Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 13 of 103
Found at i:5032840 original size:137 final size:137
Alignment explanation
Indices: 5032589--5032848 Score: 322
Period size: 137 Copynumber: 1.9 Consensus size: 137
5032579 GTATAACAGT
* ** * * * * *
5032589 TAAATTTTCAACATGCTGTGTAACAATTACATTTTTCAATATGGCGTGTAACAACTCAATTTTCA
1 TAAATCTTCAACATGAGGTATAACAATTACATTTTTCAACATGACGTATAACAACTAAATTTTCA
* * * * * * ** *
5032654 ACATGACGTATGATAATTACATTTTTTAACATGATGTGTAATAACTAAATTTTCAACACTGTGTG
66 ACATGACCTATAACAATTAAATTTTTCAACATAACATATAATAACTAAATTTTCAACACTGTGTG
5032719 TAACGAC
131 TAACGAC
* *
5032726 TAAATCTTCAACATGAGGTATAACAATTACATTTTTCAACATGATGTATAACAATTAAATTTTCA
1 TAAATCTTCAACATGAGGTATAACAATTACATTTTTCAACATGACGTATAACAACTAAATTTTCA
* * *
5032791 ATATGACCTATAACAATTAAATTTTTCAACATAACATATAATAATTAAATTTTTAACA
66 ACATGACCTATAACAATTAAATTTTTCAACATAACATATAATAACTAAATTTTCAACA
5032849 TGGCATATAA
Statistics
Matches: 101, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
137 101 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (137 bp):
TAAATCTTCAACATGAGGTATAACAATTACATTTTTCAACATGACGTATAACAACTAAATTTTCA
ACATGACCTATAACAATTAAATTTTTCAACATAACATATAATAACTAAATTTTCAACACTGTGTG
TAACGAC
Found at i:5037564 original size:23 final size:24
Alignment explanation
Indices: 5037522--5037569 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5037512 ATCTTCTTGC
** *
5037522 TCTTTCTTT-TTTTTTTTTTTCTT
1 TCTTTCTTTCTTTTGCTTTTGCTT
5037545 TCTTTCTTTCTTTTGCTTTTGCTT
1 TCTTTCTTTCTTTTGCTTTTGCTT
5037569 T
1 T
5037570 GAAATGATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (24 bp):
TCTTTCTTTCTTTTGCTTTTGCTT
Found at i:5039100 original size:32 final size:33
Alignment explanation
Indices: 5039046--5039116 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
5039036 TAAAGTCTAT
*
5039046 AATATA-AAAATTATATTAAAAAATAAAAATAA
1 AATATATAAAATTATAATAAAAAATAAAAATAA
* *
5039078 AATATATAAGATTATAAT-AAAAATAAAAATCA
1 AATATATAAAATTATAATAAAAAATAAAAATAA
5039110 AATATAT
1 AATATAT
5039117 GACATTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (33 bp):
AATATATAAAATTATAATAAAAAATAAAAATAA
Found at i:5053140 original size:18 final size:18
Alignment explanation
Indices: 5053119--5053153 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5053109 AATCCAAAAA
5053119 TAAAAAAGAAAAAGAAAG
1 TAAAAAAGAAAAAGAAAG
* *
5053137 TAAAAATGTAAAAGAAA
1 TAAAAAAGAAAAAGAAA
5053154 ATAATTGTTG
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:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (18 bp):
TAAAAAAGAAAAAGAAAG
Found at i:5053476 original size:18 final size:18
Alignment explanation
Indices: 5053444--5053495 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
5053434 ACTTAACTAT
**
5053444 TTGAACAAATTTAATTGA
1 TTGAACAAACATAATTGA
*
5053462 TTGAACAAACATAATT-C
1 TTGAACAAACATAATTGA
*
5053479 TTGAACAATCATAATTG
1 TTGAACAAACATAATTG
5053496 TTCAAAAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.35
Consensus pattern (18 bp):
TTGAACAAACATAATTGA
Found at i:5057678 original size:34 final size:35
Alignment explanation
Indices: 5057607--5057685 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
5057597 TTCAATATGG
* *
5057607 TCAAGTGTAACCTTTATAACATGCCTTTTGCAGGA
1 TCAAGTGTAACCTTTACAACATGCCTTTTGCAAGA
*
5057642 TCAAGCGTAACCTTTACAACATGCC-TTTGCAAGA
1 TCAAGTGTAACCTTTACAACATGCCTTTTGCAAGA
5057676 TCAAGTGTAA
1 TCAAGTGTAA
5057686 TTTTTAGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 17 0.43
35 23 0.57
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (35 bp):
TCAAGTGTAACCTTTACAACATGCCTTTTGCAAGA
Found at i:5067495 original size:29 final size:27
Alignment explanation
Indices: 5067438--5067498 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
5067428 TCTTTTTAGT
* *
5067438 TATTTTTTATATTTTTTTTTGTTCGAA
1 TATTTTTTATATTTTTTTTTGATCAAA
5067465 TATTTGTTTATATCTATTTTTTT-ATCAAA
1 TATTT-TTTATAT-T-TTTTTTTGATCAAA
5067494 TATTT
1 TATTT
5067499 ACCCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 7 0.24
29 10 0.34
30 7 0.24
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (27 bp):
TATTTTTTATATTTTTTTTTGATCAAA
Found at i:5081419 original size:29 final size:27
Alignment explanation
Indices: 5081362--5081422 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
5081352 TCTTTTTAGT
* *
5081362 TATTTTTTATATTTTTTTTTGTTCGAA
1 TATTTTTTATATTTTTTTTTGATCAAA
5081389 TATTTGTTTATATCTATTTTTTT-ATCAAA
1 TATTT-TTTATAT-T-TTTTTTTGATCAAA
5081418 TATTT
1 TATTT
5081423 ACCCATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 7 0.24
29 10 0.34
30 7 0.24
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (27 bp):
TATTTTTTATATTTTTTTTTGATCAAA
Found at i:5081862 original size:72 final size:72
Alignment explanation
Indices: 5081762--5081918 Score: 233
Period size: 72 Copynumber: 2.2 Consensus size: 72
5081752 TCCTTTTTTT
* * * * * *
5081762 TTTCTTTCCTTTCCTTTCTCTCTGCCCGCTGGCTTCTTCTTTCTCTTTCTTTTTTCTTTTTTTTT
1 TTTCTCTCCTTTCCTTTCTCTCTCCCCGCTGGCTTCTTCTTTCTCTTTCCTCTTTCTTTCTTTCT
*
5081827 TCTTCTC
66 CCTTCTC
*
5081834 TTTCTCTCCTTTCCTTTCTCTCTCCCCGCTGGCTTCTTCTTTCTTTTTCCTCTTTCTTTCTTTCT
1 TTTCTCTCCTTTCCTTTCTCTCTCCCCGCTGGCTTCTTCTTTCTCTTTCCTCTTTCTTTCTTTCT
5081899 CCTTCTC
66 CCTTCTC
*
5081906 TTTCTCTCATTTC
1 TTTCTCTCCTTTC
5081919 TCCCTGTTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.01, C:0.34, G:0.04, T:0.61
Consensus pattern (72 bp):
TTTCTCTCCTTTCCTTTCTCTCTCCCCGCTGGCTTCTTCTTTCTCTTTCCTCTTTCTTTCTTTCT
CCTTCTC
Found at i:5081892 original size:17 final size:16
Alignment explanation
Indices: 5081870--5081910 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
5081860 CGCTGGCTTC
*
5081870 TTCTTTCTTTTTCCTCT
1 TTCTTTCTTTCTCCT-T
5081887 TTCTTTCTTTCTCCTT
1 TTCTTTCTTTCTCCTT
*
5081903 CTCTTTCT
1 TTCTTTCT
5081911 CTCATTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTTTCTTTCTCCTT
Found at i:5081906 original size:20 final size:21
Alignment explanation
Indices: 5081883--5081921 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5081873 TTTCTTTTTC
*
5081883 CTCTTTCTTTC-TTTCTCCTT
1 CTCTTTCTCTCATTTCTCCTT
5081903 CTCTTTCTCTCATTTCTCC
1 CTCTTTCTCTCATTTCTCC
5081922 CTGTTTGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (21 bp):
CTCTTTCTCTCATTTCTCCTT
Found at i:5081977 original size:15 final size:17
Alignment explanation
Indices: 5081948--5081989 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5081938 CTTCTCCTCT
5081948 TCTCTCTTCCTCCTTCC
1 TCTCTCTTCCTCCTTCC
*
5081965 TCTCT-TTCCCCTTCTTCC
1 TCTCTCTT--CCTCCTTCC
5081983 TCTCTCT
1 TCTCTCT
5081990 CCTAACCGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 5 0.24
18 13 0.62
19 1 0.05
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTCTCTTCCTCCTTCC
Found at i:5082119 original size:14 final size:15
Alignment explanation
Indices: 5082102--5082139 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5082092 ATTGTTGTTA
*
5082102 TTTTTTTGTTTGA-G
1 TTTTTTTGGTTGAGG
5082116 TTTTTTTGGTTGATGG
1 TTTTTTTGGTTGA-GG
5082132 TTTTTTTG
1 TTTTTTTG
5082140 CAGGAGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.05, C:0.00, G:0.24, T:0.71
Consensus pattern (15 bp):
TTTTTTTGGTTGAGG
Found at i:5082394 original size:12 final size:12
Alignment explanation
Indices: 5082379--5082403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5082369 TTTTTTTAAT
5082379 TATTTTATTTTA
1 TATTTTATTTTA
5082391 TATTTTATTTTA
1 TATTTTATTTTA
5082403 T
1 T
5082404 TATATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTTTA
Found at i:5082396 original size:22 final size:22
Alignment explanation
Indices: 5082367--5082418 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5082357 ATTCCTTCTC
*
5082367 TTTT-TTTTTA-ATTATTTTA-
1 TTTTATTTTTATATTATTATAT
*
5082386 TTTTATATTTTATTTTATTATAT
1 TTTTAT-TTTTATATTATTATAT
5082409 TTTTATTTTT
1 TTTTATTTTT
5082419 TTGAGGTGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 1 0.04
21 5 0.19
22 11 0.41
23 6 0.22
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTATTTTTATATTATTATAT
Found at i:5082418 original size:17 final size:17
Alignment explanation
Indices: 5082378--5082417 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
5082368 TTTTTTTTAA
*
5082378 TTATTTTATTTTATATT
1 TTATTTTATTATATATT
5082395 TTATTTTATTATAT-TT
1 TTATTTTATTATATATT
5082411 TTATTTT
1 TTATTTT
5082418 TTTGAGGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTTTATTATATATT
Found at i:5083012 original size:35 final size:35
Alignment explanation
Indices: 5082973--5083052 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
5082963 GGATCATGCA
* * * * *
5082973 TAACCTTTACAATATGCCTTTTGCAAGATTAGGCG
1 TAACCTTTACAACATGCCATTTGCAAAATCAAGCG
*
5083008 TAACCTCTACAACATGCCATTTGCAAAATCAAGCG
1 TAACCTTTACAACATGCCATTTGCAAAATCAAGCG
5083043 TAACCTTTAC
1 TAACCTTTAC
5083053 CAAGATGCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (35 bp):
TAACCTTTACAACATGCCATTTGCAAAATCAAGCG
