Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009363.1 Kokia drynarioides strain JFW-HI SEQ_124070, whole genome shotgun sequence
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: 93361
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4572 original size:27 final size:28
Alignment explanation
Indices: 4542--4603 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
4532 AAAATGAGAT
* *
4542 TTTTGGATAC-CCAAGGTAAAATGGTAA
1 TTTTGGACACTCCAAGGCAAAATGGTAA
* *
4569 TTTTGGACACTCGAGGGCAAAATGGTAA
1 TTTTGGACACTCCAAGGCAAAATGGTAA
4597 TTTTGGA
1 TTTTGGA
4604 AAAGTTCGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (28 bp):
TTTTGGACACTCCAAGGCAAAATGGTAA
Found at i:4650 original size:59 final size:59
Alignment explanation
Indices: 4587--4736 Score: 150
Period size: 59 Copynumber: 2.6 Consensus size: 59
4577 ACTCGAGGGC
4587 AAAATGGTAATTTTGGAAAAGTTCGGGAGTCAAACA-CGAAATTTTAGACATCCGACAGT
1 AAAATGGTAATTTTGGAAAAGTTCGGGAGTCAAA-ATCGAAATTTTAGACATCCGACAGT
* ** * * * * **
4646 AAAATGGTATTTTTTGG-AAAGTT-TAGAGTTTAAAATGGAATTTTTAGACATTCGAGGGT
1 AAAATGGTA-ATTTTGGAAAAGTTCGGGAG-TCAAAATCGAAATTTTAGACATCCGACAGT
4705 AAAATGGTAATTTTGGAAAA--TCGGG-GTCAAAA
1 AAAATGGTAATTTTGGAAAAGTTCGGGAGTCAAAA
4737 ATGGAATTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
56 5 0.07
57 2 0.03
58 11 0.15
59 49 0.67
60 6 0.08
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTGGAAAAGTTCGGGAGTCAAAATCGAAATTTTAGACATCCGACAGT
Found at i:4718 original size:28 final size:28
Alignment explanation
Indices: 4556--4880 Score: 143
Period size: 28 Copynumber: 11.2 Consensus size: 28
4546 GGATACCCAA
* *
4556 GGTAAAATGGTAATTTTGGACACTCGAG
1 GGTAAAATGGTAATTTTGGAAATTCGAG
*
4584 GGCAAAATGGTAATTTTGGAAAAGTTCG-G
1 GGTAAAATGGTAATTTTGG-AAA-TTCGAG
* * * * * *
4613 GAGTCAAACA-CGAAATTTTAGACATCCGAC
1 G-GT-AAA-ATGGTAATTTTGGAAATTCGAG
* * *
4643 AGTAAAATGGTATTTTTTGGAAAGTTTAGAG
1 GGTAAAATGGTA-ATTTTGGAAA--TTCGAG
** * *
4674 TTTAAAATGG-AATTTTTAGACATTCGAG
1 GGTAAAATGGTAA-TTTTGGAAATTCGAG
*
4702 GGTAAAATGGTAATTTTGGAAAATCG-G
1 GGTAAAATGGTAATTTTGGAAATTCGAG
* *
4729 GGTCAAAAATGG-AATTTTAGGAAGTTCGGG
1 GGT--AAAATGGTAATTTT-GGAAATTCGAG
**
4759 GGTAAAATTTTAAGTTTTGGAAAAATT-G-G
1 GGTAAAATGGTAA-TTTTGG--AAATTCGAG
**
4788 GGTCAAAAATGG-AATTTTTAAAAGTTC--G
1 GGT--AAAATGGTAATTTTGGAAA-TTCGAG
*
4816 GGTAAAATGGTAATTTTTGGAGAATTTG-G
1 GGTAAAATGGTAA-TTTTGGA-AATTCGAG
*
4845 GCTTAAAATGG-AATTTTGGAAAGTTCGAG
1 G-GTAAAATGGTAATTTTGGAAA-TTCGAG
4874 GGTAAAA
1 GGTAAAA
4881 ATGTAAATTT
Statistics
Matches: 221, Mismatches: 45, Indels: 62
0.67 0.14 0.19
Matches are distributed among these distances:
26 7 0.03
27 12 0.05
28 85 0.38
29 52 0.24
30 33 0.15
31 31 0.14
32 1 0.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (28 bp):
GGTAAAATGGTAATTTTGGAAATTCGAG
Found at i:4881 original size:29 final size:28
Alignment explanation
Indices: 4677--5059 Score: 224
Period size: 29 Copynumber: 13.2 Consensus size: 28
4667 TTTAGAGTTT
* *
4677 AAAATGGAATTTTTAGACA-TTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTTCG-GGGTA
*
4705 AAAATGGTAATTTTGGAAA-ATCGGGGTCA
1 AAAATGG-AATTTTGGAAAGTTCGGGGT-A
4734 AAAATGGAATTTTAGG-AAGTTCGGGGGTA
1 AAAATGGAATTTT-GGAAAGTTC-GGGGTA
* ** *
4763 AAATTTTAAGTTTTGGAAAAATT-GGGGTCA
1 AAAATGGAA-TTTTGG-AAAGTTCGGGGT-A
**
4793 AAAATGGAATTTTTAAAAGTTC-GGGT-
1 AAAATGGAATTTTGGAAAGTTCGGGGTA
* * *
4819 AAAATGGTAATTTTTGGAGAA-TTTGGGCTT
1 AAAATGG-AA-TTTTGGA-AAGTTCGGGGTA
4849 AAAATGGAATTTTGGAAAGTTCGAGGGTA
1 AAAATGGAATTTTGGAAAGTTCG-GGGTA
* *** * ** *
4878 AAAATGTAAATTTCAAAAAATTTAAGGTTAA
1 AAAATG-GAATTT-TGGAAAGTTCGGGGT-A
*
4909 AAAATGGAATTTTGGAAAGTTTGTGGGTA
1 AAAATGGAATTTTGGAAAGTTCG-GGGTA
* * *
4938 AAAATGGAATTTTGGGAAGTTAGAGCGTA
1 AAAATGGAATTTTGGAAAGTTCG-GGGTA
* *
4967 AAAATGGAATTTTTGAAAGTTTGGGGGTA
1 AAAATGGAATTTTGGAAAG-TTCGGGGTA
* * * *
4996 AAAATGTAATTTTTAGAATGTTCGGGGTT
1 AAAATGGAA-TTTTGGAAAGTTCGGGGTA
* *
5025 AAAATGGAATTTTAGAAAAGTTCAGGGGTC
1 AAAATGGAATTTT-GGAAAGTTC-GGGGTA
5055 AAAAT
1 AAAAT
5060 ATGATTTTTG
Statistics
Matches: 274, Mismatches: 55, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
26 7 0.03
27 8 0.03
28 55 0.20
29 128 0.47
30 60 0.22
