Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001446.1 Kokia drynarioides strain JFW-HI SEQ_112960, 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: 109359
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 97 characters in sequence are not A, C, G, or T
Found at i:4571 original size:43 final size:43
Alignment explanation
Indices: 4523--4825 Score: 322
Period size: 43 Copynumber: 7.1 Consensus size: 43
4513 TGTTAGTGGT
*
4523 GTTTGTGGGAAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * ** * *
4566 GTTTGTGGGAGAAGTGTTGTTAAATACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * ** * *
4609 GTTTGTGGGAGAAGTGTTGTTAAATACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
4652 GTTTGT-GTAAATGCGCCGCTAAAGACCATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * * * **
4694 GTTTATGAGATAAGCGTCGCTAAAGACCATGTTCTTTAATGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* *
4737 GTTTGT-GGAAAAGCCCCGCTAAAGAACATGTTCTTTAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
* * * * * * *
4779 ATTTATGAGATAAGCGCCGCTAAAAATCATGTTCTATAGCGGC
1 GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
4822 GTTT
1 GTTT
4826 TTCCTCATAA
Statistics
Matches: 220, Mismatches: 38, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
42 66 0.30
43 154 0.70
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
GTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGC
Found at i:4723 original size:85 final size:84
Alignment explanation
Indices: 4534--4825 Score: 332
Period size: 85 Copynumber: 3.4 Consensus size: 84
4524 TTTGTGGGAA
* * ** * *
4534 AAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAGAAGTGTTGTTAAATACCATGTT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGT-GGA-AAGCGCCGCTAAAGACCATGTT
* * *
4599 CTTTAGCGGCGTTTGTGGGAG
64 CTTTAGCGGCGTTTATGAGAT
* ** * * *
4620 AAGTGTTGTTAAATACCATGTTCTTTAGCGGCGTTTGTGTAAATGCGCCGCTAAAGACCATGTTC
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGAAA-GCGCCGCTAAAGACCATGTTC
4685 TTTAGCGGCGTTTATGAGAT
65 TTTAGCGGCGTTTATGAGAT
* ** * *
4705 AAGCGTCGCTAAAGACCATGTTCTTTAATGGCGTTTGTGGAAAAGCCCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGG-AAAGCGCCGCTAAAGACCATGTTC
*
4770 TTTAGCGGCATTTATGAGAT
65 TTTAGCGGCGTTTATGAGAT
* * *
4790 AAGCGCCGCTAAAAATCATGTTCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTT
4826 TTCCTCATAA
Statistics
Matches: 175, Mismatches: 29, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.01
85 136 0.78
86 37 0.21
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (84 bp):
AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGAAAGCGCCGCTAAAGACCATGTTCT
TTAGCGGCGTTTATGAGAT
Found at i:4796 original size:128 final size:128
Alignment explanation
Indices: 4532--4825 Score: 340
Period size: 128 Copynumber: 2.3 Consensus size: 128
4522 TGTTTGTGGG
* * * * * * *
4532 AAAAGCGCCGTTAAAGACCATGTTCTTTAGCGGCGTTTGTGGGAGAAGTGTTGTTAAATACCATG
1 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGAGAGAAGCGTCGCTAAAGACCATG
* * **** * * * * *
4597 TTCTTTAGCGGCGTTTGTGGGAGAAGTGTTGTTAAATACCATGTTCTTTAGCGGCGTTTGTGT
66 TTCTTTAACGGCGTTTGTGGGAAAAGCCCCGCTAAAGAACATGTTCTTTAGCGGCATTTATGT
* *
4660 AAATGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGAGATAAGCGTCGCTAAAGACCATG
1 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGAGAGAAGCGTCGCTAAAGACCATG
*
4725 TTCTTTAATGGCGTTTGT-GGAAAAGCCCCGCTAAAGAACATGTTCTTTAGCGGCATTTATG-
66 TTCTTTAACGGCGTTTGTGGGAAAAGCCCCGCTAAAGAACATGTTCTTTAGCGGCATTTATGT