Found at i:5084966 original size:24 final size:23
Alignment explanation
Indices: 5084908--5084968 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
5084898 TCTTTTCCTG
*
5084908 ACAAACACAACTGTCTATTTCCA
1 ACAAACACAATTGTCTATTTCCA
***
5084931 ATGGACACAATTGTCTAATTTCCA
1 ACAAACACAATTGTCT-ATTTCCA
*
5084955 ACAAACATAATTGT
1 ACAAACACAATTGT
5084969 TTGTTTTCCA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (23 bp):
ACAAACACAATTGTCTATTTCCA
Found at i:5086174 original size:28 final size:29
Alignment explanation
Indices: 5086143--5086201 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
5086133 AAATAATTAG
* *
5086143 TTATTTTTTATTTT-ATTAAATTAAATTT
1 TTATATTTTATTTTAATTAAATAAAATTT
5086171 TTATATTTTATTTTAAATTAAATAAAATTT
1 TTATATTTTATTTT-AATTAAATAAAATTT
5086201 T
1 T
5086202 ATTAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTATATTTTATTTTAATTAAATAAAATTT
Found at i:5086192 original size:25 final size:22
Alignment explanation
Indices: 5086145--5086193 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 22
5086135 ATAATTAGTT
5086145 ATTTTTTATTTTATTAAATTAA
1 ATTTTTTATTTTATTAAATTAA
5086167 ATTTTTATATTTTATTTTAAATTAA
1 ATTTTT-TATTTTA--TTAAATTAA
5086192 AT
1 AT
5086194 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
25 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTTATTTTATTAAATTAA
Found at i:5086206 original size:20 final size:20
Alignment explanation
Indices: 5086183--5086227 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
5086173 ATATTTTATT
5086183 TTAAATTAAATAA-AATTTTA
1 TTAAATT-AATAATAATTTTA
5086203 TT-AATTAATAATTAATTTTA
1 TTAAATTAATAA-TAATTTTA
5086223 TTAAA
1 TTAAA
5086228 ATATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 11 0.50
21 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATTAATAATAATTTTA
Found at i:5108754 original size:20 final size:21
Alignment explanation
Indices: 5108710--5108755 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
5108700 CTCTATAAAG
*
5108710 AAGTTGATATGTTTTTATTAA
1 AAGTTGATATGTTTTTAGTAA
* *
5108731 AAGTTGATGTG-TTTTAGTAC
1 AAGTTGATATGTTTTTAGTAA
5108751 AAGTT
1 AAGTT
5108756 TATTAGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (21 bp):
AAGTTGATATGTTTTTAGTAA
Found at i:5109057 original size:21 final size:21
Alignment explanation
Indices: 5109033--5109072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5109023 TGCTTCAAAA
5109033 GAGCCAATATTTTGCTACTTG
1 GAGCCAATATTTTGCTACTTG
*
5109054 GAGCCAATATTTTTCTACT
1 GAGCCAATATTTTGCTACT
5109073 AAGTCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (21 bp):
GAGCCAATATTTTGCTACTTG
Found at i:5109101 original size:20 final size:20
Alignment explanation
Indices: 5109072--5109111 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5109062 ATTTTTCTAC
5109072 TAAGTCTTAAAGAAATTTGT
1 TAAGTCTTAAAGAAATTTGT
* *
5109092 TAAGTTTTAAAGATATTTGT
1 TAAGTCTTAAAGAAATTTGT
5109112 CTAAACGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.45
Consensus pattern (20 bp):
TAAGTCTTAAAGAAATTTGT
Found at i:5113493 original size:19 final size:19
Alignment explanation
Indices: 5113469--5113506 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5113459 CCATTTAACT
*
5113469 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
5113488 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
5113507 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:5116835 original size:11 final size:11
Alignment explanation
Indices: 5116819--5116844 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5116809 GATATGTTAA
5116819 TGTAGCATAAT
1 TGTAGCATAAT
5116830 TGTAGCATAAT
1 TGTAGCATAAT
5116841 TGTA
1 TGTA
5116845 AACAATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (11 bp):
TGTAGCATAAT
Found at i:5134337 original size:28 final size:28
Alignment explanation
Indices: 5134295--5134450 Score: 201
Period size: 28 Copynumber: 5.6 Consensus size: 28
5134285 TTGTATTTTC
* * *
5134295 ATTATTCATCCACTTCTGGTAGGTTAAA
1 ATTATCCATCCACTTCTGGTGGGTTGAA
*
5134323 AATATTCC-TCCACTTCTGGTGGGTTGAA
1 ATTA-TCCATCCACTTCTGGTGGGTTGAA
*
5134351 ATTATCCATCCACATCTGGTGGGTTGAA
1 ATTATCCATCCACTTCTGGTGGGTTGAA
5134379 ATTATCCATCCACTTCTGGTGGGTTGAA
1 ATTATCCATCCACTTCTGGTGGGTTGAA
* **
5134407 ATTATCCATCCACTTCT-GTTGG-CAAA
1 ATTATCCATCCACTTCTGGTGGGTTGAA
*
5134433 ATTATCCATTCACTTCTG
1 ATTATCCATCCACTTCTG
5134451 ATGGTAAAAT
Statistics
Matches: 114, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
26 18 0.16
27 7 0.06
28 87 0.76
29 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (28 bp):
ATTATCCATCCACTTCTGGTGGGTTGAA
Found at i:5134499 original size:25 final size:24
Alignment explanation
Indices: 5134418--5134499 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
5134408 TTATCCATCC
* * *
5134418 ACTTCTGTTGGCAAAATTATCCATT
1 ACTTCTGATGGTAAAATTAT-TATT
*
5134443 CACTTCTGATGGTAAAATTATTCTT
1 -ACTTCTGATGGTAAAATTATTATT
*
5134468 AGATTCTGATGGTAAAATTATTATCT
1 A-CTTCTGATGGTAAAATTATTAT-T
5134494 ACTTCT
1 ACTTCT
5134500 TCCATATCCA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.02
25 26 0.55
26 20 0.43
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (24 bp):
ACTTCTGATGGTAAAATTATTATT
Found at i:5138475 original size:15 final size:16
Alignment explanation
Indices: 5138455--5138489 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5138445 TTTACACAGA
5138455 TTTTTTCCCA-TAAAG
1 TTTTTTCCCAGTAAAG
*
5138470 TTTTTTCCTAGTAAAG
1 TTTTTTCCCAGTAAAG
5138486 TTTT
1 TTTT
5138490 AACGAAGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (16 bp):
TTTTTTCCCAGTAAAG
Found at i:5148032 original size:880 final size:879
Alignment explanation
Indices: 5146332--5148090 Score: 3509
Period size: 880 Copynumber: 2.0 Consensus size: 879
5146322 GGGGATACAA
5146332 GAGGGTGATATTGTCATGATGCATGCTTGGATCACGCTCAAGCGTGGGAGCGGTCTTGTTGCTTC
1 GAGGGTGATATTGTCATGATGCATGCTTGGATCACGCTCAAGCGTGGGAGCGGTCTTGTTGCTTC
5146397 TCTTTCTCATGCTCCTTACTTCCCTTTCCACAAGGAGGAGAACTTCTGGCTACTGGTTGCTGACT
66 TCTTTCTCATGCTCCTTACTTCCCTTTCCACAAGGAGGAGAACTTCTGGCTACTGGTTGCTGACT
5146462 CTGTCTCCAATGATGTTTGGATCTCCCAAAAGGTTAGCTTCATGGATGAGGCTGTGGCCATAACA
131 CTGTCTCCAATGATGTTTGGATCTCCCAAAAGGTTAGCTTCATGGATGAGGCTGTGGCCATAACA
5146527 GCAGCATCTAAAGCAATTCAAGAGTTGAAGGAAGGTTCAGGGGCAAGTCTGAAGGCGACAAATGC
196 GCAGCATCTAAAGCAATTCAAGAGTTGAAGGAAGGTTCAGGGGCAAGTCTGAAGGCGACAAATGC
5146592 AGCTGTTAGAGAAGCCGTTGAGAAAGTAAGGAGTGGGTCAAGGTTAGTGATGTGCAAATTTCAGG
261 AGCTGTTAGAGAAGCCGTTGAGAAAGTAAGGAGTGGGTCAAGGTTAGTGATGTGCAAATTTCAGG
5146657 CTCCTGCTGAGGCAAATTACAATTTGACTGCATTCTGCTTGTGTGACTCTTGGATTGGTTGTGAT
326 CTCCTGCTGAGGCAAATTACAATTTGACTGCATTCTGCTTGTGTGACTCTTGGATTGGTTGTGAT
5146722 AAGAAGACAAACTTAAAGATGAAATAATGAAACGGAGTCGAGCAGGTACAAGGACAGGTCCCTTG
391 AAGAAGACAAACTTAAAGATGAAATAATGAAACGGAGTCGAGCAGGTACAAGGACAGGTCCCTTG
5146787 TCAGAAGAGGGAGCGGTCATGGAAGAGGGGATTGGGGAGGAAGAAGATGGATATGATGATTATGA
456 TCAGAAGAGGGAGCGGTCATGGAAGAGGGGATTGGGGAGGAAGAAGATGGATATGATGATTATGA
5146852 GAGTGAATACAGTGACGATGAAGAGGATGAACAAGATTCTAAGAGGGATGGAGCTTTGGCCAATG
521 GAGTGAATACAGTGACGATGAAGAGGATGAACAAGATTCTAAGAGGGATGGAGCTTTGGCCAATG
5146917 GTGCTGTTGATAATAAAGGAAATGGATCAAGCTCTGAAAGTTCCGACAATGAGTGAAAAACCTTT
586 GTGCTGTTGATAATAAAGGAAATGGATCAAGCTCTGAAAGTTCCGACAATGAGTGAAAAACCTTT
5146982 TATTTTTGGTTTTTCCTTTTTAGGAATACAGGGGGAGGTGATGGATCCCATTCATTTCTTTTATA
651 TATTTTTGGTTTTTCCTTTTTAGGAATACAGGGGGAGGTGATGGATCCCATTCATTTCTTTTATA
5147047 TTGTAACATTTGATTATAGGGTATACCAATCCACATGTTGATATGAACTTAAATGCCGTAATGCT
716 TTGTAACATTTGATTATAGGGTATACCAATCCACATGTTGATATGAACTTAAATGCCGTAATGCT
5147112 TGTCTCATAGAATCCTTAAAACCATTAACTGTATCTGTTGATTAACTTCCGTTAATGCATTCAGT
781 TGTCTCATAGAATCCTTAAAACCATTAACTGTATCTGTTGATTAACTTCCGTTAATGCATTCAGT
5147177 TTTCCTGTTTCAAAACCAAGACGTTTCACAAGTT
846 TTTCCTGTTTCAAAACCAAGACGTTTCACAAGTT
5147211 NGAGGGTGATATTGTCATGATGCATGCTTGGATCACGCTCAAGCGTGGGAGCGGTCTTGTTGCTT
1 -GAGGGTGATATTGTCATGATGCATGCTTGGATCACGCTCAAGCGTGGGAGCGGTCTTGTTGCTT
5147276 CTCTTTCTCATGCTCCTTACTTCCCTTTCCACAAGGAGGAGAACTTCTGGCTACTGGTTGCTGAC
65 CTCTTTCTCATGCTCCTTACTTCCCTTTCCACAAGGAGGAGAACTTCTGGCTACTGGTTGCTGAC
5147341 TCTGTCTCCAATGATGTTTGGATCTCCCAAAAGGTTAGCTTCATGGATGAGGCTGTGGCCATAAC
130 TCTGTCTCCAATGATGTTTGGATCTCCCAAAAGGTTAGCTTCATGGATGAGGCTGTGGCCATAAC
5147406 AGCAGCATCTAAAGCAATTCAAGAGTTGAAGGAAGGTTCAGGGGCAAGTCTGAAGGCGACAAATG
195 AGCAGCATCTAAAGCAATTCAAGAGTTGAAGGAAGGTTCAGGGGCAAGTCTGAAGGCGACAAATG
5147471 CAGCTGTTAGAGAAGCCGTTGAGAAAGTAAGGAGTGGGTCAAGGTTAGTGATGTGCAAATTTCAG
260 CAGCTGTTAGAGAAGCCGTTGAGAAAGTAAGGAGTGGGTCAAGGTTAGTGATGTGCAAATTTCAG
5147536 GCTCCTGCTGAGGCAAATTACAATTTGACTGCATTCTGCTTGTGTGACTCTTGGATTGGTTGTGA
325 GCTCCTGCTGAGGCAAATTACAATTTGACTGCATTCTGCTTGTGTGACTCTTGGATTGGTTGTGA
5147601 TAAGAAGACAAACTTAAAGATGAAATAATGAAACGGAGTCGAGCAGGTACAAGGACAGGTCCCTT
390 TAAGAAGACAAACTTAAAGATGAAATAATGAAACGGAGTCGAGCAGGTACAAGGACAGGTCCCTT
5147666 GTCAGAAGAGGGAGCGGTCATGGAAGAGGGGATTGGGGAGGAAGAAGATGGATATGATGATTATG
455 GTCAGAAGAGGGAGCGGTCATGGAAGAGGGGATTGGGGAGGAAGAAGATGGATATGATGATTATG