31 16 0.06
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGGGGTA
Found at i:6216 original size:3 final size:3
Alignment explanation
Indices: 6160--6201 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
6150 TAATACTTCT
6160 TTA TTA TTA TTA 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
6202 AAAATTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6224 original size:22 final size:22
Alignment explanation
Indices: 6162--6224 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
6152 ATACTTCTTT
* **
6162 ATTATTATTATTATTATT-ATT
1 ATTATTATTATAATTATTAAAA
*
6183 ATTATTATTATTATTATTAAAA
1 ATTATTATTATAATTATTAAAA
6205 ATTATTTATTATAATT-TTAA
1 ATTA-TTATTATAATTATTAA
6225 TGTACTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.49
22 9 0.24
23 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTATTATAATTATTAAAA
Found at i:6901 original size:34 final size:34
Alignment explanation
Indices: 6853--6934 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
6843 TAAATAAATT
* * *
6853 TAAACTTAATATTT-ATAATAAATTTAAATTCCAAA
1 TAAATTTAA-ATTTAAT-ATAAACTTAAATTCAAAA
** *
6888 TGGATTTAAATTTAATATAAACTTAAATTTAAAA
1 TAAATTTAAATTTAATATAAACTTAAATTCAAAA
6922 TAAATTTAAATTT
1 TAAATTTAAATTT
6935 GTTGGGCCTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
34 30 0.79
35 8 0.21
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (34 bp):
TAAATTTAAATTTAATATAAACTTAAATTCAAAA
Found at i:6913 original size:17 final size:17
Alignment explanation
Indices: 6853--6934 Score: 74
Period size: 17 Copynumber: 4.8 Consensus size: 17
6843 TAAATAAATT
*
6853 TAAACTTAATATTTATAA
1 TAAACTTAA-ATTTAAAA
* **
6871 TAAATTTAAATTCCAAA
1 TAAACTTAAATTTAAAA
** * *
6888 TGGATTTAAATTTAATA
1 TAAACTTAAATTTAAAA
6905 TAAACTTAAATTTAAAA
1 TAAACTTAAATTTAAAA
*
6922 TAAATTTAAATTT
1 TAAACTTAAATTT
6935 GTTGGGCCTG
Statistics
Matches: 50, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
17 42 0.84
18 8 0.16
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAACTTAAATTTAAAA
Found at i:15326 original size:22 final size:21
Alignment explanation
Indices: 15280--15327 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
15270 ATATTAAAAT
* *
15280 TATAAATTATATTTTATTATT
1 TATAAATTATATTTAATTATA
15301 TATATAATTATATTTAA-TATAA
1 TATA-AATTATATTTAATTAT-A
15323 TATAA
1 TATAA
15328 TTTTGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATAAATTATATTTAATTATA
Found at i:16168 original size:30 final size:32
Alignment explanation
Indices: 16095--16180 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 32
16085 ATTTATAAAA
*
16095 TTTTAAATTAATAATAATAAAATTATATTTTAATT
1 TTTTAAA--AATAATAA-AAAATTATATTTTAACT
16130 TCTTTAAAAATAATAAAAAATTA-A-TTTAACT
1 T-TTTAAAAATAATAAAAAATTATATTTTAACT
*
16161 TTTTAAAAATTATAAAAAAT
1 TTTTAAAAATAATAAAAAAT
16181 AATAAAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
30 18 0.38
31 7 0.15
32 1 0.02
33 7 0.15
34 8 0.17
35 1 0.02
36 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (32 bp):
TTTTAAAAATAATAAAAAATTATATTTTAACT
Found at i:16179 original size:31 final size:34
Alignment explanation
Indices: 16104--16179 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 34
16094 ATTTTAAATT
* *
16104 AATAATAATAAAATTATATTTTAATTTCTTTAAA
1 AATAATAAAAAAATTATATTTTAACTTCTTTAAA
16138 AATAAT-AAAAAATTA-A-TTTAACTT-TTTAAA
1 AATAATAAAAAAATTATATTTTAACTTCTTTAAA
*
16168 AATTATAAAAAA
1 AATAATAAAAAA
16180 TAATAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 11 0.29
31 12 0.32
32 1 0.03
33 8 0.21
34 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (34 bp):
AATAATAAAAAAATTATATTTTAACTTCTTTAAA
Found at i:16659 original size:13 final size:12
Alignment explanation
Indices: 16638--16666 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16628 ATAAAAATAT
16638 TTTAATTTTTTA
1 TTTAATTTTTTA
16650 TTTAATTTTTT-
1 TTTAATTTTTTA
16661 TTTAAT
1 TTTAAT
16667 CATAACTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTAATTTTTTA
Found at i:18982 original size:21 final size:21
Alignment explanation
Indices: 18956--18997 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
18946 AGTGTCAACG
18956 AGCGATAGCTCCTAGCTTACA
