Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004841.1 Kokia drynarioides strain JFW-HI SEQ_118490, 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: 19544
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Found at i:784 original size:17 final size:17
Alignment explanation
Indices: 762--796 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
752 TTTAATATTA
762 TTATTATTAAAAAATAT
1 TTATTATTAAAAAATAT
*
779 TTATTATTAATAAATAT
1 TTATTATTAAAAAATAT
796 T
1 T
797 ATGAAAACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATTATTAAAAAATAT
Found at i:784 original size:20 final size:19
Alignment explanation
Indices: 755--792 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
745 TAATATTTTT
*
755 AATATTATTATTATTAAAA
1 AATATTATTATTAATAAAA
774 AATATTTATTATTAATAAA
1 AATA-TTATTATTAATAAA
793 TATTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTATTATTAATAAAA
Found at i:878 original size:13 final size:14
Alignment explanation
Indices: 862--893 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
852 TATATTATTC
862 TTATTAATTAATA-
1 TTATTAATTAATAT
875 TTATT-ATTAATAT
1 TTATTAATTAATAT
888 TTATTA
1 TTATTA
894 CTGCAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTAATTAATAT
Found at i:1546 original size:6 final size:6
Alignment explanation
Indices: 1537--1615 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
1527 TTTTAGCTTT
* * * *
1537 ATTTAA ATTTAT A-GTAA TTTTAA ATTTGAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * *
1584 A-ATAA ATTTAA ATTGAA A-ATAA ATTTAA ATTT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1616 TTAAACAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
5 12 0.22
6 39 0.72
7 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:1578 original size:18 final size:17
Alignment explanation
Indices: 1537--1648 Score: 134
Period size: 18 Copynumber: 6.4 Consensus size: 17
1527 TTTTAGCTTT
* *
1537 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
1554 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
1572 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
1589 ATTTAAATTGAAAATAA
1 ATTTAAATTTAAAATAA
* *
1606 ATTTAAATTTTTAAACAA
1 ATTTAAA-TTTAAAATAA
*
1624 ATTTAATTTTTAAAATAA
1 ATTTAA-ATTTAAAATAA
1642 ATTTAAA
1 ATTTAAA
1649 GGGAATTTGG
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
17 39 0.49
18 41 0.51
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1578 original size:35 final size:35
Alignment explanation
Indices: 1537--1648 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
1527 TTTTAGCTTT
* *
1537 ATTTAAATTTATAGTAATTTTAAATTTGAAAATAA
1 ATTTAAATTTATAATAAATTTAAATTTGAAAATAA
*
1572 ATTTAAATTTAAAATAAATTTAAA-TTGAAAATAA
1 ATTTAAATTTATAATAAATTTAAATTTGAAAATAA
* * * *
1606 ATTTAAATTTTTAAACAAATTTAATTTTTAAAATAA
1 ATTTAAATTTAT-AATAAATTTAAATTTGAAAATAA
1642 ATTTAAA
1 ATTTAAA
1649 GGGAATTTGG
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
34 20 0.30
35 31 0.46
36 16 0.24
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTTAAATTTATAATAAATTTAAATTTGAAAATAA
Found at i:2182 original size:14 final size:15
Alignment explanation
Indices: 2157--2185 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2147 ATGTATTTGC
2157 ATAAAAATAGTAAAA
1 ATAAAAATAGTAAAA
2172 ATAAAAA-AGTAAAA
1 ATAAAAATAGTAAAA
2186 GAGAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
ATAAAAATAGTAAAA
Found at i:7058 original size:9 final size:9
Alignment explanation
Indices: 7044--7106 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
7034 TTAAATTTTT
7044 AAATTTTAA
1 AAATTTTAA
7053 AAATTTTAA
1 AAATTTTAA
7062 AAAGTATTTCAA
1 AAA-T-TTT-AA
7074 ATAATTTTAA
1 A-AATTTTAA
** *
7084 TGATTTTTA
1 AAATTTTAA
*
7093 AATTTTTAA
1 AAATTTTAA
7102 AAATT
1 AAATT
7107 AATTAAATGT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
9 27 0.64
10 3 0.07
11 6 0.14
12 4 0.10
13 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (9 bp):
AAATTTTAA
Found at i:7456 original size:30 final size:31
Alignment explanation
Indices: 7422--7492 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
7412 ATTGTTCATT
*
7422 CATTTTAG-TCACTCAACTTTAGTAAATTTA
1 CATTTTAGATCACTCAACTTTAATAAATTTA
* * *
7452 CA-TTTCGATCACTTAACTTTAATAAATTTT
1 CATTTTAGATCACTCAACTTTAATAAATTTA
7482 CATTTTA-ATCA
1 CATTTTAGATCA
7493 TATATGACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
29 4 0.12
30 27 0.79
31 3 0.09
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (31 bp):
CATTTTAGATCACTCAACTTTAATAAATTTA
Found at i:7676 original size:22 final size:20
Alignment explanation
Indices: 7651--7699 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
7641 TTTTTCCCGA
*
7651 GAAAAACCTGAGGTTTTATAGG
1 GAAAAACCTG-GGTTTTAGA-G
7673 GAAATAA-CTGGGTTTTAGAG
1 GAAA-AACCTGGGTTTTAGAG
7693 GAAAAAC
1 GAAAAAC
7700 TCGGGTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 8 0.33
22 7 0.29
23 2 0.08
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (20 bp):
GAAAAACCTGGGTTTTAGAG
Found at i:7705 original size:20 final size:21
Alignment explanation
Indices: 7662--7707 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
7652 AAAAACCTGA
*
7662 GGTTTTATAGGGAAATAACTG
1 GGTTTTAGAGGGAAATAACTG
7683 GGTTTTAGA-GGAAA-AACTCG
1 GGTTTTAGAGGGAAATAACT-G
7703 GGTTT
1 GGTTT
7708 CTACAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 11 0.48
21 8 0.35
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (21 bp):
GGTTTTAGAGGGAAATAACTG
Found at i:10001 original size:26 final size:25
Alignment explanation
Indices: 9950--10001 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
9940 TATTGTTATA
* *
9950 TGATTAATATTTTAACAATTAATGT
1 TGATAAATATTTTAACAATGAATGT
9975 TGATAAATATTTCTAACAA-GAAGTGT
1 TGATAAATATTT-TAACAATGAA-TGT
10001 T
1 T
10002 TTTCTGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (25 bp):
TGATAAATATTTTAACAATGAATGT
Found at i:17441 original size:33 final size:29
Alignment explanation
Indices: 17399--17462 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 29
17389 TGTTTGTATG
*
17399 AAATTGAAGAAAGAGGGAAGAAGGAGAAAGACT
1 AAATTGAAGAAA-AAGG-A-AAGGAGAAAG-CT
17432 AAATTGAAGAAAAAGGAAAGGAGAAAGCT
1 AAATTGAAGAAAAAGGAAAGGAGAAAGCT
17461 AA
1 AA
17463 GGTGTGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 10 0.33
31 1 0.03
32 3 0.10
33 12 0.40
ACGTcount: A:0.58, C:0.03, G:0.30, T:0.09
Consensus pattern (29 bp):
AAATTGAAGAAAAAGGAAAGGAGAAAGCT
Done.