5147731 AGAGTGAATACAGTGACGATGAAGAGGATGAACAAGATTCTAAGAGGGATGGAGCTTTGGCCAAT
520 AGAGTGAATACAGTGACGATGAAGAGGATGAACAAGATTCTAAGAGGGATGGAGCTTTGGCCAAT
5147796 GGTGCTGTTGATAATAAAGGAAATGGATCAAGCTCTGAAAGTTCCGACAATGAGTGAAAAACCTT
585 GGTGCTGTTGATAATAAAGGAAATGGATCAAGCTCTGAAAGTTCCGACAATGAGTGAAAAACCTT
5147861 TTATTTTTGGTTTTTCCTTTTTAGGAATACAGGGGGAGGTGATGGATCCCATTCATTTCTTTTAT
650 TTATTTTTGGTTTTTCCTTTTTAGGAATACAGGGGGAGGTGATGGATCCCATTCATTTCTTTTAT
5147926 ATTGTAACATTTGATTATAGGGTATACCAATCCACATGTTGATATGAACTTAAATGCCGTAATGC
715 ATTGTAACATTTGATTATAGGGTATACCAATCCACATGTTGATATGAACTTAAATGCCGTAATGC
5147991 TTGTCTCATAGAATCCTTAAAACCATTAACTGTATCTGTTGATTAACTTCCGTTAATGCATTCAG
780 TTGTCTCATAGAATCCTTAAAACCATTAACTGTATCTGTTGATTAACTTCCGTTAATGCATTCAG
5148056 TTTTCCTGTTTCAAAACCAAGACGTTTCACAAGTT
845 TTTTCCTGTTTCAAAACCAAGACGTTTCACAAGTT
5148091 CTTTCCAAAA
Statistics
Matches: 879, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
880 879 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (879 bp):
GAGGGTGATATTGTCATGATGCATGCTTGGATCACGCTCAAGCGTGGGAGCGGTCTTGTTGCTTC
TCTTTCTCATGCTCCTTACTTCCCTTTCCACAAGGAGGAGAACTTCTGGCTACTGGTTGCTGACT
CTGTCTCCAATGATGTTTGGATCTCCCAAAAGGTTAGCTTCATGGATGAGGCTGTGGCCATAACA
GCAGCATCTAAAGCAATTCAAGAGTTGAAGGAAGGTTCAGGGGCAAGTCTGAAGGCGACAAATGC
AGCTGTTAGAGAAGCCGTTGAGAAAGTAAGGAGTGGGTCAAGGTTAGTGATGTGCAAATTTCAGG
CTCCTGCTGAGGCAAATTACAATTTGACTGCATTCTGCTTGTGTGACTCTTGGATTGGTTGTGAT
AAGAAGACAAACTTAAAGATGAAATAATGAAACGGAGTCGAGCAGGTACAAGGACAGGTCCCTTG
TCAGAAGAGGGAGCGGTCATGGAAGAGGGGATTGGGGAGGAAGAAGATGGATATGATGATTATGA
GAGTGAATACAGTGACGATGAAGAGGATGAACAAGATTCTAAGAGGGATGGAGCTTTGGCCAATG
GTGCTGTTGATAATAAAGGAAATGGATCAAGCTCTGAAAGTTCCGACAATGAGTGAAAAACCTTT
TATTTTTGGTTTTTCCTTTTTAGGAATACAGGGGGAGGTGATGGATCCCATTCATTTCTTTTATA
TTGTAACATTTGATTATAGGGTATACCAATCCACATGTTGATATGAACTTAAATGCCGTAATGCT
TGTCTCATAGAATCCTTAAAACCATTAACTGTATCTGTTGATTAACTTCCGTTAATGCATTCAGT
TTTCCTGTTTCAAAACCAAGACGTTTCACAAGTT
Found at i:5151523 original size:21 final size:24
Alignment explanation
Indices: 5151497--5151567 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
5151487 ATTTATTTTT
5151497 ATTTTATTT-TT-AAATATTAATA
1 ATTTTATTTATTAAAATATTAATA
5151519 ATTTATAATTTAATTAAAATATTAATA
1 ATTT-T-ATTT-ATTAAAATATTAATA
*
5151546 A-TTTA-TAATGTAAAATATTAAT
1 ATTTTATTTAT-TAAAATATTAAT
5151568 GTTTTAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 6 0.14
23 14 0.33
24 5 0.12
25 1 0.02
26 4 0.10
27 12 0.29
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (24 bp):
ATTTTATTTATTAAAATATTAATA
Found at i:5151548 original size:20 final size:23
Alignment explanation
Indices: 5151508--5151567 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 23
5151498 TTTTATTTTT
*
5151508 AAATATTAATAATTTATAATTTAATTA
1 AAATATTAATAATTTATAA--T--GTA
5151535 AAATATTAATAATTTATAATGTA
1 AAATATTAATAATTTATAATGTA
5151558 AAATATTAAT
1 AAATATTAAT
5151568 GTTTTAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.38
25 1 0.03
27 19 0.59
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATTAATAATTTATAATGTA
Found at i:5151630 original size:53 final size:52
Alignment explanation
Indices: 5151522--5151630 Score: 114
Period size: 53 Copynumber: 2.1 Consensus size: 52
5151512 ATTAATAATT
**
5151522 TATAATTTAATTAAAATATTAATAATTTATAATGTAAAATATTAATGTTTTAA
1 TATAATTTAATTAAAATATT-ATAATTTATAATGTAAAATATTAATGTTACAA
* * * *
5151575 TATAATTTAATTACTAATATT-TTATTTATAATTTAATATTATT-ATGATTACAA
1 TATAATTTAATTA-AAATATTATAATTTATAATGTAA-AATATTAATG-TTACAA
5151628 TAT
1 TAT
5151631 TAATATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
52 16 0.34
53 25 0.53
54 6 0.13
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (52 bp):
TATAATTTAATTAAAATATTATAATTTATAATGTAAAATATTAATGTTACAA
Found at i:5159049 original size:102 final size:103
Alignment explanation
Indices: 5158810--5159073 Score: 325
Period size: 102 Copynumber: 2.6 Consensus size: 103
5158800 TTTATTTGGC
* * *
5158810 ATTAGGTGCCTGAATATTTGTTGAGCATTGTGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
* * **
5158875 ATGTTGAGCGTTGCGTGAGAGTTAATACGTGACTGAAT
66 ATGTTGAGCATTGCGTGACAGGCAATACGTGACTGAAT
* * * * *
5158913 ATTACCTGACTGAATATTTGTTGAACATTACGTGAGTTTTTTATAGGCATTACGTGATTGAATAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
* **
5158978 TTGTT-AGCATTGCGTGACAGGCGTTACGTGACCT-AAT
66 ATGTTGAGCATTGCGTGACAGGCAATACGTGA-CTGAAT
** * * *
5159015 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTATTTGTAGGCATTGCGTGACT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACT
5159074 TTAGCTACCT
Statistics
Matches: 136, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
102 73 0.54
103 63 0.46
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATAT
ATGTTGAGCATTGCGTGACAGGCAATACGTGACTGAAT
Found at i:5159067 original size:22 final size:23
Alignment explanation
Indices: 5159029--5159072 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
5159019 CGTGACTGAA
*
5159029 TATTTGTTGAGCATTGCGTGACC
1 TATTTGTAGAGCATTGCGTGACC
5159052 TATTTGTAG-GCATTGCGTGAC
1 TATTTGTAGAGCATTGCGTGAC
5159073 TTTAGCTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (23 bp):
TATTTGTAGAGCATTGCGTGACC
Found at i:5159679 original size:29 final size:29
Alignment explanation
Indices: 5159637--5159695 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5159627 AGGAGGTGCC
5159637 TTTGAGTGTGAGGGACCAGTTGCACATAT
1 TTTGAGTGTGAGGGACCAGTTGCACATAT
5159666 TTTGAGTGTGAGGGACCAGTTGCACATAT
1 TTTGAGTGTGAGGGACCAGTTGCACATAT
5159695 T
1 T
5159696 CCAGCAGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.32
Consensus pattern (29 bp):
TTTGAGTGTGAGGGACCAGTTGCACATAT
Found at i:5169984 original size:17 final size:18
Alignment explanation
Indices: 5169929--5169985 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 18
5169919 ACTCTACACC
* *
5169929 AATCAAAACCTCATAAATCA
1 AATCAAAA-CTAATAAA-AA
**
5169949 AATCAAAACTAATCCAAA
1 AATCAAAACTAATAAAAA
5169967 AATCAAAA-TAATAAAAA
1 AATCAAAACTAATAAAAA
5169984 AA
1 AA
5169986 AAGACCCCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 9 0.29
18 9 0.29
19 5 0.16
20 8 0.26
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (18 bp):
AATCAAAACTAATAAAAA
Found at i:5171741 original size:51 final size:51
Alignment explanation
Indices: 5171677--5171791 Score: 158
Period size: 51 Copynumber: 2.3 Consensus size: 51
5171667 ATTTACCAGA
* * *
5171677 AATTCATTACATCTTGTCATTAACGTTATTAATAACCCTATACTGAAAATT
1 AATTAATTTCATCTTGTCATTAACGTTATTAATAACCCTATACAGAAAATT
* * * * *
5171728 AATTAATTTCATCTTGTCATTAATGTTATTACTAACTCTATTCAGATAATT
1 AATTAATTTCATCTTGTCATTAACGTTATTAATAACCCTATACAGAAAATT
5171779 AATTAATTTCATC
1 AATTAATTTCATC
5171792 AATTGGTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (51 bp):
AATTAATTTCATCTTGTCATTAACGTTATTAATAACCCTATACAGAAAATT
Found at i:5171856 original size:17 final size:18
Alignment explanation
Indices: 5171825--5171862 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5171815 AAAACCTCTA
5171825 TAAATTAATAATTTTGAT
1 TAAATTAATAATTTTGAT
* *
5171843 TAAA-TAATATTTTTGGT
1 TAAATTAATAATTTTGAT
5171860 TAA
1 TAA
5171863 TCCCAACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (18 bp):
TAAATTAATAATTTTGAT
Found at i:5175439 original size:16 final size:16
Alignment explanation
Indices: 5175418--5175462 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
5175408 AGTAGATATT
5175418 TTATTAATTATTTTAA
1 TTATTAATTATTTTAA
5175434 TTATT-ATATATTTTAA
1 TTATTAAT-TATTTTAA
5175450 TGTAATTAATTAT
1 T-T-ATTAATTAT
5175463 ATTATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 1 0.04
18 6 0.24
19 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTATTAATTATTTTAA
Found at i:5175467 original size:30 final size:28
Alignment explanation
Indices: 5175413--5175471 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
5175403 AAATAAGTAG
*
5175413 ATATTTTATTAATTATTTTAATTATTAT
1 ATATTTTATTAATTATTATAATTATTAT
5175441 ATATTTTAATGTAATTAATTAT-ATTATTAT
1 ATATTTT-AT-TAATT-ATTATAATTATTAT
5175471 A
1 A
5175472 AAATTATAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
29 2 0.07
30 14 0.52
31 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
ATATTTTATTAATTATTATAATTATTAT
Found at i:5176100 original size:18 final size:20
Alignment explanation
Indices: 5176077--5176124 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
5176067 TGAAAATATT
5176077 TAAATATTATTTAA-TAT-A
1 TAAATATTATTTAATTATAA
*
5176095 TTAATATTATTTAATTATAA
1 TAAATATTATTTAATTATAA
5176115 TAAATATTAT
1 TAAATATTAT
5176125 AAAGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATTATTTAATTATAA
Found at i:5176108 original size:10 final size:10
Alignment explanation
Indices: 5176073--5176147 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
5176063 GAAATGAAAA
5176073 TATTTAAATAT
1 TATTT-AATAT
5176084 TATTTAATA-
1 TATTTAATAT
5176093 TA-TTAATAT
1 TATTTAATAT
5176102 TATTTAAT-T
1 TATTTAATAT
* *
5176111 ATAATAAATAT
1 -TATTTAATAT
