Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 19 of 208
Found at i:5517762 original size:24 final size:24
Alignment explanation
Indices: 5517692--5517762 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
5517682 CAGCATATAT
5517692 GCAACATTTAAGCATCAAAATTGG
1 GCAACATTTAAGCATCAAAATTGG
* * * * * *
5517716 ACAGCATATATGTAAC-AAATTGG
1 GCAACATTTAAGCATCAAAATTGG
5517739 GCAACATTTAAGCATCAAAATTGG
1 GCAACATTTAAGCATCAAAATTGG
5517763 ACAGCATATA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (24 bp):
GCAACATTTAAGCATCAAAATTGG
Found at i:5518789 original size:43 final size:42
Alignment explanation
Indices: 5518680--5518803 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 42
5518670 AACTCGTACA
* * *
5518680 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACGTATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACAC-AATCG
* **
5518723 ATGCC-ACTGTCCCAAACAAGGTCTTACACGTAAACACAAGTCG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGTAAACACAA-TCG
*
5518766 ATGCCAACGTCTCAGACGTGGTCTTACACG-ATAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACA
5518804 TCTCGAAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 4 0.06
43 61 0.91
44 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAATCG
Found at i:5519969 original size:14 final size:15
Alignment explanation
Indices: 5519950--5519978 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5519940 TCACAAAACC
5519950 TTCACACAT-ATAAA
1 TTCACACATAATAAA
5519964 TTCACACATAATAAA
1 TTCACACATAATAAA
5519979 CACATAAAAA
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:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:5521715 original size:24 final size:24
Alignment explanation
Indices: 5521667--5521713 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5521657 ACTGGTCATA
*
5521667 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
5521691 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
5521714 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:5522787 original size:27 final size:27
Alignment explanation
Indices: 5522716--5523045 Score: 311
Period size: 27 Copynumber: 12.2 Consensus size: 27
5522706 AGAGGTCGAT
* *
5522716 AAATGATCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
5522743 AATTGACTAAAATAACCCCCGTAGGGTA
1 AAATGACCGAAAT-ACCCCCATAGGGTA
* *
5522771 AAATAACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * * *
5522798 AAATAACCAAAATACCCCTAAACGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
5522825 AAATGATCGAAATACCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * * *
5522852 AAATGATCGAAATACCTCTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * ***
5522879 AAATAACCGAAATA-ACCCATAAAATA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** * *
5522905 AAACGACTAAAATACCTCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
5522932 AAATGACCGAAATACCCCCATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
5522959 GAATGACTGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
5522986 GAATGACTGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
5523013 AAATGACCGAAATACCCCCATAGAGTA
1 AAATGACCGAAATACCCCCATAGGGTA
5523040 AAATGA
1 AAATGA
5523046 TTGTTATACT
Statistics
Matches: 251, Mismatches: 50, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
26 17 0.07
27 213 0.85
28 21 0.08
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:5522964 original size:134 final size:134
Alignment explanation
Indices: 5522780--5523026 Score: 342
Period size: 134 Copynumber: 1.8 Consensus size: 134
5522770 AAAATAACCG
*
5522780 AAATACCCCCATAAGGTAAAATAACCAAAATACCCCTAAACGGTAAAATGA-TCGAAATACCC-C
1 AAATACCCCCATAAGGTAAAATAACCAAAATACCCCCAAACGGTAAAATGACT-GAAATACCCTC
5522843 TATAGGGTAAAATGA-TCGAAATA-CCTCTATAAGGTAAAATAACCGAAATAACCCATAAAATAA
65 -ATAGGGTAAAATGACT-GAAATACCCTC-ATAAGGTAAAATAACCGAAATAACCCATAAAATAA
5522906 AACGACTA
127 AACGACTA
* * * *
5522914 AAATACCTCCATAAGGTAAAATGACCGAAATACCCCCATAA-GGTAGAATGACTGAAATACCCTC
1 AAATACCCCCATAAGGTAAAATAACCAAAATACCCCCA-AACGGTAAAATGACTGAAATACCCTC
* * *
5522978 ATAGGGTAGAATGACTGAAATACCCTCATAGGGTAAAATGACCGAAATA
65 ATAGGGTAAAATGACTGAAATACCCTCATAAGGTAAAATAACCGAAATA
5523027 CCCCCATAGA
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
134 91 0.91
135 9 0.09
ACGTcount: A:0.46, C:0.21, G:0.14, T:0.19
Consensus pattern (134 bp):
AAATACCCCCATAAGGTAAAATAACCAAAATACCCCCAAACGGTAAAATGACTGAAATACCCTCA
TAGGGTAAAATGACTGAAATACCCTCATAAGGTAAAATAACCGAAATAACCCATAAAATAAAACG
ACTA
Found at i:5523316 original size:26 final size:26
Alignment explanation
Indices: 5523280--5523360 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
5523270 TTTGCCATAT
* *
5523280 ATACTGTTACTGGCAGCTTTGCTGTG
1 ATACTGATACTGGCAGCTTTGCTGCG
*
5523306 ATACTGATACTGGCAGCTCTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* * *
5523332 ATGCT-ATTATTGGTAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
5523358 ATA
1 ATA
5523361 TTGCTATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.02
26 45 0.98
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:5523489 original size:28 final size:28
Alignment explanation
Indices: 5523449--5523542 Score: 147
Period size: 28 Copynumber: 3.4 Consensus size: 28
5523439 TATTGCACTG
*
5523449 CACTGTTACTGTATTGGGCTAAAGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
5523477 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
*
5523505 CACTGTTACTGTATTGGGCTAAGGCCTA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
5523533 CACTG-TACTG
1 CACTGTTACTG
5523543 CCACGGAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
27 7 0.11
28 53 0.85
29 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:5525648 original size:19 final size:17
Alignment explanation
Indices: 5525624--5525662 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5525614 TGGGCCACAT
5525624 TGGGCTGAAATGGGTCTTG
1 TGGGCT-AAATGGG-CTTG
*
5525643 TGGGCTCAATGGGCTTG
1 TGGGCTAAATGGGCTTG
5525660 TGG
1 TGG
5525663 TCTCCACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 6 0.32
19 6 0.32
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.31
Consensus pattern (17 bp):
TGGGCTAAATGGGCTTG
Found at i:5525912 original size:27 final size:27
Alignment explanation
Indices: 5525882--5526230 Score: 301
Period size: 27 Copynumber: 12.9 Consensus size: 27
5525872 TAAATTACTT
**
5525882 AAATACCCTTATAGGGTAAAATGATAG
1 AAATACCCCCATAGGGTAAAATGATAG
* *
5525909 AAATACCCCCGTAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGATAG
* * **
5525936 AAATACCACCATATGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGATAG
* **
5525963 AAATACCCTCAATAAAGTAAAATGATAG
1 AAATACCC-CCATAGGGTAAAATGATAG
** * * * *
5525991 AAATACCCTTATCGGGTAGAATAACCA-
1 AAATACCCCCATAGGGTAAAATGA-TAG
* *
5526018 AAATACCCCCATAGAGTAGAATGACTA-
1 AAATACCCCCATAGGGTAAAATGA-TAG
* * * *
5526045 AAATACCCCTATAAGGTAGAATGATCG
1 AAATACCCCCATAGGGTAAAATGATAG
* * **
5526072 AAATACCTCCATAAGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGATAG
* * *
5526099 AAATACCTCAATAGGGTAAAATGATTG
1 AAATACCCCCATAGGGTAAAATGATAG
* *
5526126 AAATACCCCCATATGGTAGAATGACT-G
1 AAATACCCCCATAGGGTAAAATGA-TAG
* * *
5526153 AAATACCCCCATAGGGCAAAATAATTG
1 AAATACCCCCATAGGGTAAAATGATAG
*
5526180 AAATACCCCCATAGGATAAAATGATCA-
1 AAATACCCCCATAGGGTAAAATGAT-AG
5526207 AAATACCCCCATAGGGTAAAATGA
1 AAATACCCCCATAGGGTAAAATGA
5526231 CTATTATACC
Statistics
Matches: 263, Mismatches: 53, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
26 2 0.01
27 237 0.90
28 24 0.09
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGATAG
Found at i:5526122 original size:81 final size:81
Alignment explanation
Indices: 5525873--5526230 Score: 333
Period size: 81 Copynumber: 4.4 Consensus size: 81
5525863 AGAGGTCGAT
* * ** * * * *
5525873 AAATTACTTAAATACCCTTATAGGGTAAAATGATAGAAATACCCCCGTAGGGTAAAATGATCGAA
1 AAATGACTAAAATACCCCCATAAGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCGAA
* *
5525938 ATACCACCATATGGTA
66 ATACCCCCATAGGGTA
** * * ** * * *
5525954 AAATGACCGAAATACCCTCAATAAAGTAAAATGATAGAAATACCCTTATCGGGTAGAATAACCAA