* * *
4786 AGATAAGCGCCGCTAAAAATCATGTTCTATAGCGGCGTTT
1 A-A-AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTT
4826 TTCCTCATAA
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
126 1 0.01
127 34 0.24
128 104 0.75
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (128 bp):
AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGAGAGAAGCGTCGCTAAAGACCATG
TTCTTTAACGGCGTTTGTGGGAAAAGCCCCGCTAAAGAACATGTTCTTTAGCGGCATTTATGT
Found at i:5557 original size:29 final size:28
Alignment explanation
Indices: 5524--5591 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
5514 ACACACGACT
5524 ATAAAAAACTTTCAT-TTTAAACATTTAAA
1 ATAAAAAA-TTT-ATATTTAAACATTTAAA
5553 ATAAAAAATTTATAATTTAAACATTTAAA
1 ATAAAAAATTTAT-ATTTAAACATTTAAA
* *
5582 TTAAATAATT
1 ATAAAAAATT
5592 CGATCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 3 0.09
29 30 0.86
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (28 bp):
ATAAAAAATTTATATTTAAACATTTAAA
Found at i:5583 original size:14 final size:14
Alignment explanation
Indices: 5539--5583 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5529 AAACTTTCAT
5539 TTTAAACATTTAAA
1 TTTAAACATTTAAA
* * *
5553 ATAAAAAATTTATAA
1 TTTAAACATTTA-AA
5568 TTTAAACATTTAAA
1 TTTAAACATTTAAA
5582 TT
1 TT
5584 AAATAATTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAACATTTAAA
Found at i:8141 original size:291 final size:291
Alignment explanation
Indices: 7617--8199 Score: 1103
Period size: 291 Copynumber: 2.0 Consensus size: 291
7607 TCACTAATGA
7617 TCTCAATTTGTAATTGCATATTTTAAGAATAAAATGGGATATCATGGTGGAAGTCATATATATGG
1 TCTCAATTTGTAATTGCATATTTTAAGAATAAAATGGGATATCATGGTGGAAGTCATATATATGG
** *
7682 TCCATGCTGGTGGTATTTCTTAGGAGATGATCATTAAAGCTGATTATGTGGATGAAAAGGACGGC
66 TCCATGCTGGTGGTATCACTTAGGAGATGATCATTAAAGCTGATTATGAGGATGAAAAGGACGGC
7747 TTGAAAAATTAACCAAATTTTATATAGATACCAAAACCAAGTAGGATTTATTTTTTCTTGACATG
131 TTGAAAAATTAACCAAATTTTATATAGATACCAAAACCAAGTAGGATTTATTTTTTCTTGACATG
7812 GGTTGCATTGGTTTGAAGAAAATAAATAGTGGCATTGGTGAGAAAACTAACTTACTAGGATTTTA
196 GGTTGCATTGGTTTGAAGAAAATAAATAGTGGCATTGGTGAGAAAACTAACTTACTAGGATTTTA
7877 CACAAAAAAGGTCCAGTATTTAGATGGGAAT
261 CACAAAAAAGGTCCAGTATTTAGATGGGAAT
7908 TCTCAATTTGTAATTGCATATTTTAAGAATAAAATGGGATATCATGGTGGAAGTCATATATATGG
1 TCTCAATTTGTAATTGCATATTTTAAGAATAAAATGGGATATCATGGTGGAAGTCATATATATGG
* *
7973 TCCATGCTGGTGGTATCACTTAGGAGATGATCATTAAAGCTGATTATGAGGATGAGAAGGATGGC
66 TCCATGCTGGTGGTATCACTTAGGAGATGATCATTAAAGCTGATTATGAGGATGAAAAGGACGGC
8038 TTGAAAAATTAACCAAATTTTATATAGATACCAAAACCAAGTAGGATTTATTTTTTCTTGACATG
131 TTGAAAAATTAACCAAATTTTATATAGATACCAAAACCAAGTAGGATTTATTTTTTCTTGACATG
*
8103 GTTTGCATTGGTTTGAAGAAAATAAATAGTGGCATTGGTGAGAAAACTAACTTACTAGGATTTTA
196 GGTTGCATTGGTTTGAAGAAAATAAATAGTGGCATTGGTGAGAAAACTAACTTACTAGGATTTTA
*
8168 CACAACAAAGGTCCAGTATTTAGATGGGAAT
261 CACAAAAAAGGTCCAGTATTTAGATGGGAAT
8199 T
1 T
8200 AAAAGAGTTG
Statistics
Matches: 285, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 285 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (291 bp):
TCTCAATTTGTAATTGCATATTTTAAGAATAAAATGGGATATCATGGTGGAAGTCATATATATGG
TCCATGCTGGTGGTATCACTTAGGAGATGATCATTAAAGCTGATTATGAGGATGAAAAGGACGGC
TTGAAAAATTAACCAAATTTTATATAGATACCAAAACCAAGTAGGATTTATTTTTTCTTGACATG
GGTTGCATTGGTTTGAAGAAAATAAATAGTGGCATTGGTGAGAAAACTAACTTACTAGGATTTTA
CACAAAAAAGGTCCAGTATTTAGATGGGAAT
Found at i:13840 original size:7 final size:7
Alignment explanation
Indices: 13828--13857 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
