGGTAGAAGAGGCAAAGAAAAAGAGGATGCATGTAGAGAAAATGCCAACTTCTCTT
ATTCTGAATCAAGAGAAAACATTTTGAACTATTGCAAACCAACAAATAGAGCACAACATATTTAT
ATGGATTTAAAGTAGTCAACAAAGTTTGGGGAAGAAGGGGAAGCAGGGTGTTGCATGCCATTCAC
TAATCAGAGAATAAAACCCTTCAGCATACCTATCAAGGGCCATGTTTCTGGTCTGCCCGGATCCC
AGGCTGAGCACAACGAGCCATCTATCCACAAATCTTGTTCCTTTTTGGA
Found at i:27886425 original size:108 final size:109
Alignment explanation
Indices: 27886293--27886509 Score: 409
Period size: 108 Copynumber: 2.0 Consensus size: 109
27886283 TAAAAAGGAC
27886293 TTAATCGAATAAAAATAAAAATTTAGGGGTTAAAGCTAAAAGTATCTATTTATTGTTGTCTTTTT
1 TTAATCGAATAAAAATAAAAATTTAGGGGTTAAAGCTAAAAGTATCTATTTATTGTTGTCTTTTT
*
27886358 AGTTGGAAGGTTTAAACATGCAATTAGACCACTAAATAGTTAGT
66 AGTTGGAAGGTTTAAACATGCAATTAAACCACTAAATAGTTAGT
27886402 TTAATCGAAT-AAAATAAAAATTTAGGGGTTAAAGCTAAAAGTATCTATTTATTGTTGTCTTTTT
1 TTAATCGAATAAAAATAAAAATTTAGGGGTTAAAGCTAAAAGTATCTATTTATTGTTGTCTTTTT
*
27886466 AGTTGGAAGGTTTAAACATGCAATTAAACCCCTAAATAGTTAGT
66 AGTTGGAAGGTTTAAACATGCAATTAAACCACTAAATAGTTAGT
27886510 GGATGGCTAA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
108 96 0.91
109 10 0.09
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (109 bp):
TTAATCGAATAAAAATAAAAATTTAGGGGTTAAAGCTAAAAGTATCTATTTATTGTTGTCTTTTT
AGTTGGAAGGTTTAAACATGCAATTAAACCACTAAATAGTTAGT
Found at i:27890473 original size:44 final size:44
Alignment explanation
Indices: 27890381--27890473 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
27890371 ATCTCAAGGT
* * *
27890381 CCATGTTGATAACAAAGCAATTAAGGAAGATTTGACAAAAAAGT
1 CCATGTTGATAACAAAGCAATTAAGAAAGAATTGACAAAAAAGA
* ** **
27890425 CCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAAGA
1 CCATGTTGATAACAAAGCAATTAAGAAAGAATTGACAAAAAAGA
27890469 CCATG
1 CCATG
27890474 GTTGGACCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (44 bp):
CCATGTTGATAACAAAGCAATTAAGAAAGAATTGACAAAAAAGA
Found at i:27890553 original size:50 final size:50
Alignment explanation
Indices: 27890494--27890677 Score: 251
Period size: 50 Copynumber: 3.7 Consensus size: 50
27890484 GGCAGTAAGT
*
27890494 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGGA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAA
* *
27890544 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATTGGCATAGACCGAGAA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAA
* * * **
27890594 GTGCTAGTGTAAGACCATATCTGGGACATGGCATCGGCACGGATAGAGAA
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAA
* * * * *
27890644 GAGTCAGTGTAAGTCCATGTATAGGACATGGCAT
1 GTGCCAGTGTAAGACCATGTCTGGGACATGGCAT
27890678 GTAACAGCCC
Statistics
Matches: 117, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 117 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (50 bp):
GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACCGAGAA
Found at i:27893897 original size:38 final size:39
Alignment explanation
Indices: 27893845--27894003 Score: 135
Period size: 39 Copynumber: 3.9 Consensus size: 39
27893835 ATTTGCCGGC
*
27893845 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* * *
27893883 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
* * *
27893922 TTACTG-TTACAGACTCGGCACTTTGTGTGTCGAATATTGTTACTG
1 TTACTGATT----A---GGCACTTTATGTGCCGAATACTGTTACTG
* * *
27893967 TTA-TCGATTCGGCACTTTGTGTGTCGAATACTGTTAC
1 TTACT-GATTAGGCACTTTATGTGCCGAATACTGTTAC
27894004 CATTACTGTT
Statistics
Matches: 103, Mismatches: 8, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
38 16 0.16
39 52 0.50
44 1 0.01
45 32 0.31
46 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (39 bp):
TTACTGATTAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:27893926 original size:39 final size:39
Alignment explanation
Indices: 27893845--27894049 Score: 189
Period size: 45 Copynumber: 5.0 Consensus size: 39
27893835 ATTTGCCGGC
* * * *
27893845 TTACTGATTAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
27893883 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
* *
27893922 TTACTGTTACAGACTCGGCACTTTGTGTGTCGAATATTGTTACTG
1 TTAC---T---GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
27893967 TTA-TCGATTCGGCACTTTGTGTGTCGAATACTGTTACCATTACTG
1 TTACT-GATTCGGCACTTTGTGTGTCGAATACTG------TTACTG
* * * *
27894012 TTTCAGATTCAGCACTTTGTGTGTTGAATACTGTTACT
1 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACT
27894050 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 13, Indels: 27
0.78 0.07 0.15
Matches are distributed among these distances:
38 14 0.10
39 55 0.39
41 1 0.01
42 1 0.01
45 69 0.49
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (39 bp):
TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:27893940 original size:45 final size:45
Alignment explanation
Indices: 27893872--27894049 Score: 242
Period size: 45 Copynumber: 4.1 Consensus size: 45
27893862 ATGTGCCGAC
*
27893872 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* *
27893917 TACTGTTACTGTTACAGACTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
27893962 TACTGTTA----T-C-GATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
** * * *
27894001 TACCATTACTGTTTCAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
27894046 TACT
1 TACT
27894050 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
39 33 0.28
40 1 0.01
41 1 0.01
43 1 0.01
44 1 0.01
45 80 0.68
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:27894027 original size:84 final size:84
Alignment explanation
Indices: 27893863--27894049 Score: 277
Period size: 84 Copynumber: 2.2 Consensus size: 84
27893853 TAGGCACTTA
* * **
27893863 TGTGCCGACTACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTG
1 TGTGTCGAATACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCATTACTG
*
27893928 TTACAGACTCGGCACTTTG
66 TTACAGACTCAGCACTTTG
*
27893947 TGTGTCGAATATTGTTACTGTTA-TCGATTCGGCACTTTGTGTGTCGAATACTGTTACCATTACT
1 TGTGTCGAATACTGTTACTGTTACT-GATTCGGCACTTTGTGTGTCGAATACTGTTACCATTACT
* *
27894011 GTTTCAGATTCAGCACTTTG
65 GTTACAGACTCAGCACTTTG
*
27894031 TGTGTTGAATACTGTTACT
1 TGTGTCGAATACTGTTACT
27894050 NNNNNNNNNN
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 1 0.01
84 91 0.99
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (84 bp):
TGTGTCGAATACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACCATTACTG
TTACAGACTCAGCACTTTG
Found at i:27896960 original size:23 final size:23
Alignment explanation
Indices: 27896930--27896975 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
27896920 CATGTCCTTA
27896930 GTCTAATCGGAAATGAGCAAACT
1 GTCTAATCGGAAATGAGCAAACT
27896953 GTCTAATCGGAAATGAGCAAACT
1 GTCTAATCGGAAATGAGCAAACT
27896976 AATTGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (23 bp):
GTCTAATCGGAAATGAGCAAACT
Found at i:27897806 original size:12 final size:12
Alignment explanation
Indices: 27897789--27897813 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27897779 ATGTTGACTC
27897789 AAATGAACAAAA
1 AAATGAACAAAA
27897801 AAATGAACAAAA
1 AAATGAACAAAA
27897813 A
1 A
27897814 TGGAGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.08, T:0.08
Consensus pattern (12 bp):
AAATGAACAAAA
Found at i:27897914 original size:57 final size:57
Alignment explanation