1 AAATGACTAAAATACCC-CCATAAGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCGA
*
5526019 AATACCCCCATAGAGTA
65 AATACCCCCATAGGGTA
* * * * * * *
5526036 GAATGACTAAAATACCCCTATAAGGTAGAATGATCGAAATACCTCCATAAGGTAAAATGACCGAA
1 AAATGACTAAAATACCCCCATAAGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCGAA
* *
5526101 ATACCTCAATAGGGTA
66 ATACCCCCATAGGGTA
* * * * * **
5526117 AAATGATTGAAATACCCCCATATGGTAGAATGACT-GAAATACCCCCATAGGGCAAAATAATTGA
1 AAATGACTAAAATACCCCCATAAGGTAAAATGA-TAGAAATACCCCCATAGGGTAAAATAACCGA
*
5526181 AATACCCCCATAGGATA
65 AATACCCCCATAGGGTA
*
5526198 AAATGA-TCAAAATACCCCCATAGGGTAAAATGA
1 AAATGACT-AAAATACCCCCATAAGGTAAAATGA
5526231 CTATTATACC
Statistics
Matches: 221, Mismatches: 53, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
80 1 0.00
81 156 0.71
82 64 0.29
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (81 bp):
AAATGACTAAAATACCCCCATAAGGTAAAATGATAGAAATACCCCCATAGGGTAAAATAACCGAA
ATACCCCCATAGGGTA
Found at i:5526500 original size:26 final size:26
Alignment explanation
Indices: 5526464--5526544 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
5526454 TTTGCCACAT
* * *
5526464 ATACTGTTACTGGCAGCTTTACTGTG
1 ATACTGATACTGGCAGCTTTGCTGCG
5526490 ATACTGATACTGGCAGCTTTGCTGCG
1 ATACTGATACTGGCAGCTTTGCTGCG
* *
5526516 ATGCT-ATTACTGGTAGCTTTGCTGCG
1 ATACTGA-TACTGGCAGCTTTGCTGCG
5526542 ATA
1 ATA
5526545 TTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 1 0.02
26 47 0.98
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (26 bp):
ATACTGATACTGGCAGCTTTGCTGCG
Found at i:5526687 original size:28 final size:28
Alignment explanation
Indices: 5526645--5526767 Score: 171
Period size: 28 Copynumber: 4.4 Consensus size: 28
5526635 TATTGCACTG
*
5526645 CACTGTTACTATATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
5526673 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
*
5526701 CACTGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
5526729 TACTGTTACTGTAATT-GGTTAAGGCCCA
1 CACTGTTACTGT-ATTGGGCTAAGGCCCA
5526757 CACTG-TACTGT
1 CACTGTTACTGT
5526768 CACTGAATAG
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
27 8 0.09
28 74 0.85
29 5 0.06
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:5528438 original size:23 final size:23
Alignment explanation
Indices: 5528403--5528478 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
5528393 GCACATAAGT
*
5528403 GCTA-CACTGATATGTAGCCGAA
1 GCTACCACTAATATGTAGCCGAA
*
5528425 GCTACCACTAATATGTAGCCGTA
1 GCTACCACTAATATGTAGCCGAA
*
5528448 GCTACCACTGAA-ATGTAGCTGAA
1 GCTACCACT-AATATGTAGCCGAA
5528471 GCTACCAC
1 GCTACCAC
5528479 AGATCAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
22 4 0.08
23 42 0.88
24 2 0.04
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
GCTACCACTAATATGTAGCCGAA
Found at i:5528734 original size:18 final size:17
Alignment explanation
Indices: 5528708--5528746 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
5528698 ATTTTCTTTC
5528708 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
5528725 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
5528743 CACA
1 CACA
5528747 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:5536953 original size:30 final size:30
Alignment explanation
Indices: 5536919--5536978 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
5536909 GAATTAGATC
5536919 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
* *
5536949 AAATCAAATTTTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
5536979 TATTAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:5542367 original size:49 final size:49
Alignment explanation
Indices: 5542294--5542397 Score: 156
Period size: 49 Copynumber: 2.1 Consensus size: 49
5542284 TCATGTGTTA
* * *
5542294 TAATTTTATAAATTGTTGATCTTTTGATTCAAGATATTGAACTTAATTT
1 TAATTTTATAAATTGTTCACCTTTTGATTCAAGATATTAAACTTAATTT
*
5542343 TAATTTTATAAAGTT-TTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAA-TTGTTCACCTTTTGATTCAAGATATTAAACTTAATTT
5542392 TAATTT
1 TAATTT
5542398 ATTTTTTTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
49 48 0.96
50 2 0.04
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAATTGTTCACCTTTTGATTCAAGATATTAAACTTAATTT
Found at i:5543823 original size:21 final size:21
Alignment explanation
Indices: 5543782--5543824 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5543772 AATAAAGTAG
*
5543782 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
5543803 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
5543824 A
1 A
5543825 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:5543925 original size:120 final size:120
Alignment explanation
Indices: 5543789--5544148 Score: 688
Period size: 120 Copynumber: 3.0 Consensus size: 120
5543779 TAGATTATAT
5543789 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
5543853 AATTTTATTAAATTATATATATTTT-TTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATAT-TTTTATTAAATTATATTTAATAATAATTATTTTAA
5543908 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
5543973 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
5544028 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
5544093 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
5544148 A
1 A
5544149 ATATGATTAA
Statistics
Matches: 238, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
119 9 0.04
120 229 0.96
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAA
Found at i:5544379 original size:45 final size:44
Alignment explanation
Indices: 5544288--5544380 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5544278 ATTACAACAT
5544288 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
*
5544332 CATTCCATTCAACCAAACA-ATTA-AATTATTATTACGCCTCTATTC
1 CATTCCATTCAACCAAACACA--AGAA-TACTATTACGCCTCTATTC
5544377 CATT
1 CATT
5544381 ACACCTCTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 1 0.02
44 21 0.47
45 23 0.51
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTC
Found at i:5544387 original size:16 final size:16
Alignment explanation
Indices: 5544362--5544399 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
5544352 TTAAATTATT
*
5544362 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
5544378 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
5544394 ATTACA
1 ATTACA
5544400 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:5546130 original size:18 final size:20
Alignment explanation
Indices: 5546095--5546135 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
5546085 ATATTATTTT
*
5546095 AAAATATATATAATACATCA
1 AAAATATATATAAAACATCA
*
5546115 AAAATAT-TA-AAAACATTA
1 AAAATATATATAAAACATCA
5546133 AAA
1 AAA
5546136 TAAATGTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATATATATAAAACATCA
Found at i:5550350 original size:20 final size:20
Alignment explanation
Indices: 5550304--5550350 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5550294 GCTTTTGAAA
*
5550304 AATAATTTTTAAAAAATATT
1 AATATTTTTTAAAAAATATT
5550324 AAT-TTTTTTAAAAAA-AGTT
1 AATATTTTTTAAAAAATA-TT
5550343 AATATTTT
1 AATATTTT
5550351 CTGGTGTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATTTTTTAAAAAATATT
Found at i:5552168 original size:19 final size:18
Alignment explanation
Indices: 5552128--5552168 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
5552118 AATGCCTCTA
5552128 AATAATAACAAAATTAAC
1 AATAATAACAAAATTAAC
5552146 AATAA-AACAAAAGTTATAC
1 AATAATAACAAAA-TTA-AC
5552165 AATA
1 AATA
5552169 TCCAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAATAACAAAATTAAC
Found at i:5555071 original size:21 final size:21
Alignment explanation
Indices: 5555046--5555098 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
5555036 TTTAATTTAT
5555046 ATAAATTATAAATAACATAAA
1 ATAAATTATAAATAACATAAA
* * * **
5555067 ATAAAATAAAAATTACATATT
1 ATAAATTATAAATAACATAAA
5555088 ATAAATT-TAAA
1 ATAAATTATAAA
5555099 AATGAATAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAATTATAAATAACATAAA
Found at i:5561472 original size:23 final size:23
