Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015088.1 Kokia drynarioides strain JFW-HI SEQ_130132, 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: 62829
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:65 original size:21 final size:20
Alignment explanation
Indices: 33--83 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
23 GGTTCTGATC
*
33 AGAGTTCACAGGGGCTTACA
1 AGAGTTCACAGGAGCTTACA
* *
53 AGAGATTCTCAGGAGCTTCCA
1 AGAG-TTCACAGGAGCTTACA
74 AG-G-TCACAGG
1 AGAGTTCACAGG
84 GTCAAAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 6 0.23
20 5 0.19
21 15 0.58
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (20 bp):
AGAGTTCACAGGAGCTTACA
Found at i:3918 original size:15 final size:17
Alignment explanation
Indices: 3894--3933 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
3884 TTAATATATC
*
3894 TATATCTATAA-A-AAT
1 TATATTTATAAGATAAT
3909 TATATTTATAAGATAAT
1 TATATTTATAAGATAAT
3926 TA-ATTTAT
1 TATATTTAT
3934 TTACATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
16 7 0.32
17 5 0.23
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATTTATAAGATAAT
Found at i:7510 original size:6 final size:6
Alignment explanation
Indices: 7487--7553 Score: 57
Period size: 6 Copynumber: 11.2 Consensus size: 6
7477 GAGGGACGTG
* * * *
7487 GAGGGA GA-GGA CGGGGGA GAGGGA GAGGAA G-GGGA GGAGGAA GAGGAA
1 GAGGGA GAGGGA -GAGGGA GAGGGA GAGGGA GAGGGA -GAGGGA GAGGGA
*
7535 GAGGGA GAGGGA GGGGGA G
1 GAGGGA GAGGGA GAGGGA G
7554 GTTCGGCTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 6 0.12
6 38 0.76
7 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:7510 original size:18 final size:17
Alignment explanation
Indices: 7487--7547 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
7477 GAGGGACGTG
7487 GAGGGAGAGGACGGGGGA
1 GAGGGAGAGGA-GGGGGA
*
7505 GAGGGAGAGGAAGGGGA
1 GAGGGAGAGGAGGGGGA
* *
7522 GGAGGAAGAGGAAGAGGGA
1 -GAGGGAGAGG-AGGGGGA
7541 GAGGGAG
1 GAGGGAG
7548 GGGGAGGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.14
18 26 0.72
19 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.64, T:0.00
Consensus pattern (17 bp):
GAGGGAGAGGAGGGGGA
Found at i:10085 original size:20 final size:20
Alignment explanation
Indices: 10060--10098 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10050 TAAAATTGGC
*
10060 GTAATTGTAGTTTTTTTTTT
1 GTAATTGTACTTTTTTTTTT
*
10080 GTAATTTTACTTTTTTTTT
1 GTAATTGTACTTTTTTTTT
10099 ATATTGAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (20 bp):
GTAATTGTACTTTTTTTTTT
Found at i:11611 original size:21 final size:21
Alignment explanation
Indices: 11585--11625 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
11575 AGACATCTTA
11585 ATTTATATTTGAAGATTGATT
1 ATTTATATTTGAAGATTGATT
11606 ATTTATATTTGAAGATTGAT
1 ATTTATATTTGAAGATTGAT
11626 GAACTAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
ATTTATATTTGAAGATTGATT
Found at i:18043 original size:17 final size:17
Alignment explanation
Indices: 18023--18055 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18013 TAATTGCAAG
18023 ATCTAAATATAAATTAC
1 ATCTAAATATAAATTAC
*
18040 ATCTAAATATTAATTA
1 ATCTAAATATAAATTA
18056 GAAAAAACGA
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:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
ATCTAAATATAAATTAC
Found at i:48742 original size:7 final size:7
Alignment explanation
Indices: 48730--48758 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
48720 GAAGCAAGCC
48730 AAGAGAG
1 AAGAGAG
48737 AAGAGAG
1 AAGAGAG
48744 AAGAGAG
1 AAGAGAG
48751 AAGAGAG
1 AAGAGAG
48758 A
1 A
48759 GAATGGACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AAGAGAG
Found at i:52281 original size:30 final size:28
Alignment explanation