1 AGCGATAGCTCCTAGCTTACA
18977 AGCGATAGCTCCTAGCTTACA
1 AGCGATAGCTCCTAGCTTACA
18998 TTCGAGTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
AGCGATAGCTCCTAGCTTACA
Found at i:19805 original size:24 final size:24
Alignment explanation
Indices: 19772--19823 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19762 TTTCTAGAAG
* *
19772 ATTTAGTATTTATTAGTATAATAT
1 ATTTAATATTTATTAGCATAATAT
*
19796 ATTTAATATTTATTAGCATAATTT
1 ATTTAATATTTATTAGCATAATAT
19820 ATTT
1 ATTT
19824 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
ATTTAATATTTATTAGCATAATAT
Found at i:22450 original size:18 final size:19
Alignment explanation
Indices: 22427--22462 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22417 TTCTTTTAGT
22427 TTATTTTTATTT-ATTAAA
1 TTATTTTTATTTAATTAAA
*
22445 TTATTTTTCTTTAATTAA
1 TTATTTTTATTTAATTAA
22463 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTATTTAATTAAA
Found at i:23561 original size:30 final size:31
Alignment explanation
Indices: 23506--23571 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
23496 AATATCCTAT
*
23506 ATTTTTATCATTTTTAAAGGATCAAATTA-A
1 ATTTTTATCATTTTTAAAGGATCAAAATACA
*
23536 ATTTTTATCATTTTTAGGAGG-TCAAAATACA
1 ATTTTTATCATTTTTA-AAGGATCAAAATACA
23567 ATTTT
1 ATTTT
23572 ACTTTTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 23 0.72
31 9 0.28
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (31 bp):
ATTTTTATCATTTTTAAAGGATCAAAATACA
Found at i:32165 original size:81 final size:81
Alignment explanation
Indices: 32050--32254 Score: 302
Period size: 81 Copynumber: 2.5 Consensus size: 81
32040 AGTTTAATTG
* * * * *
32050 ACTAGTGCTGGGCACACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATTA
1 ACTAGAGCTAGGCTCACTTTTGCGATTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATTA
32115 TTCGTTGGTTAATCCA
66 TTCGTTGGTTAATCCA
* * * * *
32131 ACTAGAGCTTGGCTCACTTTTGCGATATATCCGCTAGGCATTGGGTGCCATGATTTGACGGATTA
1 ACTAGAGCTAGGCTCACTTTTGCGATTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATTA
*
32196 TTTGTTGGTTAATCCA
66 TTCGTTGGTTAATCCA
*
32212 ACTAGAGCTAGGCTCACTTTTGTGATTTATCCGCTAGGCACTG
1 ACTAGAGCTAGGCTCACTTTTGCGATTTATCCGCTAGGCACTG
32255 AGTGTTAGGA
Statistics
Matches: 110, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 110 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (81 bp):
ACTAGAGCTAGGCTCACTTTTGCGATTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATTA
TTCGTTGGTTAATCCA
Found at i:32427 original size:67 final size:67
Alignment explanation
Indices: 32311--32443 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
32301 ATTGGTTAAA
**
32311 CCAACTAGAGCTGGACTCACTTATTGCGGTTTATCCTTTAGGCACTGGGTG-CTAGGAATTGACG
1 CCAACTAGAGCTGGACTCACTTATTGCGGTTTATCCGCTAGGCACTGGGTGTC-AGGAATTGACG
32375 GAT
65 GAT
* * * * * *
32378 CCAACTAGAGTTGGGCTCACTTATTGTGGTTTATCCGCTAGGGATTGGGTGTCATGAATTGACGG
1 CCAACTAGAGCTGGACTCACTTATTGCGGTTTATCCGCTAGGCACTGGGTGTCAGGAATTGACGG
32443 A
66 A
32444 ACTATATTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 56 0.98
68 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (67 bp):
CCAACTAGAGCTGGACTCACTTATTGCGGTTTATCCGCTAGGCACTGGGTGTCAGGAATTGACGG
AT
Found at i:32516 original size:2 final size:2
Alignment explanation
Indices: 32509--32542 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
32499 AAAGAAATAC
*
32509 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32543 GTACTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32670 original size:24 final size:24
Alignment explanation
Indices: 32643--32689 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
32633 TAAATTTACT
*
32643 TTTAAATTTAAAATTAATAAAAGA
1 TTTAAACTTAAAATTAATAAAAGA
32667 TTTAAACTTAAAATTAATAAAAG
1 TTTAAACTTAAAATTAATAAAAG
32690 TCCAAATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (24 bp):
TTTAAACTTAAAATTAATAAAAGA
Found at i:34503 original size:30 final size:29
Alignment explanation
Indices: 34432--34778 Score: 212
Period size: 29 Copynumber: 12.0 Consensus size: 29
34422 GCCCAAAAGG
* **
34432 CCCCTAAACTGTCCAAAAATTATGTTTTGA
1 CCCCTAAACTTTCCAAAAATTACATTTT-A
* * **
34462 CCTC-GAACTTTCCAAAAATTATGTTTTGA
1 CCCCTAAACTTTCCAAAAATTACATTTT-A
