Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 20 of 175
Found at i:5366038 original size:16 final size:17
Alignment explanation
Indices: 5366006--5366038 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5365996 AAAAGTTTTC
5366006 TTTTTTCAAAAAGTTCA
1 TTTTTTCAAAAAGTTCA
*
5366023 TTTTTTCTAAAA-TTCA
1 TTTTTTCAAAAAGTTCA
5366039 AAAATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTTTTCAAAAAGTTCA
Found at i:5367099 original size:67 final size:67
Alignment explanation
Indices: 5366991--5367135 Score: 263
Period size: 67 Copynumber: 2.2 Consensus size: 67
5366981 TTTAACTTAG
*
5366991 TAATTTAACGGTTGGTGACCAAAAAGCATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
5367056 CA
66 CA
* *
5367058 TAATTTAACGGTTGGTGACTAAAAAACATAAAATTAAATAGTTAGTTAACTATTTTAAAACTTTT
1 TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
5367123 CA
66 CA
5367125 TAATTTAACGG
1 TAATTTAACGG
5367136 AAAAAGAAGT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 75 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (67 bp):
TAATTTAACGGTTGGTGACCAAAAAACATAAAATCAAATAGTTAGTTAACTATTTTAAAACTTTT
CA
Found at i:5367476 original size:43 final size:42
Alignment explanation
Indices: 5367428--5367653 Score: 229
Period size: 43 Copynumber: 5.0 Consensus size: 42
5367418 TTTTTAAAAG
*
5367428 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCATTTTATACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TTTTACACAAA
*
5367471 CGCCGCTAAAGCACATGTTCTTTAGCTGCTTTAGCGGCGCTTTTTACACAAA
1 CGCCGCTAAAGAACATG-----T---T-CTTTAGCGGCGC-TTTTACACAAA
* * *
5367523 CGCCGCTAAAGCACATGTTCTTTAGCGGCGCTTTTAAAAATAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT--ACACAAA
*
5367567 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTCTAACACAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT-TTACACAAA
* *
5367610 CGCCGCTAAAGCTA-ATGTTCTTTAGCGGCGCTTTTTTCACAAA
1 CGCCGCTAAAG-AACATGTTCTTTAGCGGCGC-TTTTACACAAA
5367653 C
1 C
5367654 ACCACTTTTT
Statistics
Matches: 157, Mismatches: 12, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
42 4 0.03
43 69 0.44
44 41 0.26
45 1 0.01
47 1 0.01
48 1 0.01
51 1 0.01
52 39 0.25
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTTACACAAA
Found at i:5367509 original size:52 final size:52
Alignment explanation
Indices: 5367447--5367548 Score: 186
Period size: 52 Copynumber: 2.0 Consensus size: 52
5367437 AGAACATGTT
*
5367447 CTTTAGCGGCGCATTTTATACAAACGCCGCTAAAGCACATGTTCTTTAGCTG
1 CTTTAGCGGCGCATTTTACACAAACGCCGCTAAAGCACATGTTCTTTAGCTG
*
5367499 CTTTAGCGGCGCTTTTTACACAAACGCCGCTAAAGCACATGTTCTTTAGC
1 CTTTAGCGGCGCATTTTACACAAACGCCGCTAAAGCACATGTTCTTTAGC
5367549 GGCGCTTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (52 bp):
CTTTAGCGGCGCATTTTACACAAACGCCGCTAAAGCACATGTTCTTTAGCTG
Found at i:5368082 original size:66 final size:66
Alignment explanation
Indices: 5368005--5368140 Score: 209
Period size: 66 Copynumber: 2.1 Consensus size: 66
5367995 CTCGCTGCAG
* * * *
5368005 CCTCTGCTTCTCTGGATGATGCATCAGCTTTAAGTTGTTGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
5368070 A
66 A
* * *
5368071 CCTCTGCTTCTCTCGCTGCCGCATCTGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
5368136 A
66 A
5368137 CCTC
1 CCTC
5368141 AACTGTGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (66 bp):
CCTCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
A
Found at i:5373529 original size:9 final size:9
Alignment explanation
Indices: 5373515--5373636 Score: 172
Period size: 9 Copynumber: 13.4 Consensus size: 9
5373505 GTTACTTAAT
5373515 TTATGTAAG
1 TTATGTAAG
5373524 TTATGTAAG
1 TTATGTAAG
* *
5373533 TTATTTAAT
1 TTATGTAAG
*
5373542 TTATGTACG
1 TTATGTAAG
5373551 TTATGTAAG
1 TTATGTAAG
5373560 TTATGTAAG
1 TTATGTAAG
* *
5373569 TTATTTAAT
1 TTATGTAAG
*
5373578 TTATGCAAG
1 TTATGTAAG
5373587 TTTATGTAAG
1 -TTATGTAAG
5373597 TTATGTAAG
1 TTATGTAAG
*
5373606 TTATGTAGG
1 TTATGTAAG
5373615 TTATGTAAG
1 TTATGTAAG
5373624 TTATGTAAG
1 TTATGTAAG
5373633 TTAT
1 TTAT
5373637 TTTATTTATG
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
9 90 0.92
10 8 0.08
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5373645 original size:27 final size:27
Alignment explanation
Indices: 5373515--5373653 Score: 152
Period size: 27 Copynumber: 5.1 Consensus size: 27
5373505 GTTACTTAAT
* * *
5373515 TTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAATTTATGTAAG
* *
5373542 TTATGTACGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAATTTATGTAAG
* * *
5373569 TTATTTAATTTATGCAAGTTTATGTAAG
1 TTATGTAAGTTATGTAA-TTTATGTAAG
**
5373597 TTATGTAAGTTATGTAGGTTATGTAAG
1 TTATGTAAGTTATGTAATTTATGTAAG
* * *
5373624 TTATGTAAGTTATTTTATTTATGTAGG
1 TTATGTAAGTTATGTAATTTATGTAAG
5373651 TTA
1 TTA
5373654 GAGGTGCTCA
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
27 71 0.76
28 22 0.24
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.50
Consensus pattern (27 bp):
TTATGTAAGTTATGTAATTTATGTAAG
Found at i:5373929 original size:39 final size:39
Alignment explanation
Indices: 5373821--5373995 Score: 243
Period size: 39 Copynumber: 4.5 Consensus size: 39
5373811 GGCCCATTTT
*
5373821 TATTTTAAAAATTTAAAAAAGTATTTTAAAAA-TATTTT-AAAA
1 TATTTT-AAAA-TTAAAAAA--A-TTAAAAAAGTATTTTAAAAA
5373863 TATTTTAAAATTAAAAAAATT--AAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
5373900 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
*
5373939 TATTTTAAAATTTAAAAAAATTAAAAAAGTA-TGTAAAAA
1 TATTTTAAAA-TTAAAAAAATTAAAAAAGTATTTTAAAAA
5373978 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
5373996 TAACTATATT
Statistics
Matches: 127, Mismatches: 1, Indels: 14
0.89 0.01 0.10
Matches are distributed among these distances:
35 4 0.03
36 6 0.05
37 27 0.21
38 9 0.07
39 43 0.34
40 28 0.22
41 4 0.03
42 6 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:5373930 original size:86 final size:78
Alignment explanation
Indices: 5373827--5373995 Score: 230
Period size: 86 Copynumber: 2.1 Consensus size: 78
5373817 TTTTTATTTT
*
5373827 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATATTTTAAAATTAAAAAAATTAAAAGTAT
1 AAAAAATTAAAAAAGTATTTTAAAAATATTTT-AAA-A-TTTAAAA--AAAAAAA--AAAAGTA-
*
5373892 TTTAAAAATATTTTAAAATTA
58 TGTAAAAATATTTTAAAATTA
**
5373913 AAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAA
1 AAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAAAAAAAAAGTATGTAAAAA
5373978 TATTTTAAAATTA
66 TATTTTAAAATTA
5373991 AAAAA
1 AAAAA
5373996 TAACTATATT
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
78 25 0.32
79 7 0.09
81 5 0.06
83 7 0.09
84 1 0.01
85 3 0.04
86 31 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (78 bp):
AAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAAAAAAAAAGTATGTAAAAA
TATTTTAAAATTA
Found at i:5373987 original size:11 final size:11
Alignment explanation
Indices: 5373821--5373948 Score: 81
Period size: 11 Copynumber: 12.9 Consensus size: 11
5373811 GGCCCATTTT
5373821 TATTTT-AAAA
1 TATTTTAAAAA
*
5373831 -ATTTAAAAAA
1 TATTTTAAAAA
5373841 GTATTTTAAAAA
1 -TATTTTAAAAA
5373853 TATTTT-AAAA
1 TATTTTAAAAA
5373863 TATTTT--AAA
1 TATTTTAAAAA
5373872 -A--TTAAAAA
1 TATTTTAAAAA
* *
5373880 -A-ATTAAAAG
1 TATTTTAAAAA
5373889 TATTTTAAAAA
1 TATTTTAAAAA
5373900 TATTTT--AAA
1 TATTTTAAAAA
5373909 -A--TTAAAAA
1 TATTTTAAAAA
* *
5373917 -AATTAAAAAA
1 TATTTTAAAAA
5373927 GTATTTTAAAAA
1 -TATTTTAAAAA
5373939 TATTTTAAAA
1 TATTTTAAAA
5373949 TTTAAAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
6 4 0.04
8 10 0.10
9 16 0.17
10 21 0.22
11 28 0.29
12 17 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:5374212 original size:9 final size:9
Alignment explanation
Indices: 5374194--5374249 Score: 78
Period size: 9 Copynumber: 6.2 Consensus size: 9
5374184 AGCACCTCTA
*
5374194 ATGTAGGTT
1 ATGTAAGTT
5374203 ATGTAAGTT
1 ATGTAAGTT
5374212 ATGTAAGTT
1 ATGTAAGTT
*
5374221 ACT-TAATTT
1 A-TGTAAGTT
5374230 ATGTAAGTT
1 ATGTAAGTT
5374239 ATGTAAGTT
1 ATGTAAGTT
5374248 AT
1 AT
5374250 TGTTTTTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 1 0.02
9 40 0.95
10 1 0.02
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:5374326 original size:12 final size:12
Alignment explanation
Indices: 5374303--5374372 Score: 81
Period size: 12 Copynumber: 6.0 Consensus size: 12
5374293 TTATGTATTG
*
5374303 TTATATAAGTTA
1 TTATGTAAGTTA
*
5374315 TTATGTAGGTTA
1 TTATGTAAGTTA
5374327 TTATGTAAGTT-
1 TTATGTAAGTTA
5374338 TT-TGTAAGTTA
1 TTATGTAAGTTA
* *
5374349 TTATGTACGATA
1 TTATGTAAGTTA
*
5374361 CTATGTAAGTTA
1 TTATGTAAGTTA
5374373 GGATATTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.17
11 4 0.08
12 36 0.75
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:5374690 original size:29 final size:29
Alignment explanation
Indices: 5374649--5374706 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5374639 CAAAATATAT
5374649 TTTTGGAAATGAAATAGTTGACAAATGGA
1 TTTTGGAAATGAAATAGTTGACAAATGGA
5374678 TTTTGGAAATGAAATAGTTGACAAATGGA
1 TTTTGGAAATGAAATAGTTGACAAATGGA
5374707 AGAAGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (29 bp):
TTTTGGAAATGAAATAGTTGACAAATGGA
Found at i:5378777 original size:22 final size:21
Alignment explanation
Indices: 5378733--5378778 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
5378723 CTAAGACTCT
5378733 AACTATAAAAACTAAACTCCA
1 AACTATAAAAACTAAACTCCA
*
5378754 AACTTTAAAACACTAAA-TCACA
1 AACTATAAAA-ACTAAACTC-CA
5378776 AAC
1 AAC
5378779 CCAATATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (21 bp):
AACTATAAAAACTAAACTCCA
Found at i:5378823 original size:16 final size:16
Alignment explanation
Indices: 5378802--5378871 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
5378792 CCCTAAACCA
5378802 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
* * **
5378818 TAAACTA-CATACTAT
1 TAAACTATAAAACCCT
*
5378833 AGTAAAC-ATTAAA-CCT
1 --TAAACTATAAAACCCT
5378849 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
5378865 TAAACTA
1 TAAACTA
5378872 CATACTATAG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
14 5 0.12
15 9 0.22
16 19 0.47
17 7 0.17
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.27
Consensus pattern (16 bp):
TAAACTATAAAACCCT
Found at i:5378831 original size:23 final size:23
Alignment explanation
Indices: 5378805--5378880 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
5378795 TAAACCATAA
5378805 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
*
5378828 ACTATAGTAAA-CATTAAACCTTA-A-
1 ACTATA--AAACCCTTAAA-C-TACAT
5378852 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
5378875 ACTATA
1 ACTATA
5378881 GCCCTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
21 2 0.05
22 5 0.11
23 18 0.41
24 12 0.27
25 5 0.11
26 2 0.05
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (23 bp):
ACTATAAAACCCTTAAACTACAT
Found at i:5379354 original size:41 final size:40
Alignment explanation
Indices: 5379309--5379461 Score: 234
Period size: 41 Copynumber: 3.7 Consensus size: 40
5379299 GCCTGCGAAC
* *
5379309 TAGCGGCGCATCAATAAAAACGCCACTAAATCCCAGAACAT
1 TAGCGGCGC-TTAATAAAAACGCCGCTAAATCCCAGAACAT
5379350 TAGCGGCGCTTAAATAAAAACGCCGCTAAATCCCAGAACAT
1 TAGCGGCGCTT-AATAAAAACGCCGCTAAATCCCAGAACAT
*
5379391 TAGCGGCGCTTAAAACAAAACGCCGCTAAATCCCAGAACAT
1 TAGCGGCGCTTAATA-AAAACGCCGCTAAATCCCAGAACAT
*
5379432 TAGCAGCGCTTACATAAAAACGCCGCTAAA
1 TAGCGGCGCTTA-ATAAAAACGCCGCTAAA
5379462 GCCCTCGAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
40 4 0.04
41 98 0.94
42 2 0.02
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (40 bp):
TAGCGGCGCTTAATAAAAACGCCGCTAAATCCCAGAACAT
Found at i:5379379 original size:82 final size:82
Alignment explanation
Indices: 5379282--5379470 Score: 249
Period size: 82 Copynumber: 2.3 Consensus size: 82
5379272 GCGTTTTTTA
* *
5379282 AAAAAGCGCCGCTAAAGGCCTGCGAAC-TAGCGGCGCATCAATA-AAAACGCCACTAAATCCCAG
1 AAAAA-CGCCGCTAAAGCCCT-CGAACATAGCGGCGC-TCAAAACAAAACGCCACTAAATCCCAG
*
5379345 AACATTAGCGGCGCTTAAAT
63 AACATTAGCAGCGCTTAAAT
* * * *
5379365 AAAAACGCCGCTAAATCCC-AGAACATTAGCGGCGCTTAAAACAAAACGCCGCTAAATCCCAGAA
1 AAAAACGCCGCTAAAGCCCTCGAACA-TAGCGGCGCTCAAAACAAAACGCCACTAAATCCCAGAA
*
5379429 CATTAGCAGCGCTTACAT
65 CATTAGCAGCGCTTAAAT
5379447 AAAAACGCCGCTAAAGCCCTCGAA
1 AAAAACGCCGCTAAAGCCCTCGAA
5379471 AAGTCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
80 4 0.04
81 4 0.04
82 76 0.83
83 8 0.09
ACGTcount: A:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (82 bp):
AAAAACGCCGCTAAAGCCCTCGAACATAGCGGCGCTCAAAACAAAACGCCACTAAATCCCAGAAC
ATTAGCAGCGCTTAAAT
Found at i:5382470 original size:26 final size:28
Alignment explanation
Indices: 5382434--5382486 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
