Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015107.1 Kokia drynarioides strain JFW-HI SEQ_130151, 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: 118470
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 236 characters in sequence are not A, C, G, or T
Found at i:5655 original size:2 final size:2
Alignment explanation
Indices: 5650--5679 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5640 GTGCGTCTGT
5650 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5680 TGGAACCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9033 original size:15 final size:15
Alignment explanation
Indices: 9015--9044 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9005 CTACAATCCT
9015 CCACCTGACAAACTG
1 CCACCTGACAAACTG
9030 CCACCTGACAAACTG
1 CCACCTGACAAACTG
9045 AACGACAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.13, T:0.13
Consensus pattern (15 bp):
CCACCTGACAAACTG
Found at i:9169 original size:3 final size:3
Alignment explanation
Indices: 9161--9189 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9151 ACCTTTTACC
9161 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
9190 GAGAACAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:9428 original size:21 final size:21
Alignment explanation
Indices: 9389--9428 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9379 AAGATCACCG
*
9389 TCCCATTTCCAGTCATTCAAA
1 TCCCATTTACAGTCATTCAAA
9410 TCCCATTCTACAGTC-TTCA
1 TCCCATT-TACAGTCATTCA
9429 TGTCAGCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (21 bp):
TCCCATTTACAGTCATTCAAA
Found at i:11621 original size:92 final size:91
Alignment explanation
Indices: 11517--11698 Score: 274
Period size: 92 Copynumber: 2.0 Consensus size: 91
11507 TGTGTATATA
* * * * * **
11517 TATATATAAATATATTGCGAGTCTAATAAGGGCGGGTTTGGATGGGCGGTACGGTGCGTTTAGCT
1 TATATATAAATATATTACAAGTCTAATAAAGGCGGGTTTGGATGCGCGGCACAATGCGTTTAGCT
*
11582 TATTTTTTTGTCTCATGTTACAGTATC
66 TA-TTTTTTGTCTCATATTACAGTATC
*
11609 TATATATCAATATATTACAAGTCTAATAAAGGCGGGTTTGGATGCGCGGCACAATGCGTTTAGCT
1 TATATATAAATATATTACAAGTCTAATAAAGGCGGGTTTGGATGCGCGGCACAATGCGTTTAGCT
11674 TATTTTTTGTCTCATATTACAGTAT
66 TATTTTTTGTCTCATATTACAGTAT
11699 ATAATTTCAC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
91 22 0.27
92 59 0.73
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (91 bp):
TATATATAAATATATTACAAGTCTAATAAAGGCGGGTTTGGATGCGCGGCACAATGCGTTTAGCT
TATTTTTTGTCTCATATTACAGTATC
Found at i:15104 original size:23 final size:23
Alignment explanation
Indices: 15047--15097 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
15037 AGTGTTGGGC
*
15047 AACAGTAGGCACACAAAGTGCTG
1 AACAGTAGGCACACAAACTGCTG
15070 AACAGTAGGCACACAAACTGCTG
1 AACAGTAGGCACACAAACTGCTG
15093 AACAG
1 AACAG
15098 AGGGCACGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGTAGGCACACAAACTGCTG
Found at i:15225 original size:24 final size:26
Alignment explanation
Indices: 15187--15234 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
15177 TCTACATGGG
15187 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
15213 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
15235 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:18695 original size:24 final size:24
Alignment explanation
Indices: 18667--18733 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
18657 AGAAATAATC
* *
18667 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTATGTTTAATTG
* * *
18691 TTTCAATTAAATTTTGTTTATTTG
1 TTTCAATTAAACTATGTTTAATTG
18715 TTTCAATTAAACTATGTTT
1 TTTCAATTAAACTATGTTT
18734 GAGTCAAACT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTAATTG
Found at i:18979 original size:20 final size:21
Alignment explanation
Indices: 18947--18988 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
18937 ATTATAGTAA
18947 CATTATCTCTTG-ATCCAGCT
1 CATTATCTCTTGAATCCAGCT
18967 CATT-TCTCATTGAATCCAGCT
1 CATTATCTC-TTGAATCCAGCT
18988 C
1 C
18989 TAAAGTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (21 bp):
CATTATCTCTTGAATCCAGCT
Found at i:20324 original size:7 final size:7
Alignment explanation
Indices: 20312--20350 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
20302 GCTAATGCAT
20312 ATGGCAC
1 ATGGCAC
20319 ATGGCAC
1 ATGGCAC
20326 ATGGCAC
1 ATGGCAC
20333 ATGGCAC
1 ATGGCAC
20340 ATGGCAC
1 ATGGCAC
20347 ATGG
1 ATGG
20351 GGTTCATCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.31, T:0.15
Consensus pattern (7 bp):
ATGGCAC
Found at i:40026 original size:25 final size:25
Alignment explanation
Indices: 39974--40027 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
39964 GTGTGTCTCG
* **
39974 TATTTTTCTTTCAGTTAAATTTTGT
1 TATTTTTCTTCCAGTTAAATTTCAT
39999 TATTTTT-TTCCAGTTAAACTTTCAT
1 TATTTTTCTTCCAGTTAAA-TTTCAT
40024 TATT
1 TATT
40028 CCAACAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.22, C:0.11, G:0.06, T:0.61
Consensus pattern (25 bp):
TATTTTTCTTCCAGTTAAATTTCAT
Found at i:40447 original size:25 final size:26
Alignment explanation
Indices: 40404--40470 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
40394 TATTTGATGT
* *
40404 TTTTTTTTTTTTTAATTTTA-TGAAC
1 TTTTTATTTTTTGAATTTTACTGAAC
* ** *
40429 TTTTTATTTTTTGAGTTTTACTTTAT
1 TTTTTATTTTTTGAATTTTACTGAAC
40455 TTTTTATTTTTTGAAT
1 TTTTTATTTTTTGAAT
40471 ATTTTAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (26 bp):
TTTTTATTTTTTGAATTTTACTGAAC
Found at i:41049 original size:24 final size:25
Alignment explanation
Indices: 41003--41049 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
40993 TGTATAATCA
* *
41003 AATTAAAATCAAAATTTATATTTAC
1 AATTAAAATCAAAATTAAAATTTAC
*
41028 AATT-AAATTAAAATTAAAATTT
1 AATTAAAATCAAAATTAAAATTT
41050 GATGTGTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
AATTAAAATCAAAATTAAAATTTAC
Found at i:46734 original size:20 final size:20
Alignment explanation
Indices: 46709--46750 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
46699 ATATTAATTT
46709 AACATTTAA-ATCATGCTTTA
1 AACATTTAAGATCATG-TTTA
*
46729 AACATTTAAGATCTTGTTTA
1 AACATTTAAGATCATGTTTA
46749 AA
1 AA
46751 TGAATGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
AACATTTAAGATCATGTTTA
Found at i:51030 original size:2 final size:2
Alignment explanation
Indices: 51025--51056 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51015 GAAGAGTTGG
51025 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
51057 TGCTGCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56575 original size:28 final size:28
Alignment explanation
Indices: 56538--56591 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
56528 CATTTGACTT
*
56538 TGTAAGAAATAATTTAGTAATAGCATAC
1 TGTAAAAAATAATTTAGTAATAGCATAC
56566 TGTAAAAAATAATTTAGTAATAGCAT
1 TGTAAAAAATAATTTAGTAATAGCAT
56592 TTAACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (28 bp):
TGTAAAAAATAATTTAGTAATAGCATAC
Found at i:72804 original size:57 final size:57
Alignment explanation
Indices: 72679--72797 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 57
72669 GATTTAGTGC
* * * *
72679 CTAAACTTTTTTTGACCCAAATTGATACCTGAACTTTACACTTTTTTAATTTGGTAT
1 CTAAACTTTTTTCGACCCAAATTGATACCTGAACTTGACACTTTTCTAATTTGGCAT
* *
72736 CTAAACTTTTTTCGACCCAATTTGATACCTGAACTTGATA-TTTTCCCTAATTTGGCAT