**
5176122 TATAAAGAATAT
1 TAT--TTAATAT
5176134 TATTTAATAT
1 TATTTAATAT
5176144 TATT
1 TATT
5176148 ATTTGAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.12
9 5 0.10
10 26 0.51
11 6 0.12
12 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (10 bp):
TATTTAATAT
Found at i:5176159 original size:45 final size:45
Alignment explanation
Indices: 5176099--5176192 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
5176089 AATATATTAA
*
5176099 TATTATTTAATTATAATAAATATTATAAAGAATATTATTTAATAT
1 TATTATTTAATTATAATAAATATAATAAAGAATATTATTTAATAT
* *
5176144 TATTATTTGAA-TATAATAAATGTAATAAAGAATATTATTTAGTAT
1 TATTATTT-AATTATAATAAATATAATAAAGAATATTATTTAATAT
5176189 TATT
1 TATT
5176193 TAAATTTAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
45 43 0.96
46 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (45 bp):
TATTATTTAATTATAATAAATATAATAAAGAATATTATTTAATAT
Found at i:5176252 original size:30 final size:29
Alignment explanation
Indices: 5176213--5176270 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
5176203 GAAGATTATA
* *
5176213 TTTTGTCTTTTAATTTTAAATATTATTTT
1 TTTTATCTTTTAATATTAAATATTATTTT
5176242 NTTTTATCTTTTAATATTAAATATTATTT
1 -TTTTATCTTTTAATATTAAATATTATTT
5176271 AATTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTATCTTTTAATATTAAATATTATTTT
Found at i:5177006 original size:33 final size:33
Alignment explanation
Indices: 5176943--5177006 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5176933 GCATGTTATG
* *
5176943 TCATCATCAATTATGATATGTTAATCTGTCAAA
1 TCATCATCAATTATGATATGCTAATATGTCAAA
*
5176976 TCATCATTAATTATGATAT-CTAAGTATGTCA
1 TCATCATCAATTATGATATGCTAA-TATGTCA
5177007 CGTCAGTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (33 bp):
TCATCATCAATTATGATATGCTAATATGTCAAA
Found at i:5177098 original size:30 final size:29
Alignment explanation
Indices: 5177064--5177128 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
5177054 AATAATTAGT
* *
5177064 TATAAAAATTTATTTGATTCAAAATAAAA
1 TATAAAAACTTATTTGACTCAAAATAAAA
*
5177093 GTATAAAGACTTATTTGACTCAAAATAAAA
1 -TATAAAAACTTATTTGACTCAAAATAAAA
5177123 TATAAA
1 TATAAA
5177129 TGTTTGATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (29 bp):
TATAAAAACTTATTTGACTCAAAATAAAA
Found at i:5177139 original size:29 final size:29
Alignment explanation
Indices: 5177064--5177166 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
5177054 AATAATTAGT
* * *
5177064 TATAAAAATTTATTTGATTCAAAATAAAA
1 TATAAAGACTTATTTGAATCAAAATAAAA
*
5177093 GTATAAAGACTTATTTGACTCAAAATAAAA
1 -TATAAAGACTTATTTGAATCAAAATAAAA
* *
5177123 TATAAATG-TTTGA-TTGAATGCAATA-AAAA
1 TATAAA-GACTT-ATTTGAAT-CAAAATAAAA
*
5177152 TATAAAGATTTATTT
1 TATAAAGACTTATTT
5177167 TAAATTTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
28 2 0.03
29 28 0.45
30 32 0.52
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.37
Consensus pattern (29 bp):
TATAAAGACTTATTTGAATCAAAATAAAA
Found at i:5180269 original size:13 final size:13
Alignment explanation
Indices: 5180253--5180279 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5180243 TATTATTTAT
5180253 TTTTATCAAGTAA
1 TTTTATCAAGTAA
5180266 TTTTATCAAGTAA
1 TTTTATCAAGTAA
5180279 T
1 T
5180280 AATTTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTATCAAGTAA
Found at i:5180602 original size:10 final size:10
Alignment explanation
Indices: 5180587--5180614 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5180577 CTTAACATAA
5180587 TATATTTATT
1 TATATTTATT
5180597 TATATTTATT
1 TATATTTATT
5180607 TATATTTA
1 TATATTTA
5180615 CTTTTTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTTATT
Found at i:5180927 original size:18 final size:17
Alignment explanation
Indices: 5180889--5180927 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
5180879 TGTATATATT
*
5180889 TTTATTTTTATATTATA
1 TTTATTTTTATATTAGA
5180906 -TTATTTTTATATATAGA
1 TTTATTTTTATAT-TAGA
5180923 TTTAT
1 TTTAT
5180928 ATCTCTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 12 0.63
17 3 0.16
18 4 0.21
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTATTTTTATATTAGA
Found at i:5181410 original size:34 final size:34
Alignment explanation
Indices: 5181372--5181626 Score: 261
Period size: 34 Copynumber: 7.4 Consensus size: 34
5181362 ATCACCCCCC
*
5181372 ACCGGCGGCAAACACTCCAA-AT-TTCACTCCTCCT
1 ACCGGCGGCAAAC-CTCCAAGCTGTT-ACTCCTCCT
* *
5181406 ACCGGCGGCAAACCACCAAGCTGTTGCTCCTCCT
1 ACCGGCGGCAAACCTCCAAGCTGTTACTCCTCCT
*
5181440 AACCGGCGGCAAACCCCCAAGCTGTTACTCCTCTCT
1 -ACCGGCGGCAAACCTCCAAGCTGTTACTCCTC-CT
* *
5181476 -CCGGCAGCAAACCTCCAAGCT-TTCACTCTTCCT
1 ACCGGCGGCAAACCTCCAAGCTGTT-ACTCCTCCT
* * * *
5181509 ACCGGCAGCAAACACTCC-AGAT-TTCAGTCTTCCT
1 ACCGGCGGCAAAC-CTCCAAGCTGTT-ACTCCTCCT
* *
5181543 ACCGGCGGCCAACCTCCAAGCTGTTGCTCCTCTCT
1 ACCGGCGGCAAACCTCCAAGCTGTTACTCCTC-CT
* *
5181578 AAACGGCGGCAAACCTCCAAGCTGTTGCTCCTCCT
1 -ACCGGCGGCAAACCTCCAAGCTGTTACTCCTCCT
5181613 ACCGGCGGCAAACC
1 ACCGGCGGCAAACC
5181627 AGCCCAGATT
Statistics
Matches: 191, Mismatches: 19, Indels: 22
0.82 0.08 0.09
Matches are distributed among these distances:
33 13 0.07
34 104 0.54
35 42 0.22
36 32 0.17
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.20
Consensus pattern (34 bp):
ACCGGCGGCAAACCTCCAAGCTGTTACTCCTCCT
Found at i:5181452 original size:35 final size:34
Alignment explanation
Indices: 5181398--5181660 Score: 232
Period size: 34 Copynumber: 7.6 Consensus size: 34
5181388 CCAAATTTCA
5181398 CTCCTCCTACCGGCGGCAAACCACCAAGCTGTTG
1 CTCCTCCTACCGGCGGCAAACCACCAAGCTGTTG
* *
5181432 CTCCTCCTAACCGGCGGCAAACCCCCAAGCTGTTA
1 CTCCTCCT-ACCGGCGGCAAACCACCAAGCTGTTG
* * *
5181467 CTCCTCTCT-CCGGCAGCAAACCTCCAAGCT-TTCA
1 CTCCTC-CTACCGGCGGCAAACCACCAAGCTGTT-G
* * * *
5181501 CTCTTCCTACCGGCAGCAAA-CACTCCAGAT-TT-
1 CTCCTCCTACCGGCGGCAAACCAC-CAAGCTGTTG
* * *
5181533 CAGTCTTCCTACCGGCGGCCAACCTCCAAGCTGTTG
1 C--TCCTCCTACCGGCGGCAAACCACCAAGCTGTTG
* *
5181569 CTCCTCTCTAAACGGCGGCAAACCTCCAAGCTGTTG
1 CTCCTC-CT-ACCGGCGGCAAACCACCAAGCTGTTG
* * *
5181605 CTCCTCCTACCGGCGGCAAACCAGCCCAGAT-TTCT
1 CTCCTCCTACCGGCGGCAAACCA-CCAAGCTGTT-G
*
5181640 CTCCTCCTACCGGCAGCAAAC
1 CTCCTCCTACCGGCGGCAAAC
5181661 ACTCTCTCCC
Statistics
Matches: 193, Mismatches: 22, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.01
33 6 0.03
34 90 0.47
35 63 0.33
36 33 0.17
ACGTcount: A:0.21, C:0.41, G:0.17, T:0.21
Consensus pattern (34 bp):
CTCCTCCTACCGGCGGCAAACCACCAAGCTGTTG
Found at i:5181486 original size:69 final size:70
Alignment explanation
Indices: 5181372--5181664 Score: 284
Period size: 69 Copynumber: 4.2 Consensus size: 70
5181362 ATCACCCCCC
5181372 ACCGGCGGCAAACACTCCAA-ATTTCACTCCTCCTACCGGCGGCAAACCACCAAGCTGTTGCTCC
1 ACCGGCGGCAAACACTCCAAGATTTCACTCCTCCTACCGGCGGCAAACCACCAAGCTGTTGCTCC
5181436 TCCTA
66 TCCTA
* * * * *
5181441 ACCGGCGGCAAAC-CCCCAAGCTGTT-ACTCCTCTCT-CCGGCAGCAAACCTCCAAGCT-TTCAC
1 ACCGGCGGCAAACACTCCAAGAT-TTCACTCCTC-CTACCGGCGGCAAACCACCAAGCTGTT-GC
*
5181502 TCTTCCT-
63 TCCTCCTA
* * * * *
5181509 ACCGGCAGCAAACACTCC-AGATTTCAGTCTTCCTACCGGCGGCCAACCTCCAAGCTGTTGCTCC
1 ACCGGCGGCAAACACTCCAAGATTTCACTCCTCCTACCGGCGGCAAACCACCAAGCTGTTGCTCC
5181573 TCTCTA
66 TC-CTA
* * * * * *
5181579 AACGGCGGCAAAC-CTCCAAGCTGTT-GCTCCTCCTACCGGCGGCAAACCAGCCCAGAT-TTCTC
1 ACCGGCGGCAAACACTCCAAGAT-TTCACTCCTCCTACCGGCGGCAAACCA-CCAAGCTGTT-GC
5181641 TCCTCCT-
63 TCCTCCTA
*
5181648 ACCGGCAGCAAACACTC
1 ACCGGCGGCAAACACTC
5181665 TCTCCCTCCT
Statistics
Matches: 181, Mismatches: 28, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
67 4 0.02
68 51 0.28
69 69 0.38
70 44 0.24
71 13 0.07
ACGTcount: A:0.23, C:0.41, G:0.17, T:0.20
Consensus pattern (70 bp):
ACCGGCGGCAAACACTCCAAGATTTCACTCCTCCTACCGGCGGCAAACCACCAAGCTGTTGCTCC
TCCTA
Found at i:5183239 original size:2 final size:2
Alignment explanation
Indices: 5183234--5183266 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5183224 ATGCTCAACA
5183234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5183267 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5183271 original size:2 final size:2
Alignment explanation
Indices: 5183266--5183298 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5183256 ATATATATAT
5183266 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5183299 ATGAATGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5184595 original size:71 final size:71
Alignment explanation
Indices: 5184479--5184621 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
5184469 TTTTGCTTTA
*
5184479 TTTAATGCTTTTCATTACTGGGGTCATGACGTAAATTTACAATACAAAGAGCCCTT-ACTGGATG
1 TTTAATGCTTTTCATTACTGAGGTCATGACGTAAATTTACAATACAAAGAGCCCTTCA-TGGATG
5184543 TTGTCGG
65 TTGTCGG
*
5184550 TTTAATGCTTTTCATTACTGAGGTCATGACGTTAATTTACAATACAAAGAGCCCTTCATGGATGT
1 TTTAATGCTTTTCATTACTGAGGTCATGACGTAAATTTACAATACAAAGAGCCCTTCATGGATGT
5184615 TGTCGG
66 TGTCGG
5184621 T
1 T
5184622 AATCTCACTT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 68 0.99
72 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (71 bp):