5382424 ACCAAAAATT
5382434 TATTTTCAAAA-TAAAAAAATAAAAAAG
1 TATTTTCAAAATTAAAAAAATAAAAAAG
* *
5382461 TATTTT-AAAATTAAAAATATTAAAAA
1 TATTTTCAAAATTAAAAAAATAAAAAA
5382487 TATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
TATTTTCAAAATTAAAAAAATAAAAAAG
Found at i:5400241 original size:13 final size:13
Alignment explanation
Indices: 5400225--5400286 Score: 58
Period size: 12 Copynumber: 5.0 Consensus size: 13
5400215 TAAAAAATAT
5400225 AAAAAAAAG-AAA
1 AAAAAAAAGAAAA
*
5400237 AAAAAAAA-AAAG
1 AAAAAAAAGAAAA
5400249 AAAAAAAAG-AAA
1 AAAAAAAAGAAAA
* * *
5400261 GAAGAAGAGAAAA
1 AAAAAAAAGAAAA
*
5400274 TAAAAAAAGAAAA
1 AAAAAAAAGAAAA
5400287 GGAGAGGCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 26 0.67
13 13 0.33
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:5401260 original size:24 final size:24
Alignment explanation
Indices: 5401226--5401279 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5401216 ATGTCCCAAA
*
5401226 ATTACAGTGGACTT-AACCTTGAAG
1 ATTACAATGGA-TTGAACCTTGAAG
**
5401250 ATTACAATGGATTGAAGTTTGAAG
1 ATTACAATGGATTGAACCTTGAAG
5401274 ATTACA
1 ATTACA
5401280 GTGGGGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.31
Consensus pattern (24 bp):
ATTACAATGGATTGAACCTTGAAG
Found at i:5401675 original size:45 final size:45
Alignment explanation
Indices: 5401552--5401775 Score: 198
Period size: 45 Copynumber: 5.0 Consensus size: 45
5401542 CAATGAAGTT
* * * * * *
5401552 GCAGATATTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACA
1 GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
* * * * * * * *
5401597 CCAG-CCTTGCCTTCCTATACTGACAGCGGAGTAGATTGAAGATA
1 GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
* * * *
5401641 ACAGATCTTGTCTTCTTGTATTTGCAGCGAAGTAGATCAAAGATA
1 GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
* ** *
5401686 GCAGATCCTGTCTTCCAATATTGGCAGCGAAGTAGATCGAATATA
1 GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
* * * * *
5401731 GCAGATCTTGCCTTCTTATACTGACAGTGAAGCAGATCGAAGATA
1 GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
5401776 CCATAGTTTG
Statistics
Matches: 142, Mismatches: 36, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
44 36 0.25
45 106 0.75
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (45 bp):
GCAGATCTTGTCTTCTTATATTGGCAGCGAAGTAGATCGAAGATA
Found at i:5401768 original size:90 final size:88
Alignment explanation
Indices: 5401552--5401778 Score: 240
Period size: 90 Copynumber: 2.5 Consensus size: 88
5401542 CAATGAAGTT
* * * *
5401552 GCAGATATTGCCTTCCTATACTGGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTTCCTATAC
1 GCAGATCTTGCCTTCTTATACT-GCAGCGAAGCAGATCGAAGATACCAGCCTTGCCTTCCAATAC
* *
5401617 TGACAGCGGAGTAGATTGAAGATA
65 TGACAGCGAAGTAGATCGAAGATA
* * * * * * * *
5401641 ACAGATCTTGTCTTCTTGTATTTGCAGCGAAGTAGATCAAAGATAGCAGATCC-TGTCTTCCAAT
1 GCAGATCTTGCCTTCTTATA-CTGCAGCGAAGCAGATCGAAGATACCAG--CCTTGCCTTCCAAT
* * *
5401705 ATTGGCAGCGAAGTAGATCGAATATA
63 ACTGACAGCGAAGTAGATCGAAGATA
*
5401731 GCAGATCTTGCCTTCTTATACTGACAGTGAAGCAGATCGAAGATACCA
1 GCAGATCTTGCCTTCTTATACTG-CAGCGAAGCAGATCGAAGATACCA
5401779 TAGTTTGCAG
Statistics
Matches: 109, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
89 39 0.36
90 68 0.62
91 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (88 bp):
GCAGATCTTGCCTTCTTATACTGCAGCGAAGCAGATCGAAGATACCAGCCTTGCCTTCCAATACT
GACAGCGAAGTAGATCGAAGATA
Found at i:5401811 original size:76 final size:76
Alignment explanation
Indices: 5401715--5401855 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 76
5401705 ATTGGCAGCG
* * ** * *
5401715 AAGTAGATCGAATATAGCAGATCTTGCCTTCTTATACTGACAGTGAAGCAGATCGAAGATACCAT
1 AAGTAGATCGAAGATAGCAGATCTTGCCTTCCTATACTGACAACGAAGCAAATCGAAGACACCAT
5401780 AGTTTGCAGTA
66 AGTTTGCAGTA
*
5401791 AAGTAGA-CTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGCAAATCGAAGACACCA
1 AAGTAGATC-GAAGATAGCAGATCTTGCCTTCCTATACTGACAACGAAGCAAATCGAAGACACCA
5401855 T
65 T
5401856 CCTTACCTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 1 0.02
76 56 0.98
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (76 bp):
AAGTAGATCGAAGATAGCAGATCTTGCCTTCCTATACTGACAACGAAGCAAATCGAAGACACCAT
AGTTTGCAGTA
Found at i:5401979 original size:44 final size:44
Alignment explanation
Indices: 5401817--5402116 Score: 163
Period size: 44 Copynumber: 6.8 Consensus size: 44
5401807 GCAGATCTTG
* * *
5401817 CCTTCCTGTACTGACAACGAAGCA-AATCGAAGACACCATCCTTA
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACA-CAGCCTTA
* * *
5401861 CCTTCCTGTACTGAC-G-G-AGCAGACT-GAAGATAGCAGATCTTG
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACA-CAG-CCTTA
* *
5401903 CCTTCCTGTACTGGCAGTGAAGCAGA-TCGAAGACACTAGCCTTA
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACAC-AGCCTTA
* * * * * *
5401947 CCTTCCTGTACTGACAGCGGAGCCGACT-GAAGATAGCAGATCATG
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACA-CAG-CCTTA
* * * ** * *
5401992 GCTTCCTGTACCGGCAGTAAAGCAGA-TCGAAGAGACCAGCCTTG
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACA-CAGCCTTA
* * * * * *
5402036 CCTTCTTGTACTGACAG-AATAGCAGAC-GGAAGATAGCAGATCTTG
1 CCTTCCTGTACTGACAGCGA-AGCAGACTCGAAGACA-CAG-CCTTA
* * *
5402081 CATTTCTGTACTGACAGTGAAGCAGA-TCGAAGACAC
1 CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACAC
5402117 CATAATTTGC
Statistics
Matches: 196, Mismatches: 44, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
41 12 0.06
42 20 0.10
43 3 0.02
44 84 0.43
45 76 0.39
46 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (44 bp):
CCTTCCTGTACTGACAGCGAAGCAGACTCGAAGACACAGCCTTA
Found at i:5402008 original size:89 final size:89
Alignment explanation
Indices: 5401795--5402118 Score: 438
Period size: 89 Copynumber: 3.7 Consensus size: 89
5401785 GCAGTAAAGT
** * *
5401795 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAACGAAGCAAATCGAAGACACCATCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTT
5401860 ACCTTCCTGTACTG--A-CGGAGC
66 ACCTTCCTGTACTGACAGCGGAGC
* *
5401881 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACACTAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTT
5401946 ACCTTCCTGTACTGACAGCGGAGC
66 ACCTTCCTGTACTGACAGCGGAGC
* * * * * * *
5401970 CGACTGAAGATAGCAGATCATGGCTTCCTGTACCGGCAGTAAAGCAGATCGAAGAGACCAGCCTT
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTT
* * ***
5402035 GCCTTCTTGTACTGACAGAATAGC
66 ACCTTCCTGTACTGACAGCGGAGC
* * *
5402059 AGACGGAAGATAGCAGATCTTGCATTTCTGTACTGACAGTGAAGCAGATCGAAGACACCA
1 AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCA
5402119 TAATTTGCAG
Statistics
Matches: 207, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
86 73 0.35
88 1 0.00
89 133 0.64
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (89 bp):
AGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATCGAAGACACCAGCCTT
ACCTTCCTGTACTGACAGCGGAGC
Found at i:5402380 original size:44 final size:43
Alignment explanation
Indices: 5402281--5402703 Score: 186
Period size: 44 Copynumber: 9.7 Consensus size: 43
5402271 TGATAGATCT
* ** * * * *
5402281 TATCTCTCTGAAGTTGCAGTAAAGCAGATCGCATC-C-AATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCACTAATCC
* * *
5402322 TATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGCTACTAGTCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-ACTAATCC
** * * *
5402366 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC-ATATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-GAAGCACTA-ATCC
* * * * *
5402410 TATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CA-CATCCAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCA-CTAATCC
* * *
5402451 TATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGAAATCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCACT-AATCC
* * * * *
5402495 TATCTTCCTAAAGTTGCAGTGAAGC-GAATTAAAATG-AC-AGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAG-ATT-GAA-GCACTA-ATCC
* * * * * * * *
5402539 TATCTCTCTAAAGTTGCAGTAGAGCGGA-TCACACCATGATAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-AGCA--CTAA-TCC
* ** *
5402585 TATCTCCCT-AAGGTTGCAGTGGAGCAGACTGGAGATAAC-AAACC
1 TATCTCCCTGAA-GTTGCAGTGGAGCAGA-TTGA-AGCACTAATCC
* * *
5402629 TTATCTCCCTGAAGTTGAAATGGAGCAAATTGAAGCTACTAATCC
1 -TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-ACTAATCC
* * *
5402674 TATCTCCTTGAAGTTGCAATGGAGCGGATT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT
5402704 AAAATGATAA
Statistics
Matches: 288, Mismatches: 65, Indels: 55
0.71 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 58 0.20
42 3 0.01
43 9 0.03
44 146 0.51
45 38 0.13
46 29 0.10
48 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCACTAATCC
Found at i:5402425 original size:129 final size:129
Alignment explanation
Indices: 5402275--5402645 Score: 424
Period size: 129 Copynumber: 2.8 Consensus size: 129
5402265 CGAAGATGAT
* *
5402275 AGATCTTATCTCTCTGAAGTTGCAGTAAAGCAGATCGCATCCAATCTTATCTCCCTAAAGTTGCA
1 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTGCA
* * ** * * * * *
5402340 GTGGAGTAGATTGAAGCTA-CTAGTCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCAC
66 GTGGAGCAAATTGAAGAAATC-AATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACCAC
* *
5402404 ATATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTGAAGTTGCA
1 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTGCA
* **
5402469 GTGGAGCAAATTGAAGAAATCAATCCTATCTTCCTAAAGTTGCAGTGAAGCGAATTAAAATGAC
66 GTGGAGCAAATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACCAC
* * *
5402533 AGATCTTATCTCTCTAAAGTTGCAGTAGAGCGGATCACA-CCATGATAAGTCTTATCTCCCTAAG
1 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCC-----AA-TCTTATCTCCCTAAA
* * * * *
5402597 GTTGCAGTGGAGCAGACTGGAGATAA-CAAACCTTATCTCCCTGAAGTTG
60 GTTGCAGTGGAGCAAATTGAAGA-AATCAATCC-TATCTCCCTAAAGTTG
5402646 AAATGGAGCA
Statistics
Matches: 206, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
128 2 0.01
129 147 0.71
130 1 0.00
133 2 0.01
134 38 0.18
135 16 0.08
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (129 bp):
AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAATCTTATCTCCCTAAAGTTGCA
GTGGAGCAAATTGAAGAAATCAATCCTATCTCCCTAAAGTTGCAGTGAAGCGAATTAAAACCAC
Found at i:5403363 original size:11 final size:11
Alignment explanation
Indices: 5403347--5403371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5403337 TTCGGTATAA
5403347 AAACCGATTGT
1 AAACCGATTGT
5403358 AAACCGATTGT
1 AAACCGATTGT
5403369 AAA
1 AAA
5403372 GGGGAAATCG
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (11 bp):
AAACCGATTGT
Found at i:5404427 original size:13 final size:13
Alignment explanation
Indices: 5404397--5404421 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5404387 TTTTCATATT
5404397 TTTTAGATATGTA
1 TTTTAGATATGTA
5404410 TTTTAGATATGT
1 TTTTAGATATGT
5404422 TCTTTATATT
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:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTTAGATATGTA
Found at i:5407364 original size:14 final size:14
Alignment explanation
Indices: 5407345--5407372 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5407335 CTGATAGCGA
5407345 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
5407359 CAGCAAGACTCCGG
1 CAGCAAGACTCCGG
5407373 TATTCAGCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (14 bp):
CAGCAAGACTCCGG
Found at i:5408920 original size:20 final size:21
Alignment explanation
Indices: 5408882--5408923 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5408872 ATTTCATAAT
*
5408882 TTTTATATACCTACATATATA
1 TTTTATATACATACATATATA
*
5408903 TTTTA-ATACATACTTATATA
1 TTTTATATACATACATATATA
5408923 T
1 T
5408924 ATTGTACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTATATACATACATATATA
Found at i:5409643 original size:73 final size:73
Alignment explanation
Indices: 5409539--5409674 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
5409529 CAAACTCAAG
* *
5409539 TTTTAAACGATCTCAGGAAGTAAGAAGAGATCGTGTCCTAACTTACT-GCGCATGATCCCTTTTT
1 TTTTAAACAATCTCAGGAAGTAAGAAAAGATCGTGTCCTAACTTACTAG-GCATGATCCCTTTTT
5409603 TCCTCAATT
65 TCCTCAATT
* *
5409612 TTTTAAACAATCTC-GGAAATTAAGAAAAGATCGTGTCTTAACTTACTAGGCATGATCCCTTTT
1 TTTTAAACAATCTCAGG-AAGTAAGAAAAGATCGTGTCCTAACTTACTAGGCATGATCCCTTTT
5409675 CTAAACCCGA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
72 2 0.04
73 54 0.95
74 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (73 bp):
TTTTAAACAATCTCAGGAAGTAAGAAAAGATCGTGTCCTAACTTACTAGGCATGATCCCTTTTTT
CCTCAATT
Found at i:5417930 original size:22 final size:22
Alignment explanation
Indices: 5417903--5417945 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5417893 TACTTTTTAA
5417903 TTTAATTT-TTAATAGAATAATT
1 TTTAATTTATT-ATAGAATAATT