13818 CTAATTTGTT
13828 TTTAAAA
1 TTTAAAA
13835 TTTAAAA
1 TTTAAAA
13842 TTTAAAA
1 TTTAAAA
13849 TTTATAAA
1 TTTA-AAA
13857 T
1 T
13858 ATACAAAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:22746 original size:6 final size:6
Alignment explanation
Indices: 22735--22764 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
22725 ATATTTATTG
22735 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
22765 GGTGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:24792 original size:10 final size:10
Alignment explanation
Indices: 24777--24822 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
24767 ATAATTTTAT
24777 ATTTAAAAAA
1 ATTTAAAAAA
*
24787 ATTTAAATTAA
1 ATTTAAA-AAA
* *
24798 TTTTAAAATA
1 ATTTAAAAAA
24808 ATTTAAAAAA
1 ATTTAAAAAA
24818 ATTTA
1 ATTTA
24823 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:24820 original size:21 final size:21
Alignment explanation
Indices: 24778--24821 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24768 TAATTTTATA
**
24778 TTTAAAAAAATTTAAATTAAT
1 TTTAAAAAAATTTAAAAAAAT
*
24799 TTTAAAATAATTTAAAAAAAT
1 TTTAAAAAAATTTAAAAAAAT
24820 TT
1 TT
24822 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAAAAAATTTAAAAAAAT
Found at i:30743 original size:12 final size:12
Alignment explanation
Indices: 30726--30777 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
30716 AAAGACATAC
30726 GTATATATATAT
1 GTATATATATAT
30738 GTATATATATA-
1 GTATATATATAT
*
30749 -TATATATGTAT
1 GTATATATATAT
* *
30760 GTATGTATGTAT
1 GTATATATATAT
30772 GTATAT
1 GTATAT
30778 TTTTTGTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.26
12 26 0.74
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (12 bp):
GTATATATATAT
Found at i:35952 original size:3 final size:3
Alignment explanation
Indices: 35909--35935 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35899 GGTAGTGACC
35909 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
35936 GGGGTGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:37972 original size:16 final size:17
Alignment explanation
Indices: 37948--37995 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
37938 TTATCATTTA
37948 TTAAATAAAA-ATTATC
1 TTAAATAAAATATTATC
*
37964 TTAATTAAAATATTAT-
1 TTAAATAAAATATTATC
*
37980 TTCAATAAAATTATTA
1 TTAAATAAAA-TATTA
37996 AATTTCACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAAAATATTATC
Found at i:39895 original size:3 final size:3
Alignment explanation
Indices: 39887--39923 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
39877 GAACAAATCA
39887 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39924 CAAGCTCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43432 original size:13 final size:13
Alignment explanation
Indices: 43396--43422 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43386 TGTTATATAC
43396 ATAAAAATATTAA
1 ATAAAAATATTAA
43409 ATAAAAATATTAA
1 ATAAAAATATTAA
43422 A
1 A
43423 AAATTATATT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAAATATTAA
Found at i:50012 original size:2 final size:2
Alignment explanation
Indices: 50005--50033 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49995 CATGGACTAC
50005 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
50034 CATAACAAGC
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:52653 original size:31 final size:30
Alignment explanation
Indices: 52589--52653 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
52579 AGTTTAGGTG
* * * *