* *
34491 CCCCTAAACTTTCCAAAAATCACATTTTT
1 CCCCTAAACTTTCCAAAAATTACATTTTA
* *
34520 CCTCC-AAA-ATTCCAAAAATCACATTTTTA
1 CC-CCTAAACTTTCCAAAAATTACA-TTTTA
* ** *
34549 CCCCTAAATTTTTTAAAAATCACATTTTA
1 CCCCTAAACTTTCCAAAAATTACATTTTA
* * *
34578 CCCCCAAACTTTCTAAAAATCACATTTTA
1 CCCCTAAACTTTCCAAAAATTACATTTTA
* * * *
34607 ACCCTCAAACATTCCAAAAATCACATTTTT
1 CCCCT-AAACTTTCCAAAAATTACATTTTA
*
34637 CCCCTAAAC-TTAC-AAAATTACCATTTTA
1 CCCCTAAACTTTCCAAAAATTA-CATTTTA
* * *
34665 -CCCTCGAAC-TTCAAAAAATTGCATTTTTGA
1 CCCCT-AAACTTTCCAAAAATTACA-TTTT-A
* **
34695 -CCCTAAATTTTCCAAAAATTATGTTTTTA
1 CCCCTAAACTTTCCAAAAATTA-CATTTTA
* *
34724 CCCCTGAAC-ATCCAAAAATTACCATTTT-
1 CCCCTAAACTTTCCAAAAATTA-CATTTTA
** *
34752 CCCCTGGA-TGTCCAAAAATTACATTTT
1 CCCCTAAACTTTCCAAAAATTACATTTT
34779 TTTCCCTTTA
Statistics
Matches: 258, Mismatches: 44, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
27 16 0.06
28 50 0.19
29 106 0.41
30 86 0.33
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCCTAAACTTTCCAAAAATTACATTTTA
Found at i:34779 original size:28 final size:29
Alignment explanation
Indices: 34472--34779 Score: 100
Period size: 30 Copynumber: 10.6 Consensus size: 29
34462 CCTCGAACTT
** * * *
34472 TCCAAAAATTATGTTTTGACCCCTAAACTT
1 TCCAAAAATTACATTTTTACCCCTGAAC-A
* *
34502 TCCAAAAATCACATTTTT-CCTCC--AAAA
1 TCCAAAAATTACATTTTTACC-CCTGAACA
* * **
34529 TTCCAAAAATCACATTTTTACCCCTAAATTT
1 -TCCAAAAATTACATTTTTACCCCTGAA-CA
** * ** *
34560 TTTAAAAATCACA-TTTTACCCCCAAACTT
1 TCCAAAAATTACATTTTTACCCCTGAAC-A
* * * *
34589 TCTAAAAATCACA-TTTTAACCCTCAAACA
1 TCCAAAAATTACATTTTTACCCCT-GAACA
* * *
34618 TTCCAAAAATCACATTTTT-CCCCTAAACT
1 -TCCAAAAATTACATTTTTACCCCTGAACA
* *
34647 TAC-AAAATTACCA-TTTTA-CCCTCGAACT
1 TCCAAAAATTA-CATTTTTACCCCT-GAACA
* * * **
34675 TCAAAAAATTGCATTTTTGA-CCCTAAATTT
1 TCCAAAAATTACATTTTT-ACCCCTGAA-CA
**
34705 TCCAAAAATTATGTTTTTACCCCTGAACA
1 TCCAAAAATTACATTTTTACCCCTGAACA
* **
34734 TCCAAAAATTACCA-TTTT-CCCCTGGATG
1 TCCAAAAATTA-CATTTTTACCCCTGAACA
34762 TCCAAAAATTACATTTTT
1 TCCAAAAATTACATTTTT
34780 TTCCCTTTAG
Statistics
Matches: 219, Mismatches: 39, Indels: 42
0.73 0.13 0.14
Matches are distributed among these distances:
27 16 0.07
28 55 0.25
29 69 0.32
30 75 0.34
31 4 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCCTGAACA
Found at i:43153 original size:97 final size:97
Alignment explanation
Indices: 42987--43180 Score: 379
Period size: 97 Copynumber: 2.0 Consensus size: 97
42977 GATGTGTTTT
42987 TGAAAATAAAAGAAGAGGTCAAGAAACAATTTGATGCTGGGTTTCTCCAAGTAATTAAATACTCT
1 TGAAAATAAAAGAAGAGGTCAAGAAACAATTTGATGCTGGGTTTCTCCAAGTAATTAAATACTCT
43052 GAATGGGTAGCTAACATAGTCCCTGTTCCTAA
66 GAATGGGTAGCTAACATAGTCCCTGTTCCTAA
43084 TGAAAATAAAAGAAGAGGTCAAGAAACAATTTGATGCTGGGTTTCTCCAAGTAATTAAATACTCT
1 TGAAAATAAAAGAAGAGGTCAAGAAACAATTTGATGCTGGGTTTCTCCAAGTAATTAAATACTCT
*
43149 GAATGGGTAGCTAACATAGTTCCTGTTCCTAA
66 GAATGGGTAGCTAACATAGTCCCTGTTCCTAA
43181 AAGAGATGGA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (97 bp):
TGAAAATAAAAGAAGAGGTCAAGAAACAATTTGATGCTGGGTTTCTCCAAGTAATTAAATACTCT
GAATGGGTAGCTAACATAGTCCCTGTTCCTAA
Found at i:47397 original size:209 final size:208
Alignment explanation
Indices: 47009--47482 Score: 727
Period size: 209 Copynumber: 2.3 Consensus size: 208
46999 CGATTATCGA
* *
47009 AAACAA-CGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAGG
1 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGG
* * * * * *
47073 CTCAAAGTGAGCAAATCTTCAAACCTAGCTTCCTGATGAGATACTGAGAAATAGGTCGAAGCAAT
66 CTCAAACTAAGCAAATCTGCAAACCCAACTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAAT
* * * *
47138 AAAATGATCGCCTTCTTGATAAGATACAGAGAAGAGGACCAAACCCGTCTTCTTGATGAGGTATA
131 AAAATGATCGCCTTCCTGATAAGATACAGAGAAGAGGACCAAACCCGTCTTCCTGATGAGATACA
47203 AAGAAGTGGGTTG
196 AAGAAGTGGGTTG
*
47216 AAACAAGCGATGCGGTCATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGG
1 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGG
* * *
47281 CTCAAACTAAGCAAATCTGCGAACCCCAACTTCCTTATGAGATACTGAGAAACAGGTTGAAGCAA
66 CTCAAACTAAGCAAATCTGC-AAACCCAACTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAA
* * *