*
5417925 TTTAATTTATTATATAATAAT
1 TTTAATTTATTATAGAATAAT
5417946 ATTATTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTTATTATAGAATAATT
Found at i:5418448 original size:12 final size:13
Alignment explanation
Indices: 5418431--5418460 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5418421 GACTAAAAAA
5418431 TTCTTCTT-CTTT
1 TTCTTCTTCCTTT
5418443 TTCTTCTTCCTTT
1 TTCTTCTTCCTTT
5418456 TTCTT
1 TTCTT
5418461 TTTATGGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCTTCTTCCTTT
Found at i:5421372 original size:33 final size:30
Alignment explanation
Indices: 5421297--5421377 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 30
5421287 TTAATTAATT
*
5421297 TTTTTAAATTTAAAAAATATTTTTTAATAA
1 TTTTTAAATTTTAAAAATATTTTTTAATAA
**
5421327 -TTTTAAATTTTTAAAAATAGTTTTCTTTTTGAA
1 TTTTTAAA-TTTTAAAAATA-TTTT-TTAAT-AA
5421360 TTTTTAAATTTTAAAAAT
1 TTTTTAAATTTTAAAAAT
5421378 TAATTAAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 7 0.16
30 10 0.23
31 4 0.09
32 3 0.07
33 12 0.28
34 7 0.16
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTAAATTTTAAAAATATTTTTTAATAA
Found at i:5434302 original size:50 final size:50
Alignment explanation
Indices: 5434197--5434303 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
5434187 TTATTAAGGT
* * **
5434197 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCGTTGGTGCCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGA
* * * * *
5434247 GATGAGATGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGA
5434297 TATGAGA
1 TATGAGA
5434304 ACCCTCATGT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGGCACCGA
Found at i:5434610 original size:12 final size:12
Alignment explanation
Indices: 5434593--5434631 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5434583 ATGAGTTATT
5434593 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
5434605 TAAGTAAACAAG
1 TAAGTAAGCAAG
5434617 TAAG-AGAGCAAG
1 TAAGTA-AGCAAG
5434629 TAA
1 TAA
5434632 AGAAGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 23 0.96
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:5437072 original size:64 final size:64
Alignment explanation
Indices: 5436987--5437143 Score: 197
Period size: 64 Copynumber: 2.5 Consensus size: 64
5436977 CGCGACTCGG
* * * * **
5436987 CACACGCCCGTGTCTCCTGCCCGTGTGACTCTAAAACTTAACTCAAGGAGTTACATGGCCTAGA
1 CACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAAGGAGTTACACAGCCTAGA
* ** *
5437051 CACACGCCAGTGTGTCTTGCCCATGTGACTCCAAGTCTTAACTCAGGGAGTTACACAGCCTAGA
1 CACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAAGGAGTTACACAGCCTAGA
* * *
5437115 AAAACGCCTGTGTGTCTTGCCCGTGTGAC
1 CACACGCCAGTGTGTCTTGCCCGTGTGAC
5437144 CCTTGCACCT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (64 bp):
CACACGCCAGTGTGTCTTGCCCGTGTGACTCCAAAACTTAACTCAAGGAGTTACACAGCCTAGA
Found at i:5455288 original size:20 final size:20
Alignment explanation
Indices: 5455263--5455300 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5455253 GTATGTAACA
5455263 TATATATA-TCATGACATACT
1 TATATATAGTCAT-ACATACT
5455283 TATATATAGTCATACATA
1 TATATATAGTCATACATA
5455301 ACATAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
TATATATAGTCATACATACT
Found at i:5458899 original size:24 final size:24
Alignment explanation
Indices: 5458871--5458923 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5458861 ATTCGCAAGT
* *
5458871 TAAATAAATTATGCTAATAAATGC
1 TAAATAAATTATACTAATAAATAC
*
5458895 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
5458919 TAAAT
1 TAAAT
5458924 TTTTTAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:5461189 original size:40 final size:36
Alignment explanation
Indices: 5461129--5461214 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
5461119 AAATTAGTAT
* * *
5461129 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
5461165 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
5461205 TATTATTATT
1 TATTATTATT
5461215 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:5463519 original size:3 final size:3
Alignment explanation
Indices: 5463511--5463561 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
5463501 GCTATGATTT
*
5463511 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5463559 TTA
1 TTA
5463562 CTACCACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5468519 original size:6 final size:7
Alignment explanation
Indices: 5468496--5468530 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
5468486 AAAAGTGATG
5468496 TGAAAAA
1 TGAAAAA
5468503 TGAAAAGA
1 TGAAAA-A
5468511 TG-AAAA
1 TGAAAAA
5468517 TGAAAAA
1 TGAAAAA
5468524 TGAAAAA
1 TGAAAAA
5468531 GTAAAAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:5468537 original size:21 final size:21
Alignment explanation
Indices: 5468496--5468538 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5468486 AAAAGTGATG
*
5468496 TGAAAAATGAAAAGATGAAAA
1 TGAAAAATGAAAAGATAAAAA
5468517 TGAAAAATGAAAA-AGTAAAAA
1 TGAAAAATGAAAAGA-TAAAAA
5468538 T
1 T
5468539 CGAGAGGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.67, C:0.00, G:0.16, T:0.16
Consensus pattern (21 bp):
TGAAAAATGAAAAGATAAAAA
Found at i:5470249 original size:89 final size:89
Alignment explanation
Indices: 5469695--5470245 Score: 861
Period size: 89 Copynumber: 6.2 Consensus size: 89
5469685 GAGTAGGTTG
* * * * *
5469695 AAAGATAACAGATCTTTCCTTCCCATACTGGTGGTGAGGTAGATCGAAGAAAGCGGATCTTGTCT
1 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
*
5469760 TCATGTACTGGCGTGAACTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * *
5469784 AGAGATACCAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCAAAAAAAGCAGATCTTGTCT
1 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
5469849 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
*
5469873 AAAGATAACAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
5469938 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * * *
5469962 AAAGATACCAGATCTTGTCTCCCCATACTAGTGGCGAAGCAGATCAAAGAAAGCAGATCTTGTCT
1 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
5470027 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
*
5470051 AAAGATAACAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
1 AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
5470116 TCATGTACTGGCGTGAAGTAGATC
66 TCATGTACTGGCGTGAAGTAGATC
* * * * *
5470140 AAAGATACCATATCTTGTC-TCTCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATCTTGTC
1 AAAGATACCAGATCTTGCCTTC-CCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTC
5470204 TTCATGTACTGGCGTGAAGTAGATC
65 TTCATGTACTGGCGTGAAGTAGATC
* **
5470229 GAAGATTTCAGATCTTG
1 AAAGATACCAGATCTTG
5470246 TCTCCCTAAG
Statistics
Matches: 424, Mismatches: 37, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
88 2 0.00
89 422 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (89 bp):
AAAGATACCAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGAAAGCAGATCTTGTCT
TCATGTACTGGCGTGAAGTAGATC
Found at i:5470591 original size:132 final size:132
Alignment explanation
Indices: 5470230--5470591 Score: 607
Period size: 132 Copynumber: 2.7 Consensus size: 132
5470220 AAGTAGATCG
*
5470230 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGAGAATTTTACCTCC
1 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGTGAATTTTACCTCC
* * * * *
5470295 CTGTGGTTACAGTGGTGTATATTGAAGCCAATAATTCTACTTCCTTGGGCAGCAGTGGAATAGAT
66 CTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGAT
*
5470360 TG
131 TA
5470362 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGTGAATTTTACCTCC
1 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGTGAATTTTACCTCC
*
5470427 CTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGAT
66 CTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGAT
5470492 TA
131 TA
* * * *
5470494 AAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCC
1 AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGTGAATTTTACCTCC
*
5470559 CTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
66 CTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
5470592 TTCCTATCTC
Statistics
Matches: 216, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 216 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (132 bp):
AAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGGGCAGATCAAAGATGGTGAATTTTACCTCC
CTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGAT
TA
Found at i:5472087 original size:3 final size:3
Alignment explanation
Indices: 5472079--5472108 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5472069 GCTATGATTT
*
5472079 TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5472109 CTGCCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5475499 original size:24 final size:25
Alignment explanation
Indices: 5475467--5475513 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
5475457 ATATTATTTC
5475467 ATTACATTTTGTTT-GAAATTTTTGT
1 ATTACATTTTGTTTCG-AATTTTTGT
*
5475492 ATTA-ATTTTTTTTCGAATTTTT
1 ATTACATTTTGTTTCGAATTTTT
5475514 AAAAAAGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (25 bp):
ATTACATTTTGTTTCGAATTTTTGT
Found at i:5475779 original size:325 final size:322
Alignment explanation
Indices: 5475188--5476268 Score: 1780
Period size: 325 Copynumber: 3.4 Consensus size: 322
5475178 GCAAGTTGAA
*
5475188 AAAAAAGTTAGTAAAATACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
* *
5475253 ACTTTAAAAAATTCTCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
*
5475318 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAATTTCAACCCTTATTCTT
131 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT-AAAAAAA-TACAACCCTTATT-TT
*
5475383 GCCCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTT
193 GCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTT
*
5475448 TATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTTCGAATTTT
258 TATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAA-TTTTTTCCGAATTTT
5475513 T
322 T
5475514 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTT-TCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
* *
5475578 ACTTTAAAAAAATATCATAATTTCTAGTTTTGTAATTTTACATTATTTCAGTGCATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
5475643 TCTTTATTAATTTAGTGTGTTTTTTTAAATTAATTTAGTGTAAAAGAAATACAACCCTTATTTTT
131 TCTTTATTAATTTAGTGTG-TTTTTTAAATTAATTTAGTGTAAAA-AAATACAACCCTTA-TTTT
* *
5475708 GCCCTTTGCTCGTATTATTTTTCCGAATTTTATTACTTCTAAAAAAATATATTATTTTCGTATTT
193 GCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTT
*
5475773 TATTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTCCGAATTTTT
258 TATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTCCGAATTTTT
*
5475838 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGCATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
5475903 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
* *
5475968 TCTTTATTAATTTAGTGTGTTTTTAAAATTAATTTAGTGT--AAAAA-A-AACCC--A----ACC
131 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAATACAACCCTTATTTTGCC
* *
5476023 C--T--T-ATATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATATTTTAT
196 CTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTAT
* * * *
5476083 TATTTTAAATTATTTCAGTACATTTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATTTTT
261 TATTTTATATTATTTCATTACA-TTTTGTTTGAAATTTTTGTATTAATTTTTTCCGAATTTTT
*
5476146 AAAAAAGTTAGTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
*
5476211 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTA
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTA
5476269 CTTCGGCCTT
Statistics
Matches: 722, Mismatches: 28, Indels: 28
0.93 0.04 0.04
Matches are distributed among these distances:
307 73 0.10
308 158 0.22
310 1 0.00
312 3 0.00
317 1 0.00
319 5 0.01
320 1 0.00
321 3 0.00
322 2 0.00
324 85 0.12
325 314 0.43
326 76 0.11
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (322 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAATACAACCCTTATTTTGCC
CTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTAT
TATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTCCGAATTTTT
Found at i:5476322 original size:98 final size:98
Alignment explanation
Indices: 5476168--5476365 Score: 251
Period size: 98 Copynumber: 2.0 Consensus size: 98
5476158 AAAACACTTT
* * ***
5476168 TTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAAATATCA-TAAT
1 TTACTTCGGCCATTTGCTCGTATTATTTTCTCCAAATTTTATTACTTTAAAAAAATAT-ATTAAT
5476232 TTC-TAATTTTATAATTTTACATTATTTCAGTACA
65 TTCGT-ATTTTATAATTTTACATTATTTCAGTACA
*
5476266 TTACTTCGGCC-TTTGCTCGTATTATTTTC-CCAAATTTTATTACTTTCAATAAAAATATATTAT
1 TTACTTCGGCCATTTGCTCGTATTATTTTCTCCAAATTTTATTACTTT-AA-AAAAATATATTAA
* * *
5476329 TTTCGTATTTTATTATTTTATATTATTTTAGTACA