1 CTAAACTTTTTTCGACCCAAATTGATACCTGAACTTGACACTTTT--CTAATTTGGCAT
72794 CTAA
1 CTAA
72798 GTTTTTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
56 4 0.07
57 36 0.67
58 14 0.26
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (57 bp):
CTAAACTTTTTTCGACCCAAATTGATACCTGAACTTGACACTTTTCTAATTTGGCAT
Found at i:72994 original size:31 final size:31
Alignment explanation
Indices: 72959--73075 Score: 109
Period size: 31 Copynumber: 3.9 Consensus size: 31
72949 AACAATTAAA
*
72959 TACCAAATTAGAAAAAAGAGTCAAGTTCAGG
1 TACCAAATTAGAAAAAAGAGTCAAGTTTAGG
*** *
72990 TACCAAATTAGACCCCAA-A---AAGTTTAAG
1 TACCAAATTAGA-AAAAAGAGTCAAGTTTAGG
* * *
73018 TACCAACTTA-AAAAAGGTGTCAAGTTTAGG
1 TACCAAATTAGAAAAAAGAGTCAAGTTTAGG
*
73048 TACCAAATTAGAAAAAAGTGTCAAGTTT
1 TACCAAATTAGAAAAAAGAGTCAAGTTT
73076 GAGTAGTAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 16 0.24
30 17 0.26
31 29 0.44
32 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (31 bp):
TACCAAATTAGAAAAAAGAGTCAAGTTTAGG
Found at i:73087 original size:31 final size:32
Alignment explanation
Indices: 73009--73075 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
72999 AGACCCCAAA
* *
73009 AAGTTTAAGTACCAACTT--AAAAAAGGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGGTGTC
73039 AAGTTTAGGTACCAAATTAGAAAAAA-GTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGGTGTC
73070 AAGTTT
1 AAGTTT
73076 GAGTAGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.48
31 11 0.33
32 6 0.18
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.28
Consensus pattern (32 bp):
AAGTTTAGGTACCAAATTAGAAAAAAGGTGTC
Found at i:73118 original size:89 final size:89
Alignment explanation
Indices: 72959--73121 Score: 204
Period size: 89 Copynumber: 1.8 Consensus size: 89
72949 AACAATTAAA
**
72959 TACCAAATTAGAAAAAAGAGTCAAGTTCAGGTACCAAATTAGACCCCAAAAAGTTTAAGTACCAA
1 TACCAAATTAGAAAAAAGAGTCAAGTTCAGGTACCAAATTAGACCAAAAAAAGTTTAAGTACCAA
*
73024 CTTAAAAAAGGTGTCAAGTTTAGG
66 ATTAAAAAAGGTGTCAAGTTTAGG
* * ** * * *
73048 TACCAAATTAGAAAAAAGTGTCAAGTT-TGAGTAGTAAATTGGATCAAAAAAAGTTT-AGATATC
1 TACCAAATTAGAAAAAAGAGTCAAGTTCAG-GTACCAAATTAGACCAAAAAAAGTTTAAG-TACC
73111 AAATTAAAAAA
64 AAATTAAAAAA
73122 ATATCAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
88 3 0.05
89 59 0.95
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (89 bp):
TACCAAATTAGAAAAAAGAGTCAAGTTCAGGTACCAAATTAGACCAAAAAAAGTTTAAGTACCAA
ATTAAAAAAGGTGTCAAGTTTAGG
Found at i:89057 original size:22 final size:22
Alignment explanation
Indices: 89013--89058 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
89003 CTTAGCTTTT
* **
89013 TTTTTTTTTTTAATAATCCAAA
1 TTTTTTTATTTAATAATAAAAA
*
89035 TTTTTTTATTTAATTATAAAAA
1 TTTTTTTATTTAATAATAAAAA
89057 TT
1 TT
89059 ATAAAATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTTATTTAATAATAAAAA
Found at i:96477 original size:19 final size:19
Alignment explanation
Indices: 96455--96514 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
96445 AGAATTAATT
*
96455 AATTTTTTAAAATTTTAAA
1 AATTTTTAAAAATTTTAAA
**
96474 AA-TTCAAAATAATTTTAAA
1 AATTTTTAAA-AATTTTAAA
* *
96493 AATTATTGAAAATTTATAAA
1 AATTTTTAAAAATTT-TAAA
96513 AA
1 AA
96515 AAATTTAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 4 0.13
19 18 0.58
20 9 0.29
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
AATTTTTAAAAATTTTAAA
Found at i:97076 original size:64 final size:65
Alignment explanation
Indices: 96997--97164 Score: 218
Period size: 64 Copynumber: 2.6 Consensus size: 65
96987 TTTGAACCCG
* * *
96997 TCCCGTCTTAGTTTAATTAATATTAT-TGTTGTTGCAATAACTCAAATATAAATATTATATTTGA
1 TCCCGTCTTAGTTTAATTAATATTATAAGTTGTTGCAATAACTCAAACATAAATATCATATTTGA