47346 TAAAATGGTCGCCTTCCTGATGAGATACAGAGAAGTGGACCAAACCCGTCTTCCTGATGAGATAC
130 TAAAATGATCGCCTTCCTGATAAGATACAGAGAAGAGGACCAAACCCGTCTTCCTGATGAGATAC
47411 AAAGAAGTGGGTTG
195 AAAGAAGTGGGTTG
* *
47425 AAACAAGTGATGCGGTCATTTTCCTGATGAGA-AGCTGAGAAGTAGACCAAATCAATGA
1 AAACAAGCGATGCGGTCATCTTCCTGATGAGATA-CTGAGAAGTAGACCAAATCAATGA
47483 CCAAACCATT
Statistics
Matches: 242, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
207 6 0.02
208 73 0.30
209 163 0.67
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (208 bp):
AAACAAGCGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAGG
CTCAAACTAAGCAAATCTGCAAACCCAACTTCCTGATGAGATACTGAGAAACAGGTCGAAGCAAT
AAAATGATCGCCTTCCTGATAAGATACAGAGAAGAGGACCAAACCCGTCTTCCTGATGAGATACA
AAGAAGTGGGTTG
Found at i:47791 original size:6 final size:6
Alignment explanation
Indices: 47780--47876 Score: 78
Period size: 6 Copynumber: 16.8 Consensus size: 6
47770 CCAAACCTTT
* *
47780 TTTAAA TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
** * **
47826 TTT-GT TTTAAA TTTAAA -TTAAG TTTAAA TTTACT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
47872 ATTAA
1 TTTAA
47877 TAAAAGTCTA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
5 16 0.23
6 54 0.77
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:47801 original size:17 final size:17
Alignment explanation
Indices: 47779--47857 Score: 115
Period size: 17 Copynumber: 4.6 Consensus size: 17
47769 ACCAAACCTT
47779 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
47796 TTTTAAGA-TTAAATTTA
1 TTTTAA-ATTTAAATTTA
*
47813 TTTTAAATTTAAATTTG
1 TTTTAAATTTAAATTTA
*
47830 TTTTAAATTTAAATTAA
1 TTTTAAATTTAAATTTA
*
47847 GTTTAAATTTA
1 TTTTAAATTTA
47858 CTTTTAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
16 1 0.02
17 54 0.96
18 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:47818 original size:11 final size:11
Alignment explanation
Indices: 47784--47877 Score: 55
Period size: 11 Copynumber: 8.3 Consensus size: 11
47774 ACCTTTTTTA
47784 AATTTAAATTT
1 AATTTAAATTT
* *
47795 ATTTTAAGATTA
1 AATTTAA-ATTT
*
47807 AATTT-ATTTT
1 AATTTAAATTT
47817 AAATTTAAATTT
1 -AATTTAAATTT
**
47829 GTTTTAAATTT
1 AATTTAAATTT
* *
47840 AAATTAAGTTT
1 AATTTAAATTT
**
47851 AAATTTACTTTT
1 -AATTTAAATTT
*
47863 AAATTTAAAATT
1 -AATTTAAATTT
47875 AAT
1 AAT
47878 AAAAGTCTAA
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
10 2 0.03
11 31 0.51
12 28 0.46
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:49651 original size:30 final size:30
Alignment explanation
Indices: 49617--50004 Score: 182
Period size: 30 Copynumber: 13.2 Consensus size: 30
49607 TTGCCCAAAA
*
49617 GACCCCTAAA-TTGTCCAAAAATTATGTTTT
1 GACCCCTAAACTT-TCCAAAAATTATATTTT
*
49647 GACCCTTAAACTTTCCAAAAATTATATTTT
1 GACCCCTAAACTTTCCAAAAATTATATTTT
* * * *
49677 -AACACTCAAACTTTCTAAAAATTATAATTT
1 GACCCCT-AAACTTTCCAAAAATTATATTTT
* * * *
49707 AACCCCTAAACTTTTCAAAAATCACATTTT
1 GACCCCTAAACTTTCCAAAAATTATATTTT
* * * * *
49737 TA-CTCTCGAAC-TTCCAAAAATCACATTTT
1 GACCCCT-AAACTTTCCAAAAATTATATTTT
* * * * *
49766 TA-CCCTCGAACTTTTCAAAAATCACATTTT
1 GACCCCT-AAACTTTCCAAAAATTATATTTT
* * *
49796 -A--CCTACGAACTTCCCAAAAATCACATTTT
1 GACCCCTA--AACTTTCCAAAAATTATATTTT
* * *
49825 -A-CCCTCGAACTTTCC-AAAATCAAATTTTT
1 GACCCCT-AAACTTTCCAAAAATTATA-TTTT
* * * * *
49854 TACCCAC-GAACTTTCTAAAAATCACATTTT
1 GACCC-CTAAACTTTCCAAAAATTATATTTT
*
49884 -A-CCCTAAAC-TTCCAAAAATTACCATTTT
1 GACCCCTAAACTTTCCAAAAATTA-TATTTT
* *
49912 G-CCCCTAAACTTTCTAAAAATTACATTTT
1 GACCCCTAAACTTTCCAAAAATTATATTTT
* * *
49941 TACCCCCAAAAC-ATCCAAAAATTATATTTT
1 GA-CCCCTAAACTTTCCAAAAATTATATTTT
* * *
49971 TA-TCCTAAACTTTCCAAAAATTATGTTTT
1 GACCCCTAAACTTTCCAAAAATTATATTTT
*
50000 TACCC
1 GACCC
50005 TCGAACATCT
Statistics
Matches: 293, Mismatches: 42, Indels: 46
0.77 0.11 0.12
Matches are distributed among these distances:
27 11 0.04
28 28 0.10
29 99 0.34
30 130 0.44
31 24 0.08
32 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
GACCCCTAAACTTTCCAAAAATTATATTTT
Found at i:49754 original size:29 final size:29
Alignment explanation
Indices: 49722--50063 Score: 261
Period size: 29 Copynumber: 11.7 Consensus size: 29
49712 CTAAACTTTT
*
49722 CAAAAATCACATTTTTACTCTCGAACTTC