64 TTTCGTATTTTATAATTTTACATTATTTCAGTACA
5476364 TT
1 TT
5476366 TTGTGAGAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
96 14 0.16
97 19 0.22
98 53 0.61
99 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (98 bp):
TTACTTCGGCCATTTGCTCGTATTATTTTCTCCAAATTTTATTACTTTAAAAAAATATATTAATT
TCGTATTTTATAATTTTACATTATTTCAGTACA
Found at i:5476591 original size:258 final size:257
Alignment explanation
Indices: 5476026--5476597 Score: 700
Period size: 258 Copynumber: 2.2 Consensus size: 257
5476016 CCCAACCCTT
* * * *
5476026 ATATTATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCATATTTTATTATTTTAA
1 ATATCATTTTCCCAAATTTTATTACTTCC-AATAAATATATTATTTTCGTATTTTATTATTTTAA
* ** * *
5476091 ATTATTTCAGTACATTTTTTTTTGAAATTTTTGTATTAATTTTTTCCAAATTTTTAAAAAAGTTA
65 ATTATTTCAGTACATTTTTGTGAGAAATATTTGTATTAATTATTTCCAAATTTTTAAAAAAGTTA
* *
5476156 GTAAAACACTTTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAA
130 GTAAAACACTTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAA
* *** ** *
5476221 AATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGGCCTTTGCTC
195 AATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGAAATTTAATA
* * *
5476284 GTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTA
1 ATATCATTTTCCCAAATTTTATTACTTCCAAT--AAATATATTATTTTCGTATTTTATTATTTTA
* * **
5476349 TATTATTTTAGTACA-TTTTGTGAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTT
64 AATTATTTCAGTACATTTTTGTGAGAAATATTTGTATTAATTATTTCCAAATTTTTAAAAAAGTT
**
5476413 AGTAAAACAC-TCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCTTATTTTATTACTTT-AAA
129 AGTAAAACACTTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAA
* * * * *
5476476 AAATATCCTAAATTCTAATTTTATAATTTTACGTTATTTCAGTGCATTATGTTTGAAATTTAATA
194 AAATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTA-CTTCGAAATTTAAT-
5476541 A
257 A
** ** * * * *
5476542 ATATACCATTTTTTCGGATTTTATTACTTCCAGTGAATATATAATTTTCGTTTTTT
1 ATAT--CATTTTCCCAAATTTTATTACTTCCAATAAATATATTATTTTCGTATTTT
5476598 TTCTTCTCGT
Statistics
Matches: 267, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
256 48 0.18
257 55 0.21
258 100 0.37
259 43 0.16
260 21 0.08
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (257 bp):
ATATCATTTTCCCAAATTTTATTACTTCCAATAAATATATTATTTTCGTATTTTATTATTTTAAA
TTATTTCAGTACATTTTTGTGAGAAATATTTGTATTAATTATTTCCAAATTTTTAAAAAAGTTAG
TAAAACACTTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTTAAAAAA
ATATCATAAATTCTAATTTTATAATTTTACATTATTTCAGTACATTACTTCGAAATTTAATA
Found at i:5480587 original size:19 final size:19
Alignment explanation
Indices: 5480547--5480588 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5480537 GTCTCTTTTC
* *
5480547 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
5480566 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
5480585 GCAT
1 GCAT
5480589 CAAACACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:5482501 original size:20 final size:20
Alignment explanation
Indices: 5482476--5482516 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
5482466 GCAAATGTTC
5482476 TTTCATTCTTT-ACGATTTTT
1 TTTCATTCTTTCA-GATTTTT
5482496 TTTCATTCTTTCAGATTTTT
1 TTTCATTCTTTCAGATTTTT
5482516 T
1 T
5482517 CTGCCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTCAGATTTTT
Found at i:5483471 original size:7 final size:7
Alignment explanation
Indices: 5483446--5483487 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
5483436 AGTGATGTGA
5483446 AAAAATG
1 AAAAATG
5483453 AAAAGATG
1 AAAA-ATG
5483461 -AAAATG
1 AAAAATG
5483467 AAAAATG
1 AAAAATG
5483474 AAAAA-G
1 AAAAATG
5483480 TAAAAATG
1 -AAAAATG
5483488 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:5483485 original size:21 final size:21
Alignment explanation
Indices: 5483446--5483487 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5483436 AGTGATGTGA
*
5483446 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
5483467 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
5483488 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Found at i:5484851 original size:44 final size:44
Alignment explanation
Indices: 5484788--5485588 Score: 659
Period size: 44 Copynumber: 18.1 Consensus size: 44
5484778 GCAGATTTTA
*
5484788 TCTTCATGTATTGACATGAAGTAGATCAAAAATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
* * * *
5484832 TCTTCATGTATTGACATGAAGTAGATCAGAGATAGTAGATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
*
5484876 TCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
* * **** *
5484920 TCTTCATGTATTGACATGAAATAGATCAAGGATAGCAAATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
*** * *** *
5484964 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTA-TTGACATGAAGTAGATCAAAGATAATGGATCTTG
* ** **
5485009 TCTTCATGTATTGACATGAAATAGATCAGGGATAACAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
*** * *** *
5485053 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTG
1 TCTTCATGTA-TTGACATGAAGTAGATCAAAGATAATGGATCTTG
* * ****
5485098 TCTTCATGTATTGACATGAAGTAGATTAGAGATGGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
*** * *** * *
5485142 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTA
1 TCTTCATGTA-TTGACATGAAGTAGATCAAAGATAATGGATCTTG
* *** *
5485187 TCTTCATGTATTGACATGAAGTAGATCAGAGATAGCAGATCTTA
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
* *
5485231 TCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
* *
5485275 TCTTCATGTATTGACATGAAGTAGATTAAA-A-AAAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATG--GATCTTG
* * *
5485319 TCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATG--GATCTTG
* * * * *
5485363 TCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGTAGATCCTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAA-TGGATCTTG
* * * *
5485407 TCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCATG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATG--GATCTTG
* * **
5485451 TCTTCATGTATTGGCGTGAAGTAGATTGAAGA-AA-GCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATG--GATCTTG
* * **
5485495 TCTTTC-TGTACTGGCAGTGAAGTAGATCAAAGATAACAGATCTTG
1 TC-TTCATGTATTGACA-TGAAGTAGATCAAAGATAATGGATCTTG
* * ***
5485540 TCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCTTG
1 TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
5485584 TCTTC
1 TCTTC
5485589 CCATACTGGT
Statistics
Matches: 613, Mismatches: 129, Indels: 30
0.79 0.17 0.04
Matches are distributed among these distances:
42 3 0.00
43 1 0.00
44 481 0.78
45 126 0.21
46 2 0.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.32
Consensus pattern (44 bp):
TCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTG
Found at i:5484934 original size:88 final size:88
Alignment explanation
Indices: 5484777--5485588 Score: 902
Period size: 88 Copynumber: 9.2 Consensus size: 88
5484767 GTTGAAAAGC
* * * * *
5484777 AGCAGATTTTATCTTCATGTATTGACATGAAGTAGATCAAAAATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
5484842 TTGACATGAAGTAGATCAGAGAT
66 TTGACATGAAGTAGATCAGAGAT
* * *
5484865 AGTAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
*
5484930 TTGACATGAAATAGATCA-AGGAT
66 TTGACATGAAGTAGATCAGA-GAT
* * *** * **
5484953 AGCAAATCTTATCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTA-TTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
* *
5485018 ATTGACATGAAATAGATCAGGGAT
65 ATTGACATGAAGTAGATCAGAGAT
* *** * **
5485042 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTA-TTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
*
5485107 ATTGACATGAAGTAGATTAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* *** * ** *
5485131 GGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTATCTTCATGT
1 AGCAGATCTTGTCTTCATGTA-TTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGT
5485196 ATTGACATGAAGTAGATCAGAGAT
65 ATTGACATGAAGTAGATCAGAGAT
* * *
5485220 AGCAGATCTTATCTTCATGTATTGACATGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTA
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
* * * *
5485285 TTGACATGAAGTAGATTAAAAAA
66 TTGACATGAAGTAGATCAGAGAT
*
5485308 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATG
* * *
5485371 TATTGGCGTGAAGTAGATC-GAAGAA
64 TATTGACATGAAGTAGATCAG-AGAT
* * * *
5485396 AGTAGATCCTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AA-GCAGATCATGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATG
* * * *
5485459 TATTGGCGTGAAGTAGAT-TGAAGAA
64 TATTGACATGAAGTAGATCAG-AGAT
* * * **
5485484 AGCAGATCTTGTCTTTC-TGTACTGGCAGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCATG
1 AGCAGATCTTGTC-TTCATGTATTGAC-GTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATG
* * *
5485548 TATTGGCGTGAAGTAGATCAAAGAT
64 TATTGACATGAAGTAGATCAGAGAT
5485573 AGCAGATCTTGTCTTC
1 AGCAGATCTTGTCTTC
5485589 CCATACTGGT
Statistics
Matches: 651, Mismatches: 61, Indels: 24
0.88 0.08 0.03
Matches are distributed among these distances:
86 1 0.00
87 3 0.00
88 333 0.51
89 312 0.48
90 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (88 bp):
AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTA
TTGACATGAAGTAGATCAGAGAT
Found at i:5485621 original size:89 final size:89
Alignment explanation
Indices: 5484804--5485619 Score: 910
Period size: 89 Copynumber: 9.2 Consensus size: 89
5484794 TGTATTGACA
* * * *
5484804 TGAAGTAGATCAAAAATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGTA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
* *** * ***
5484869 GATCTTATCTTCATGTA-TTGACA
66 GATCTTGTCTTCCCATACTGGTGG
* *
5484892 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAATAGATCAAGGATAGCA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
* *
5484957 AATCTTATCTTCCCATACTGGTGG
66 GATCTTGTCTTCCCATACTGGTGG
* ** *
5484981 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAATAGATCAGGGATAACA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
5485046 GATCTTGTCTTCCCATACTGGTGG
66 GATCTTGTCTTCCCATACTGGTGG
* * *
5485070 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATTAGAGATGGCA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
5485135 GATCTTGTCTTCCCATACTGGTGG
66 GATCTTGTCTTCCCATACTGGTGG
* *
5485159 TGAAGTAGATCGAAGATAATGGATCTTATCTTCATGTATTGACATGAAGTAGATCAGAGATAGCA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
* *** * ***
5485224 GATCTTATCTTCATGTA-TTGACA
66 GATCTTGTCTTCCCATACTGGTGG
* * * *
5485247 TGAAGTTGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATTAAAAAAAGCA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
*** * *
5485312 GATCTTGTCTTCATGTATTGG-CG
66 GATCTTGTCTTCCCATACTGGTGG
* * * *
5485335 TGAAGTAGATCGAAGA-AA-GCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAG
1 TGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAG
* * *** * *
5485398 TAGATCCTGTCTTCATGTATTGG-CG
64 CAGATCTTGTCTTCCCATACTGGTGG
* * * ** *
5485423 TGAAGTAGATCGAAGA-AA-GCAGATCATGTCTTCATGTATTGGCGTGAAGTAGATTGAAGAAAG
1 TGAAGTAGATCGAAGATAATG--GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAG
* ** **
5485486 CAGATCTTGTCTTTCTGTACTGGCAG
64 CAGATCTTGTCTTCCCATACTGGTGG
* ** * *
5485512 TGAAGTAGATCAAAGATAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCA
1 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
5485577 GATCTTGTCTTCCCATACTGGTGG
66 GATCTTGTCTTCCCATACTGGTGG
*
5485601 CGAAGTAGATCGAAGATAA
1 TGAAGTAGATCGAAGATAA
5485620 CAAGTCTTAA
Statistics
Matches: 649, Mismatches: 72, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
86 1 0.00
87 2 0.00
88 304 0.47
89 340 0.52
90 2 0.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (89 bp):
TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCA
GATCTTGTCTTCCCATACTGGTGG
Found at i:5485653 original size:37 final size:37
Alignment explanation
Indices: 5485607--5485682 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
5485597 GTGGCGAAGT
5485607 AGATCGAAGATA-ACAAGTCTTAACCCCCTGAAGTTGC
1 AGATCGAAGATAGACAA-TCTTAACCCCCTGAAGTTGC
* ** * *
5485644 AGATTGAAGATAGTGAATCTTATCTCCCTGAAGTTGC
1 AGATCGAAGATAGACAATCTTAACCCCCTGAAGTTGC
5485681 AG
1 AG
5485683 TGGAGCGGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (37 bp):
AGATCGAAGATAGACAATCTTAACCCCCTGAAGTTGC
Found at i:5489124 original size:16 final size:15
Alignment explanation
Indices: 5489103--5489132 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5489093 CCAAAAAATA
5489103 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
5489119 TATTATTTTATATT
1 TATTATTTTATATT
5489133 ATTTAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:5489444 original size:164 final size:160
Alignment explanation
Indices: 5488895--5489787 Score: 669
Period size: 164 Copynumber: 5.5 Consensus size: 160
5488885 ACTTCGGCCA
* * * * *