* * * *
97061 TTCTGTCTTATTTTAATTAATATT-TAAGTTGTTGCAATAACTCGAACATAAATATCATATTTGA
1 TCCCGTCTTAGTTTAATTAATATTATAAGTTGTTGCAATAACTCAAACATAAATATCATATTTGA
* * *
97125 TCCCATCTTAGTTTAATTAA-ATTA-AAGTGGTTGTAATAAC
1 TCCCGTCTTAGTTTAATTAATATTATAAGTTGTTGCAATAAC
97165 AAGGAAGAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 18 0.20
64 71 0.80
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (65 bp):
TCCCGTCTTAGTTTAATTAATATTATAAGTTGTTGCAATAACTCAAACATAAATATCATATTTGA
Found at i:100638 original size:11 final size:10
Alignment explanation
Indices: 100619--100651 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
100609 ATATAATTAC
100619 AAAAA-TGTA
1 AAAAATTGTA
100628 TAAAAATTGTA
1 -AAAAATTGTA
100639 AAAAATTGTA
1 AAAAATTGTA
100649 AAA
1 AAA
100652 TTTTAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (10 bp):
AAAAATTGTA
Found at i:100860 original size:27 final size:27
Alignment explanation
Indices: 100830--100886 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
100820 TTTATAAAAA
*
100830 TATATTTTAAACTT-TATTTTAATATAT
1 TATATATT-AACTTATATTTTAATATAT
**
100857 TATATATTATTTTATATTTTAATATAT
1 TATATATTAACTTATATTTTAATATAT
100884 TAT
1 TAT
100887 TAGTAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATATTAACTTATATTTTAATATAT
Found at i:100866 original size:20 final size:20
Alignment explanation
Indices: 100843--100887 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
100833 ATTTTAAACT
100843 TTATTTTAATATATT-ATATA
1 TTATTTT-ATATATTAATATA
*
100863 TTATTTTATATTTTAATATA
1 TTATTTTATATATTAATATA
100883 TTATT
1 TTATT
100888 AGTAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTATATATTAATATA
Found at i:105757 original size:19 final size:19
Alignment explanation
Indices: 105724--105774 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
105714 ATAAATAATT
*
105724 AATAAA-TTAAATTAAA-A
1 AATAAACTTAATTTAAAGA
*
105741 AATAACTCTTAATTTAAAGA
1 AATAA-ACTTAATTTAAAGA
105761 AATAAACTTAATTT
1 AATAAACTTAATTT
105775 TATAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.18
19 17 0.61
20 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (19 bp):
AATAAACTTAATTTAAAGA
Found at i:108397 original size:27 final size:27
Alignment explanation
Indices: 108377--108435 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
108367 ATTTATATGG
*
108377 TTTTTTAGAT-TATATATATTTCTTAA
1 TTTTTTAGATATATATATATTTATTAA
* *
108403 TTTTTTATATATATATATATTT-TTTA
1 TTTTTTAGATATATATATATTTATTAA
108429 TTTTTTA
1 TTTTTTA
108436 TACACATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTTTAGATATATATATATTTATTAA
Found at i:109612 original size:18 final size:18
Alignment explanation
Indices: 109589--109623 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
109579 TGAGCAGCAC
*
109589 TTCTTTTTCTCCCTCCCG
1 TTCTTTGTCTCCCTCCCG
109607 TTCTTTGTCTCCCTCCC
1 TTCTTTGTCTCCCTCCC
109624 TTTCCCCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.46, G:0.06, T:0.49
Consensus pattern (18 bp):
TTCTTTGTCTCCCTCCCG
Found at i:118417 original size:23 final size:23
Alignment explanation
Indices: 118387--118470 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 23
118377 AGTGTTGGGT
118387 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
118410 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
118429 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
118449 ATCAGAGAGCACACACAGTGCT
1 AACAGAGAGCACACAAAGTGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
16 10 0.21
18 3 0.06
19 1 0.02
20 1 0.02
21 2 0.04
23 31 0.65
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Done.