Alignment explanation
Indices: 5561446--5561528 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
5561436 GCGCATTCTA
* * *
5561446 TTTGGCCTGTGTGGTGTATTTTG
1 TTTGGCCTTTGTGGCGTAATTTG
*
5561469 TTTGGCCTTTGTGGCGTACATATG
1 TTTGGCCTTTGTGGCGTA-ATTTG
5561493 TTTGGCCTTTGTGGCGTAATTTG
1 TTTGGCCTTTGTGGCGTAATTTG
* *
5561516 TTTAGCCTCTGTG
1 TTTGGCCTTTGTG
5561529 ATGTACCCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 31 0.60
24 21 0.40
ACGTcount: A:0.08, C:0.14, G:0.30, T:0.47
Consensus pattern (23 bp):
TTTGGCCTTTGTGGCGTAATTTG
Found at i:5566710 original size:19 final size:20
Alignment explanation
Indices: 5566688--5566728 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5566678 GATTAATAAA
5566688 AATTT-AAATATATAA-TTTT
1 AATTTCAAATA-ATAACTTTT
5566707 AATTTCAAATAATAACTTTT
1 AATTTCAAATAATAACTTTT
5566727 AA
1 AA
5566729 ATGTGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTCAAATAATAACTTTT
Found at i:5569295 original size:27 final size:27
Alignment explanation
Indices: 5569265--5569329 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
5569255 ACAACAATTC
**
5569265 CAACAGCAACAACTCCTCCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
** *
5569292 CAACAGCAACTGCAACTTCAACAACAA
1 CAACAGCAACAACAACTCCAACAACAA
*
5569319 CAAGAGCAACA
1 CAACAGCAACA
5569330 TGAACAACAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.49, C:0.35, G:0.08, T:0.08
Consensus pattern (27 bp):
CAACAGCAACAACAACTCCAACAACAA
Found at i:5569327 original size:21 final size:21
Alignment explanation
Indices: 5569283--5569338 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
5569273 ACAACTCCTC
* * *
5569283 CAACAACAACAACAGCAACTG
1 CAACATCAACAACAACAACAG
* *
5569304 CAACTTCAACAACAACAAGAG
1 CAACATCAACAACAACAACAG
*
5569325 CAACATGAACAACA
1 CAACATCAACAACA
5569339 GTTACAGTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.54, C:0.30, G:0.09, T:0.07
Consensus pattern (21 bp):
CAACATCAACAACAACAACAG
Found at i:5571018 original size:17 final size:18
Alignment explanation
Indices: 5570981--5571018 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5570971 TTTCATTTTC
*
5570981 TTTTGTTAAAAATAAAGA
1 TTTTGTTAAAAATAAAAA
*
5570999 TTTTTTTAAAAA-AAAAA
1 TTTTGTTAAAAATAAAAA
5571016 TTT
1 TTT
5571019 AAGTTAGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
TTTTGTTAAAAATAAAAA
Found at i:5582695 original size:22 final size:23
Alignment explanation
Indices: 5582649--5582695 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5582639 TCTTAAATTG
* *
5582649 TTTTGAGTTTAATTTCAAATCTA
1 TTTTGAGTTTAAATTCAAATATA
*
5582672 TTTTGA-TTTAAATTCGAATATA
1 TTTTGAGTTTAAATTCAAATATA
5582694 TT
1 TT
5582696 GTAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (23 bp):
TTTTGAGTTTAAATTCAAATATA
Found at i:5590253 original size:13 final size:13
Alignment explanation
Indices: 5590209--5590258 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
5590199 ATTTAATAAT
*
5590209 ATTTTAATTGATA
1 ATTTTAATTTATA
* *
5590222 ATTTTTAAAATTATT
1 A-TTTT-AATTTATA
5590237 ATTTTAATTTATA
1 ATTTTAATTTATA
5590250 ATTTTAATT
1 ATTTTAATT
5590259 AAAAAATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 16 0.53
14 8 0.27
15 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
ATTTTAATTTATA
Found at i:5591428 original size:60 final size:60
Alignment explanation
Indices: 5591355--5591474 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
5591345 ATGTGTTATT
5591355 ATGATTAATGAATTTCAAACCATACATATATTTATTTATTATATATTATTTTTAAACACA
1 ATGATTAATGAATTTCAAACCATACATATATTTATTTATTATATATTATTTTTAAACACA
*
5591415 ATGATTAATGAATTTCAAATCATACATATATTTATTTATTATATATTATTTTTAAACACA
1 ATGATTAATGAATTTCAAACCATACATATATTTATTTATTATATATTATTTTTAAACACA
5591475 CATCTCATGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (60 bp):
ATGATTAATGAATTTCAAACCATACATATATTTATTTATTATATATTATTTTTAAACACA
Found at i:5593541 original size:28 final size:28
Alignment explanation
Indices: 5593504--5593560 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
5593494 AGTAGTACGC
5593504 TGGGACAGTAAACAC-AGATAAAGTTTGT
1 TGGGACAGTAAACACGAGATAAA-TTTGT
*
5593532 TGGGACAGTAAACACGAGGTAAATTTGT
1 TGGGACAGTAAACACGAGATAAATTTGT
5593560 T
1 T
5593561 AGGAGGCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (28 bp):
TGGGACAGTAAACACGAGATAAATTTGT
Found at i:5594557 original size:35 final size:35
Alignment explanation
Indices: 5594504--5594573 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
5594494 GACCTAGTTA
*
5594504 AAGAACTCACTAATTTCATTTGAACTTACAGTAGT
1 AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
*
5594539 AAGAACTCACTTAGTTCATTTGAACTTACAGTAGT
1 AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
5594574 GTGGCTGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (35 bp):
AAGAACTCACTAAGTTCATTTGAACTTACAGTAGT
Found at i:5595747 original size:23 final size:23
Alignment explanation
Indices: 5595717--5595765 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5595707 GAGTAGGGAA
5595717 ACCAACAAACTGGTAAGGTTCTT
1 ACCAACAAACTGGTAAGGTTCTT
5595740 ACCAACAAACTGGTAAGGTTCTT
1 ACCAACAAACTGGTAAGGTTCTT
5595763 ACC
1 ACC
5595766 CTTTCTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (23 bp):
ACCAACAAACTGGTAAGGTTCTT
Found at i:5595969 original size:15 final size:15
Alignment explanation
Indices: 5595949--5595980 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5595939 TAAACTATTG
5595949 AAATAATGAAGCTTC
1 AAATAATGAAGCTTC
5595964 AAATAATGAAGCTTC
1 AAATAATGAAGCTTC
5595979 AA
1 AA
5595981 GTGAGTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (15 bp):
AAATAATGAAGCTTC
Found at i:5596474 original size:58 final size:58
Alignment explanation
Indices: 5596382--5596516 Score: 164
Period size: 58 Copynumber: 2.3 Consensus size: 58
5596372 ATACGTAGCT
* * * * *
5596382 TAAGACCATGGATGAAAGCCGCCATGACAGCATGGTACAAGGTAAAATGTATATGGCG
1 TAAGACCATAGATGAAAGACGCCATGACAGCATGGTACAAAGTAAAAGGTATATGACG
* * *
5596440 TAAGACCATAGATGAAAGACGCCATGGC-GACATGGTACAAAGTATAAGGTATATGATG
1 TAAGACCATAGATGAAAGACGCCATGACAG-CATGGTACAAAGTAAAAGGTATATGACG
* *
5596498 TAAAACCATAGACGAAAGA
1 TAAGACCATAGATGAAAGA
5596517 TGTTATGGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
57 1 0.02
58 65 0.98
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.19
Consensus pattern (58 bp):
TAAGACCATAGATGAAAGACGCCATGACAGCATGGTACAAAGTAAAAGGTATATGACG
Found at i:5597884 original size:15 final size:16
Alignment explanation
Indices: 5597847--5597885 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5597837 TTATTTTTTA
*
5597847 TTTTATTATTAGATTG
1 TTTTATTATTAGACTG
*
5597863 TTTTATTTTTAGACTG
1 TTTTATTATTAGACTG
5597879 -TTTATTA
1 TTTTATTA
5597886 GCAGTTGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (16 bp):
TTTTATTATTAGACTG
Found at i:5604804 original size:2 final size:2
Alignment explanation
Indices: 5604797--5604828 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
5604787 CGTTGACCCA
*
5604797 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5604829 TCCTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5605671 original size:18 final size:18
Alignment explanation
Indices: 5605648--5605683 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5605638 AATTTTTATG
5605648 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
5605666 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
5605684 CTTTAGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.50, T:0.39
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:5606122 original size:27 final size:26
Alignment explanation
Indices: 5606091--5606144 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5606081 CGATATTGGA
*
5606091 TCAAGTGATGAGAAGTTTGATTTTCCT
1 TCAAGGGATGAG-AGTTTGATTTTCCT
* **
5606118 TCAAGGGTTTCGAGTTTGATTTTCCT
1 TCAAGGGATGAGAGTTTGATTTTCCT
5606144 T
1 T
5606145 TGCCCCTTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.20, C:0.13, G:0.22, T:0.44
Consensus pattern (26 bp):
TCAAGGGATGAGAGTTTGATTTTCCT
Found at i:5608328 original size:21 final size:18