5488895 TTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAAATATCATAATTTCTAATTTTATA
1 TTTGCTCGTATTATTTTC-CAGAATTTTATTACTTCAAAAAAATATCATAATTTCTAATTTTATA
* * *
5488960 ATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTCAGTGTGTTTTTTAAATTAATT
65 ATTTTATATTATTTCAGTGAATTATGTTATTTCTTTATTAATTTAGTGTG-TTTTTAAATTAATT
* *
5489025 TAGTGTAAAAAAAATCCAACCCTTATTCTTGCCC
129 TAGTGTAAAAAAAA-ACAACCCTTATTC-CGCCC
* * * *
5489059 TTTGCTTGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATAT-ATTATTT-TCATATTTTAT
1 TTTGCTCGTATTATTTTCCAGAATTTTATTACTTCAAAAAAATATCATAATTTCT-A-ATTTTAT
* * * * ** * *
5489122 TATTTTATATTATTT-AATTACATTTTGTTTGAAATTT-TTGTATTAATTTTTTTCTAATTTTTA
64 AATTTTATATTATTTCAGTGA-ATTATG-TT---ATTTCTT-TATTAA-TTTAGTGT-GTTTTTA
** * * *
5489185 AA--AA---AGT-T--AGTAAAAC-ACTCTTTACTTCGGCCA
121 AATTAATTTAGTGTAAAAAAAAACAAC-CCTTA-TTCCGCCC
* * * * * *
5489218 TTTGTTCATATTTTTTTCTC-GTCATTTTATTACTT-TAAAAAATATCATAATTTCTAATTTTGT
1 TTTGCTCGTATTATTTTC-CAG-AATTTTATTACTTCAAAAAAATATCATAATTTCTAATTTTAT
5489281 AATTTTATATTATTTCAGTGAATTATGTTATTTCTTTATTAATTTAGTGTGTGTTTTAAATTAAT
64 AATTTTATATTATTTCAGTGAATTATGTTATTTCTTTATTAATTTAGTGTGT-TTTTAAATTAAT
*
5489346 TTAGTGTAAAAAAAATACAACCCTTATTCTTGCCC
128 TTAGTGTAAAAAAAA-ACAACCCTTATTC-CGCCC
* *
5489381 TTTGCTCGTATTATTTTCCAGAATTTTATTACTTCCAAAAAAATAT-ATTATTTTCGT-ATTTTG
1 TTTGCTCGTATTATTTTCCAGAATTTTATTACTT-CAAAAAAATATCA-TAATTTC-TAATTTTA
* * * * *
5489444 TTATTTTATATTATTTCA-TTACATTTTGTTTAAAATTT-TTGTATTAATTT-TTTTCGAATTTT
63 TAATTTTATATTATTTCAGTGA-ATTATG-TT---ATTTCTT-TATTAATTTAGTGT-G--TTTT
** * * *
5489506 TAAA--AA---AGT-T--AGTAAAAC-ACTCTTTACTTCGGCCA
119 TAAATTAATTTAGTGTAAAAAAAAACAAC-CCTTA-TTCCGCCC
* * * * *
5489541 TTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAAATATCATAATTTCTAATTTTATA
1 TTTGCTCGTATTATTTTC-CAGAATTTTATTACTTCAAAAAAATATCATAATTTCTAATTTTATA
* * *
5489606 ATTTTACATTATTTCAGTGCATTATGTTATTTCTTTATTAATTTAGTGCGTTTTTTAAATTAATT
65 ATTTTATATTATTTCAGTGAATTATGTTATTTCTTTATTAATTTAGTGTG-TTTTTAAATTAATT
5489671 TAGTGTAAAAAAAAACCCAACCCTTATTCCCGCCC
129 TAGTGTAAAAAAAAA--CAACCCTTATT-CCGCCC
* * *
5489706 TTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATAT-ATTATTTTCGT-ATTTTAT
1 TTTGCTCGTATTATTTTCCAGAATTTTATTACTTCAAAAAAATATCA-TAATTTC-TAATTTTAT
*
5489769 TATTTTATATTATTTCAGT
64 AATTTTATATTATTTCAGT
5489788 ACATTTTGTT
Statistics
Matches: 571, Mismatches: 92, Indels: 132
0.72 0.12 0.17
Matches are distributed among these distances:
153 1 0.00
154 12 0.02
155 18 0.03
156 18 0.03
157 5 0.01
158 4 0.01
159 65 0.11
160 101 0.18
161 26 0.05
162 30 0.05
163 86 0.15
164 120 0.21
165 29 0.05
166 6 0.01
167 16 0.03
168 26 0.05
169 7 0.01
170 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (160 bp):
TTTGCTCGTATTATTTTCCAGAATTTTATTACTTCAAAAAAATATCATAATTTCTAATTTTATAA
TTTTATATTATTTCAGTGAATTATGTTATTTCTTTATTAATTTAGTGTGTTTTTAAATTAATTTA
GTGTAAAAAAAAACAACCCTTATTCCGCCC
Found at i:5489782 original size:324 final size:323
Alignment explanation
Indices: 5488861--5489896 Score: 1817
Period size: 323 Copynumber: 3.2 Consensus size: 323
5488851 GCAAGTTGAA
5488861 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
5488926 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
* *
5488991 TCTTTATTAATTCAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAATCCAACCCTTATTCTTG
131 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAACCAACCCTTATTCTTG
* *
5489056 CCCTTTGCTTGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCATATTTTA
196 CCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCGTATTTTA
* *
5489121 TTATTTTATATTATTTAATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCTAATTTTT
261 TTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATTTTT
* *
5489184 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCATATTTTTTTCTCGTCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
* * *
5489249 ACTTT-AAAAAATATCATAATTTCTAATTTTGTAATTTTATATTATTTCAGTGAATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
*
5489313 TCTTTATTAATTTAGTGTGTGTTTTAAATTAATTTAGTGTAAAAAAAATA-CAACCCTTATTCTT
131 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAA-ACCAACCCTTATTCTT
*
5489377 GCCCTTTGCTCGTATTATTTTCCAGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTT
195 GCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCC-AAAAAATATATTATTTTCGTATTT
* * *
5489442 TGTTATTTTATATTATTTCATTACATTTTGTTTAAAATTTTTGTATTAATTTTTTTCGAATTTTT
259 TATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATTTTT
5489507 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
5489572 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
66 ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
* **
5489637 TCTTTATTAATTTAGTGCGTTTTTTAAATTAATTTAGTGTAAAAAAAAACCCAACCCTTATTCCC
131 TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAA-CCAACCCTTATTCTT
5489702 GCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCGTATTTT
195 GCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCGTATTTT
* *
5489767 ATTATTTTATATTATTTCAGTACATTTTGTTTGAAATTTTTGTATTAATTTTTTCCAAATTTTT
260 ATTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATTTTT
* *
5489831 AAAAAATTTAGTAAAATACTCTTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
5489895 AC
66 AC
5489897 ATTATTTCAG
Statistics
Matches: 676, Mismatches: 32, Indels: 10
0.94 0.04 0.01
Matches are distributed among these distances:
322 154 0.23
323 243 0.36
324 228 0.34
325 51 0.08
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (323 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATT
ACTTTAAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATT
TCTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAAAACCAACCCTTATTCTTG
CCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCGTATTTTA
TTATTTTATATTATTTCATTACATTTTGTTTGAAATTTTTGTATTAATTTTTTTCAAATTTTT
Found at i:5490027 original size:216 final size:216
Alignment explanation
Indices: 5489704--5490112 Score: 662
Period size: 216 Copynumber: 1.9 Consensus size: 216
5489694 TTATTCCCGC
* *
5489704 CCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAAAAAATATATTATTTTCGTATTTTAT
1 CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCAAAAAAATATATTATTTTCGTATTTTAT
* * *
5489769 TATTTTATATTATTTCAGTACATTTTGTTTGAAATTTTTGTATTAATTTTTTCCAAATTTTTAAA
66 TATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCCAAATTTTTAAA
* * *
5489834 AAATTTAGTAAAATACTCTTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCGGCATTTTATTACA
131 AAAGTTAGTAAAACACTC-TTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACA
5489898 TTATTTCAGTACATTACTTCGG
195 TTATTTCAGTACATTACTTCGG
*
5489920 CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATTTTCTTATTTT
1 CCTTTGCTCGTATTATTTTCCCAAATTTTATTAC-TTCAA-AAAAATATATTATTTTCGTATTTT
* **
5489985 CTTATTTTATATTATTT-AGTACATTTT-TTAGAAATATTTGTATTAATTATTTCTGAATTTTTA
64 ATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCCAAATTTTTA
5490048 AAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAC
129 AAAAAGTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAC
5490113 TTTAAAAATA
Statistics
Matches: 178, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
215 22 0.12
216 103 0.58
217 14 0.08
218 39 0.22
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.52
Consensus pattern (216 bp):
CCTTTGCTCGTATTATTTTCCCAAATTTTATTACTTCAAAAAAATATATTATTTTCGTATTTTAT
TATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCCAAATTTTTAAA
AAAGTTAGTAAAACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACAT
TATTTCAGTACATTACTTCGG
Found at i:5490524 original size:24 final size:24
Alignment explanation
Indices: 5490497--5490638 Score: 134
Period size: 24 Copynumber: 6.0 Consensus size: 24
5490487 AAAATACTTT
* *
5490497 TTTTCTTTCCCTCTTCTCCTTTCC
1 TTTTCTTTCCTTCTTCTTCTTTCC
*
5490521 TTTTCTTTCCTTCTTTTTCTTT-C
1 TTTTCTTTCCTTCTTCTTCTTTCC
5490544 -TTT-TTT-CTTCTTCTTCTTTCC
1 TTTTCTTTCCTTCTTCTTCTTTCC
*
5490565 TTTTCTTTCTTTCTGTCTTTCTTTCC
1 TTTTCTTTCCTTCT-TC-TTCTTTCC
* * *
5490591 TCTCCTTTCCTT-TTCTTTCTTT-T
1 TTTTCTTTCCTTCTTC-TTCTTTCC
*
5490614 TCTTTCTTTCTTTCTTCTTCTTTCC
1 T-TTTCTTTCCTTCTTCTTCTTTCC
5490639 CTCTCCTTCT
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
20 12 0.12
21 4 0.04
22 6 0.06
23 5 0.05
24 46 0.48
25 6 0.06
26 17 0.18
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (24 bp):
TTTTCTTTCCTTCTTCTTCTTTCC
Found at i:5490530 original size:10 final size:10
Alignment explanation
Indices: 5490515--5490638 Score: 84
Period size: 10 Copynumber: 12.6 Consensus size: 10
5490505 CCCTCTTCTC
5490515 CTTTCCTTTT
1 CTTTCCTTTT
5490525 CTTTCCTTCTT
1 CTTTCCTT-TT
*
5490536 -TTTCTTTCTT
1 CTTTCCTT-TT
*
5490546 TTTTCTTCTTCTT
1 CTTTC--CTT-TT
5490559 CTTTCCTTTT
1 CTTTCCTTTT
5490569 CTTT-C-TTT
1 CTTTCCTTTT
*
5490577 CTGT-C-TTT
1 CTTTCCTTTT
* *
5490585 CTTTCCTCTC
1 CTTTCCTTTT
5490595 CTTTCCTTTT
1 CTTTCCTTTT
*
5490605 CTTTCTTTTT
1 CTTTCCTTTT
5490615 CTTT-C-TTT
1 CTTTCCTTTT
5490623 CTTT-CTTCTT
1 CTTTCCTT-TT
5490633 CTTTCC
1 CTTTCC
5490639 CTCTCCTTCT
Statistics
Matches: 94, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
8 21 0.22
9 3 0.03
10 51 0.54
11 10 0.11
13 9 0.10
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:5490538 original size:14 final size:14
Alignment explanation
Indices: 5490515--5490637 Score: 106
Period size: 14 Copynumber: 8.4 Consensus size: 14
5490505 CCCTCTTCTC
*
5490515 CTTTCCTTTTCTTT
1 CTTTCTTTTTCTTT
*
5490529 CCTTCTTTTTCTTT
1 CTTTCTTTTTCTTT
5490543 CTTT-TTTCTTCTTCTT
1 CTTTCTTT-TTC-T-TT
*
5490559 CTTTCCTTTTCTTT
1 CTTTCTTTTTCTTT
5490573 CTTTCTGTCTTTCTTT
1 CTTTCT-T-TTTCTTT
* * *
5490589 CCTCTCCTTTCCTTTT
1 -CTTTCTTTTTC-TTT
5490605 CTTTCTTTTTCTTT
1 CTTTCTTTTTCTTT
5490619 CTTTCTTTCTTC-TT
1 CTTTCTTT-TTCTTT
5490633 CTTTC
1 CTTTC
5490638 CCTCTCCTTC
Statistics
Matches: 89, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
13 3 0.03
14 43 0.48
15 17 0.19
16 20 0.22
17 6 0.07
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (14 bp):
CTTTCTTTTTCTTT
Found at i:5490543 original size:4 final size:4
Alignment explanation
Indices: 5490522--5490637 Score: 81
Period size: 4 Copynumber: 30.0 Consensus size: 4
5490512 CTCCTTTCCT
*
5490522 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC -TTC -TTC -TTC TTTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C
* *
5490565 TTTTC TTTC TTTC TGTC TTTC TTTCC TCTCC TTTCC TTTTC TTTC -TT-
1 -TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTT-C -TTTC TTTC TTTC
5490612 TTTC TTTC TTTC TTTC -TTC -TTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
5490638 CCTCTCCTTC
Statistics
Matches: 94, Mismatches: 5, Indels: 26
0.75 0.04 0.21
Matches are distributed among these distances:
3 26 0.28
4 53 0.56
5 8 0.09
6 7 0.07
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:5492913 original size:16 final size:16
Alignment explanation
Indices: 5492892--5492924 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5492882 CATAATTTAA
5492892 TTTAATT-TTTGATTTC
1 TTTAATTGTTT-ATTTC
5492908 TTTAATTGTTTATTTC
1 TTTAATTGTTTATTTC
5492924 T
1 T
5492925 ACTATCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTAATTGTTTATTTC
Found at i:5495561 original size:25 final size:24
Alignment explanation
Indices: 5495479--5495562 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
5495469 CATGTGATCC
* *
5495479 GCATGTAATAACA-ATAAGGGGTTT
1 GCATGTAATAATAGATAA-GGGCTT
* *
5495503 GCATGAAATAATAGATAAGGGCTC
1 GCATGTAATAATAGATAAGGGCTT
*
5495527 GCATGTAATAATAGATAAGTGACTT
1 GCATGTAATAATAGATAAG-GGCTT
5495552 GCATGTAATAA
1 GCATGTAATAA
5495563 CATATATTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
24 33 0.65
25 18 0.35
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (24 bp):
GCATGTAATAATAGATAAGGGCTT
Found at i:5495574 original size:25 final size:24
Alignment explanation
Indices: 5495524--5495601 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
5495514 TAGATAAGGG
* * *
5495524 CTCGCATGTAATAATAGATAAGTGA
1 CTCGCATGTAATAACATAT-ATTGA
*
5495549 CTTGCATGTAATAACATATATTTGA
1 CTCGCATGTAATAACATATA-TTGA
*
5495574 CTCGCATGTAGTAACATATCATTGA
1 CTCGCATGTAATAACATAT-ATTGA
5495599 CTC
1 CTC
5495602 ACATAAACAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.96
26 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (24 bp):
CTCGCATGTAATAACATATATTGA
Found at i:5495667 original size:60 final size:60
Alignment explanation
Indices: 5495571--5495924 Score: 418
Period size: 60 Copynumber: 6.0 Consensus size: 60
5495561 AACATATATT
* * * *
5495571 TGACTCGCATGTAGTAACATATCATTGACTCA-CATAAACAGTGGTTCGCATGTAATAATC
1 TGACTCGCATGTAATAACATATCATTGACT-AGCATAAACAATGGTTCACATGTAATAATG
* * *