Indices: 52236--52294 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
52226 ATTTCTAGTA
52236 ATTTATATTTTTAAATTTT-TAACTTTT
1 ATTTATATTTTTAAATTTTATAACTTTT
52263 ATTTAATATTCTTATAAATTTTAATAACTTTT
1 ATTT-ATATT-TT-TAAATTTT-ATAACTTTT
52295 TACAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 4 0.15
28 5 0.19
29 2 0.07
30 8 0.30
32 8 0.30
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTATATTTTTAAATTTTATAACTTTT
Found at i:52322 original size:20 final size:20
Alignment explanation
Indices: 52299--52336 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52289 ACTTTTTACA
52299 AATTTATA-AATTATAAAATT
1 AATTTATATAATT-TAAAATT
*
52319 AATTTTTATAATTTAAAA
1 AATTTATATAATTTAAAA
52337 AAATGAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTATATAATTTAAAATT
Found at i:53228 original size:17 final size:17
Alignment explanation
Indices: 53143--53230 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
53133 AAAATCTTTA
53143 AAAATTGCAAAAATATT
1 AAAATTGCAAAAATATT
* *
53160 AAAATAGGAAAAAT-TAT
1 AAAATTGCAAAAATAT-T
53177 AAAATT---AAAAT-TT
1 AAAATTGCAAAAATATT
**
53190 AAAATTTTAAAAATATTT
1 AAAATTGCAAAAATA-TT
*
53208 AAAATTGCAAAGATATT
1 AAAATTGCAAAAATATT
53225 AAAATT
1 AAAATT
53231 AGTAAAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
13 7 0.12
14 6 0.10
16 6 0.10
17 26 0.44
18 14 0.24
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (17 bp):
AAAATTGCAAAAATATT
Found at i:53668 original size:20 final size:20
Alignment explanation
Indices: 53639--53711 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
53629 AAATATTCTA
*
53639 ATATGTTTTTAATATATTTT
1 ATATTTTTTTAATATATTTT
** *
53659 ATATTTTTTTTTTGTAATTTT
1 ATATTTTTTTAATAT-ATTTT
* *
53680 ATATTTTTTT-CTCTATTTT
1 ATATTTTTTTAATATATTTT
53699 -TAATTTTTTTAAT
1 AT-ATTTTTTTAAT
53712 TTCTATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 14 0.33
21 15 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (20 bp):
ATATTTTTTTAATATATTTT
Found at i:53686 original size:19 final size:20
Alignment explanation
Indices: 53654--53708 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
53644 TTTTTAATAT
* *
53654 ATTTTATATTTTTTTTTTGTA
1 ATTTTATA-TTTTTTTCTCTA
53675 ATTTTATATTTTTTTCTCTA
1 ATTTTATATTTTTTTCTCTA
*
53695 TTTTTA-ATTTTTTT
1 ATTTTATATTTTTTT
53709 AATTTCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 8 0.26
20 15 0.48
21 8 0.26
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (20 bp):
ATTTTATATTTTTTTCTCTA
Found at i:53707 original size:21 final size:20
Alignment explanation
Indices: 53654--53724 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
53644 TTTTTAATAT
*
53654 ATTTTATATTTTTTTTTTGTA
1 ATTTTA-ATTTTTTTTTTCTA
*
53675 ATTTT-ATATTTTTTTCTCTA
1 ATTTTAAT-TTTTTTTTTCTA
*
53695 TTTTTAATTTTTTTAATTTCTA
1 ATTTTAATTTTTTT--TTTCTA
53717 TATTTTAA
1 -ATTTTAA
53725 GATTTTTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 2 0.05
20 20 0.50
21 7 0.17
22 5 0.12
23 6 0.15
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (20 bp):
ATTTTAATTTTTTTTTTCTA
Found at i:53730 original size:23 final size:22
Alignment explanation
Indices: 53691--53733 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
53681 TATTTTTTTC
**
53691 TCTATTTTTAATTTTTTTAATT
1 TCTATTTTTAAGATTTTTAATT
53713 TCTATATTTTAAGATTTTTAA
1 TCTAT-TTTTAAGATTTTTAA
53734 GGACAATGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
TCTATTTTTAAGATTTTTAATT
Found at i:62374 original size:2 final size:2
Alignment explanation
Indices: 62367--62398 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62357 TAGTTTATTA
62367 AG 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 AG
62399 TGGAAAGAAT
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):
AG
Done.