Alignment explanation
Indices: 5608277--5608340 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
5608267 AAAAACTCAT
5608277 TAAAAATATATAA-AAATTA
1 TAAAAA-AT-TAATAAATTA
*
5608296 T-TAAAATTAATAAATATTA
1 TAAAAAATTAAT-AA-ATTA
5608315 TAAAAAAGTTAATAAATTA
1 TAAAAAA-TTAATAAATTA
5608334 TAAAAAA
1 TAAAAAA
5608341 AACATAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.08
17 2 0.05
18 5 0.13
19 17 0.45
20 6 0.16
21 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAAAAATTAATAAATTA
Found at i:5608333 original size:19 final size:20
Alignment explanation
Indices: 5608298--5608340 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5608288 AAAAATTATT
5608298 AAAATTAATAAATATTATAA
1 AAAATTAATAAATATTATAA
5608318 AAAAGTTAAT-AA-ATTATAA
1 AAAA-TTAATAAATATTATAA
5608337 AAAA
1 AAAA
5608341 AACATAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 6 0.27
21 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTAATAAATATTATAA
Found at i:5608341 original size:21 final size:20
Alignment explanation
Indices: 5608298--5608342 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5608288 AAAAATTATT
5608298 AAAATTAATAAATATTATAAA
1 AAAATTAATAAATATTA-AAA
*
5608319 AAAGTTAATAAAT-TATAAAA
1 AAAATTAATAAATAT-TAAAA
5608339 AAAA
1 AAAA
5608343 CATAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATTAATAAATATTAAAA
Found at i:5608377 original size:9 final size:9
Alignment explanation
Indices: 5608277--5608378 Score: 62
Period size: 9 Copynumber: 10.7 Consensus size: 9
5608267 AAAAACTCAT
5608277 TAAAAATATA
1 TAAAAAT-TA
5608287 TAAAAATTA
1 TAAAAATTA
*
5608296 TTAAAATTAA
1 TAAAAATT-A
*
5608306 TAAATATTA
1 TAAAAATTA
5608315 TAAAAAAGTTA
1 T-AAAAA-TTA
*
5608326 -ATAAATTA
1 TAAAAATTA
**
5608334 TAAAAAAAACA
1 T--AAAAATTA
*
5608345 TAAAACTTA
1 TAAAAATTA
* *
5608354 TAAACATGA
1 TAAAAATTA
5608363 TAAAAAATTA
1 T-AAAAATTA
5608373 TAAAAA
1 TAAAAA
5608379 AAATCTAATA
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
8 3 0.04
9 32 0.46
10 25 0.36
11 9 0.13
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5608736 original size:13 final size:13
Alignment explanation
Indices: 5608718--5608744 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5608708 TCGAACTGGT
5608718 CGAATAGGCAAAG
1 CGAATAGGCAAAG
5608731 CGAATAGGCAAAG
1 CGAATAGGCAAAG
5608744 C
1 C
5608745 AATGGCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.19, G:0.30, T:0.07
Consensus pattern (13 bp):
CGAATAGGCAAAG
Found at i:5609153 original size:16 final size:16
Alignment explanation
Indices: 5609132--5609191 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
5609122 TAAATGATTT
5609132 TTTTTATAATTTATAG
1 TTTTTATAATTTATAG
5609148 TTTTTATAATTTTTAATAG
1 TTTTTATAA--TTT-ATAG
* *
5609167 TTTTGATATTTTTATA-
1 TTTTTATA-ATTTATAG
5609183 TTTTTATAA
1 TTTTTATAA
5609192 GCTTTTATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 16 0.44
17 3 0.08
18 6 0.17
19 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (16 bp):
TTTTTATAATTTATAG
Found at i:5609300 original size:29 final size:30
Alignment explanation
Indices: 5609256--5609322 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
5609246 TTATAAAATC
5609256 TTTTATAATATATTATAACTTATTAGATT-T
1 TTTTATAATATATTATAACTT-TTAGATTAT
**
5609286 TTTTATAATAT-TTATAACTTTTTTATTAT
1 TTTTATAATATATTATAACTTTTAGATTAT
5609315 TTTTATAA
1 TTTTATAA
5609323 GTTTATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 5 0.15
29 18 0.53
30 11 0.32
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTATAATATATTATAACTTTTAGATTAT
Found at i:5609373 original size:10 final size:9
Alignment explanation
Indices: 5609132--5609386 Score: 101
Period size: 10 Copynumber: 27.0 Consensus size: 9
5609122 TAAATGATTT
5609132 TTTTTATAA
1 TTTTTATAA
*
5609141 --TTTATAG
1 TTTTTATAA
5609148 TTTTTATAA
1 TTTTTATAA
*
5609157 TTTTTAATAG
1 TTTTT-ATAA
*
5609167 TTTTGAT-A
1 TTTTTATAA
5609175 TTTTTAT-A
1 TTTTTATAA
5609183 TTTTTATAA
1 TTTTTATAA
* *
5609192 GCTTTTATGAC
1 -TTTTTAT-AA
5609203 TTTTTATAA
1 TTTTTATAA
5609212 GTTTTTATATA
1 -TTTTTATA-A
* *
5609223 TTTTAAGTATG
1 TTTTTA-TA-A
5609234 TTTTTATTAAA
1 TTTTTA-T-AA
* *
5609245 TTTATAAAA
1 TTTTTATAA
5609254 TCTTTTATAA
1 T-TTTTATAA
*
5609264 TATATTATAA
1 T-TTTTATAA
* * *
5609274 CTTATTAGATT
1 -TTTTTATA-A
5609285 TTTTTATAA
1 TTTTTATAA
*
5609294 TATTTATAA
1 TTTTTATAA
*
5609303 CTTTTTTATTA
1 --TTTTTATAA
5609314 TTTTTATAA
1 TTTTTATAA
*
5609323 GTTTATATTAA
1 -TTTTTA-TAA
* *
5609334 TGTTAAT-A
1 TTTTTATAA
5609342 TTTGTTA-AA
1 TTT-TTATAA
**
5609351 TTTAAATAA
1 TTTTTATAA
5609360 -TTTTATAA
1 TTTTTATAA
*
5609368 TTTTTTATGA
1 -TTTTTATAA
5609378 TTTTTATAA
1 TTTTTATAA
5609387 GAAAATATAA
Statistics
Matches: 182, Mismatches: 42, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.03
8 24 0.13
9 51 0.28
10 73 0.40
11 27 0.15
12 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5610540 original size:18 final size:18
Alignment explanation
Indices: 5610512--5610556 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5610502 CGTTCGTTTC
*
5610512 CAAAACATTATTC-ATTT
1 CAAAACGTTATTCAATTT
*
5610529 ACAAATCGTTATTCAATTT
1 -CAAAACGTTATTCAATTT
5610548 CAAAACGTT
1 CAAAACGTT
5610557 TTCTTATTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCAATTT
Found at i:5611097 original size:23 final size:24
Alignment explanation
Indices: 5611053--5611097 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5611043 AAAACCCTAC
*
5611053 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
5611077 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
5611098 GTGGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:5616041 original size:25 final size:24
Alignment explanation
Indices: 5615982--5616050 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 24
5615972 AGGAGAGGCG
* *
5615982 TTTTTCAATATTAATATAATTATT
1 TTTTTAAATATTAATATAAATATT
*
5616006 TTTATTTAATATTAATATAAAATATT
1 TTT-TTAAATATTAATAT-AAATATT
5616032 TTTTTAAATACATTAATAT
1 TTTTTAAAT--ATTAATAT
5616051 CCAGTTATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 3 0.08
25 18 0.47
26 9 0.24
27 8 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTAAATATTAATATAAATATT
Found at i:5618751 original size:15 final size:15
Alignment explanation
Indices: 5618727--5618756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5618717 CCAGCAAAAT
*
5618727 ATTTTTAACTTGTAA
1 ATTTTCAACTTGTAA
5618742 ATTTTCAACTTGTAA
1 ATTTTCAACTTGTAA
5618757 GTTGTGTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTTTCAACTTGTAA
Found at i:5623553 original size:43 final size:43
Alignment explanation
Indices: 5623506--5623601 Score: 156
Period size: 43 Copynumber: 2.2 Consensus size: 43
5623496 TCCTAAACAG
5623506 GGTCTTACACAAAAATACAAGTCGACGCCAACGCCCCAGACGT
1 GGTCTTACACAAAAATACAAGTCGACGCCAACGCCCCAGACGT
** * *
5623549 GGTCTTACATGAAAATACAAGTCGATGCCAACGTCCCAGACGT
1 GGTCTTACACAAAAATACAAGTCGACGCCAACGCCCCAGACGT
5623592 GGTCTTACAC
1 GGTCTTACAC
5623602 GAACGTATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (43 bp):
GGTCTTACACAAAAATACAAGTCGACGCCAACGCCCCAGACGT
Found at i:5623596 original size:86 final size:86
Alignment explanation
Indices: 5623444--5623601 Score: 203
Period size: 86 Copynumber: 1.8 Consensus size: 86
5623434 AGCTCGTACA
* * * ** *
5623444 ACGCCAATGTCCCAGACGTGGTCTTACATGTAATCACAAATCAATGCCATTGTCCTAAACAGGGT
1 ACGCCAACGCCCCAGACGTGGTCTTACATGAAATCACAAATCAATGCCAACGTCCCAAACAGGGT
5623509 CTTACACAAAAATACAAGTCG
66 CTTACACAAAAATACAAGTCG
* * *
5623530 ACGCCAACGCCCCAGACGTGGTCTTACATGAAAAT-ACAAGTCGATGCCAACGTCCCAGAC-GTG
1 ACGCCAACGCCCCAGACGTGGTCTTACATG-AAATCACAAATCAATGCCAACGTCCCAAACAG-G
5623593 GTCTTACAC
64 GTCTTACAC
5623602 GAACGTATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
85 1 0.02
86 57 0.93
87 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (86 bp):
ACGCCAACGCCCCAGACGTGGTCTTACATGAAATCACAAATCAATGCCAACGTCCCAAACAGGGT
CTTACACAAAAATACAAGTCG
Found at i:5630373 original size:94 final size:93
Alignment explanation
Indices: 5630210--5630508 Score: 340