5495631 TGACTCGCATGTAATAGCATATCATTTACTAGCATAAACAATGGTTCGCATGTAATAATG
1 TGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGTAATAATG
* * * * *
5495691 TGATTCGTATGTAATAACATATCATT-ACCTCA-CATAAATAGTGGTTTCGCATGTAATAATG
1 TGACTCGCATGTAATAACATATCATTGA-CT-AGCATAAACAATGG-TTCACATGTAATAATG
* * * *
5495752 TGACTCGCATGTAATAACATATTATTGACTCGCATAAGCAATGATTCACATGTAATAATG
1 TGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGTAATAATG
* * *
5495812 TGACTTGCATGTAATAACATATCATTGACTCGCATAAACAGTGGTTCACATGTAATAATG
1 TGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGTAATAATG
* * *
5495872 TGACTCACATG---T--CATATCATTGACTTGCATGAACAATGGTTCACATGTAATAA
1 TGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGTAATAA
5495925 CATATACTTG
Statistics
Matches: 259, Mismatches: 29, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
55 38 0.15
57 1 0.00
59 2 0.01
60 167 0.64
61 50 0.19
62 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
TGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGTAATAATG
Found at i:5495794 original size:121 final size:118
Alignment explanation
Indices: 5495571--5495924 Score: 468
Period size: 121 Copynumber: 3.0 Consensus size: 118
5495561 AACATATATT
* * *
5495571 TGACTCGCATGTAGTAACATATCATTGACTCACATAAACAGTGGTTCGCATGTAATAATCTGACT
1 TGACTTGCATGTAATAACATATCATTGACTCACATAAACAGTGGTTCGCATGTAATAATGTGACT
* *
5495636 CGCATGTAATAGCATATCATTTACTAGCATAAACAATGGTTCGCATGTAATAATG
66 CGCATGTAATA-CATATCATTGACTAGCAT-AACAATGGTTCACATGTAATAATG
* *
5495691 TGA-TTCGTATGTAATAACATATCATT-ACCTCACATAAATAGTGGTTTCGCATGTAATAATGTG
1 TGACTT-GCATGTAATAACATATCATTGA-CTCACATAAACAGTGG-TTCGCATGTAATAATGTG
* * *
5495754 ACTCGCATGTAATAACATATTATTGACTCGCATAAGCAATGATTCACATGTAATAATG
63 ACTCGCATGTAAT-ACATATCATTGACTAGCATAA-CAATGGTTCACATGTAATAATG
* *
5495812 TGACTTGCATGTAATAACATATCATTGACTCGCATAAACAGTGGTTCACATGTAATAATGTGACT
1 TGACTTGCATGTAATAACATATCATTGACTCACATAAACAGTGGTTCGCATGTAATAATGTGACT
* *
5495877 CACATG---T-CATATCATTGACTTGCATGAACAATGGTTCACATGTAATAA
66 CGCATGTAATACATATCATTGACTAGCAT-AACAATGGTTCACATGTAATAA
5495925 CATATACTTG
Statistics
Matches: 208, Mismatches: 18, Indels: 21
0.84 0.07 0.09
Matches are distributed among these distances:
115 35 0.17
116 2 0.01
117 1 0.00
119 2 0.01
120 63 0.30
121 101 0.49
122 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (118 bp):
TGACTTGCATGTAATAACATATCATTGACTCACATAAACAGTGGTTCGCATGTAATAATGTGACT
CGCATGTAATACATATCATTGACTAGCATAACAATGGTTCACATGTAATAATG
Found at i:5495939 original size:181 final size:183
Alignment explanation
Indices: 5495553--5495942 Score: 447
Period size: 181 Copynumber: 2.1 Consensus size: 183
5495543 AAGTGACTTG
* * *
5495553 CATGTAATAACATATATTTGACTCGCATGTAGTAACATATCATTGACTCACATAAACAGTGGTTC
1 CATGTAATAACATATA-TTGACTCGCATGTAATAACATATCATTGACTCACATAAACAATGATTC
* * * *
5495618 GCATGTAATAATCTGACTCGCATGTAATAGCATATCATTTACTAGCATAAACAATGGTTCGCATG
65 ACATGTAATAATCTGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATG
* ** * * *
5495683 TAATAATGTGATTCGTATGTAATAACATATCATTACCTCACATAAATAGTGGTTTCG
130 TAATAATGTGACTCACATG--AT-ACATATCATTACCTCACATAAACAATGGTTTCA
* * * *
5495740 CATGTAAT---A-AT-GTGACTCGCATGTAATAACATATTATTGACTCGCATAAGCAATGATTCA
1 CATGTAATAACATATATTGACTCGCATGTAATAACATATCATTGACTCACATAAACAATGATTCA
* * * *
5495800 CATGTAATAATGTGACTTGCATGTAATAACATATCATTGACTCGCATAAACAGTGGTTCACATGT
66 CATGTAATAATCTGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGT
** *
5495865 AATAATGTGACTCACATG-T-CATATCATTGA-CTTGCATGAACAATGG-TTCA
131 AATAATGTGACTCACATGATACATATCATT-ACCTCACATAAACAATGGTTTCA
5495915 CATGTAATAACATATACTTGACTCGCAT
1 CATGTAATAACATATA-TTGACTCGCAT
5495943 AAACAGTGGT
Statistics
Matches: 171, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
175 11 0.06
176 20 0.12
177 1 0.01
178 2 0.01
179 2 0.01
181 124 0.73
183 2 0.01
184 1 0.01
187 8 0.05
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (183 bp):
CATGTAATAACATATATTGACTCGCATGTAATAACATATCATTGACTCACATAAACAATGATTCA
CATGTAATAATCTGACTCGCATGTAATAACATATCATTGACTAGCATAAACAATGGTTCACATGT
AATAATGTGACTCACATGATACATATCATTACCTCACATAAACAATGGTTTCA
Found at i:5498453 original size:115 final size:115
Alignment explanation
Indices: 5498243--5498593 Score: 478
Period size: 112 Copynumber: 3.1 Consensus size: 115
5498233 CTTTTTGAAT
* * * * * *
5498243 TTTTTTTTAACTTTTTTCGAACACTAGTGCCGACCATTGACATGAAAAAAGTAAAAAAAAAATTT
1 TTTTTTTTAACTTTTTTCGTATACTGGTGCTG-CCATTGACACGAAAAAAGT-AAAAAAAAATTC
* *
5498308 CCAGAAAGGTGGTGCCGGCCATTAGCAGGCCACCACCAAATTTTTTTTTTAC
64 CCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTTAC
5498360 TTTTTTTTAACTTTTTTCGTATACTGGTGCTTGCCATTGACACGAAAAAAGT-AAAAAAAATTCC
1 TTTTTTTTAACTTTTTTCGTATACTGGTGC-TGCCATTGACACGAAAAAAGTAAAAAAAAATTCC
* *
5498424 CATAAAGGTGGTGCCGACCATTGGCAGGCCACCGCCAAA-TTTTTTTTT--
65 CATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTTAC
* * *
5498472 TTCTTTTTAACTTTTTTCGTATAATGGTGCCTGCCATTGACAC-AAAAAAGTAAAAAAAAATTCT
1 TTTTTTTTAACTTTTTTCGTATACTGGTG-CTGCCATTGACACGAAAAAAGTAAAAAAAAATTCC
* * *
5498536 CATAAAGGTGGTGCTGGCCATTGGCAGGCCACCACAAAAATTTTTTTTTAAC
65 CATAAAGGTGGTGCCGGCCATTGGCAGGCCACCAC-CAAATTTTTTTTTTAC
5498588 TTTTTT
1 TTTTTT
5498594 CTTATATTGG
Statistics
Matches: 208, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
111 8 0.04
112 82 0.39
113 4 0.02
114 17 0.08
115 46 0.22
116 5 0.02
117 45 0.22
118 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (115 bp):
TTTTTTTTAACTTTTTTCGTATACTGGTGCTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCC
ATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAATTTTTTTTTTAC
Found at i:5498507 original size:112 final size:111
Alignment explanation
Indices: 5498242--5498641 Score: 476
Period size: 112 Copynumber: 3.6 Consensus size: 111
5498232 CCTTTTTGAA
* * * *
5498242 TTTTTTTTTAACTTTTTTCGAACACTAGTGCCGACCATTGACATGAAAAAAGTAAAAAAAAAATT
1 TTTTTTTTTAACTTTTTTCGTATACTGGTGCCGACCATTGACACGAAAAAAGT-AAAAAAAAATT
* * *
5498307 TCCAGAAAGGTGGTGCCGGCCATTAGCAGGCCACCACCAAATTTTTTTTT
65 CCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACC-CCAAA--TTTTTTT
*
5498357 TACTTTTTTTTAACTTTTTTCGTATACTGGTGCTTG-CCATTGACACGAAAAAAGT-AAAAAAAA
1 T--TTTTTTTTAACTTTTTTCGTATACTGGTGC-CGACCATTGACACGAAAAAAGTAAAAAAAAA
*
5498420 TTCCCATAAAGGTGGTGCCGACCATTGGCAGGCCACCGCCAAATTTTTTT
63 TTCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACC-CCAAATTTTTTT
*
5498470 TTTTCTTTTTAACTTTTTTCGTATAATGGTGCCTG-CCATTGACAC-AAAAAAGTAAAAAAAAAT
1 TTTT-TTTTTAACTTTTTTCGTATACTGGTGCC-GACCATTGACACGAAAAAAGTAAAAAAAAAT
* * * **
5498533 TCTCATAAAGGTGGTGCTGGCCATTGGCAGGCCACCACAAA-----AA
64 TCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCCCAAATTTTTTT
* * *
5498576 TTTTTTTTTAACTTTTTTCTTATATTGGTGCCGACCATTAACACGAAAAAAAGTAAAAAAAAATT
1 TTTTTTTTTAACTTTTTTCGTATACTGGTGCCGACCATTGACACG-AAAAAAGTAAAAAAAAATT
5498641 C
65 C
5498642 TGGTGCCAGC
Statistics
Matches: 255, Mismatches: 21, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
104 1 0.00
105 35 0.14
106 4 0.02
107 20 0.08
111 15 0.06
112 79 0.31
113 8 0.03
115 47 0.18
117 45 0.18
118 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (111 bp):
TTTTTTTTTAACTTTTTTCGTATACTGGTGCCGACCATTGACACGAAAAAAGTAAAAAAAAATTC
CCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCCCAAATTTTTTT
Found at i:5502106 original size:35 final size:35
Alignment explanation
Indices: 5502055--5502125 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
5502045 TAGGGAGAAA
*
5502055 TCCGACGGTAAGCGTTGTGGATTATGTAGGTTAAG
1 TCCGACGGTAAACGTTGTGGATTATGTAGGTTAAG
5502090 TCCGACGGTAAACGTTGTGGATTATGTAGGTTAAG
1 TCCGACGGTAAACGTTGTGGATTATGTAGGTTAAG
5502125 T
1 T
5502126 GGTCATAGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.32, T:0.32
Consensus pattern (35 bp):
TCCGACGGTAAACGTTGTGGATTATGTAGGTTAAG
Found at i:5507579 original size:17 final size:17
Alignment explanation
Indices: 5507559--5507603 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
5507549 TATTTATACT
5507559 TGTATTATATTTGTGAA
1 TGTATTATATTTGTGAA
5507576 TGTATTATATTTGTGAA
1 TGTATTATATTTGTGAA
*
5507593 TGTAATATATT
1 TGTATTATATT
5507604 AAGATTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (17 bp):
TGTATTATATTTGTGAA
Found at i:5513017 original size:23 final size:23
Alignment explanation
Indices: 5512938--5513017 Score: 58
Period size: 23 Copynumber: 3.4 Consensus size: 23
5512928 TTATTATACT
*
5512938 TATATACATGCA--TTTTT-ATA
1 TATATATATGCATTTTTTTAATA
* *
5512958 TAGTATATACGCATATTTTTATATAACA
1 TA-TATATATGC--ATTTTT-T-TAATA
*
5512986 TACATATATGCATTTTTTTAATA
1 TATATATATGCATTTTTTTAATA
5513009 TATATATAT
1 TATATATAT
5513018 ATATTAAGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
20 2 0.04
21 7 0.16
23 13 0.29
24 1 0.02
25 9 0.20
26 1 0.02
27 8 0.18
28 4 0.09
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (23 bp):
TATATATATGCATTTTTTTAATA
Found at i:5513019 original size:27 final size:26
Alignment explanation
Indices: 5512954--5513021 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
5512944 CATGCATTTT
*
5512954 TATATAGTATATACGCATATTTTTATA
1 TATATA-TATATATGCATATTTTTATA
* * *
5512981 TAACATACATATATGCATTTTTTTAATA
1 T-ATATATATATATGCATATTTTT-ATA
5513009 TATATATATATAT
1 TATATATATATAT
5513022 TAAGCTCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 25 0.76
28 8 0.24
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (26 bp):
TATATATATATATGCATATTTTTATA
Found at i:5517521 original size:42 final size:43
Alignment explanation
Indices: 5517472--5517702 Score: 171
Period size: 43 Copynumber: 5.4 Consensus size: 43
5517462 CCGCTATAGG
* *
5517472 ACATGACCTTTAGCGGTGCTTTTTCCACAAACGCCACTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGA
* * * * *
5517515 A-ATGACCTTTAACGGCACTTTTCCCACAAACGGCGCTATAGA
1 ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGA
* * *
5517557 ACATGACCTTTAGTGGCGCTTTTCCCACAAATGCCGCTATAA-A
1 ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTA-AAGA
* * * * * ***
5517600 ACATGATC-ATAGCGGTGCTTTCCCCACAAATGCTGTTAAAGA
1 ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGA
* * ** * * * *
5517642 ACAAGACTTTTAGTTGCGCTTTTACTAAAAACGCCACTAAAGG
1 ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGA
* **
5517685 TCATGTTCTTTAGCGGCG
1 ACATGACCTTTAGCGGCG
5517703 TCTGTAGAAA
Statistics
Matches: 141, Mismatches: 43, Indels: 8
0.73 0.22 0.04
Matches are distributed among these distances:
41 2 0.01
42 65 0.46
43 73 0.52
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
ACATGACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGA
Found at i:5517579 original size:43 final size:43
Alignment explanation
Indices: 5517418--5517629 Score: 202
Period size: 42 Copynumber: 5.1 Consensus size: 43
5517408 TTATGTGGAA
* * *
5517418 AAACGCCGCTATAGAACATGACCTTTTGCTGCG-TTTT--TA-
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
** * * *
5517457 TGACGCCGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * *
5517500 AAACGCCACTAAAGAA-ATGACCTTTAACGGCACTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
5517542 AAACGGCGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
5517585 AAATGCCGCTATAAAACATGATC-ATAGCGGTGCTTTCCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
5517627 AAA
1 AAA
5517630 TGCTGTTAAA
Statistics
Matches: 138, Mismatches: 30, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
39 27 0.20
40 4 0.03
42 54 0.39
43 53 0.38
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:5517626 original size:85 final size:84
Alignment explanation
Indices: 5517463--5517683 Score: 203
Period size: 85 Copynumber: 2.6 Consensus size: 84
5517453 TTTATGACGC
* * * * *
5517463 CGCTATAGGACATGACCTTTAGCGGTGCTTTTTCCACAAACGCCACTAAAGAAATGACCTTTAAC
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTATAAC
*
5517528 GGCACTTTTCCCACAAACGG
66 GGCACTTTCCCCACAAA-GG
* * *
5517548 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAATGCCGCTATAA-AACATGATC-ATA
1 CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTA-AAGAA-ATGACCTATA
* ** *
5517611 GCGGTGCTTTCCCCACAAATG
64 ACGGCACTTTCCCCACAAAGG
* * * * * * * *
5517632 CTGTTAAAGAACAAGACTTTTAGTTGCGCTTTTACTAAAAACGCCACTAAAG
1 C-GCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAG
5517684 GTCATGTTCT
Statistics
Matches: 109, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
84 4 0.04
85 98 0.90
86 7 0.06
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (84 bp):
CGCTATAGAACATGACCTTTAGTGGCGCTTTTCCCACAAACGCCACTAAAGAAATGACCTATAAC
GGCACTTTCCCCACAAAGG
Found at i:5518052 original size:21 final size:21
Alignment explanation
Indices: 5518027--5518076 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5518017 TTTTGCTTTG
*
5518027 CTCTGCTTCCCTTGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
5518048 CTCTGTTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
5518069 CTCCGCTT
1 CTCTGCTT
5518077 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.44, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:5522768 original size:40 final size:40
Alignment explanation
Indices: 5522713--5522792 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
5522703 ATATATTCTG
*
5522713 TATTCATATTCATCCAACGAGATTTATCGCAAACATGACA
1 TATTCATATTCATCCAACGAGATTTACCGCAAACATGACA
*
5522753 TATTCATATTCATCCAATGAGATTTACCGCAAACATGACA
1 TATTCATATTCATCCAACGAGATTTACCGCAAACATGACA
5522793 AGGCTGTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (40 bp):
TATTCATATTCATCCAACGAGATTTACCGCAAACATGACA
Found at i:5523004 original size:15 final size:15
Alignment explanation
Indices: 5522980--5523009 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5522970 TCTGGTCCAC
*
5522980 CCTCCTAAACATTTT
1 CCTCCCAAACATTTT
5522995 CCTCCCAAACATTTT
1 CCTCCCAAACATTTT
5523010 AAGTGAAAAA
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:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (15 bp):
CCTCCCAAACATTTT
Found at i:5523535 original size:20 final size:20
Alignment explanation
Indices: 5523510--5523550 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5523500 GAAAAGTTTG
5523510 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
5523530 TACTCCATTTCGATAGTCAT
1 TACTCCATTTCGATAGTCAT
5523550 T
1 T
5523551 GCTTACCTTG
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:0.24, C:0.24, G:0.10, T:0.41
Consensus pattern (20 bp):
TACTCCATTTCGATAGTCAT
Found at i:5523772 original size:9 final size:9
Alignment explanation
Indices: 5523758--5523870 Score: 104
Period size: 9 Copynumber: 12.6 Consensus size: 9
5523748 TATTTATGTA
5523758 TTATGTAAG
1 TTATGTAAG
5523767 TTATGTAAG
1 TTATGTAAG
*
5523776 TTATGATATG
1 TTATG-TAAG
* * *
5523786 ATATAT-AT
1 TTATGTAAG
5523794 TTATGTAAG
1 TTATGTAAG
*
5523803 TTATGTAAA
1 TTATGTAAG
*
5523812 TTATGAAAG
1 TTATGTAAG
5523821 TTATGTAAG
1 TTATGTAAG
*
5523830 TTATGATATG
1 TTATG-TAAG
* * *
5523840 ATATAT-AT
1 TTATGTAAG
5523848 TTATGTAAG
1 TTATGTAAG
5523857 TTATGTAAG
1 TTATGTAAG
5523866 TTATG
1 TTATG
5523871 ATTATCATCT
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
8 8 0.10
9 60 0.75
10 12 0.15
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5523798 original size:27 final size:27
Alignment explanation
Indices: 5523767--5523861 Score: 131
Period size: 27 Copynumber: 3.5 Consensus size: 27
5523757 ATTATGTAAG
5523767 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
* * *
5523794 TTATGTAAGTTATG-TA-AATTATGAAAG
1 TTATGTAAGTTATGATATGA-TAT-ATAT
5523821 TTATGTAAGTTATGATATGATATATAT
1 TTATGTAAGTTATGATATGATATATAT
5523848 TTATGTAAGTTATG
1 TTATGTAAGTTATG
5523862 TAAGTTATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.02
26 5 0.09
27 46 0.79
28 5 0.09
29 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (27 bp):
TTATGTAAGTTATGATATGATATATAT
Found at i:5523822 original size:54 final size:54
Alignment explanation
Indices: 5523757--5523871 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
5523747 ATATTTATGT
*
5523757 ATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
1 ATTATGAAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
5523811 ATTATGAAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
1 ATTATGAAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
*
5523865 GTTATGA
1 ATTATGA
5523872 TTATCATCTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.45
Consensus pattern (54 bp):
ATTATGAAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATGTAA
Found at i:5524694 original size:43 final size:43
Alignment explanation
Indices: 5524647--5524839 Score: 234
Period size: 43 Copynumber: 4.5 Consensus size: 43
5524637 AAAGAAAAAT
* *
5524647 GCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTAAAGACCATAACCTTTAGCGACGCTTTTATCACAAAC
* *
5524690 GCCGCTAAAGACCATGACCTTTAGCGACGCTTTTATCACAAAT
1 GCCGCTAAAGACCATAACCTTTAGCGACGCTTTTATCACAAAC
*
5524733 GCCGCTAAAGACCATAACCTTTAGC-AGCGCTTCTATCACAAAC
1 GCCGCTAAAGACCATAACCTTTAGCGA-CGCTTTTATCACAAAC
* * *
5524776 GCCGCTATAA-AACA-AACCTTTAGCGACGCTTCTCA-CAAAAAC
1 GCCGCTA-AAGACCATAACCTTTAGCGACGCTT-TTATCACAAAC
* *
5524818 GCCGCTAAA-AACATAACATTTA
1 GCCGCTAAAGACCATAACCTTTA
5524840 AAAAAATTAT
Statistics
Matches: 135, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
41 6 0.04
42 36 0.27
43 91 0.67
44 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGACCATAACCTTTAGCGACGCTTTTATCACAAAC
Found at i:5524770 original size:86 final size:85
Alignment explanation
Indices: 5524643--5524806 Score: 258
Period size: 86 Copynumber: 1.9 Consensus size: 85
5524633 GCCCAAAGAA
* * * * *
5524643 AAATGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTA-AAGACCATGA
1 AAATGCCGCTAAAGACCATAACCTTTAGCAGCGCTTCTATCACAAACGCCGCTATAA-AACA-AA
5524707 CCTTTAGCGACGCTTTTATCAC
64 CCTTTAGCGACGCTTTTATCAC
5524729 AAATGCCGCTAAAGACCATAACCTTTAGCAGCGCTTCTATCACAAACGCCGCTATAAAACAAACC
1 AAATGCCGCTAAAGACCATAACCTTTAGCAGCGCTTCTATCACAAACGCCGCTATAAAACAAACC
5524794 TTTAGCGACGCTT
66 TTTAGCGACGCTT
5524807 CTCACAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 16 0.22
86 54 0.75
87 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (85 bp):
AAATGCCGCTAAAGACCATAACCTTTAGCAGCGCTTCTATCACAAACGCCGCTATAAAACAAACC
TTTAGCGACGCTTTTATCAC
Found at i:5526601 original size:15 final size:15
Alignment explanation
Indices: 5526578--5526616 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5526568 TAACTTTTAA
*
5526578 CCCTAAAACATCTAAC
1 CCCT-AAACACCTAAC
*
5526594 CCCTAAACCCCTAAC
1 CCCTAAACACCTAAC
5526609 CCCTAAAC
1 CCCTAAAC
5526617 TTTAAATCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (15 bp):
CCCTAAACACCTAAC
Found at i:5526636 original size:21 final size:22
Alignment explanation
Indices: 5526597--5526637 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5526587 ATCTAACCCC
5526597 TAAACCCCTAACCCCTAAACTT
1 TAAACCCCTAACCCCTAAACTT
* *
5526619 TAAATCCC-AACCCTTAAAC
1 TAAACCCCTAACCCCTAAAC
5526638 CATAATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAACCCCTAACCCCTAAACTT
Found at i:5526679 original size:15 final size:15
Alignment explanation
Indices: 5526633--5526670 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5526623 TCCCAACCCT
5526633 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
5526647 T-GATCCATAATCCC
1 TAAATCCATAATCCC
5526661 TAAATCCATA
1 TAAATCCATA
5526671 CTCCTTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 1 0.05
14 12 0.60
15 7 0.35
ACGTcount: A:0.39, C:0.32, G:0.03, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:5526942 original size:21 final size:22
Alignment explanation
Indices: 5526901--5526944 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5526891 ACGTCTAACT
5526901 CTTAAACCCCTAACCCCTAAAC
1 CTTAAACCCCTAACCCCTAAAC
* *
5526923 CTTAAATCCC-AACCCTTAAAC
1 CTTAAACCCCTAACCCCTAAAC
5526944 C
1 C
5526945 ATAATCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.20
Consensus pattern (22 bp):
CTTAAACCCCTAACCCCTAAAC
Found at i:5526955 original size:57 final size:59
Alignment explanation
Indices: 5526859--5526985 Score: 154
Period size: 57 Copynumber: 2.2 Consensus size: 59
5526849 CCTGAATCCT
* * * * *
5526859 TAAACCCTAAATCCTTAACTCTTAACCTCATAACGTCTAACTCTTAAACCCCTAAC-CCC
1 TAAACCTTAAATCCTCAACCCTTAAACTCATAACGTCTAACTCTTAAACCCAT-ACTCCC
*
5526918 TAAACCTTAAATCC-CAACCCTTAAAC-CATAATC-TCTAATTCTTAAACCCATACTCCC
1 TAAACCTTAAATCCTCAACCCTTAAACTCATAA-CGTCTAACTCTTAAACCCATACTCCC
5526975 TAAACCTTAAA
1 TAAACCTTAAA
5526986 ATAGTAATTC
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
56 2 0.03
57 35 0.58
58 10 0.17
59 13 0.22
ACGTcount: A:0.37, C:0.35, G:0.01, T:0.28
Consensus pattern (59 bp):
TAAACCTTAAATCCTCAACCCTTAAACTCATAACGTCTAACTCTTAAACCCATACTCCC
Found at i:5526977 original size:22 final size:21
Alignment explanation
Indices: 5526937--5526977 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5526927 AATCCCAACC
*
5526937 CTTAAACCATAATCTCTAATT
1 CTTAAACCATAATCCCTAATT
*
5526958 CTTAAACCCATACTCCCTAA
1 CTTAAA-CCATAATCCCTAA
5526978 ACCTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (21 bp):
CTTAAACCATAATCCCTAATT
Found at i:5526983 original size:22 final size:21
Alignment explanation
Indices: 5526908--5526985 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
5526898 ACTCTTAAAC
* * *
5526908 CCCTAACCCCTAAACCTTAAAT
1 CCCTAAACCTTAAACCAT-AAT
*
5526930 CCC-AACCCTTAAACCATAAT
1 CCCTAAACCTTAAACCATAAT
* ** *
5526950 CTCTAATTCTTAAACCCATACT
1 CCCTAAACCTTAAA-CCATAAT
5526972 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
5526986 ATAGTAATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 5 0.11
21 20 0.44
22 20 0.44
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (21 bp):
CCCTAAACCTTAAACCATAAT
Found at i:5527019 original size:306 final size:303
Alignment explanation
Indices: 5526447--5527051 Score: 961
Period size: 306 Copynumber: 2.0 Consensus size: 303
5526437 TCAATATATT
5526447 AAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAACTA
1 AAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAACTA
* *
5526512 ATTAATCTAAACCCAAAACCCTAACCCGACCCTTAAATCCCTAAACCCTAAACCTTTAACTTTTA
66 ATTAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAAACCCTAAACCTTTAACTCTTA
*
5526577 ACCCTAAAACATCTAACCCCTAAACCCCTAACCCCTAAACTTTAAATCCCAACCCTTAAACCATA
131 ACCCTAAAACATCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATA
* *
5526642 ATCCCTGATCCATAATCCCTAAATCCATACTCCTTAAACCTTAAAATAGTAACTCCTAAACCGAC
196 AT-CC--ATCCATAATCCCTAAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGAC
5526707 CTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAAC
258 CTTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAAC
5526753 AAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAACTA
1 AAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAACTA
* * *
5526818 ATTAATCTAAACCCAAAACCCTAACCTGACCCCTGAATCCTTAAACCCTAAATCC-TTAACTCTT
66 ATTAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAAACCCTAAA-CCTTTAACTCTT
* * * *
5526882 AA-CCTCATAACGTCTAACTCTTAAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCA
130 AACCCT-AAAACATCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCA
* * * *
5526946 TAAT-C-T-C-TAATTCTTAAACCCATACTCCCTAAACCTTAAAATAGTAATTCCTAAACCGGCC
194 TAATCCATCCATAATCCCTAAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGACC
* *
5527007 TTAAATCTTAAATTAATCATATGCCCTAAACCAAAAACCCTAAAC
259 TTAAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAAC
5527052 TATAGTGATA
Statistics
Matches: 279, Mismatches: 18, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
299 91 0.33
300 1 0.00
301 1 0.00
304 1 0.00
305 3 0.01
306 180 0.65
307 2 0.01
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (303 bp):
AAATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAACTA
ATTAATCTAAACCCAAAACCCTAACCCGACCCCTAAATCCCTAAACCCTAAACCTTTAACTCTTA
ACCCTAAAACATCTAACCCCTAAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATA
ATCCATCCATAATCCCTAAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGACCTT
AAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAAC
Found at i:5529013 original size:121 final size:123
Alignment explanation
Indices: 5528795--5529552 Score: 918
Period size: 121 Copynumber: 6.1 Consensus size: 123
5528785 CGTTTGTAGT
* *
5528795 GTTTTTTACCTAGCGCCACTAATGCTCGATCTATTGCGGCG-TTTTCACCTAGTACCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
* * *
5528859 CACTAAAGACGCCACTTAAAATGGCACTATTTTGTTTAAAGT-AAA-TTTTTTACAGC
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAATTTTTTTGCAGC
* * ** * *
5528915 GTTTTTTACCTAGCGTCGCTAATGCTCTATCTATTGTAGCGTTTTTCACCTAGCGCCGCCAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
* * *
5528980 CACTAAAGACGCTACTTAAAATGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCGGC
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAA----TTTTTTTGCAGC
* * * **
5529042 GTTTTTTACTTAGTGCCGCTAATGCTTGATCTATTGCGGCGTTTTTCACCTAGTGCCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
* * * ** *
5529107 CATTAAAGACGCCACTTAAAACGGCGTCATTTT-TTTAAAGTAAAATGTTTTTTGTGGT
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAAT-TTTTTTGCAGC
* * ** **
5529165 GTTTTTTACCTAGCGCCGCTAACGCTCGATCTATTGTGGTTTTTTTCACCTAATACCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
* ** *
5529230 CACTAAAGACGCCACTTAAAATGGCACTGTTTTGTTTAAAGT-AAA-TTTTTTACAGC
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAATTTTTTTGCAGC
* * *