Indices: 27897810--27897925 Score: 139
Period size: 57 Copynumber: 2.0 Consensus size: 57
27897800 AAAATGAACA
* *
27897810 AAAATGGAGAAATAGGAAACATTTGAAAATGATTAAGATTTTCTCCAAAATGAAAATG
1 AAAATGGAGAAATA-GAAACATTTGAAAATGATTAAGATTTTATCCAAAAGGAAAATG
* *
27897868 AAAATGGAGAAATA-AAATCATTTGGAAATGAATGT-TG-TTTTATCCAAAAGGAAAATG
1 AAAATGGAGAAATAGAAA-CATTTGAAAATG-AT-TAAGATTTTATCCAAAAGGAAAATG
27897925 A
1 A
27897926 CCTAAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
56 3 0.06
57 30 0.59
58 17 0.33
59 1 0.02
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (57 bp):
AAAATGGAGAAATAGAAACATTTGAAAATGATTAAGATTTTATCCAAAAGGAAAATG
Found at i:27901015 original size:12 final size:12
Alignment explanation
Indices: 27900998--27901022 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27900988 ACCAAAACAG
27900998 GCTTTTAGCGGC
1 GCTTTTAGCGGC
27901010 GCTTTTAGCGGC
1 GCTTTTAGCGGC
27901022 G
1 G
27901023 TTTGTACAAA
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:0.08, C:0.24, G:0.36, T:0.32
Consensus pattern (12 bp):
GCTTTTAGCGGC
Found at i:27901115 original size:40 final size:40
Alignment explanation
Indices: 27901014--27901120 Score: 133
Period size: 40 Copynumber: 2.6 Consensus size: 40
27901004 AGCGGCGCTT
*
27901014 TTAGCGGCGTTTGTACAAAAAATGCCGCTAAAAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAAAAATCGAGCA
* ** * *
27901055 TTAGCGGCGCTTCCCAAAAAACGCCGCTAAAGATCGAGTA
1 TTAGCGGCGTTTTACAAAAAACGCCGCTAAAAATCGAGCA
*
27901095 TTAGCGGCGTTTTTCTAAAAAACGCC
1 TTAGCGGCGTTTTAC-AAAAAACGCC
27901121 ACAAAAAACC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 35 0.62
41 21 0.38
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTTACAAAAAACGCCGCTAAAAATCGAGCA
Found at i:27901223 original size:41 final size:41
Alignment explanation
Indices: 27901166--27901468 Score: 439
Period size: 41 Copynumber: 7.4 Consensus size: 41
27901156 CCTTGTGGGT
* * **
27901166 CTTTAGCGGCATTTTTCAAGAAGCGTCGCTAATGCGTGGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
*
27901207 CTTTAGCAGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
*
27901248 CTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
*
27901289 CTTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* * *
27901330 CTTTAGCGGCGTTTTTCAGGAAGCGCCGCTAATGCACTGAC
1 CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
* * * *
27901371 CTTTAGCGGCGTTTGT-AAGGAATCGCCGCTAATGTGCAAAC
1 CTTTAGCGGCGTTTTTCAA-GAAGCGCCGCTAATGCGCAGAC
*
27901412 CTTTAGC-GCGTTTTTTCATGAAGCGCCGCTAATGCGCAGAC
1 CTTTAGCGGCG-TTTTTCAAGAAGCGCCGCTAATGCGCAGAC
27901453 CTTTAGCGGCGTTTTT
1 CTTTAGCGGCGTTTTT
27901469 TGTAAAGCGC
Statistics
Matches: 235, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
40 4 0.02
41 227 0.97
42 4 0.02
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTCAAGAAGCGCCGCTAATGCGCAGAC
Found at i:27902308 original size:14 final size:15
Alignment explanation
Indices: 27902291--27902331 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
27902281 GAGTTTGGGA
*
27902291 TTAGAGGTTTAGAG-
1 TTAGAGATTTAGAGT
*
27902305 TTAGAGATTTAGGGT
1 TTAGAGATTTAGAGT
27902320 TTAGAGATTTAG
1 TTAGAGATTTAG
27902332 GGTCGAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TTAGAGATTTAGAGT
Found at i:27903434 original size:152 final size:153
Alignment explanation
Indices: 27903099--27903435 Score: 622
Period size: 153 Copynumber: 2.2 Consensus size: 153
27903089 AAAAACCAAA
*
27903099 ATAGCAAAACGGCGTCATTTTGTTCAAAATGGAAACTTTTTTGTGGCGTTTTTAATAAAAACGCC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGCGTTTTTAATAAAAACGCC
*
27903164 GCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCCGCAAAAAATAAATCAATTTATAAAA
66 GCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCAGCAAAAAATAAATCAATTTATAAAA
27903229 AAAATAAAATAAAAAATTTTAGC
131 AAAATAAAATAAAAAATTTTAGC
*
27903252 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGCGTTTTTATTAAAAACGCC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGCGTTTTTAATAAAAACGCC
27903317 GCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCAGCAAAAAATAAATCAATTTAT-AAA
66 GCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCAGCAAAAAATAAATCAATTTATAAAA
27903381 AAAATAAAATAAAAAATTTTAGC
131 AAAATAAAATAAAAAATTTTAGC
* *
27903404 ATAGCAAAACGGTGTCATTTTATTCAAAATGA
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGA
27903436 TGGAATTTAA
Statistics
Matches: 179, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
152 56 0.31
153 123 0.69
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (153 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAACTTTTTTGTGGCGTTTTTAATAAAAACGCC
GCAAAAGATAAGCAATAGCGGCGTTTTTATAAAAAGCGCAGCAAAAAATAAATCAATTTATAAAA
AAAATAAAATAAAAAATTTTAGC
Found at i:27905228 original size:86 final size:87
Alignment explanation
Indices: 27905114--27905283 Score: 216
Period size: 86 Copynumber: 2.0 Consensus size: 87
27905104 TCCTCTTATT
* * * * * *
27905114 TTATAAAAATTGAAAATTTAGTCTGGTTTTTGGTGAATATATGA-ACTTGTATTGTTAATTTGTG
1 TTATAAAAATTGAAAAGTTAGTCCGGTTTTTGGTAAATACATGATACATGAATTGTTAATTTGTG
* *
27905178 TTAATTTGTTGCATTTAAAATG
66 CTAATTTGTTGCATGTAAAATG
* * * *
27905200 TTATAAAAATTGACAAGTTGGTCCGGTTTTTGGTAAATACATTATACATGAATTGTTAATTTTTG
1 TTATAAAAATTGAAAAGTTAGTCCGGTTTTTGGTAAATACATGATACATGAATTGTTAATTTGTG
*
27905265 CTAATTTTTTGCATGTAAA
66 CTAATTTGTTGCATGTAAA
27905284 TACATGATAC
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
86 37 0.53
87 33 0.47
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (87 bp):
TTATAAAAATTGAAAAGTTAGTCCGGTTTTTGGTAAATACATGATACATGAATTGTTAATTTGTG
CTAATTTGTTGCATGTAAAATG
Found at i:27905300 original size:54 final size:54
Alignment explanation
Indices: 27905236--27905338 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
27905226 TTTTTGGTAA
*
27905236 ATACATTATACATGAATTGTTAATTTTTGCTAATTTTTTGCATGTAAATACATG
1 ATACATTATACATGAACTGTTAATTTTTGCTAATTTTTTGCATGTAAATACATG
27905290 ATACATTATACATGAACTGTTAATTTTTGCTAATTTTTTGCATGTAAAT
1 ATACATTATACATGAACTGTTAATTTTTGCTAATTTTTTGCATGTAAAT
27905339 TGTTGAAATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.47
Consensus pattern (54 bp):
ATACATTATACATGAACTGTTAATTTTTGCTAATTTTTTGCATGTAAATACATG
Found at i:27905604 original size:86 final size:86
Alignment explanation
Indices: 27905434--27905684 Score: 256
Period size: 86 Copynumber: 2.9 Consensus size: 86
27905424 TAAAAATTGA
* * * *
27905434 AAATTGAAAATTTAGTCTGCTTGTTGGTAAATGCATGAACTTGATCCATTTATTTTTGCTAATTT
1 AAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTT
* * **
27905499 GTTGCATGTAAGTTTTTATA-
66 GTTGCATATAAATCATTATAG
* *
27905519 AATATTGACAAA-TTAGTCTGATTTTTGGTAAATACATGAACTTGAACCATTGATTTTTGTTAAT
1 AA-ATTGA-AAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCTAAT
27905583 TTGTTGCATATAAATCATTATAG
64 TTGTTGCATATAAATCATTATAG
* * * ** * **
27905606 AAATTGAAGATTTAGCCCT-AATGCCGGTAAATATATGAACTATGAATAATTGATTTTTTGCTAA
1 AAATTGAAAATTTAG-TCTGATTGTTGGTAAATACATGAACT-TGAACCATTGA-TTTTTGCTAA
* *
27905670 TTTGTTTCACATAAA
63 TTTGTTGCATATAAA
27905685 CTGTTGTAAG
Statistics
Matches: 137, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
85 4 0.03
86 95 0.69
87 16 0.12
88 22 0.16