52589 TTTGGTCACTTTGGCCATTATCGTTTTTTT
1 TTTGCTCACTTTGGCCACTAACCTTTTTTT
*
52619 TTTGCTCACTTTGGCCCCTAACCTTTGTTTT
1 TTTGCTCACTTTGGCCACTAACCTTT-TTTT
52650 TTTG
1 TTTG
52654 GTTAAATTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.09, C:0.22, G:0.15, T:0.54
Consensus pattern (30 bp):
TTTGCTCACTTTGGCCACTAACCTTTTTTT
Found at i:52828 original size:20 final size:19
Alignment explanation
Indices: 52800--52848 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
52790 CCATGTCAGC
* *
52800 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAAATA-TA
52820 AAATTATTTTTTAAAAATATA
1 AAATTA--TTTTAAAAATATA
52841 AAATTATT
1 AAATTATT
52849 AAAATAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.08
20 5 0.20
21 8 0.32
22 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATTATTTTAAAAATATA
Found at i:52842 original size:21 final size:22
Alignment explanation
Indices: 52806--52848 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
52796 CAGCAAATGA
*
52806 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
52828 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
52849 AAAATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:53564 original size:13 final size:13
Alignment explanation
Indices: 53546--53590 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
53536 GTCATCAAGG
53546 AAGGGAAAAGGAA
1 AAGGGAAAAGGAA
*
53559 AAGGG-AAAGGGA
1 AAGGGAAAAGGAA
*
53571 AAGGGAAAGGGAA
1 AAGGGAAAAGGAA
53584 AAGGGAA
1 AAGGGAA
53591 GCGGGGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (13 bp):
AAGGGAAAAGGAA
Found at i:53607 original size:7 final size:6
Alignment explanation
Indices: 53546--53590 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
53536 GTCATCAAGG
*
53546 AAGGGAA AAGGAA AAGGGA AAGGGA AAGGGA AAGGGAA AAGGGA A
1 AAGGG-A AAGGGA AAGGGA AAGGGA AAGGGA AAGGG-A AAGGGA A
53591 GCGGGGAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
6 25 0.71
7 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:53676 original size:18 final size:16
Alignment explanation
Indices: 53645--53704 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 16
53635 AAATGATGAT
53645 TATTTTAATAATTTTA
1 TATTTTAATAATTTTA
53661 TATTTTAATTTAATTTTAAAA
1 TATTTTAA--TAATTTT---A
*
53682 TAATTTTAGTAATTTTA
1 T-ATTTTAATAATTTTA
53699 TATTTT
1 TATTTT
53705 TAAAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
16 13 0.35
17 2 0.05
18 7 0.19
20 7 0.19
21 2 0.05
22 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTTTAATAATTTTA
Found at i:53686 original size:29 final size:29
Alignment explanation
Indices: 53651--53728 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
53641 TGATTATTTT
*
53651 AATAATTTTAT-ATTTTAAT-TTAATTTTAA
1 AATAATTTTATAATTTTAATATT--TTTAAA
53680 AATAATTTTAGTAATTTT-ATATTTTTAAA
1 AATAATTTTA-TAATTTTAATATTTTTAAA
53709 AATAATTTTAATAATTTTAA
1 AATAATTTT-ATAATTTTAA
53729 AATCACTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 31 0.72
30 5 0.12
31 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
AATAATTTTATAATTTTAATATTTTTAAA
Found at i:53714 original size:20 final size:21
Alignment explanation
Indices: 53691--53730 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53681 ATAATTTTAG
*
53691 TAATTTT-ATATTTTTAAAAA
1 TAATTTTAATAATTTTAAAAA
53711 TAATTTTAATAATTTTAAAA
1 TAATTTTAATAATTTTAAAA
53731 TCACTTGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTTTAATAATTTTAAAAA
Found at i:53722 original size:38 final size:37
Alignment explanation