1 CAAAAATCACATTTTTACCCTCGAACTTC
*
49751 CAAAAATCACATTTTTACCCTCGAACTTTT
1 CAAAAATCACATTTTTACCCTCGAAC-TTC
49781 CAAAAATCACA-TTTTA-CCTACGAACTTCC
1 CAAAAATCACATTTTTACCCT-CGAACTT-C
49810 CAAAAATCACA-TTTTACCCTCGAACTTTC
1 CAAAAATCACATTTTTACCCTCGAAC-TTC
* *
49839 C-AAAATCAAATTTTTTACCCACGAACTTTC
1 CAAAAATCACA-TTTTTACCCTCGAAC-TTC
* *
49869 TAAAAATCACA-TTTTACCCT-AAACTTC
1 CAAAAATCACATTTTTACCCTCGAACTTC
* ** *
49896 CAAAAATTACCATTTTGCCCCT-AAACTTTC
1 CAAAAATCA-CATTTTTACCCTCGAAC-TTC
* * * * *
49926 TAAAAATTACATTTTTACCCCCAAAACATC
1 CAAAAATCACATTTTTACCCTC-GAACTTC
* * * *
49956 CAAAAATTATATTTTTATCCT-AAACTTTC
1 CAAAAATCACATTTTTACCCTCGAAC-TTC
* ** *
49985 CAAAAATTATGTTTTTACCCTCGAACATC
1 CAAAAATCACATTTTTACCCTCGAACTTC
* * * *
50014 TAAAAATTACCA-TTTTACCCTCGAACGTG
1 CAAAAATCA-CATTTTTACCCTCGAACTTC
* *
50043 CAAAAATTACATTTTTGCCCT
1 CAAAAATCACATTTTTACCCT
50064 TGAGTGACCA
Statistics
Matches: 262, Mismatches: 34, Indels: 34
0.79 0.10 0.10
Matches are distributed among these distances:
27 10 0.04
28 24 0.09
29 148 0.56
30 68 0.26
31 12 0.05
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATCACATTTTTACCCTCGAACTTC
Found at i:49842 original size:88 final size:86
Alignment explanation
Indices: 49655--49945 Score: 286
Period size: 88 Copynumber: 3.3 Consensus size: 86
49645 TTGACCCTTA
* * * * * * * * *
49655 AACTTTCCAAAAATTATATTTTAACACTCAAACTTTCTAAAAATTATAATTTAACCCCTAAACTT
1 AACTTTCCAAAAATCACATTTTTACCCACGAACTTTCTAAAAATCA-CATTTTA-CCCTAAAC-T
* *
49720 TTCAAAAATCACATTTTTACTCTCG
63 TCCAAAAATCACA-TTTTACCCTCG
*
49745 AAC-TTCCAAAAATCACATTTTTACCCTCGAACTTT-TCAAAAATCACATTTTA-CCTACGAACT
1 AACTTTCCAAAAATCACATTTTTACCCACGAACTTTCT-AAAAATCACATTTTACCCTA--AACT
49807 TCCCAAAAATCACATTTTACCCTCG
63 T-CCAAAAATCACATTTTACCCTCG
*
49832 AACTTTCC-AAAATCAAATTTTTTACCCACGAACTTTCTAAAAATCACATTTTACCCTAAACTTC
1 AACTTTCCAAAAATCACA-TTTTTACCCACGAACTTTCTAAAAATCACATTTTACCCTAAACTTC
* * *
49896 CAAAAATTACCATTTTGCCC-CTA
65 CAAAAATCA-CATTTTACCCTC-G
* *
49919 AACTTTCTAAAAATTACATTTTTACCC
1 AACTTTCCAAAAATCACATTTTTACCC
49946 CCAAAACATC
Statistics
Matches: 172, Mismatches: 18, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
86 14 0.08
87 53 0.31
88 63 0.37
89 39 0.23
90 3 0.02
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (86 bp):
AACTTTCCAAAAATCACATTTTTACCCACGAACTTTCTAAAAATCACATTTTACCCTAAACTTCC
AAAAATCACATTTTACCCTCG
Found at i:49911 original size:59 final size:57
Alignment explanation
Indices: 49643--49945 Score: 245
Period size: 59 Copynumber: 5.1 Consensus size: 57
49633 AAAAATTATG
* * * * * * *
49643 TTTTGACCCTTAAACTTTCCAAAAATTATATTTTAACACTCAAACTTTCTAAAAATTATAA
1 TTTT-ACCC-TAAACTTTCCAAAAATCACATTTT-ACCCACGAACTTTCTAAAAATCA-CA
* * * * *
49704 TTTAACCCCTAAACTTTTCAAAAATCACATTTTTACTCTCGAAC-TTCCAAAAATCACA
1 TTTTA-CCCTAAACTTTCCAAAAATCACA-TTTTACCCACGAACTTTCTAAAAATCACA
* * * * *
49762 TTTTTACCCTCGAACTTTTCAAAAATCACATTTTACCTACGAACTTCCCAAAAATCACA
1 -TTTTACCCT-AAACTTTCCAAAAATCACATTTTACCCACGAACTTTCTAAAAATCACA
* *
49821 TTTTACCCTCGAACTTTCC-AAAATCAAATTTTTTACCCACGAACTTTCTAAAAATCACA
1 TTTTACCCT-AAACTTTCCAAAAATCACA--TTTTACCCACGAACTTTCTAAAAATCACA
* * * *
49880 TTTTACCCTAAAC-TTCCAAAAATTACCATTTTGCCC-CTAAACTTTCTAAAAATTACA
1 TTTTACCCTAAACTTTCCAAAAATCA-CATTTTACCCAC-GAACTTTCTAAAAATCACA
49937 TTTTTACCC
1 -TTTTACCC
49946 CCAAAACATC
Statistics
Matches: 205, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 36 0.18
58 51 0.25
59 81 0.40
60 26 0.13
61 10 0.05
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (57 bp):
TTTTACCCTAAACTTTCCAAAAATCACATTTTACCCACGAACTTTCTAAAAATCACA
Found at i:49990 original size:59 final size:59
Alignment explanation
Indices: 49862--50058 Score: 197
Period size: 59 Copynumber: 3.4 Consensus size: 59
49852 TTTACCCACG
* * * *
49862 AACTTTCTAAAAATCACA-TTTTA-CCCTAAACTTCCAAAAATTACCATTTTGCCCCTA
1 AACTTTCTAAAAATTACATTTTTACCCCCAAACATCCAAAAATTACCATTTTGACCCTA
* * *
49919 AACTTTCTAAAAATTACATTTTTACCCCCAAAACATCCAAAAATTA-TATTTTTATCCTA
1 AACTTTCTAAAAATTACATTTTTACCCCC-AAACATCCAAAAATTACCATTTTGACCCTA
* ** * * * *
49978 AACTTTCCAAAAATTATGTTTTTACCCTCGAACATCTAAAAATTACCATTTT-ACCCTCG
1 AACTTTCTAAAAATTACATTTTTACCCCCAAACATCCAAAAATTACCATTTTGACCCT-A