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (86 bp):
AAATTGAAAATTTAGTCTGATTGTTGGTAAATACATGAACTTGAACCATTGATTTTTGCTAATTT
GTTGCATATAAATCATTATAG
Found at i:27905740 original size:40 final size:40
Alignment explanation
Indices: 27905696--27905780 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
27905686 TGTTGTAAGA
* * *
27905696 TTGATTTGTGTTAATTTCTTGCATA-TAAATTATTGAAATG
1 TTGATTTGTGATAATTCCTTACATATTAAA-TATTGAAATG
* *
27905736 TTGATTTTTGATAATTCCTTACATATTAAATATTGAAGTG
1 TTGATTTGTGATAATTCCTTACATATTAAATATTGAAATG
27905776 TTGAT
1 TTGAT
27905781 ATTCAAGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (40 bp):
TTGATTTGTGATAATTCCTTACATATTAAATATTGAAATG
Found at i:27905871 original size:17 final size:18
Alignment explanation
Indices: 27905849--27905884 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
27905839 TCAGGTTTTG
27905849 TAAATTAAGGGGA-AAAA
1 TAAATTAAGGGGATAAAA
27905866 TAAATTAAGGGGATAAAA
1 TAAATTAAGGGGATAAAA
27905884 T
1 T
27905885 TCATAATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
TAAATTAAGGGGATAAAA
Found at i:27907965 original size:40 final size:40
Alignment explanation
Indices: 27907881--27907973 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
27907871 AAATTGTACT
* * *
27907881 TTTAGCGGCGTTTGTGATAAAGCGTCGCTAAAGATCATGTTC
1 TTTAGCGGCG--TGGGAAAAAGCGTCGCTAAAGATCATGGTC
* *
27907923 TTTAGCGGCGTGGGAAAAAGCG-CTGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTGGGAAAAAGCGTC-GCTAAAGATCATGGTC
*
27907963 TTTAACGGCGT
1 TTTAGCGGCGT
27907974 TTTTAGGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 33 0.75
42 10 0.23
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (40 bp):
TTTAGCGGCGTGGGAAAAAGCGTCGCTAAAGATCATGGTC
Found at i:27907995 original size:43 final size:43
Alignment explanation
Indices: 27907938--27908083 Score: 150
Period size: 43 Copynumber: 3.4 Consensus size: 43
27907928 CGGCGTGGGA
* * *
27907938 AAAAGCGCTGCTAAAGGTCTTGGTCTTTAACGGCGTTTTTAGG
1 AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTTTAGG
* * * * * *
27907981 AAAAGCGCCACTAAAGCTCATGTTCTATAGCAGCGTTTGT-GG
1 AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTTTAGG
* * *
27908023 TTAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCTGCGTTTTTAGA
1 -AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTTTAGG
*
27908067 AATAAACGCCGCTAAAG
1 AA-AAGCGCCGCTAAAG
27908084 TTAGCGACGC
Statistics
Matches: 80, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
42 2 0.03
43 64 0.80
44 14 0.17
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCTTGGTCTTTAGCAGCGTTTTTAGG
Found at i:27908305 original size:35 final size:36
Alignment explanation
Indices: 27908265--27908336 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
27908255 TCTAGGATCA
*
27908265 CATATCTCCA-AAGATCACCTTCCATATTTGCCAAG
1 CATATCTCCAGAAAATCACCTTCCATATTTGCCAAG
** * *
27908300 CATATCTTTAGAAAATCACTTTCCTTATTTGCCAAG
1 CATATCTCCAGAAAATCACCTTCCATATTTGCCAAG
27908336 C
1 C
27908337 TCCGGAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 8 0.26
36 23 0.74
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (36 bp):
CATATCTCCAGAAAATCACCTTCCATATTTGCCAAG
Found at i:27919694 original size:17 final size:16
Alignment explanation
Indices: 27919663--27919706 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
27919653 GATTTATTTA
27919663 ATAATATAATATCATT
1 ATAATATAATATCATT
*
27919679 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
27919696 AATTATATAAT
1 -ATAATATAAT
27919707 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Done.