Period size: 94 Copynumber: 3.1 Consensus size: 93
5630200 TCTGATCAGC
*
5630210 GATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGATAAGTGATAAGC
1 GATAAGTGATAAGT-GTAGCTTTAGCTACACTTATCTG---A-T--C-AGTGATAAGTGATAAGT
* *
5630275 GGTAGCTTGGCTACACTTATTTGATCAGTGACAAGT
58 GGTAGCTTAGCTACACTTATCTGATCAGTGACAAGT
* *
5630311 GATAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGATAAGTGATAAGTGGTAGTT
1 GATAAGTGATAAGTG-TAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGATAAGTGGTAGCT
5630376 TAGCTACACTTATCTGATCAGTGACAAGT
65 TAGCTACACTTATCTGATCAGTGACAAGT
5630405 GATAA--G-T--G-GTAGCTTTAGCTACACTTATCTGATCAGTGGCAAGTGACAAGTGATAAGTG
1 GATAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAGT-G--A-T---AAGTGATAAGTG
* * *
5630464 GTAGCTTAGCTACACTTATCTAATCAGGGATAAGT
59 GTAGCTTAGCTACACTTATCTGATCAGTGACAAGT
5630499 GATAAGTGAT
1 GATAAGTGAT
5630509 CATACGTAAG
Statistics
Matches: 177, Mismatches: 10, Indels: 26
0.83 0.05 0.12
Matches are distributed among these distances:
87 27 0.15
88 2 0.01
89 1 0.01
90 1 0.01
91 2 0.01
92 1 0.01
94 102 0.58
95 1 0.01
96 1 0.01
97 2 0.01
98 1 0.01
100 1 0.01
101 35 0.20
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (93 bp):
GATAAGTGATAAGTGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGATAAGTGGTAGCTT
AGCTACACTTATCTGATCAGTGACAAGT
Found at i:5632109 original size:9 final size:9
Alignment explanation
Indices: 5632095--5632131 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
5632085 TGAAGAAACA
5632095 TCATCGTCC
1 TCATCGTCC
5632104 TCATCG-CC
1 TCATCGTCC
5632112 GTCATCGTCC
1 -TCATCGTCC
5632122 TCATCGTCC
1 TCATCGTCC
5632131 T
1 T
5632132 TTTTGCAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.11, C:0.43, G:0.14, T:0.32
Consensus pattern (9 bp):
TCATCGTCC
Found at i:5634329 original size:20 final size:20
Alignment explanation
Indices: 5634304--5634344 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5634294 TTGTACTGGG
5634304 ATATCAGAGAAAGAAAAAAT
1 ATATCAGAGAAAGAAAAAAT
5634324 ATATCAGAGAAAGAAAAAAT
1 ATATCAGAGAAAGAAAAAAT
5634344 A
1 A
5634345 AAACAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (20 bp):
ATATCAGAGAAAGAAAAAAT
Found at i:5635080 original size:16 final size:16
Alignment explanation
Indices: 5635059--5635094 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5635049 TGGCACCGAT
5635059 GCCGTCGTGTACGGTG
1 GCCGTCGTGTACGGTG
5635075 GCCGTCGTGTACGGTG
1 GCCGTCGTGTACGGTG
5635091 GCCG
1 GCCG
5635095 GCGAAGGTAA
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:0.06, C:0.28, G:0.44, T:0.22
Consensus pattern (16 bp):
GCCGTCGTGTACGGTG
Found at i:5637208 original size:17 final size:17
Alignment explanation
Indices: 5637186--5637220 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5637176 AAACTAATTT
5637186 ATTTATATCGAATTTGC
1 ATTTATATCGAATTTGC
5637203 ATTTATATCGAATTTGC
1 ATTTATATCGAATTTGC
5637220 A
1 A
5637221 GACATCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
ATTTATATCGAATTTGC
Found at i:5656459 original size:7 final size:7
Alignment explanation
Indices: 5656447--5656485 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
5656437 TGTGTCTCAT
5656447 TTTTTTA
1 TTTTTTA
5656454 TTTTTTA
1 TTTTTTA
5656461 TTTTTTA
1 TTTTTTA
*
5656468 TTTTTGAA
1 TTTTT-TA
5656476 TTTTTT-
1 TTTTTTA
5656482 TTTT
1 TTTT
5656486 CGCCAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 4 0.14
7 19 0.66
8 6 0.21
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:5657175 original size:20 final size:19
Alignment explanation
Indices: 5657128--5657177 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
5657118 TTACAAAAAT
*
5657128 AAAATA-AAATAATTTTTA
1 AAAATATAAATTATTTTTA
* *
5657146 AAATTTTAAATTATTTATTA
1 AAAATATAAATTATTT-TTA
5657166 AAAATATAAATT
1 AAAATATAAATT
5657178 TACATCATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATATAAATTATTTTTA
Found at i:5657940 original size:6 final size:7
Alignment explanation
Indices: 5657914--5657939 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5657904 TTTAAAATAC
5657914 TTTTTTA
1 TTTTTTA
5657921 TTTTTTA
1 TTTTTTA
5657928 TTTTTTA
1 TTTTTTA
5657935 TTTTT
1 TTTTT
5657940 AAAATAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:5657961 original size:33 final size:33
Alignment explanation
Indices: 5657900--5657962 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
5657890 AATTTTAAAA
** * *
5657900 TATTTTTAAAATACTTTTTTATTTTTTATTTTT
1 TATTTTTAAAATAAATTTTTAGTGTTTATTTTT
*
5657933 TATTTTTAAAATAAATTTTTGGTGTTTATT
1 TATTTTTAAAATAAATTTTTAGTGTTTATT
5657963 AAAAAATGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (33 bp):
TATTTTTAAAATAAATTTTTAGTGTTTATTTTT
Found at i:5659657 original size:91 final size:91
Alignment explanation
Indices: 5659496--5659669 Score: 244
Period size: 91 Copynumber: 1.9 Consensus size: 91
5659486 CTTTGTTTTT
* * * *
5659496 TTTTTTTGCACTCATTTGGGTATTTGAACTTTCAAAATGCATTAAAAAAATCCCTCAAACCATTT
1 TTTTTTTGCACCCAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAATCCCTCAAACCATTT
* **
5659561 CAAAAAATTCAATTAAGCTCCTACTA
66 AAAAAAAAGCAATTAAGCTCCTACTA
*
5659587 TTTTTTTGCACCCAATTGGGTACTTGAACTTTCAAAATACATT-AAAAAGTCCCTCAAACTC-TT
1 TTTTTTTGCACCCAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAATCCCTCAAAC-CATT
5659650 TAAAAAAAAAGCAATTAAGC
65 T-AAAAAAAAGCAATTAAGC
5659670 CCCTGCTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
90 18 0.25
91 55 0.75
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.34
Consensus pattern (91 bp):
TTTTTTTGCACCCAATTGGGTACTTGAACTTTCAAAATACATTAAAAAAATCCCTCAAACCATTT
AAAAAAAAGCAATTAAGCTCCTACTA
Found at i:5659803 original size:20 final size:19
Alignment explanation
Indices: 5659767--5659851 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 19
5659757 AAATTAGAAG
*
5659767 ATATATATAAATAGTAAAA
1 ATATATAAAAATAGTAAAA
* *
5659786 ATATATACAAAATTGTAATA
1 ATATATA-AAAATAGTAAAA
* *
5659806 TTTTATAAAAATAGTAAAA
1 ATATATAAAAATAGTAAAA
* * *
5659825 AAATAAAAAAATA-TAGAA
1 ATATATAAAAATAGTAAAA
5659843 ATATA-AAAA
1 ATATATAAAA
5659852 CTATAAATTT
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
17 4 0.08
18 8 0.15
19 26 0.50
20 14 0.27
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (19 bp):
ATATATAAAAATAGTAAAA
Found at i:5659848 original size:18 final size:19
Alignment explanation
Indices: 5659812--5659851 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5659802 AATATTTTAT
5659812 AAAAATAGTAAAAAAATAA
1 AAAAATAGTAAAAAAATAA
* *
5659831 AAAAATA-TAGAAATATAA
1 AAAAATAGTAAAAAAATAA
5659849 AAA
1 AAA
5659852 CTATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAATAGTAAAAAAATAA
Found at i:5660133 original size:18 final size:16
Alignment explanation
Indices: 5660110--5660161 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 16
5660100 ATTTTTACGG
5660110 TTTTATAAAAATTCTAAT
1 TTTTAT-AAAATT-TAAT
*
5660128 TTTTATTAAATTTAATT
1 TTTTATAAAATTTAA-T
5660145 TTTTATTAAAATTTAAT
1 TTTTA-TAAAATTTAAT
5660162 AATTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.10
17 12 0.40
18 15 0.50
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTATAAAATTTAAT
Found at i:5660138 original size:17 final size:17
Alignment explanation
Indices: 5660118--5660161 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
5660108 GGTTTTATAA
5660118 AAATTCTAA-TTTTTATT
1 AAATT-TAATTTTTTATT
5660135 AAATTTAATTTTTTATT
1 AAATTTAATTTTTTATT
5660152 AAAATTTAAT
1 -AAATTTAAT
5660162 AATTATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.12
17 13 0.52
18 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATTTAATTTTTTATT
Found at i:5660319 original size:91 final size:92
Alignment explanation
Indices: 5660225--5660398 Score: 221
Period size: 91 Copynumber: 1.9 Consensus size: 92
5660215 CTTAATTACT
* * *
5660225 TTTTTTTAA-AAATTTGAGGGTC-TTTTTGATG-ATTTTGAAAGTTCAAGTACCCAATTGAGTG-
1 TTTTTTTAAGAAATTTAAGGG-CATTTTTGATGCATTTAGAAAGTTCAAGTACCCAACTGAGTGC
* *
5660286 AAAAAAAGTAGGGGCTTAATTGTTTTTA
65 AAAAAAAGGACGGGCTTAATTGTTTTTA
* * * * *
5660314 TTTTTTTAAGAAGTTTAAGGGCATTTTTGATGCATTTAGAAAGTTTAAGTGCTCAACTGGGTGCA