* *
50037 AACGTGC-AAAAATTACATTTTT
1 AACTTTCTAAAAATTACATTTTT
50059 GCCCTTGAGT
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
57 17 0.15
58 36 0.31
59 47 0.41
60 15 0.13
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
AACTTTCTAAAAATTACATTTTTACCCCCAAACATCCAAAAATTACCATTTTGACCCTA
Found at i:56929 original size:23 final size:24
Alignment explanation
Indices: 56884--56940 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 24
56874 TATTATTACA
56884 TTCAAATCCAAAACAAAAACAAAG
1 TTCAAATCCAAAACAAAAACAAAG
*
56908 TTCAAATCCAAATC-AAAACAAAG
1 TTCAAATCCAAAACAAAAACAAAG
56931 TTCAAA-CCAA
1 TTCAAATCCAA
56941 GTATGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 4 0.12
23 15 0.47
24 13 0.41
ACGTcount: A:0.58, C:0.23, G:0.04, T:0.16
Consensus pattern (24 bp):
TTCAAATCCAAAACAAAAACAAAG
Found at i:64226 original size:87 final size:87
Alignment explanation
Indices: 64080--64253 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
64070 AAAGCACAAT
64080 AACGTCGAATTCCCACTTGGAACAACCATTGAACTCTTAACCATCAACTAAACTAGTTCTTCCTT
1 AACGTCGAATTCCCACTTGGAACAACCATTGAACTCTTAACCATCAACTAAACTAGTTCTTCCTT
64145 TAGGAGAAAGATCTCATCCCTC
66 TAGGAGAAAGATCTCATCCCTC
64167 AACGTCGAATTCCCACTTGGAACAACCATTGAACTCTTAACCATCAACTAAACTAGTTCTTCCTT
1 AACGTCGAATTCCCACTTGGAACAACCATTGAACTCTTAACCATCAACTAAACTAGTTCTTCCTT
64232 TAGGAGAAAGATCTCATCCCTC
66 TAGGAGAAAGATCTCATCCCTC
64254 CCCATCGTAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.28
Consensus pattern (87 bp):
AACGTCGAATTCCCACTTGGAACAACCATTGAACTCTTAACCATCAACTAAACTAGTTCTTCCTT
TAGGAGAAAGATCTCATCCCTC
Found at i:65013 original size:31 final size:30
Alignment explanation
Indices: 64950--65014 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
64940 TTAATTATAT
*
64950 TTTTATAAATTTTAAAAGATTAAATTAAAA
1 TTTTATAAATTTTAAAAGATTAAAATAAAA
*
64980 TTTTATAAATTTTAGAAA-ATTCAAAATACAA
1 TTTTATAAATTTTA-AAAGATT-AAAATAAAA
65011 TTTT
1 TTTT
65015 GTTTTTATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTATAAATTTTAAAAGATTAAAATAAAA
Found at i:65211 original size:10 final size:10
Alignment explanation
Indices: 65196--65222 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
65186 AATTCCTAAC
65196 TAATTAATAT
1 TAATTAATAT
65206 TAATTAATAT
1 TAATTAATAT
65216 TAATTAA
1 TAATTAA
65223 AAGAGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAATTAATAT
Found at i:68225 original size:5 final size:5
Alignment explanation
Indices: 68215--68242 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
68205 CAAAACCAAC
68215 ATCAT ATCAT ATCAT ATCAT ATCAT ATC
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATC
68243 TCAACCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
ATCAT
Found at i:74827 original size:14 final size:14
Alignment explanation
Indices: 74808--74836 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
74798 CGTAAACAGT
74808 TGTGAATATTACAA
1 TGTGAATATTACAA
74822 TGTGAATATTACAA
1 TGTGAATATTACAA
74836 T
1 T
74837 AATTTCATAA
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:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (14 bp):
TGTGAATATTACAA
Found at i:82773 original size:53 final size:54
Alignment explanation
Indices: 82641--82847 Score: 148
Period size: 54 Copynumber: 3.9 Consensus size: 54
82631 TTATAGTTTG
* * * * * * * * *
82641 TCGATTTACTATCACAACCTCCCACTTAAAAGATTTTTAGAGTCTTACGATTCG
1 TCGATTTACAATCACAACCTTCTACTTACATGATTTTCAGAATCTTACAATTCA
* * *** *
82695 CCAATTTACAATCGTGACCTCCTACTTACATGATTTTCAGAATCTT-CAATTCA
1 TCGATTTACAATCACAACCTTCTACTTACATGATTTTCAGAATCTTACAATTCA
* * * * * *
82748 TCGATTTACGATCACAACCTTCTACTTTCAAGATTTTTAGAATCTTACAGTTCG
1 TCGATTTACAATCACAACCTTCTACTTACATGATTTTCAGAATCTTACAATTCA
* ** * * *
82802 TTGATTTACAATTGCAACCTTTTACATACAAT-ATTTTCAAAATCTT
1 TCGATTTACAATCACAACCTTCTACTTAC-ATGATTTTCAGAATCTT
82848 GCATCTTGTC
Statistics
Matches: 116, Mismatches: 35, Indels: 4
0.75 0.23 0.03
Matches are distributed among these distances:
53 41 0.35
54 74 0.64
55 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (54 bp):
TCGATTTACAATCACAACCTTCTACTTACATGATTTTCAGAATCTTACAATTCA
Found at i:82838 original size:107 final size:107