TTTAATGCTTTTCATTACTGAGGTCATGACGTAAATTTACAATACAAAGAGCCCTTCATGGATGT
TGTCGG
Found at i:5203798 original size:2 final size:2
Alignment explanation
Indices: 5203791--5203822 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5203781 TAAAAATAGA
5203791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5203823 ATGAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5212342 original size:17 final size:17
Alignment explanation
Indices: 5212322--5212354 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5212312 AATTATATGA
5212322 TATAAAATTATGAGGTT
1 TATAAAATTATGAGGTT
*
5212339 TATAAAATTGTGAGGT
1 TATAAAATTATGAGGT
5212355 CTAAAGCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (17 bp):
TATAAAATTATGAGGTT
Found at i:5218098 original size:10 final size:11
Alignment explanation
Indices: 5218069--5218102 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
5218059 ACTCTAAAAC
5218069 AAATATTTTAGA
1 AAATATTTTA-A
5218081 AAATATTTTAA
1 AAATATTTTAA
5218092 AAA-ATTTTAA
1 AAATATTTTAA
5218102 A
1 A
5218103 TTTAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 4 0.18
12 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:5227541 original size:15 final size:15
Alignment explanation
Indices: 5227521--5227555 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5227511 ACTTTTGAAA
* *
5227521 TTTTTTCTCTCTGGT
1 TTTTTTCTCCCTGAT
5227536 TTTTTTCTCCCTGAT
1 TTTTTTCTCCCTGAT
5227551 TTTTT
1 TTTTT
5227556 GGCTACGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.03, C:0.20, G:0.09, T:0.69
Consensus pattern (15 bp):
TTTTTTCTCCCTGAT
Found at i:5227842 original size:7 final size:7
Alignment explanation
Indices: 5227841--5227933 Score: 91
Period size: 7 Copynumber: 12.9 Consensus size: 7
5227831 TTTTTTTATT
5227841 TTTTTTA
1 TTTTTTA
5227848 TTTTTTTA
1 -TTTTTTA
5227856 TTTTTTTA
1 -TTTTTTA
5227864 TTTTTTA
1 TTTTTTA
*
5227871 -TTATTA
1 TTTTTTA
5227877 TTTTTTA
1 TTTTTTA
5227884 TTTTTTA
1 TTTTTTA
5227891 GCTTTTTTA
1 --TTTTTTA
* *
5227900 -ATTATA
1 TTTTTTA
5227906 TTTTATTA
1 TTTT-TTA
*
5227914 TTATTTA
1 TTTTTTA
5227921 TTTTTTA
1 TTTTTTA
5227928 TTTTTT
1 TTTTTT
5227934 GAAATAGGTG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
6 9 0.12
7 36 0.50
8 20 0.28
9 7 0.10
ACGTcount: A:0.18, C:0.01, G:0.01, T:0.80
Consensus pattern (7 bp):
TTTTTTA
Found at i:5227852 original size:17 final size:17
Alignment explanation
Indices: 5227830--5227933 Score: 97
Period size: 17 Copynumber: 5.9 Consensus size: 17
5227820 TTCATTCATC
5227830 ATTTTTTTATTTTTTTT
1 ATTTTTTTATTTTTTTT
5227847 ATTTTTTTA-TTTTTTT
1 ATTTTTTTATTTTTTTT
5227863 ATTTTTTATTATTATTTTTT
1 A-TTTTT-TTATT-TTTTTT
* *
5227883 A-TTTTTTAGCTTTTTTA
1 ATTTTTTTA-TTTTTTTT
*
5227900 ATTATATTTTATTATTATTT
1 ATT-T-TTTTATT-TTTTTT
5227920 A-TTTTTTATTTTTT
1 ATTTTTTTATTTTTT
5227934 GAAATAGGTG
Statistics
Matches: 72, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
16 11 0.15
17 30 0.42
18 10 0.14
19 4 0.06
20 17 0.24
ACGTcount: A:0.18, C:0.01, G:0.01, T:0.80
Consensus pattern (17 bp):
ATTTTTTTATTTTTTTT
Found at i:5227897 original size:37 final size:34
Alignment explanation
Indices: 5227831--5227933 Score: 127
Period size: 37 Copynumber: 2.9 Consensus size: 34
5227821 TCATTCATCA
*
5227831 TTTTTTTATT-TTTTTTATTTTTTTATTTTTTTAT
1 TTTTTTTATTATTTTTTA-TTTTTTATTTTTTAAT
5227865 TTTTTATTATTATTTTTTATTTTTTAGCTTTTTTAAT
1 TTTTT-TTATTATTTTTTATTTTTTA--TTTTTTAAT
* *
5227902 TATATTTTATTATTATTTATTTTTTATTTTTT
1 T-TTTTTTATTATTTTTTATTTTTTATTTTTT
5227934 GAAATAGGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.08
35 18 0.30
36 7 0.11
37 28 0.46
38 3 0.05
ACGTcount: A:0.17, C:0.01, G:0.01, T:0.81
Consensus pattern (34 bp):
TTTTTTTATTATTTTTTATTTTTTATTTTTTAAT
Found at i:5227920 original size:10 final size:9
Alignment explanation
Indices: 5227830--5227926 Score: 69
Period size: 10 Copynumber: 10.6 Consensus size: 9
5227820 TTCATTCATC
5227830 ATTTTT-TT
1 ATTTTTATT
*
5227838 ATTTTTTTT
1 ATTTTTATT
5227847 ATTTTT-TT
1 ATTTTTATT
5227855 ATTTTT-TT
1 ATTTTTATT
5227863 ATTTTTTATT
1 A-TTTTTATT
*
5227873 ATTATTTTTT
1 ATT-TTTATT
5227883 ATTTTTTAGCTT
1 A-TTTTTA--TT
*
5227895 -TTTTAATT
1 ATTTTTATT
5227903 ATATTTTATT
1 AT-TTTTATT
5227913 ATTATTTATT
1 ATT-TTTATT
5227923 -TTTT
1 ATTTT
5227927 ATTTTTTGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
8 21 0.28
9 19 0.25
10 31 0.41
11 2 0.03
12 2 0.03
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.79
Consensus pattern (9 bp):
ATTTTTATT
Found at i:5240530 original size:2 final size:2
Alignment explanation
Indices: 5240523--5240557 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5240513 GGTAAGCCAC
5240523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5240558 CANNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5245400 original size:17 final size:17
Alignment explanation
Indices: 5245378--5245411 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5245368 GTTCTTGATA
5245378 AAATAA-AACTCCTTATT
1 AAATAATAACT-CTTATT
5245395 AAATAATAACTCTTATT
1 AAATAATAACTCTTATT
5245412 TATTATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAACTCTTATT
Found at i:5245609 original size:28 final size:28
Alignment explanation
Indices: 5245557--5245719 Score: 148
Period size: 28 Copynumber: 5.6 Consensus size: 28
5245547 TTTTGTCTTT
* *
5245557 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACAT-GTTT-TCTTGTCTA
* * *
5245587 AATTGAGATAAATATGTTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* * * *
5245615 CATTAAGATAAAAAATATTTTTCTTGTCTTA
1 AATTAAGA-CAAACAT-GTTTTCTTGTC-TA
* *
5245646 AATTAAGACAAACATATTTTCTTGT-TT
1 AATTAAGACAAACATGTTTTCTTGTCTA
* *
5245673 AATTAAGACCAAACATGTTTCCTTGTTTA
1 AATTAAGA-CAAACATGTTTTCTTGTCTA
5245702 AATTAAGACAAACATGTT
1 AATTAAGACAAACATGTT
5245720 AAAGTTGCCA
Statistics
Matches: 111, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
27 9 0.08
28 40 0.36
29 26 0.23
30 27 0.24
31 9 0.08
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:5245640 original size:58 final size:58
Alignment explanation
Indices: 5245556--5245716 Score: 170
Period size: 59 Copynumber: 2.8 Consensus size: 58
5245546 TTTTTGTCTT
* * * * *
5245556 TAATTAAGACAAAAATATTTTATCTTGTC-TAAATTGAGATAAATATGTTTTCTTGTC
1 TAATTAAGAAAAAAATATTTTATCTTGTCTTAAATTAAGACAAACATATTTTCTTGTC
*
5245613 TACATTAAGATAAAAAATATTTT-TCTTGTCTTAAATTAAGACAAACATATTTTCTTGTT
1 TA-ATTAAGA-AAAAAATATTTTATCTTGTCTTAAATTAAGACAAACATATTTTCTTGTC
* * * *
5245672 TAATTAAGACCAAACAT-GTTT-CCTTGT-TTAAATTAAGACAAACAT
1 TAATTAAGA-AAAAAATATTTTATCTTGTCTTAAATTAAGACAAACAT
5245717 GTTAAAGTTG
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
56 18 0.20
57 10 0.11
58 26 0.29
59 36 0.40
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (58 bp):
TAATTAAGAAAAAAATATTTTATCTTGTCTTAAATTAAGACAAACATATTTTCTTGTC
Found at i:5253092 original size:253 final size:250
Alignment explanation
Indices: 5252478--5253192 Score: 827
Period size: 253 Copynumber: 2.8 Consensus size: 250
5252468 TTTTTGTAGT
* * * * * * *
5252478 GTTACCATAGCAAGTCAATTTAAACAAGATAAACATACATTTAGTGAAAATTAAGTA-TTT-ACA
1 GTTACCACAACAAGTCAATTTAGATAAAATAAACATACTTTTAGTGAAAATTAA--ACTTTAAAA
* * *
5252541 TATATAATCTCGAGCAAAAAATATTTAACCATTTACAAATTCTAATTTTCAAATGTATAATAACA
64 T-TATATTCTTGAGCAAAAAATATTTAACCATTTACAAATT-TAATTTT-AAATGTATAATAATA
** *
5252606 AAAATAAAAAC-ATCTGTAATGAAAATTAGTTATTTAAAAATCTT-CTTGTAAA-TTATAAGAAT
126 AAAATAAAAACAAT-TGTAATGAAAATTAGCCATTTAAAAATCTTAC-TATAAATTTATAAGAAT
* * * *
5252668 GAAAGTAAAAAA-AATAAAATTGAAATAAGCATTGTTAAAATGTTAATGTAAGTGTGTAAGA
189 GAAAGTAAAAAATCATAAAATTGAAATAAGCATTGTTAAAATATTAATGTAAATATGTAAGA
* * * * *
5252729 GTTTCCATAACAAGTCAATTTAGATAAAATAAACAT-CTTTTTAGTGAAAATTAATCATTTATAT
1 GTTACCACAACAAGTCAATTTAGATAAAATAAACATAC-TTTTAGTGAAAATTAAAC-TTTAAAA
*
5252793 TTATTTTCTTGAGCAAAAAATATTTAACCATTTACAAATGTTAATTTGTAAACT-TATAATAATA
64 TTATATTCTTGAGCAAAAAATATTTAACCATTTACAAAT-TTAATTT-TAAA-TGTATAATAATA
*
5252857 AAAATAAAAACAATTGTAATGAAAATTAACCATTTAAAAATCTTACTATAAATTTATAAGAATGA
126 AAAATAAAAACAATTGTAATGAAAATTAGCCATTTAAAAATCTTACTATAAATTTATAAGAATGA
* * *
5252922 AAGTAAAAAATCATAAAGTTGAAATAAGCATTGTTAAGATATTGATGTAAATATGTAAGA
191 AAGTAAAAAATCATAAAATTGAAATAAGCATTGTTAAAATATTAATGTAAATATGTAAGA
** *
5252982 GTTACTGCAACAAGTCAATTTGGATAATAATAAACATACTTTTAGTGAAAATTAAACTTGTAAAA
1 GTTACCACAACAAGTCAATTTAGATAA-AATAAACATACTTTTAGTGAAAATTAAACTT-TAAAA
** * * *
5253047 TTATATTCTTGAGCATTAAA-ATTTAACCATTTACGAATATTAATTTATAAATGCATAAGAATAA
64 TTATATTCTTGAGCAAAAAATATTTAACCATTTACAAAT-TTAATTT-TAAATGTATAATAATAA
* * * * * *
5253111 AAATAAAAACACTTGTGATGAAAATTAGCCATTTAAAAATCTTAATTTAAATTTTAAAAAAAATG
127 AAATAAAAACAATTGTAATGAAAATTAGCCATTTAAAAATCTTACTATAAA-TTT-ATAAGAATG
*
5253176 AACGTAAAAAATCATAA
190 AAAGTAAAAAATCATAA
5253193 GGGTCTGTTT
Statistics
Matches: 398, Mismatches: 49, Indels: 30
0.83 0.10 0.06
Matches are distributed among these distances:
250 1 0.00
251 145 0.36