1 TTTTTTTAAGAAATTTAAGGGCATTTTTGATGCATTTAGAAAGTTCAAGTACCCAACTGAGTGCA
5660379 AAAAAAGGACGGGCTTAATT
66 AAAAAAGGACGGGCTTAATT
5660399 ACTTTTCTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
89 10 0.14
90 18 0.25
91 24 0.34
92 19 0.27
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.39
Consensus pattern (92 bp):
TTTTTTTAAGAAATTTAAGGGCATTTTTGATGCATTTAGAAAGTTCAAGTACCCAACTGAGTGCA
AAAAAAGGACGGGCTTAATTGTTTTTA
Found at i:5663380 original size:16 final size:17
Alignment explanation
Indices: 5663359--5663391 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5663349 AAATGATCAT
*
5663359 CTCTCG-TTTTTTTTTC
1 CTCTCGCTTTTCTTTTC
5663375 CTCTCGCTTTTCTTTTC
1 CTCTCGCTTTTCTTTTC
5663392 TACCAAACAC
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:0.00, C:0.30, G:0.06, T:0.64
Consensus pattern (17 bp):
CTCTCGCTTTTCTTTTC
Found at i:5663801 original size:16 final size:16
Alignment explanation
Indices: 5663764--5663817 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
5663754 TAAAGTGGAA
*
5663764 AGAAAATTGGAAGG-T
1 AGAAAATTAGAAGGAT
* *
5663779 TGAAAAATTAGAGGGAT
1 AG-AAAATTAGAAGGAT
5663796 AGAAAATTAGAAGGAT
1 AGAAAATTAGAAGGAT
*
5663812 GGAAAA
1 AGAAAA
5663818 CATAATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 1 0.03
16 28 0.90
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.19
Consensus pattern (16 bp):
AGAAAATTAGAAGGAT
Found at i:5677813 original size:30 final size:30
Alignment explanation
Indices: 5677774--5677842 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
5677764 AAATTACACC
* *
5677774 AACAATCACTCAATTTT-GAGAAAATAATAA
1 AACAGTCACTCAATTTTAG-GAAAATAACAA
5677804 AACAGTCACTCAATTTTAGGAAAATAACAA
1 AACAGTCACTCAATTTTAGGAAAATAACAA
5677834 AACAGTCAC
1 AACAGTCAC
5677843 CCGCTAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (30 bp):
AACAGTCACTCAATTTTAGGAAAATAACAA
Found at i:5679018 original size:20 final size:19
Alignment explanation
Indices: 5678995--5679032 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5678985 TCTTTTAACA
5678995 TTATCATATTTCTCTCAAAT
1 TTATCATA-TTCTCTCAAAT
*
5679015 TTATCTTATTCTCTCAAA
1 TTATCATATTCTCTCAAA
5679033 GACCCTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATCATATTCTCTCAAAT
Found at i:5679554 original size:7 final size:7
Alignment explanation
Indices: 5679542--5679608 Score: 62
Period size: 7 Copynumber: 8.9 Consensus size: 7
5679532 ATGAAAGTTT
5679542 AATTTTA
1 AATTTTA
5679549 AATTTTA
1 AATTTTA
5679556 AATTTTA
1 AATTTTA
*
5679563 AATATTTT
1 AAT-TTTA
*
5679571 TATTTTCCAA
1 AATTTT---A
*
5679581 AGATTTTT
1 A-ATTTTA
5679589 AATTTTA
1 AATTTTA
5679596 AATTTTA
1 AATTTTA
5679603 AATTTT
1 AATTTT
5679609 TAAGAAGTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
7 38 0.78
8 6 0.12
11 5 0.10
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:5679655 original size:30 final size:29
Alignment explanation
Indices: 5679620--5679694 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
5679610 AAGAAGTACA
* *
5679620 ACTAAATTGATAGAATG-TGTAAAGTTGAGG
1 ACTAAATTGATA-AATGATGTAAAATT-AAG
* *
5679650 ACTAAATTTATTAAATGATTTAAAATTAAG
1 ACTAAATTGA-TAAATGATGTAAAATTAAG
5679680 ACTAAATTGATAAAT
1 ACTAAATTGATAAAT
5679695 ATTATAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.13
30 24 0.63
31 9 0.24
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (29 bp):
ACTAAATTGATAAATGATGTAAAATTAAG
Found at i:5688479 original size:19 final size:20
Alignment explanation
Indices: 5688455--5688494 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
5688445 AAATTGATAA
5688455 AAAATTA-AA-TTAATCTTTT
1 AAAATTATAATTTAAT-TTTT
5688474 AAAATTATAATTTAATTTTT
1 AAAATTATAATTTAATTTTT
5688494 A
1 A
5688495 CCCCTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTATAATTTAATTTTT
Found at i:5688961 original size:31 final size:31
Alignment explanation
Indices: 5688919--5689017 Score: 128
Period size: 31 Copynumber: 3.2 Consensus size: 31
5688909 AATTTTTAAA
* *
5688919 TTTTTTTAATTTTGAAATATTTTTAAAATAC
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
5688950 TTTTTTAAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
* *** *
5688981 ATTTTTAAATTTTTTTA-ATTTTTAAAATAT
1 TTTTTTAAATTTTAAAATATTTTTAAAATAC
5689011 TTTTTTA
1 TTTTTTA
5689018 GTATTTATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 18 0.30
31 42 0.70
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (31 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATAC
Found at i:5688972 original size:41 final size:39
Alignment explanation
Indices: 5688927--5689013 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 39
5688917 AATTTTTTTA
*
5688927 ATTTTGAAAT-ATTTTTAAAATACTTTTTTAAATTTTAAAAT
1 ATTTTAAAATAATTTTT-AAAT--TTTTTTAAATTTTAAAAT
*
5688968 ATTTTTAAAATACATTTTTAAATTTTTTTAATTTTTAAAAT
1 A-TTTTAAAATA-ATTTTTAAATTTTTTTAAATTTTAAAAT
5689009 ATTTT
1 ATTTT
5689014 TTTAGTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
40 4 0.10
41 19 0.46
42 8 0.20
43 4 0.10
44 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (39 bp):
ATTTTAAAATAATTTTTAAATTTTTTTAAATTTTAAAAT
Found at i:5688986 original size:13 final size:11
Alignment explanation
Indices: 5688928--5689014 Score: 64
Period size: 11 Copynumber: 8.4 Consensus size: 11
5688918 ATTTTTTTAA
*
5688928 TTTTGAAATAT
1 TTTTAAAATAT
5688939 TTTTAAAATACT
1 TTTTAAAATA-T
*
5688951 TTTT-TAA-A-
1 TTTTAAAATAT
5688959 TTTTAAAATAT
1 TTTTAAAATAT
5688970 TTTTAAAATACAT
1 TTTTAAAAT--AT
5688983 TTTT-AAAT-T
1 TTTTAAAATAT
*
5688992 TTTT--TA-AT
1 TTTTAAAATAT
5689000 TTTTAAAATAT
1 TTTTAAAATAT
5689011 TTTT
1 TTTT
5689015 TTAGTATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
8 10 0.16
9 7 0.11
10 3 0.05
11 26 0.43
12 9 0.15
13 6 0.10
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5689000 original size:9 final size:9
Alignment explanation
Indices: 5688895--5689014 Score: 54
Period size: 9 Copynumber: 12.8 Consensus size: 9
5688885 AAATATATTT
5688895 ATTTTTT-A
1 ATTTTTTAA
5688903 A-TTTTT-A
1 ATTTTTTAA
5688910 A-TTTTTAA
1 ATTTTTTAA
*
5688918 ATTTTTTTA
1 ATTTTTTAA
*
5688927 A-TTTTGAA
1 ATTTTTTAA
5688935 ATATTTTTAAAA
1 AT-TTTTT--AA
5688947 TACTTTTTTAA
1 -A-TTTTTTAA
*
5688958 A-TTTTAAA
1 ATTTTTTAA
5688966 ATATTTTTAAA
1 AT-TTTTT-AA
5688977 ATACATTTTTAA
1 AT---TTTTTAA
*
5688989 ATTTTTTTA
1 ATTTTTTAA
*
5688998 ATTTTTAAA
1 ATTTTTTAA
5689007 ATATTTTT
1 AT-TTTTT
5689015 TTAGTATTTA
Statistics
Matches: 88, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
7 12 0.14
8 16 0.18
9 22 0.25
10 13 0.15
11 6 0.07
12 6 0.07
13 12 0.14
14 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:5694581 original size:20 final size:20
Alignment explanation
Indices: 5694558--5694640 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
5694548 AACTATAATT
5694558 TTTTAAATATAAATTTTGAA
1 TTTTAAATATAAATTTTGAA
**
5694578 TTTT-TTTATACATATTTTGAA
1 TTTTAAATATA-A-ATTTTGAA
**
5694599 TTTTAAA-ATTTATTTTGAA
1 TTTTAAATATAAATTTTGAA
*
5694618 TATTTGAAAT-T-TATTTTGAA
1 T-TTT-AAATATAAATTTTGAA
5694638 TTT
1 TTT
5694641 ATTTTGAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
19 15 0.29
20 18 0.35
21 18 0.35
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.58
Consensus pattern (20 bp):
TTTTAAATATAAATTTTGAA
Found at i:5694582 original size:22 final size:21
Alignment explanation
Indices: 5694554--5694602 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5694544 AAAAAACTAT
*
5694554 AATTTTTTAAATATAAATTTTG
1 AATTTTTT-AATACAAATTTTG
* *
5694576 AATTTTTTTATACATATTTTG
1 AATTTTTTAATACAAATTTTG
5694597 AATTTT
1 AATTTT
5694603 AAAATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTTTTTAATACAAATTTTG
Found at i:5694612 original size:19 final size:19
Alignment explanation
Indices: 5694590--5694640 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
5694580 TTTTTATACA
5694590 TATTTTGAATTTTAAAATT
1 TATTTTGAATTTTAAAATT
*
5694609 TATTTTGAATATTTGAAATT
1 TATTTTGAAT-TTTAAAATT
5694629 TATTTTGAATTT
1 TATTTTGAATTT