Alignment explanation
Indices: 82641--82847 Score: 238
Period size: 107 Copynumber: 1.9 Consensus size: 107
82631 TTATAGTTTG
* *
82641 TCGATTTACTATCACAACCTCCCACTTAAAAGATTTTTAGAGTCTTACGATTCGCCAATTTACAA
1 TCGATTTACGATCACAACCTCCCACTTAAAAGATTTTTAGAATCTTACGATTCGCCAATTTACAA
** * *
82706 TCGTGACCTCCTACTTACATGATTTTCAGAATCTTCAATTCA
66 TCGCAACCTCCTACATACATGATTTTCAAAATCTTCAATTCA
* * ** ***
82748 TCGATTTACGATCACAACCTTCTACTTTCAAGATTTTTAGAATCTTAC-AGTTCGTTGATTTACA
1 TCGATTTACGATCACAACCTCCCACTTAAAAGATTTTTAGAATCTTACGA-TTCGCCAATTTACA
* **
82812 ATTGCAACCTTTTACATACAAT-ATTTTCAAAATCTT
65 ATCGCAACCTCCTACATAC-ATGATTTTCAAAATCTT
82848 GCATCTTGTC
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
106 1 0.01
107 79 0.96
108 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (107 bp):
TCGATTTACGATCACAACCTCCCACTTAAAAGATTTTTAGAATCTTACGATTCGCCAATTTACAA
TCGCAACCTCCTACATACATGATTTTCAAAATCTTCAATTCA
Found at i:83551 original size:31 final size:31
Alignment explanation
Indices: 83475--83593 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 31
83465 GATAAAAGTA
* *
83475 ACCTCACAAGGTGATCCCATCACACTTAATC
1 ACCTCACAAGGTGATCCCATCACACCTCATC
** *
83506 ATATCATTAA-GTGATCCCATCACACCTCATC
1 ACCTCA-CAAGGTGATCCCATCACACCTCATC
* * * *
83537 ACCTCGCAAGGTGATCACATCGCACCTCACC
1 ACCTCACAAGGTGATCCCATCACACCTCATC
* *
83568 ATCT-ACTAA-GTGATCCAATCACACCT
1 ACCTCAC-AAGGTGATCCCATCACACCT
83594 TACCACCTTG
Statistics
Matches: 68, Mismatches: 17, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
30 17 0.25
31 49 0.72
32 2 0.03
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.24
Consensus pattern (31 bp):
ACCTCACAAGGTGATCCCATCACACCTCATC
Found at i:83670 original size:62 final size:62
Alignment explanation
Indices: 83577--83734 Score: 140
Period size: 62 Copynumber: 2.5 Consensus size: 62
83567 CATCTACTAA
** * * ** **
83577 GTGATCCAATCACACCTTACCACCTTGCGAGGTG-ACCCTACCACGCCTCACCATCTT-ATTAG
1 GTGATCCCGTCACACATAACCACCTAACGAGGTGAACCC-ACCACGCCTCACCAT-TTAACGAG
* * * * * * *
83639 GTGATCTCGTCACGCATCACCACCTCACGAGGTGAACCCATCACTCTTCACCATTTAACGAG
1 GTGATCCCGTCACACATAACCACCTAACGAGGTGAACCCACCACGCCTCACCATTTAACGAG
*
83701 GTGATCCCGTCACACCTAACCACCTAACGAGGTG
1 GTGATCCCGTCACACATAACCACCTAACGAGGTG
83735 GAGCATTAGG
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
61 2 0.03
62 70 0.92
63 4 0.05
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.22
Consensus pattern (62 bp):
GTGATCCCGTCACACATAACCACCTAACGAGGTGAACCCACCACGCCTCACCATTTAACGAG
Found at i:83672 original size:31 final size:31
Alignment explanation
Indices: 83637--83734 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 31
83627 CCATCTTATT
* * *
83637 AGGTGATCTCGTCACGCATCACCACCTCACG
1 AGGTGATCCCGTCACACATCACCACCTAACG
* * * * **
83668 AGGTGAACCCATCACTCTTCACCATTTAACG
1 AGGTGATCCCGTCACACATCACCACCTAACG
* *
83699 AGGTGATCCCGTCACACCTAACCACCTAACG
1 AGGTGATCCCGTCACACATCACCACCTAACG
83730 AGGTG
1 AGGTG
83735 GAGCATTAGG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (31 bp):
AGGTGATCCCGTCACACATCACCACCTAACG
Found at i:85538 original size:17 final size:17
Alignment explanation
Indices: 85516--85550 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
85506 GTCCAGAGTC
85516 TAGATAACTTCACATAA
1 TAGATAACTTCACATAA
85533 TAGATAACTTCACATAA
1 TAGATAACTTCACATAA
85550 T
1 T
85551 TCCACAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
TAGATAACTTCACATAA
Found at i:86347 original size:18 final size:18
Alignment explanation
Indices: 86319--86353 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
86309 CAGTAGCAAG
86319 AGAAGTGAAG-AAGAAAA
1 AGAAGTGAAGAAAGAAAA
86336 AGAAGATGAAGAAAGAAA
1 AGAAG-TGAAGAAAGAAA
86354 GGGAAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (18 bp):
AGAAGTGAAGAAAGAAAA
Found at i:91733 original size:22 final size:22
Alignment explanation
Indices: 91705--91748 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
91695 CCGTGAGGTA
91705 GAACTGAACGAGATGCCATGAT
1 GAACTGAACGAGATGCCATGAT
91727 GAACTGAACGAGATGCCATGAT
1 GAACTGAACGAGATGCCATGAT
91749 CTATAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
GAACTGAACGAGATGCCATGAT
Done.