252 30 0.08
253 149 0.37
254 49 0.12
255 24 0.06
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (250 bp):
GTTACCACAACAAGTCAATTTAGATAAAATAAACATACTTTTAGTGAAAATTAAACTTTAAAATT
ATATTCTTGAGCAAAAAATATTTAACCATTTACAAATTTAATTTTAAATGTATAATAATAAAAAT
AAAAACAATTGTAATGAAAATTAGCCATTTAAAAATCTTACTATAAATTTATAAGAATGAAAGTA
AAAAATCATAAAATTGAAATAAGCATTGTTAAAATATTAATGTAAATATGTAAGA
Found at i:5255329 original size:2 final size:2
Alignment explanation
Indices: 5255322--5255348 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5255312 NNNNNNNNAT
5255322 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5255349 CATTAATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5260486 original size:3 final size:3
Alignment explanation
Indices: 5260480--5260504 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5260470 TTGAATGATG
5260480 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5260505 CTATGTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5261196 original size:37 final size:37
Alignment explanation
Indices: 5261146--5261216 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
5261136 TCTGGAGACT
5261146 CTGAATGCAAATATGATTCACAAACACAGAGCTGTAG
1 CTGAATGCAAATATGATTCACAAACACAGAGCTGTAG
* *
5261183 CTGAATGCAAATATGATTTACAAATACAGAGCTG
1 CTGAATGCAAATATGATTCACAAACACAGAGCTG
5261217 CAACTGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (37 bp):
CTGAATGCAAATATGATTCACAAACACAGAGCTGTAG
Found at i:5261754 original size:24 final size:24
Alignment explanation
Indices: 5261709--5261754 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5261699 TCAGCTGCAG
* * *
5261709 CAGGTGCGGCAGCGGCACCAGCTC
1 CAGGTGCAGCAGCGGAAACAGCTC
*
5261733 CAGGTGCAGCAGCTGAAACAGC
1 CAGGTGCAGCAGCGGAAACAGC
5261755 AACACCACCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.35, T:0.09
Consensus pattern (24 bp):
CAGGTGCAGCAGCGGAAACAGCTC
Found at i:5264948 original size:2 final size:2
Alignment explanation
Indices: 5264941--5264969 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5264931 TGTCTTTTGG
5264941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5264970 CATGTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5265829 original size:27 final size:29
Alignment explanation
Indices: 5265795--5265861 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 29
5265785 AACTTCTAAT
*
5265795 AAAATATTAATATTAAAT-TATAAA-ATA
1 AAAATATTAATATTAAATAAATAAATATA
5265822 AAAATATTAATATTAAATCAAATAAATATA
1 AAAATATTAATATTAAAT-AAATAAATATA
5265852 AAAAT-TTAAT
1 AAAATATTAAT
5265862 TATCAATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
27 18 0.50
29 10 0.28
30 8 0.22
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATATTAATATTAAATAAATAAATATA
Found at i:5265889 original size:27 final size:28
Alignment explanation
Indices: 5265850--5265919 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
5265840 CAAATAAATA
* * *
5265850 TAAAAATTTAATTATCAATTATTAATATT
1 TAAAAA-TAAATTATAAACTATTAATATT
* *
5265879 T-AAAATAAATTATAAACTATTACTCTT
1 TAAAAATAAATTATAAACTATTAATATT
5265906 TAAAAAATAAATTA
1 T-AAAAATAAATTA
5265920 AATTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 18 0.53
28 4 0.12
29 12 0.35
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAAATAAATTATAAACTATTAATATT
Found at i:5265953 original size:13 final size:12
Alignment explanation
Indices: 5265905--5265961 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 12
5265895 CTATTACTCT
*
5265905 TTAAAAAATAAA
1 TTAAATAATAAA
*
5265917 TTAAATTAAAAAA
1 TTAAA-TAATAAA
*
5265930 ATAACATAATAACA
1 TTAA-ATAATAA-A
5265944 TTAAATAATAAA
1 TTAAATAATAAA
5265956 -TAAATA
1 TTAAATA
5265962 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 6 0.16
12 6 0.16
13 20 0.54
14 5 0.14
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAATAATAAA
Found at i:5266618 original size:21 final size:20
Alignment explanation
Indices: 5266557--5266610 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
5266547 AATATTTAAG
*
5266557 TTAAATAAAATATTAATA-T
1 TTAAATAAATTATTAATATT
5266576 TTAAATTAATATTATTAATATT
1 TTAAA-TAA-ATTATTAATATT
5266598 TTAAATAAATTAT
1 TTAAATAAATTAT
5266611 CAATTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 5 0.16
20 8 0.26
21 12 0.39
22 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAATAAATTATTAATATT
Found at i:5274853 original size:16 final size:16
Alignment explanation
Indices: 5274832--5274865 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5274822 AAGCATCTGA
5274832 CTGTGAAAGACTGTTT
1 CTGTGAAAGACTGTTT
*
5274848 CTGTGAAAGATTGTTT
1 CTGTGAAAGACTGTTT
5274864 CT
1 CT
5274866 TCATAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (16 bp):
CTGTGAAAGACTGTTT
Found at i:5283928 original size:22 final size:22
Alignment explanation
Indices: 5283898--5283950 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5283888 AATTGAAGTT
* *
5283898 AAAGGAAGAAATAGTAAATGAG
1 AAAGGAAGAAAGAGCAAATGAG
*
5283920 AAAGAAAGAAAGAGCAAATGAG
1 AAAGGAAGAAAGAGCAAATGAG
5283942 AAAGGAAGA
1 AAAGGAAGA
5283951 TTTCAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.28, T:0.08
Consensus pattern (22 bp):
AAAGGAAGAAAGAGCAAATGAG
Found at i:5286953 original size:13 final size:13
Alignment explanation
Indices: 5286935--5286959 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5286925 TTCCAGAAAA
5286935 TTTATAAAATCAT
1 TTTATAAAATCAT
5286948 TTTATAAAATCA
1 TTTATAAAATCA
5286960 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5288354 original size:19 final size:19
Alignment explanation
Indices: 5288330--5288367 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5288320 CTGCCAAACC
*
5288330 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
5288349 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
5288368 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:5288952 original size:35 final size:35
Alignment explanation
Indices: 5288913--5289021 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
5288903 GTTAGGTATT
5288913 AGGTTTTAGTTGAGCCCGTGAAAAACCATTGTGAA
1 AGGTTTTAGTTGAGCCCGTGAAAAACCATTGTGAA
* * * **
5288948 AGGTTGTGGTTAAGCCTTTGAAAAACCACTT-TG--
1 AGGTTTTAGTTGAGCCCGTGAAAAACCA-TTGTGAA
* ** *
5288981 -GGTTATAGTTGAGCCCGAAAAAAACTATTGTGAA
1 AGGTTTTAGTTGAGCCCGTGAAAAACCATTGTGAA
5289015 AGGTTTT
1 AGGTTTT
5289022 GGCTAAGCCT
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
31 2 0.04
32 21 0.38
35 30 0.55
36 2 0.04
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (35 bp):
AGGTTTTAGTTGAGCCCGTGAAAAACCATTGTGAA
Found at i:5303571 original size:13 final size:13
Alignment explanation
Indices: 5303553--5303577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5303543 TTCCAGAAAA
5303553 TTTATAAAATCAT
1 TTTATAAAATCAT
5303566 TTTATAAAATCA
1 TTTATAAAATCA
5303578 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5304754 original size:28 final size:27
Alignment explanation
Indices: 5304718--5304770 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
5304708 ATATCCTGGT
*
5304718 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
5304745 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
5304771 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:5304838 original size:20 final size:20
Alignment explanation
Indices: 5304815--5304860 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
5304805 CTTCTAAACC
5304815 TCAAATCATACT-TCAATAAG
1 TCAAATCATACTCT-AATAAG
*
5304835 TCAAATTATACTCTAATAAG
1 TCAAATCATACTCTAATAAG
5304855 TCAAAT
1 TCAAAT
5304861 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (20 bp):
TCAAATCATACTCTAATAAG
Found at i:5311785 original size:34 final size:34
Alignment explanation
Indices: 5311736--5311812 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
5311726 TTGGTTGCTG
*
5311736 AAAATTTGAGCTGTTTGCTGCCAATTTATGCAAA
1 AAAATTGGAGCTGTTTGCTGCCAATTTATGCAAA
* * * **
5311770 AAAATTGGAGTTGTTTGTTGCCAATTTGTGCAGG
1 AAAATTGGAGCTGTTTGCTGCCAATTTATGCAAA
5311804 AAAATTGGA
1 AAAATTGGA
5311813 CAGCATTGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (34 bp):
AAAATTGGAGCTGTTTGCTGCCAATTTATGCAAA
Found at i:5311955 original size:10 final size:10
Alignment explanation
Indices: 5311937--5311978 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
5311927 AGAAACGTGG
*
5311937 AAGAGAGAAA
1 AAGAAAGAAA
5311947 AAGAAAGAAA
1 AAGAAAGAAA
5311957 AAGAAA-AGAA
1 AAGAAAGA-AA
*
5311967 AAGAAATAAA
1 AAGAAAGAAA
5311977 AA
1 AA
5311979 ATAAATGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 1 0.03
10 27 0.93
11 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:5311999 original size:25 final size:25
Alignment explanation
Indices: 5311971--5312058 Score: 131
Period size: 25 Copynumber: 3.5 Consensus size: 25
5311961 AAAGAAAAGA
*
5311971 AATAAAAAATAAATGGGCATGGCCC
1 AATAGAAAATAAATGGGCATGGCCC
*
5311996 AATAGAAAATAAATGGGCATGACCC
1 AATAGAAAATAAATGGGCATGGCCC
* *
5312021 AATAGAAAATAAGTGGGCATGGCAC
1 AATAGAAAATAAATGGGCATGGCCC