Indices: 53646--53728 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
53636 AATGATGATT
**
53646 ATTTTAATAATTTTATATTTTAATTTAATTTTAAAATA
1 ATTTTAATAATTTTATATTTTAAAATAATTTT-AAATA
*
53684 ATTTTAGTAATTTTATATTTTTAAAAATAATTTT-AATA
1 ATTTTAATAATTTTATA-TTTT-AAAATAATTTTAAATA
53722 ATTTTAA
1 ATTTTAA
53729 AATCACTTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
38 26 0.67
39 4 0.10
40 9 0.23
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (37 bp):
ATTTTAATAATTTTATATTTTAAAATAATTTTAAATA
Found at i:53731 original size:20 final size:19
Alignment explanation
Indices: 53651--53731 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 19
53641 TGATTATTTT
53651 AATAATTTTAT-ATTTTAA
1 AATAATTTTATAATTTTAA
**
53669 TTTAATTTTAAAATAATTTT--
1 AATAATTTT---ATAATTTTAA
* *
53689 AGTAATTTTATATTTTTAAA
1 AATAATTTTATAATTTT-AA
53709 AATAATTTTAATAATTTTAA
1 AATAATTTT-ATAATTTTAA
53729 AAT
1 AAT
53732 CACTTGCTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.15
18 7 0.15
20 20 0.42
21 9 0.19
22 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (19 bp):
AATAATTTTATAATTTTAA
Found at i:54094 original size:7 final size:7
Alignment explanation
Indices: 54082--54109 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
54072 ATAAAGGAAG
54082 TTGATTC
1 TTGATTC
54089 TTGATTC
1 TTGATTC
54096 TTGATTC
1 TTGATTC
54103 TTGATTC
1 TTGATTC
54110 AATCATTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
TTGATTC
Found at i:54175 original size:7 final size:7
Alignment explanation
Indices: 54165--54195 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
54155 ATTTTAAACC
54165 ATTGAAA
1 ATTGAAA
54172 ATTGAAA
1 ATTGAAA
54179 ATTGAAA
1 ATTGAAA
54186 ATTGAAA
1 ATTGAAA
54193 ATT
1 ATT
54196 AAATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (7 bp):
ATTGAAA
Found at i:56474 original size:18 final size:18
Alignment explanation
Indices: 56441--56486 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
56431 TCAAAATTTT
* *
56441 ATTTTAAATTTGTTATAC
1 ATTTTAATTTTATTATAC
*
56459 ATTTTAATTTTATTATGC
1 ATTTTAATTTTATTATAC
*
56477 ATATTAATTT
1 ATTTTAATTT
56487 AAATCCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (18 bp):
ATTTTAATTTTATTATAC
Found at i:62246 original size:14 final size:14
Alignment explanation
Indices: 62229--62274 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
62219 CCTCATCGTA
*
62229 AATTCTCAATCTTC
1 AATTTTCAATCTTC
*
62243 AATTTTCAATTTTC
1 AATTTTCAATCTTC
*
62257 AATTTTCAATCCTC
1 AATTTTCAATCTTC
62271 AATT
1 AATT
62275 ATTTTCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTCAATCTTC
Found at i:62250 original size:7 final size:7
Alignment explanation
Indices: 62229--62266 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
62219 CCTCATCGTA
*
62229 AATTCTC
1 AATTTTC
*
62236 AATCTTC
1 AATTTTC
62243 AATTTTC
1 AATTTTC
62250 AATTTTC
1 AATTTTC
62257 AATTTTC
1 AATTTTC
62264 AAT
1 AAT
62267 CCTCAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (7 bp):
AATTTTC
Found at i:62458 original size:24 final size:25
Alignment explanation
Indices: 62430--62477 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
62420 ATCATTTAAT
62430 TTTAAACAATTAA-TTATTATGTTG
1 TTTAAACAATTAATTTATTATGTTG
** *
62454 TTTAAATTATTAATTTTTTATGTT
1 TTTAAACAATTAATTTATTATGTT
62478 TATATACTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.58
Consensus pattern (25 bp):
TTTAAACAATTAATTTATTATGTTG
Found at i:66022 original size:5 final size:5
Alignment explanation