5529286 GTTTTTTACCTAGCGTCGCTAATGCTCGATCTATTGCGGAGTTTTTCACCTAGCGCCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
* *** * *
5529351 CACTAAAGACACCACTTAAAACAACGCCTTTTTGTTTAAAGTAAACTATTTTTTTGCAAC
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAA--ATTTTTTTGCAGC
* * * * *
5529411 GTTTTTAACCTAGCGCCGCTAATGCTTGATCTATTGCAGCGTCTTTCACCTAGCATCGCTAATGC
1 GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
**
5529476 CACTAAAGACGCCACTTAAAATGATGCCATTTTGTTTAAAGTAAAATGTTTTTTTGC-GAC
66 CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAA--TTTTTTTGCAG-C
5529536 GTTTTTTACCTAGCGCC
1 GTTTTTTACCTAGCGCC
5529553 AGTAACGCTA
Statistics
Matches: 541, Mismatches: 81, Indels: 27
0.83 0.12 0.04
Matches are distributed among these distances:
120 36 0.07
121 157 0.29
122 6 0.01
123 96 0.18
124 9 0.02
125 132 0.24
126 12 0.02
127 93 0.17
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (123 bp):
GTTTTTTACCTAGCGCCGCTAATGCTCGATCTATTGCGGCGTTTTTCACCTAGCACCGCTAATGC
CACTAAAGACGCCACTTAAAATGGCGCCATTTTGTTTAAAGTAAAATTTTTTTGCAGC
Found at i:5529531 original size:371 final size:370
Alignment explanation
Indices: 5528787--5529561 Score: 1144
Period size: 371 Copynumber: 2.1 Consensus size: 370
5528777 AAAATGATCG
* * * *
5528787 TTTGTAGTGTTTTTTACCTAGCGCCACTAATGCTCGATCTATTGCGGCGTTTTCACCTAGTACCG
1 TTTGTGGTGTTTTTTACCTAGCGCCGCTAACGCTCGATCTATTGCGGCGTTTTCACCTAATACCG
5528852 CTAATGCCACTAAAGACGCCACTTAAAATGGCACTATTTTGTTTAAAGTAAATTTTTTACAGCGT
66 CTAATGCCACTAAAGACGCCACTTAAAATGGCACTATTTTGTTTAAAGTAAATTTTTTACAGCGT
* * *
5528917 TTTTTACCTAGCGTCGCTAATGCTCTATCTATTGTAGCGTTTTTCACCTAGCGCCGCCAATGCCA
131 TTTTTACCTAGCGTCGCTAATGCTCGATCTATTGCAGAGTTTTTCACCTAGCGCCGCCAATGCCA
* * *** * * **
5528982 CTAAAGACGCTACTTAAAATGGCGCCGTTTTGTTTAAAGTAAAATGTTTTTTTTTGCGGCGTTTT
196 CTAAAGACACCACTTAAAACAACGCCGTTTTGTTTAAAGTAAAATCTATTTTTTTGCAACGTTTT
* * * * * ** *
5529047 TTACTTAGTGCCGCTAATGCTTGATCTATTGCGGCGTTTTTCACCTAGTGCCGCTAATGCCATTA
261 TAACCTAGCGCCGCTAATGCTTGATCTATTGCAGCGTCTTTCACCTAGCACCGCTAATGCCACTA
* *
5529112 AAGACGCCACTTAAAACGGCGTCATTTTTTTAAAGTAAAATGTTT
326 AAGACGCCACTTAAAACGACGCCATTTTTTTAAAGTAAAATGTTT
* **
5529157 TTTGTGGTGTTTTTTACCTAGCGCCGCTAACGCTCGATCTATTGTGGTTTTTTTCACCTAATACC
1 TTTGTGGTGTTTTTTACCTAGCGCCGCTAACGCTCGATCTATTGCGG-CGTTTTCACCTAATACC
*
5529222 GCTAATGCCACTAAAGACGCCACTTAAAATGGCACTGTTTTGTTTAAAGTAAATTTTTTACAGCG
65 GCTAATGCCACTAAAGACGCCACTTAAAATGGCACTATTTTGTTTAAAGTAAATTTTTTACAGCG
* *
5529287 TTTTTTACCTAGCGTCGCTAATGCTCGATCTATTGCGGAGTTTTTCACCTAGCGCCGCTAATGCC
130 TTTTTTACCTAGCGTCGCTAATGCTCGATCTATTGCAGAGTTTTTCACCTAGCGCCGCCAATGCC
*
5529352 ACTAAAGACACCACTTAAAACAACGCCTTTTTGTTTAAAGT-AAA-CTATTTTTTTGCAACGTTT
195 ACTAAAGACACCACTTAAAACAACGCCGTTTTGTTTAAAGTAAAATCTATTTTTTTGCAACGTTT
*
5529415 TTAACCTAGCGCCGCTAATGCTTGATCTATTGCAGCGTCTTTCACCTAGCATCGCTAATGCCACT
260 TTAACCTAGCGCCGCTAATGCTTGATCTATTGCAGCGTCTTTCACCTAGCACCGCTAATGCCACT
* *
5529480 AAAGACGCCACTTAAAATGATGCCATTTTGTTTAAAGTAAAATGTTT
325 AAAGACGCCACTTAAAACGACGCCATTTT-TTTAAAGTAAAATGTTT
*
5529527 TTT-TGCGACGTTTTTTACCTAGCGCCAG-TAACGCT
1 TTTGTG-G-TGTTTTTTACCTAGCGCC-GCTAACGCT
5529562 AGGTTTTTTT
Statistics
Matches: 363, Mismatches: 37, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
369 98 0.27
370 67 0.18
371 197 0.54
372 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (370 bp):
TTTGTGGTGTTTTTTACCTAGCGCCGCTAACGCTCGATCTATTGCGGCGTTTTCACCTAATACCG
CTAATGCCACTAAAGACGCCACTTAAAATGGCACTATTTTGTTTAAAGTAAATTTTTTACAGCGT
TTTTTACCTAGCGTCGCTAATGCTCGATCTATTGCAGAGTTTTTCACCTAGCGCCGCCAATGCCA
CTAAAGACACCACTTAAAACAACGCCGTTTTGTTTAAAGTAAAATCTATTTTTTTGCAACGTTTT
TAACCTAGCGCCGCTAATGCTTGATCTATTGCAGCGTCTTTCACCTAGCACCGCTAATGCCACTA
AAGACGCCACTTAAAACGACGCCATTTTTTTAAAGTAAAATGTTT
Found at i:5530452 original size:15 final size:15
Alignment explanation
Indices: 5530416--5530554 Score: 99
Period size: 15 Copynumber: 9.6 Consensus size: 15
5530406 CAAAATCCCT
* *
5530416 AACCCTAAAACAT-A
1 AACCCTAAACCCTAA
* *
5530430 AACACTAAATCCTAA
1 AACCCTAAACCCTAA
* * *
5530445 AACCCTAAATCTTTA
1 AACCCTAAACCCTAA
**
5530460 AACCCTAAACTATAA
1 AACCCTAAACCCTAA
**
5530475 AAAACTAAACCC--A
1 AACCCTAAACCCTAA
* *
5530488 AACCCCAAACCCCAA
1 AACCCTAAACCCTAA
*
5530503 AA-CATAAACCCTAA
1 AACCCTAAACCCTAA
*
5530517 AACCATAAACCCTAA
1 AACCCTAAACCCTAA
*
5530532 AACCATAAACCCT-A
1 AACCCTAAACCCTAA
5530546 AACCCTAAA
1 AACCCTAAA
5530555 TCTTAAATCT
Statistics
Matches: 100, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.10
14 30 0.30
15 60 0.60
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (15 bp):
AACCCTAAACCCTAA
Found at i:5530517 original size:7 final size:7
Alignment explanation
Indices: 5530412--5530582 Score: 85
Period size: 7 Copynumber: 24.0 Consensus size: 7
5530402 TTATCAAAAT
5530412 CCCT-AA
1 CCCTAAA
5530418 CCCTAAA
1 CCCTAAA
* *
5530425 ACATAAA
1 CCCTAAA
*
5530432 CACTAAA
1 CCCTAAA
*
5530439 TCCTAAAA
1 CCCT-AAA
5530447 CCCTAAA
1 CCCTAAA
**
5530454 TCTTTAAA
1 -CCCTAAA
5530462 CCCTAAA
1 CCCTAAA
**
5530469 CTATAAAA
1 CCCT-AAA
**
5530477 AACTAAA
1 CCCTAAA
5530484 CCC-AAA
1 CCCTAAA
*
5530490 CCCCAAA
1 CCCTAAA
*
5530497 CCCCAAA
1 CCCTAAA
* *
5530504 ACATAAA
1 CCCTAAA
5530511 CCCTAAAA
1 CCCT-AAA
*
5530519 CCATAAA
1 CCCTAAA
5530526 CCCTAAAA
1 CCCT-AAA
*
5530534 CCATAAA
1 CCCTAAA
5530541 CCCTAAA
1 CCCTAAA
5530548 CCCTAAA
1 CCCTAAA
* *
5530555 TCTTAAA
1 CCCTAAA
* *
5530562 TCTTAAA
1 CCCTAAA
* *
5530569 TCATAAA
1 CCCTAAA
5530576 CCCTAAA
1 CCCTAAA
5530583 ATAAAATGAT
Statistics
Matches: 125, Mismatches: 33, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
6 10 0.08
7 88 0.70
8 27 0.22
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:5530703 original size:41 final size:41
Alignment explanation
Indices: 5530608--5530732 Score: 169
Period size: 41 Copynumber: 3.0 Consensus size: 41
5530598 GCGGCGTTTT
* * * * * *
5530608 CGCTACTACTAGATCTTTTGCAGCGTTTATGATAAAAAACGC
1 CGCTACTACTTGACCTTTTGCAGCATTT-TTATCATAAACGC
5530650 CGCTACTACTTGACCTTTTGCAGCATTTTTATCATAAACGC
1 CGCTACTACTTGACCTTTTGCAGCATTTTTATCATAAACGC
* *
5530691 CGCTACTGCTTGACCTTTTGCGGCATTTTTATCATAAACGC
1 CGCTACTACTTGACCTTTTGCAGCATTTTTATCATAAACGC
5530732 C
1 C
5530733 ACTATCGCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 50 0.67
42 25 0.33
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (41 bp):
CGCTACTACTTGACCTTTTGCAGCATTTTTATCATAAACGC
Found at i:5532469 original size:11 final size:11
Alignment explanation
Indices: 5532440--5532469 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5532430 TATTTTTAAT
5532440 TAATATTAAAA
1 TAATATTAAAA
5532451 TAAATATTAAAA
1 T-AATATTAAAA
5532463 TAATATT
1 TAATATT
5532470 CTTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:5532517 original size:17 final size:17
Alignment explanation
Indices: 5532495--5532531 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5532485 AACTCGCTTA
5532495 ATTTTAAATGTTTAACT
1 ATTTTAAATGTTTAACT
*
5532512 ATTTTAAATGTTTAATT
1 ATTTTAAATGTTTAACT
5532529 ATT
1 ATT
5532532 CAATTCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATGTTTAACT
Found at i:5535160 original size:34 final size:34
Alignment explanation
Indices: 5535117--5535182 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5535107 TAAACTCTGT
* *
5535117 TTATTTATTTCAGTTAAACACTGATTAGTTTAGA
1 TTATTTATTTCAATCAAACACTGATTAGTTTAGA
*
5535151 TTATTTATTTCAATCAAACATTGATTAGTTTA
1 TTATTTATTTCAATCAAACACTGATTAGTTTA
5535183 CAACCTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (34 bp):
TTATTTATTTCAATCAAACACTGATTAGTTTAGA
Found at i:5539219 original size:41 final size:41
Alignment explanation
Indices: 5539162--5539243 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
5539152 TTTGTAATAG
5539162 AATGAGCCTTTCAATTTAGTGGTTAAACTTTAATGTACTCT
1 AATGAGCCTTTCAATTTAGTGGTTAAACTTTAATGTACTCT
5539203 AATGAGCCTTTCAATTTAGTGGTTAAACTTTAATGTACTCT
1 AATGAGCCTTTCAATTTAGTGGTTAAACTTTAATGTACTCT
5539244 TTAATCTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (41 bp):
AATGAGCCTTTCAATTTAGTGGTTAAACTTTAATGTACTCT
Found at i:5542743 original size:14 final size:14
Alignment explanation
Indices: 5542724--5542752 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5542714 TAATGTCTAG
5542724 GCTGAGTTTAGAGT
1 GCTGAGTTTAGAGT
5542738 GCTGAGTTTAGAGT
1 GCTGAGTTTAGAGT
5542752 G
1 G
5542753 TTTCACCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.38, T:0.34
Consensus pattern (14 bp):
GCTGAGTTTAGAGT
Found at i:5544962 original size:19 final size:18
Alignment explanation
Indices: 5544929--5544967 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5544919 AACTTAAATC
**
5544929 CTAGACCTTTTTTTAGACA
1 CTAGACCTTAATTTA-ACA
5544948 CTAGACCTTAATTTAACA
1 CTAGACCTTAATTTAACA
5544966 CT
1 CT
5544968 TCCTCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (18 bp):
CTAGACCTTAATTTAACA
Found at i:5546687 original size:28 final size:28
Alignment explanation
Indices: 5546656--5546711 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5546646 TATAATTTTT
*
5546656 TTTTATTTACTAAAATATTA-TAAAAAAA
1 TTTTATTTACCAAAATA-TACTAAAAAAA
5546684 TTTTATTTACCAAAATATACTAAAAAAA
1 TTTTATTTACCAAAATATACTAAAAAAA
5546712 CACAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.08
28 24 0.92
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (28 bp):
TTTTATTTACCAAAATATACTAAAAAAA
Found at i:5546778 original size:27 final size:26
Alignment explanation
Indices: 5546740--5546797 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
5546730 GCCTGATCAC
* *
5546740 GCCAATGTCATTGGTGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAAT-GT
5546767 GCCAATGCCATTGGCGGCACCAATGT
1 GCCAATGCCATTGGCGGCACCAATGT
5546793 GCCAA
1 GCCAA
5546798 AGGACTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (26 bp):
GCCAATGCCATTGGCGGCACCAATGT
Found at i:5547321 original size:19 final size:19
Alignment explanation
Indices: 5547297--5547357 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
5547287 TCTAATTAAG
5547297 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
5547316 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
* *
5547334 TAATAACTATATTTTAAAT
1 TAATAACTCTATTTTAATT
5547353 TAATA
1 TAATA
5547358 GAAATATCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:5547326 original size:18 final size:18
Alignment explanation
Indices: 5547305--5547357 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
5547295 AGTAATAACT
5547305 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* *
5547323 CTATTCTCATTTAAT-AA
1 CTATTTTAATTTAATAAA
*
5547340 CTATATTTTAAATTAATA
1 C--TATTTTAATTTAATA
5547358 GAAATATCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:5547878 original size:27 final size:26
Alignment explanation
Indices: 5547842--5547898 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
5547832 TTTTAGTCCT
*
5547842 TTGGCACATTGGTGCCGCCAATGACA
1 TTGGCACATTGGTGCCACCAATGACA
*
5547868 TTGGCACCATTGGTGCCACCAATGGCA
1 TTGGCA-CATTGGTGCCACCAATGACA
5547895 TTGG
1 TTGG
5547899 GGTGCCGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (26 bp):
TTGGCACATTGGTGCCACCAATGACA
Found at i:5547904 original size:20 final size:20
Alignment explanation
Indices: 5547879--5547918 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5547869 TGGCACCATT
5547879 GGTGCCACCAATGGCATTGG
1 GGTGCCACCAATGGCATTGG
*
5547899 GGTGCCGCCAATGGCATTGG
1 GGTGCCACCAATGGCATTGG
5547919 CGTGATCAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.38, T:0.20
Consensus pattern (20 bp):
GGTGCCACCAATGGCATTGG
Found at i:5554718 original size:19 final size:19
Alignment explanation
Indices: 5554694--5554740 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
5554684 ATGATAATTA
*
5554694 CCTTTGATTCGTTTTAAAT
1 CCTTTGATTCATTTTAAAT
5554713 CCTTTGATTCATTTTAAAT
1 CCTTTGATTCATTTTAAAT
5554732 CCTTTGATT
1 CCTTTGATT
5554741 GAAATTCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
CCTTTGATTCATTTTAAAT
Found at i:5555259 original size:18 final size:18
Alignment explanation
Indices: 5555236--5555270 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5555226 TTAAAATTAG
5555236 TTTTTCAAAAATATTTTA
1 TTTTTCAAAAATATTTTA
* *
5555254 TTTTTCTAAATTATTTT
1 TTTTTCAAAAATATTTT
5555271 TTAATTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTCAAAAATATTTTA
Found at i:5560603 original size:18 final size:20
Alignment explanation
Indices: 5560572--5560608 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
5560562 TAATATTTTA
*
5560572 TTTTATATTAAATTTAAATT
1 TTTTATATTAAATTAAAATT
5560592 TTTTATA-T-AATTAAAAT
1 TTTTATATTAAATTAAAAT
5560609 GTCGTATAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 1 0.06
20 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTATATTAAATTAAAATT
Done.