*
5312046 AATAGGAAATAAA
1 AATAGAAAATAAA
5312059 AATAAATGGG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (25 bp):
AATAGAAAATAAATGGGCATGGCCC
Found at i:5312151 original size:28 final size:28
Alignment explanation
Indices: 5312107--5312166 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
5312097 CCCATGGAGG
*
5312107 AGGCTCAAAGGTTATAAAGAAATGAAAA
1 AGGCTCAAAGGTCATAAAGAAATGAAAA
5312135 AGGCTCAAAGGTCATAAAGAAATGAAAA
1 AGGCTCAAAGGTCATAAAGAAATGAAAA
5312163 AGGC
1 AGGC
5312167 ACAATGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (28 bp):
AGGCTCAAAGGTCATAAAGAAATGAAAA
Found at i:5312579 original size:2 final size:2
Alignment explanation
Indices: 5312572--5312600 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5312562 ATCATTTGAA
5312572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5312601 CTAGACGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5314580 original size:38 final size:38
Alignment explanation
Indices: 5314532--5314822 Score: 278
Period size: 38 Copynumber: 7.7 Consensus size: 38
5314522 ATAGTGCCCG
5314532 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
*
5314570 TGTGCACGATGTGGGGGGATATACATGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
5314608 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
* ** *
5314646 TGTGCACGATGTGGGGGGATGCACATGCCGGTGA-TGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGG-CACTGAT
* * ** *
5314684 GGTG---G-TAT-GGGAAATGGATA-ATGATAGTGC-CCG--
1 TGTGCACGATGTGGGGGGAT-G-TACATGAT-G-GCACTGAT
* * **
5314717 TGTGAACGATGTAGGGGGATGTACATGATGATACTGAT
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
* * * *
5314755 TGTGCACGATGTGGGGGGATGCACATGATGGCGCCGGCT
1 TGTGCACGATGTGGGGGGATGTACATGATGGC-ACTGAT
*
5314794 ATGTGCACGATGTGGGGGAATGTACATGA
1 -TGTGCACGATGTGGGGGGATGTACATGA
5314823 GCCAGGTGTG
Statistics
Matches: 204, Mismatches: 32, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
33 8 0.04
34 6 0.03
35 4 0.02
36 7 0.03
37 8 0.04
38 141 0.69
39 4 0.02
40 26 0.13
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.25
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
Found at i:5314618 original size:19 final size:19
Alignment explanation
Indices: 5314596--5314656 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
5314586 GGATATACAT
5314596 GATGGCACTGATTGTGCAC
1 GATGGCACTGATTGTGCAC
**** * *
5314615 GATGTGGGGGGA-TGTACAT
1 GATG-GCACTGATTGTGCAC
5314634 GATGGCACTGATTGTGCAC
1 GATGGCACTGATTGTGCAC
5314653 GATG
1 GATG
5314657 TGGGGGGATG
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (19 bp):
GATGGCACTGATTGTGCAC
Found at i:5314785 original size:185 final size:188
Alignment explanation
Indices: 5314460--5314822 Score: 570
Period size: 185 Copynumber: 1.9 Consensus size: 188
5314450 TAACCGTGTG
* *
5314460 TGTGCACAATGTGGGGGGGATGCACATGCCGGTGATAATAGTGGTGTGGGAGATGGATAATGATA
1 TGTGCACAATGTGGGGGGGATGCACATGCCGGTGATAATAGTGGTATGGGAAATGGATAATGATA
* * *
5314525 GTGCCCGTGTGCACGATGTGGGGGGATGTACATGATGGCACTGATTGTGCACGATGTGGGGGGAT
66 GTGCCCGTGTGAACGATGTAGGGGGATGTACATGATGACACTGATTGTGCACGATGTGGGGGGAT
* * *
5314590 ATACATGATGGC-ACTGAT-TGTGCACGATGTGGGGGGATGTACATGATGGCACTGAT
131 ACACATGATGGCGACGGATATGTGCACGATGTGGGGGAATGTACATGATGGCACTGAT
* * *
5314646 TGTGCACGATGT-GGGGGGATGCACATGCCGGTGATGATGGTGGTATGGGAAATGGATAATGATA
1 TGTGCACAATGTGGGGGGGATGCACATGCCGGTGATAATAGTGGTATGGGAAATGGATAATGATA
*
5314710 GTGCCCGTGTGAACGATGTAGGGGGATGTACATGATGATACTGATTGTGCACGATGTGGGGGGAT
66 GTGCCCGTGTGAACGATGTAGGGGGATGTACATGATGACACTGATTGTGCACGATGTGGGGGGAT
* * *
5314775 GCACATGATGGCGCCGGCTATGTGCACGATGTGGGGGAATGTACATGA
131 ACACATGATGGCGACGGATATGTGCACGATGTGGGGGAATGTACATGA
5314823 GCCAGGTGTG
Statistics
Matches: 160, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
185 119 0.74
186 14 0.09
187 27 0.17
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.25
Consensus pattern (188 bp):
TGTGCACAATGTGGGGGGGATGCACATGCCGGTGATAATAGTGGTATGGGAAATGGATAATGATA
GTGCCCGTGTGAACGATGTAGGGGGATGTACATGATGACACTGATTGTGCACGATGTGGGGGGAT
ACACATGATGGCGACGGATATGTGCACGATGTGGGGGAATGTACATGATGGCACTGAT
Found at i:5319120 original size:2 final size:2
Alignment explanation
Indices: 5319113--5319143 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5319103 ACTTTCTATA
5319113 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5319144 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5319218 original size:37 final size:37
Alignment explanation
Indices: 5319168--5319245 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
5319158 CGTGTGCATT
*
5319168 CATCATCATGTGTGCACTCTCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
5319205 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
5319242 CATC
1 CATC
5319246 CTCACACAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.24, C:0.37, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:5326103 original size:9 final size:9
Alignment explanation
Indices: 5326089--5326156 Score: 73
Period size: 9 Copynumber: 7.6 Consensus size: 9
5326079 ACACAATTAA
5326089 TAACACGTT
1 TAACACGTT
*
5326098 TAACACGAT
1 TAACACGTT
*
5326107 TAATACGTT
1 TAACACGTT
* *
5326116 TAACATGAT
1 TAACACGTT
5326125 TAACACGTT
1 TAACACGTT
* *
5326134 TAACATGGT
1 TAACACGTT
5326143 TAACACGTT
1 TAACACGTT
*
5326152 GAACA
1 TAACA
5326157 TGATTAAATA
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (9 bp):
TAACACGTT
Found at i:5326116 original size:18 final size:18
Alignment explanation
Indices: 5326089--5326163 Score: 114
Period size: 18 Copynumber: 4.2 Consensus size: 18
5326079 ACACAATTAA
*
5326089 TAACACGTTTAACACGAT
1 TAACACGTTTAACATGAT
*
5326107 TAATACGTTTAACATGAT
1 TAACACGTTTAACATGAT
*
5326125 TAACACGTTTAACATGGT
1 TAACACGTTTAACATGAT
*
5326143 TAACACGTTGAACATGAT
1 TAACACGTTTAACATGAT
5326161 TAA
1 TAA
5326164 ATAAAAATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (18 bp):
TAACACGTTTAACATGAT
Found at i:5329297 original size:8 final size:8
Alignment explanation
Indices: 5329286--5329334 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
5329276 ACGTTTAAAT
5329286 ACGATAAC
1 ACGATAAC
*
5329294 ACGATTAAAT
1 ACGA-T-AAC
5329304 ACGATAAC
1 ACGATAAC
5329312 ACGATTAAAC
1 ACGA-T-AAC
5329322 ACGATAAC
1 ACGATAAC
5329330 ACGAT
1 ACGAT
5329335 TAAGTAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 18 0.51
9 4 0.11
10 13 0.37
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.18
Consensus pattern (8 bp):
ACGATAAC
Found at i:5329301 original size:18 final size:18
Alignment explanation
Indices: 5329280--5329337 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
5329270 GTACATACGT
5329280 TTAAATACGATAACACGA
1 TTAAATACGATAACACGA
5329298 TTAAATACGATAACACGA
1 TTAAATACGATAACACGA
*
5329316 TTAAACACGATAACACGA
1 TTAAATACGATAACACGA
5329334 TTAA
1 TTAA
5329338 GTAAACGTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.22
Consensus pattern (18 bp):
TTAAATACGATAACACGA
Found at i:5329307 original size:10 final size:10
Alignment explanation
Indices: 5329291--5329337 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
5329281 TAAATACGAT
5329291 AACACGATTA
1 AACACGATTA
*
5329301 AATACGA-T-
1 AACACGATTA
5329309 AACACGATTA
1 AACACGATTA
5329319 AACACGA-T-
1 AACACGATTA
5329327 AACACGATTA
1 AACACGATTA
5329337 A
1 A
5329338 GTAAACGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 13 0.42
9 4 0.13
10 14 0.45
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (10 bp):
AACACGATTA
Found at i:5340062 original size:2 final size:2
Alignment explanation
Indices: 5340049--5340078 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5340039 AGACCAGATC
*
5340049 CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5340079 TATGTCCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:5344160 original size:21 final size:21
Alignment explanation
Indices: 5344122--5344161 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5344112 CCCACTTACG
*
5344122 AAAAAAAAGAAATCAAAAAAT
1 AAAAAAAAGAAAACAAAAAAT
*
5344143 AAAAAAAAGAAAAGAAAAA
1 AAAAAAAAGAAAACAAAAA
5344162 GGTGAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.07, T:0.05
Consensus pattern (21 bp):
AAAAAAAAGAAAACAAAAAAT
Found at i:5344713 original size:30 final size:29
Alignment explanation
Indices: 5344661--5344719 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5344651 NNNNNNNNTT
* *
5344661 TTTTTATTTTATTAAATCAAGCTTTTATA
1 TTTTTATTTTATCAAATCAAGCTCTTATA
5344690 TTTTTATTTTAAATCAAAT-AAGCTCTTATA
1 TTTTTATTTT--ATCAAATCAAGCTCTTATA
5344720 ATTAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 10 0.38
31 6 0.23
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTTATTTTATCAAATCAAGCTCTTATA
Found at i:5349485 original size:23 final size:23
Alignment explanation
Indices: 5349455--5349500 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5349445 CTACCATAGC
* *
5349455 ATGTATTTTGTATTAAATGTGCT
1 ATGTATTTCGTACTAAATGTGCT
5349478 ATGTATTTCGTACTAAATGTGCT