5694641 ATTTTGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TATTTTGAATTTTAAAATT
Found at i:5694639 original size:11 final size:11
Alignment explanation
Indices: 5694605--5694682 Score: 85
Period size: 12 Copynumber: 7.3 Consensus size: 11
5694595 TGAATTTTAA
5694605 AATTTATTTTG
1 AATTTATTTTG
5694616 AA--TA-TTTG
1 AATTTATTTTG
5694624 AAATTTATTTTG
1 -AATTTATTTTG
5694636 AATTTATTTTG
1 AATTTATTTTG
*
5694647 AAATTTATTTTAA
1 -AATTTATTTT-G
5694660 AATTTATTTTG
1 AATTTATTTTG
5694671 AA--TATTTTG
1 AATTTATTTTG
5694680 AAT
1 AAT
5694683 ATTTTAAATA
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
8 4 0.07
9 13 0.22
11 17 0.29
12 24 0.41
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
AATTTATTTTG
Found at i:5694678 original size:9 final size:9
Alignment explanation
Indices: 5694664--5694693 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5694654 TTTTAAAATT
5694664 TATTTTGAA
1 TATTTTGAA
5694673 TATTTTGAA
1 TATTTTGAA
*
5694682 TATTTTAAA
1 TATTTTGAA
5694691 TAT
1 TAT
5694694 AAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (9 bp):
TATTTTGAA
Found at i:5694698 original size:35 final size:34
Alignment explanation
Indices: 5694624--5694706 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
5694614 TGAATATTTG
* *
5694624 AAATTTATTTTGAATTTATTTTGAAATTTATTTTA
1 AAATTTATTTTGAA-TTATTTTGAAATTTAATATA
5694659 AAATTTATTTTGAA-TATTTTGAATATTTTAA-ATA
1 AAATTTATTTTGAATTATTTTGAA-A-TTTAATATA
5694693 TAAATTTATTTTGA
1 -AAATTTATTTTGA
5694707 TTTTCATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 9 0.21
34 3 0.07
35 31 0.72
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (34 bp):
AAATTTATTTTGAATTATTTTGAAATTTAATATA
Found at i:5696270 original size:4 final size:4
Alignment explanation
Indices: 5696261--5696286 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5696251 ATAAATGTAA
5696261 TATC TATC TATC TATC TATC TATC TA
1 TATC TATC TATC TATC TATC TATC TA
5696287 ATGTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:5697086 original size:2 final size:2
Alignment explanation
Indices: 5697079--5697107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5697069 TTCAAATCAT
5697079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5697108 CATNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5698584 original size:11 final size:11
Alignment explanation
Indices: 5698568--5698592 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5698558 ATCAAGACTC
5698568 TTCGTTCTTGT
1 TTCGTTCTTGT
5698579 TTCGTTCTTGT
1 TTCGTTCTTGT
5698590 TTC
1 TTC
5698593 TGAAGCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.20, G:0.16, T:0.64
Consensus pattern (11 bp):
TTCGTTCTTGT
Found at i:5700898 original size:22 final size:21
Alignment explanation
Indices: 5700863--5700905 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5700853 AATTTTTTCC
*
5700863 TTTTTATATATCTTGAATTTTT
1 TTTTTAAATATCTT-AATTTTT
*
5700885 TTTTTAAATTTCTTAATTTTT
1 TTTTTAAATATCTTAATTTTT
5700906 AAAGATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTAAATATCTTAATTTTT
Found at i:5700933 original size:25 final size:25
Alignment explanation
Indices: 5700886--5700933 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5700876 TGAATTTTTT
*
5700886 TTTTAAATTTCTTAATTTTTAAAGA
1 TTTTAAATTTCTTAATTTATAAAGA
*
5700911 TTTTAAATATTTTTAA-TTATAAA
1 TTTTAAAT-TTCTTAATTTATAAA
5700934 ACATCTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTAAATTTCTTAATTTATAAAGA
Found at i:5701116 original size:11 final size:11
Alignment explanation
Indices: 5701102--5701129 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5701092 ATATATTTAT
5701102 ATTTAAAAATA
1 ATTTAAAAATA
5701113 ATTTAAAAATA
1 ATTTAAAAATA
5701124 ATTTAA
1 ATTTAA
5701130 TTAATACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:5708982 original size:13 final size:13
Alignment explanation
Indices: 5708966--5708998 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5708956 ATTTTCATTG
5708966 ATAATTTTTGAAA
1 ATAATTTTTGAAA
*
5708979 ATAAATTTTGAAA
1 ATAATTTTTGAAA
5708992 ATAATTT
1 ATAATTT
5708999 CGAAACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (13 bp):
ATAATTTTTGAAA
Found at i:5708985 original size:14 final size:13
Alignment explanation
Indices: 5708966--5709009 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
5708956 ATTTTCATTG
*
5708966 ATAATTTTTGAAA
1 ATAAATTTTGAAA
5708979 ATAAATTTTGAAA
1 ATAAATTTTGAAA
*
5708992 AT-AATTTCGAAA
1 ATAAATTTTGAAA
5709004 CATAAA
1 -ATAAA
5709010 AATAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (13 bp):
ATAAATTTTGAAA
Found at i:5720639 original size:28 final size:27
Alignment explanation
Indices: 5720608--5720671 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
5720598 ATTTCGATTA
* *
5720608 ATTTAAAATATTTCAATTCGGTTAATG
1 ATTTAAAATAATTCAATTCAGTTAATG
* *
5720635 TATTTAAAAAAATTCGATTCAGTTAATG
1 -ATTTAAAATAATTCAATTCAGTTAATG
*
5720663 ATTAAAAAT
1 ATTTAAAAT
5720672 TTTTACATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (27 bp):
ATTTAAAATAATTCAATTCAGTTAATG
Found at i:5722469 original size:21 final size:22
Alignment explanation
Indices: 5722414--5722469 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
5722404 CATATAAAAT
*
5722414 TAATATTTTAACAAGTTAATCA
1 TAATATTTTAATAAGTTAATCA
*
5722436 TAATATTTT-ATAA-TCTATTCA
1 TAATATTTTAATAAGT-TAATCA
5722457 T-ATATTTTAATAA
1 TAATATTTTAATAA
5722470 ATAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 8 0.27
21 13 0.43
22 9 0.30
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATATTTTAATAAGTTAATCA
Found at i:5731979 original size:17 final size:17
Alignment explanation
Indices: 5731946--5731979 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5731936 AGCATTAATA
**
5731946 ATTATTTTAAATGAAAT
1 ATTATTTTAAAAAAAAT
5731963 ATTATTTTAAAAAAAAT
1 ATTATTTTAAAAAAAAT
5731980 TAATATTAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTATTTTAAAAAAAAT
Found at i:5732005 original size:21 final size:22
Alignment explanation
Indices: 5731981--5732034 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5731971 AAAAAAAATT
*
5731981 AATATTAGTATTTTAA-TGATA
1 AATATTAGTATTATAATTGATA
*
5732002 AATATATAG-ATTATAATTTATA
1 AATAT-TAGTATTATAATTGATA
5732024 AATATTTAGTA
1 AATA-TTAGTA
5732035 ATAAATGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 11 0.41
22 14 0.52
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (22 bp):
AATATTAGTATTATAATTGATA
Found at i:5733470 original size:31 final size:32
Alignment explanation
Indices: 5733414--5733473 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
5733404 AACAATCTAA
5733414 TGACTTAAATAAAAAACATTTAAATAGTTTAG
1 TGACTTAAATAAAAAACATTTAAATAGTTTAG
* *
5733446 TGACTTAAAT-AAGAACTTTTAAATAGTT
1 TGACTTAAATAAAAAACATTTAAATAGTT
5733474 CAATAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (32 bp):
TGACTTAAATAAAAAACATTTAAATAGTTTAG
Found at i:5734322 original size:31 final size:31
Alignment explanation
Indices: 5734259--5734323 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5734249 AAAAAAAAAT
* * *
5734259 AAAAGTATAAAAACTGAAATTAACCAATTTA
1 AAAAGTATAAAAAATAAAATTAACCAAATTA
* **
5734290 AAAATTATAAAAAATAAAATTAATTAAATTA
1 AAAAGTATAAAAAATAAAATTAACCAAATTA
5734321 AAA
1 AAA
5734324 TATAGATATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (31 bp):
AAAAGTATAAAAAATAAAATTAACCAAATTA
Found at i:5739892 original size:3 final size:3
Alignment explanation
Indices: 5739884--5739939 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
5739874 ACCAATAACA
* *
5739884 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5739932 AAT AAT AA
1 AAT AAT AA
5739940 AGGAAGAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5740773 original size:14 final size:16
Alignment explanation
Indices: 5740742--5740775 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
5740732 TAAAAGAAAT
5740742 TTATAAACGTTATATA
1 TTATAAACGTTATATA
5740758 TTATAAA-GTT-TATA
1 TTATAAACGTTATATA
5740772 TTAT
1 TTAT
5740776 TTTTTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (16 bp):