Indices: 66012--66037 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
66002 TTTGCCCTAA
66012 TCTTC TCTTC TCTTC TCTTC TCTTC T
1 TCTTC TCTTC TCTTC TCTTC TCTTC T
66038 TCTACATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
TCTTC
Found at i:73791 original size:5 final size:5
Alignment explanation
Indices: 73781--73807 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
73771 TTTTAAATGT
73781 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
73808 AAATAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:74831 original size:23 final size:24
Alignment explanation
Indices: 74796--74860 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
74786 CTTTGCCTTC
* ** *
74796 TAAAATGACAAAAA-ATTTATTTT
1 TAAAATGATAAAAATATAGATTAT
*
74819 TAAAATTATAAAAATATAGATTAT
1 TAAAATGATAAAAATATAGATTAT
*
74843 TAAAATGATAAAATTATA
1 TAAAATGATAAAAATATA
74861 TTTTTACCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (24 bp):
TAAAATGATAAAAATATAGATTAT
Found at i:77411 original size:16 final size:18
Alignment explanation
Indices: 77392--77424 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
77382 TTAAATGCAA
77392 AATTAAC-C-AAATTTAC
1 AATTAACACTAAATTTAC
77408 AATTAACACTAAATTTA
1 AATTAACACTAAATTTA
77425 TTCTATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAACACTAAATTTAC
Found at i:82304 original size:23 final size:24
Alignment explanation
Indices: 82253--82304 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
82243 GGGGAGTCAA
*
82253 AATT-AAATTGTAATTTTTACAAT
1 AATTAAAAATGTAATTTTTACAAT
*
82276 -AGTAAAAATGTAATTTTTA-AAT
1 AATTAAAAATGTAATTTTTACAAT
82298 AATTAAA
1 AATTAAA
82305 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (24 bp):
AATTAAAAATGTAATTTTTACAAT
Found at i:86935 original size:12 final size:12
Alignment explanation
Indices: 86912--86947 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
86902 ACTTATCTTT
*
86912 CTTAGTTTTCTC
1 CTTAGCTTTCTC
*
86924 CTTGGCTTTCTC
1 CTTAGCTTTCTC
86936 CTTAGCTTTCTC
1 CTTAGCTTTCTC
86948 TTTATCCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.31, G:0.11, T:0.53
Consensus pattern (12 bp):
CTTAGCTTTCTC
Found at i:101205 original size:12 final size:12
Alignment explanation
Indices: 101190--101231 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
101180 GTTCAATTAT
*
101190 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
101202 ATGTTCGTTTA-
1 ATGTTCGTGAAC
101213 ATGTTCGTGAAC
1 ATGTTCGTGAAC
101225 ATGTTCG
1 ATGTTCG
101232 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:101223 original size:23 final size:23
Alignment explanation
Indices: 101173--101254 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 23
101163 ACATTGTTTG
*
101173 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTTCA
* *
101197 TGAACATGTTCGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTCA
*
101220 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-CA
101243 TGAACATGTTCG
1 TGAACATGTTCG
101255 TGAACATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 3 0.06
23 34 0.67
24 14 0.27
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTCA
Found at i:101264 original size:23 final size:23
Alignment explanation
Indices: 101220--101265 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
101210 TTAATGTTCG
* *
101220 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
101243 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
101266 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Done.