1 ATGTATTTCGTACTAAATGTGCT
5349501 TTGCAATCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (23 bp):
ATGTATTTCGTACTAAATGTGCT
Found at i:5350769 original size:25 final size:25
Alignment explanation
Indices: 5350740--5350801 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
5350730 ACTTTTAAAA
*
5350740 TATATTTTTATTTTTTAAAAAATTT
1 TATATTTTTATTTTTAAAAAAATTT
*
5350765 TATATTTTTGTTTTTAAAAAAATTT
1 TATATTTTTATTTTTAAAAAAATTT
*
5350790 TAAAATTTTTAT
1 T-ATATTTTTAT
5350802 AAAATGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TATATTTTTATTTTTAAAAAAATTT
Found at i:5350770 original size:19 final size:20
Alignment explanation
Indices: 5350732--5350773 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
5350722 ATTTCAAAAC
5350732 TTTTAAAATATATTTTTATT
1 TTTTAAAATATATTTTTATT
5350752 TTTTAAAA-A-ATTTTATATT
1 TTTTAAAATATATTTT-TATT
5350771 TTT
1 TTT
5350774 GTTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAAATATATTTTTATT
Found at i:5351341 original size:141 final size:141
Alignment explanation
Indices: 5351083--5351363 Score: 472
Period size: 141 Copynumber: 2.0 Consensus size: 141
5351073 GATAAAATGT
* *
5351083 ATCTAAGCTATCAATTGGATCTATTTAAGCTTGACATTTTTTATAATCAAGCTTTGAAAAATGTA
1 ATCTAAGCTATCAATTGGATCTATTTAAGCATGACATTTTTCATAATCAAGCTTTGAAAAATGTA
* *
5351148 TCTACACTTTGTGAGCTATGCCGAGTGTTGAAGAAGATGAGAATATCAAAAGTTTACCTTTTTGT
66 TCTACACTTTGTGAGCTATGCCAAGTGATGAAGAAGATGAGAATATCAAAAGTTTACCTTTTTGT
5351213 GGACAGATTGC
131 GGACAGATTGC
*
5351224 ATCTAAGCTATCAATTGGATCTATTTAAGCATGACATTTTTCATAATCAAGTTTTGAAAAATGTA
1 ATCTAAGCTATCAATTGGATCTATTTAAGCATGACATTTTTCATAATCAAGCTTTGAAAAATGTA
* * *
5351289 TCTACACTTTTTGAGCTATGCCAAGTGATGAAGAAGATGAGAATATCCAAAGTTTACTTTTTTGT
66 TCTACACTTTGTGAGCTATGCCAAGTGATGAAGAAGATGAGAATATCAAAAGTTTACCTTTTTGT
* *
5351354 TGACCGATTG
131 GGACAGATTG
5351364 ATCCGACTTG
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 130 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (141 bp):
ATCTAAGCTATCAATTGGATCTATTTAAGCATGACATTTTTCATAATCAAGCTTTGAAAAATGTA
TCTACACTTTGTGAGCTATGCCAAGTGATGAAGAAGATGAGAATATCAAAAGTTTACCTTTTTGT
GGACAGATTGC
Found at i:5352258 original size:8 final size:7
Alignment explanation
Indices: 5352220--5352263 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
5352210 GATATTTTGC
5352220 TATTTAT
1 TATTTAT
*
5352227 TATTTGT
1 TATTTAT
*
5352234 TTTTTAT
1 TATTTAT
5352241 T-TTTAT
1 TATTTAT
5352247 TATTTAT
1 TATTTAT
5352254 ATATTTAT
1 -TATTTAT
5352262 TA
1 TA
5352264 CAAAAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (7 bp):
TATTTAT
Found at i:5361972 original size:211 final size:208
Alignment explanation
Indices: 5361723--5362101 Score: 609
Period size: 211 Copynumber: 1.8 Consensus size: 208
5361713 TATATAATAT
*
5361723 TTTATTTATTTAAATTAGGGTTTAGGGAATTAATTAAATAATTTAAGTAAATAAAAATAATAATG
1 TTTATTTAATTAAATTAGGGTTTAGGGAATTAATTAAATAATTTAAGTAAATAAAAATAATAATG
*
5361788 TATTAGTAATTAATCAATTAATTAAATTAGTACACTTAG-AGACACTAAAAATTATTTAAATTAA
66 TATTAGTAATTAATCAATTAATTAAATTAGTAAACTTAGTAGA-ACTAAAAATTATTTAAATTAA
*
5361852 TTA-AGATTTATGGTAATCAAGCAATTAATTAAATTAGTAAATTTAGAAAATTTTAAAANCATTC
130 TTAGAG-TTT-TAGTAATCAAGCAATTAATTAAATTAGTAAATTTAGAAAATTTTAAAA-CATTC
5361916 TATATTTTTAATTTTTA
192 TATATTTTTAATTTTTA
*
5361933 TTTATTTAAATTAATTTAGGGTTTAGGGAATTAATTAAATAATTTAAGTAAATAAAAATAATAAT
1 TTTATTT-AATTAAATTAGGGTTTAGGGAATTAATTAAATAATTTAAGTAAATAAAAATAATAAT
* * * *
5361998 GTATTAGTAATTAATCAATTAATTAAATTAGTAAATTTAGTAGAATTTATAATTATTTAAATTAA
65 GTATTAGTAATTAATCAATTAATTAAATTAGTAAACTTAGTAGAACTAAAAATTATTTAAATTAA
* *
5362063 TTAGAGTTTTAGTAATTAAGTAATTAATTAAATTAGTAA
130 TTAGAGTTTTAGTAATCAAGCAATTAATTAAATTAGTAA
5362102 TATTATTTAA
Statistics
Matches: 156, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
210 34 0.22
211 117 0.75
212 5 0.03
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (208 bp):
TTTATTTAATTAAATTAGGGTTTAGGGAATTAATTAAATAATTTAAGTAAATAAAAATAATAATG
TATTAGTAATTAATCAATTAATTAAATTAGTAAACTTAGTAGAACTAAAAATTATTTAAATTAAT
TAGAGTTTTAGTAATCAAGCAATTAATTAAATTAGTAAATTTAGAAAATTTTAAAACATTCTATA
TTTTTAATTTTTA
Found at i:5362125 original size:70 final size:70
Alignment explanation
Indices: 5362001--5362133 Score: 173
Period size: 70 Copynumber: 1.9 Consensus size: 70
5361991 TAATAATGTA
* * *
5362001 TTAGTAATTAATCAATTAATTAAATTAGTAAATTTAGTAGAATTTATAATTATTTAAATTAATTA
1 TTAGTAATTAATCAATTAATTAAATTAGTAAATTTAGTAGAATTAAAAAATATTTAAATTAATTA
5362066 GAGTT
66 GAGTT
* *
5362071 TTAGTAATTAAGT-AATTAATTAAATTAGT-AATATTATTTA-ACTTAAAAAATATTTAAATTAA
1 TTAGTAATTAA-TCAATTAATTAAATTAGTAAAT-TTA-GTAGAATTAAAAAATATTTAAATTAA
5362133 T
63 T
5362134 ACTTCCTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
69 3 0.05
70 49 0.89
71 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (70 bp):
TTAGTAATTAATCAATTAATTAAATTAGTAAATTTAGTAGAATTAAAAAATATTTAAATTAATTA
GAGTT
Found at i:5364211 original size:2 final size:2
Alignment explanation
Indices: 5364199--5364229 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5364189 TACATGTGTT
*
5364199 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5364230 GTTGCTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5366297 original size:19 final size:19
Alignment explanation
Indices: 5366259--5366294 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5366249 GCCACGATTG
5366259 GTGTCTTTCACAATGCCCA
1 GTGTCTTTCACAATGCCCA
5366278 GTGTCTTT-ACAATGCCC
1 GTGTCTTTCACAATGCCC
5366295 CAGCGTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (19 bp):
GTGTCTTTCACAATGCCCA
Found at i:5371274 original size:29 final size:29
Alignment explanation
Indices: 5371226--5371291 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 29
5371216 CAAAGAGAGA
5371226 GAGAGAGAGAGAGAGAGAGAGAGAAGAAA-G
1 GAGAGA-AGAGAGAGAGAGAGAGAA-AAAGG
*
5371256 GAGAGAANAGAGAGAGAGAGAGAAAAAGG
1 GAGAGAAGAGAGAGAGAGAGAGAAAAAGG
5371285 GAGAGAA
1 GAGAGAA
5371292 AGGAGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 3 0.09
29 25 0.74
30 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.44, T:0.00
Consensus pattern (29 bp):
GAGAGAAGAGAGAGAGAGAGAGAAAAAGG
Found at i:5371290 original size:2 final size:2
Alignment explanation
Indices: 5371219--5371278 Score: 81
Period size: 2 Copynumber: 31.5 Consensus size: 2
5371209 CAACAACCAA
*
5371219 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AA AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
5371259 AG A- AN AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
5371279 AAAAGGGAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 3 0.06
2 49 0.94
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5373821 original size:19 final size:19
Alignment explanation
Indices: 5373799--5373835 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5373789 TAATTGGAAT
5373799 ATCCATTAATAAATGTTTA
1 ATCCATTAATAAATGTTTA
5373818 ATCCATTAATAAATGTTT
1 ATCCATTAATAAATGTTT
5373836 GAGCCATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
ATCCATTAATAAATGTTTA
Found at i:5373842 original size:19 final size:19
Alignment explanation
Indices: 5373801--5373843 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
5373791 ATTGGAATAT
*
5373801 CCATTAATAAATGTTTAAT
1 CCATTAATAAATGTTTAAG
*
5373820 CCATTAATAAATGTTTGAG
1 CCATTAATAAATGTTTAAG
5373839 CCATT
1 CCATT
5373844 CCGCTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
CCATTAATAAATGTTTAAG
Found at i:5376252 original size:108 final size:108
Alignment explanation
Indices: 5376135--5376344 Score: 323
Period size: 108 Copynumber: 1.9 Consensus size: 108
5376125 TATAAGAAAT
* * *
5376135 TTTGAGTAAATTTAAATAAAATGTAAATTG-GTTAAGAGTTGAATAATTTCAAGAGAATGTGTAT
1 TTTGAGTAAATTTAAATAAAAGGCAAATTGAG-TAAGAGTTGAATAATTTCAAAAGAATGTGTAT
* *
5376199 TTATAAATTATGAAAGTTGTAACTAAATCAACATATTTTGCTAA
65 TTATAAATTATGAAAGTTGTAACTAAATAAAAATATTTTGCTAA
* *
5376243 TTTGAGTAAATTTAAATAAACGGCAAATTGAGTAAGAGTTGAATAATTTCAAAAGAATGTGTGTT
1 TTTGAGTAAATTTAAATAAAAGGCAAATTGAGTAAGAGTTGAATAATTTCAAAAGAATGTGTATT
* *
5376308 TGTAAATTGTGAAAGTTGTAACTAAATAAAAATATTT
66 TATAAATTATGAAAGTTGTAACTAAATAAAAATATTT
5376345 AGTCATTTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 91 0.99
109 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (108 bp):
TTTGAGTAAATTTAAATAAAAGGCAAATTGAGTAAGAGTTGAATAATTTCAAAAGAATGTGTATT
TATAAATTATGAAAGTTGTAACTAAATAAAAATATTTTGCTAA
Found at i:5385084 original size:29 final size:28
Alignment explanation
Indices: 5385012--5385085 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 28
5385002 TGCCACAATA
5385012 TTCAACTCATGT-TG-TTCATCATGATG
1 TTCAACTCATGTCTGTTTCATCATGATG
* *
5385038 TTCAACTTATTTCTTGTTTCATCATGATG
1 TTCAACTCATGTC-TGTTTCATCATGATG
5385067 TTCAACTCATGTCGTGTTT
1 TTCAACTCATGTC-TGTTT
5385086 TGCCACGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 10 0.25
28 2 0.05
29 28 0.70
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (28 bp):
TTCAACTCATGTCTGTTTCATCATGATG
Done.