TTATAAACGTTATATA
Found at i:5747048 original size:19 final size:20
Alignment explanation
Indices: 5747015--5747052 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5747005 AAAAGTTTGG
*
5747015 GTTTTTGTTTTTCAATTTTT
1 GTTTTTGTTTATCAATTTTT
5747035 GTTTTT-TTTATCAATTTT
1 GTTTTTGTTTATCAATTTT
5747053 AAATTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (20 bp):
GTTTTTGTTTATCAATTTTT
Found at i:5747859 original size:25 final size:24
Alignment explanation
Indices: 5747830--5747878 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
5747820 AATTTTTTTA
* *
5747830 AAAATTTTAGATTTTCTTTAAATAT
1 AAAATTTTAAATTTT-TATAAATAT
5747855 AAAATTTTAAATTTTTATAAATAT
1 AAAATTTTAAATTTTTATAAATAT
5747879 TTTGAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
AAAATTTTAAATTTTTATAAATAT
Found at i:5747886 original size:19 final size:20
Alignment explanation
Indices: 5747858--5747927 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 20
5747848 TAAATATAAA
*
5747858 ATTTTAAATTTTTATAAA-T
1 ATTTTGAATTTTTATAAATT
* *
5747877 ATTTTGAA-TTGTAAAAATT
1 ATTTTGAATTTTTATAAATT
**
5747896 ATTTTGAATTTTTGGAAATT
1 ATTTTGAATTTTTATAAATT
5747916 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
5747928 TTTTTGTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 7 0.16
19 22 0.51
20 14 0.33
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (20 bp):
ATTTTGAATTTTTATAAATT
Found at i:5747928 original size:20 final size:20
Alignment explanation
Indices: 5747891--5747927 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5747881 TGAATTGTAA
5747891 AAATTATTTTGAATTTTTGG
1 AAATTATTTTGAATTTTTGG
5747911 AAATTATTTTG-ATTTTT
1 AAATTATTTTGAATTTTT
5747928 TTTTTGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (20 bp):
AAATTATTTTGAATTTTTGG
Found at i:5753412 original size:21 final size:21
Alignment explanation
Indices: 5753375--5753414 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5753365 ATATATATAT
*
5753375 ATTATTAAATTATAAAAAACC
1 ATTATTAAATTAGAAAAAACC
5753396 ATTATTAAAATT-GAAAAAA
1 ATTATT-AAATTAGAAAAAA
5753415 AAAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
ATTATTAAATTAGAAAAAACC
Found at i:5758406 original size:27 final size:27
Alignment explanation
Indices: 5758364--5758415 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5758354 ATCTAAATCA
*
5758364 TCCAACACTTGTGTTTCGC-CACCAAAG
1 TCCAACACTTGAGTTTC-CTCACCAAAG
5758391 TCCAACACTTGAGTTTCCTCACCAA
1 TCCAACACTTGAGTTTCCTCACCAA
5758416 GGTTTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (27 bp):
TCCAACACTTGAGTTTCCTCACCAAAG
Found at i:5766128 original size:89 final size:91
Alignment explanation
Indices: 5766021--5766281 Score: 280
Period size: 89 Copynumber: 2.8 Consensus size: 91
5766011 CTTTTTCTTT
* *
5766021 CTCTTTTTTTCTTCGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAGA
1 CTCTTTTTTT-TT-GCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAA
* *
5766086 CTTTTTCAGAAAAA-GCAATTAAGC-C-C
64 CTTTTTCA-AAAAAGGCAACTAAACTCTC
* * * * *
5766112 CTGTTTTTTTTTGCACTCAATTGAGTACTTAAAATTTCAAAATGCATCAAAAAAATCCGCAAACT
1 CTCTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACT
*
5766177 TTTTCAAAAAAGGTAACTAAACTCTTGC
66 TTTTCAAAAAAGGCAACTAAACTC-T-C
* * * * * *
5766205 TTCTTCTTTCTTTTGCACTTAGTTGAGTACTTGAACTGTCAAGATGCATCAAAAAGACCCTCAAA
1 CTCTT-TTT-TTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAA
5766270 C-TTTT-AAAAAAG
64 CTTTTTCAAAAAAG
5766282 AACAATTAAG
Statistics
Matches: 142, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
88 5 0.04
89 60 0.42
90 3 0.02
91 9 0.06
93 11 0.08
94 7 0.05
95 47 0.33
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (91 bp):
CTCTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGCATCAAAAAAACCCTCAAACT
TTTTCAAAAAAGGCAACTAAACTCTC
Found at i:5766504 original size:10 final size:10
Alignment explanation
Indices: 5766472--5766542 Score: 55
Period size: 9 Copynumber: 7.6 Consensus size: 10
5766462 TTATAATAAA
* *
5766472 TAAAAATAAA
1 TAAAAATTAT
*
5766482 TAAAAGTTA-
1 TAAAAATTAT
*
5766491 TAAAAATTAG
1 TAAAAATTAT
5766501 T--AAATT-T
1 TAAAAATTAT
5766508 TAAAAA-TAT
1 TAAAAATTAT
5766517 TAAAAATTTAT
1 TAAAAA-TTAT
5766528 TAAAAATTA-
1 TAAAAATTAT
5766537 TAAAAA
1 TAAAAA
5766543 CCATAAAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
7 1 0.02
8 6 0.12
9 24 0.47
10 11 0.22
11 9 0.18
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:5766504 original size:19 final size:17
Alignment explanation
Indices: 5766457--5766541 Score: 52
Period size: 19 Copynumber: 4.8 Consensus size: 17
5766447 CAGGTGGCAA
5766457 AAAAATTATAATAA--AT
1 AAAAATTATAA-AATTAT
*
5766473 AAAAATAAATAAAAGTTAT
1 AAAAAT-TATAAAA-TTAT
*
5766492 AAAAATTAGT-AAATTTT
1 AAAAATTA-TAAAATTAT
5766509 AAAAA-TATTAAAAATTTATT
1 AAAAATTA-T-AAAA-TTA-T
5766529 AAAAATTATAAAA
1 AAAAATTATAAAA
5766542 ACCATAAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
16 11 0.20
17 12 0.22
18 7 0.13
19 15 0.28
20 7 0.13
21 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATTATAAAATTAT
Found at i:5766512 original size:36 final size:36
Alignment explanation
Indices: 5766472--5766540 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
5766462 TTATAATAAA
5766472 TAAAAATAA-ATAAAAGTTA-TAAAAATTAGTAAATTT
1 TAAAAATAATA-AAAAGTTATTAAAAATTA-TAAATTT
* *
5766508 TAAAAATATTAAAAATTTATTAAAAATTATAAA
1 TAAAAATAATAAAAAGTTATTAAAAATTATAAA
5766541 AACCATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (36 bp):
TAAAAATAATAAAAAGTTATTAAAAATTATAAATTT
Found at i:5774435 original size:15 final size:15
Alignment explanation
Indices: 5774415--5774447 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5774405 ACTACATAAC
*
5774415 ATTTATTATTAATAT
1 ATTTATTATTAAAAT
5774430 ATTTATTATTAAAAT
1 ATTTATTATTAAAAT
5774445 ATT
1 ATT
5774448 AATATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTATTATTAAAAT
Found at i:5781864 original size:29 final size:29
Alignment explanation
Indices: 5781825--5781881 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
5781815 AATAAAGAAA
5781825 ATATCAGTAAGACAAATATTCCTTACAAT
1 ATATCAGTAAGACAAATATTCCTTACAAT
5781854 ATATCAGTAAGACAAATATTCCTTACAA
1 ATATCAGTAAGACAAATATTCCTTACAA
5781882 ATACTAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.30
Consensus pattern (29 bp):
ATATCAGTAAGACAAATATTCCTTACAAT
Found at i:5790815 original size:3 final size:3
Alignment explanation
Indices: 5790807--5790845 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5790797 AAGAAAGCAA
5790807 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5790846 TCAAACTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5792389 original size:13 final size:13
Alignment explanation
Indices: 5792352--5792394 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
5792342 TACCCTGAAC
*
5792352 CCTAAATCTCAAA
1 CCTAAATCTTAAA
*
5792365 CACTAAACCTTAAA
1 C-CTAAATCTTAAA
5792379 CCTAAATCTTAAA
1 CCTAAATCTTAAA
5792392 CCT
1 CCT
5792395 TGAACTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (13 bp):
CCTAAATCTTAAA
Found at i:5795382 original size:27 final size:26
Alignment explanation
Indices: 5795352--5795424 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
5795342 AAATCGAATC
5795352 AAATATATTTAATTATAATTTAAATTA
1 AAATATATTTAATTA-AATTTAAATTA
* * * *
5795379 AAATAAAATTTGATGAAATTTAAATTT
1 AAAT-ATATTTAATTAAATTTAAATTA
*
5795406 AAACAT-TTTAATTTAAATT
1 AAATATATTTAA-TTAAATT
5795425 GATATTCAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
25 4 0.11
26 7 0.19
27 17 0.47
28 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
AAATATATTTAATTAAATTTAAATTA
Found at i:5797359 original size:16 final size:16
Alignment explanation
Indices: 5797338--5797378 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5797328 TTCGCTGTAT
*
5797338 TGGAATAGAGGCGTAA
1 TGGAATAGAGACGTAA
5797354 TGGAATAGAGACGTAA
1 TGGAATAGAGACGTAA
5797370 TGGAATAGA
1 TGGAATAGA
5797379 ATATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.34, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGACGTAA
Done.