Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005385.1 Kokia drynarioides strain JFW-HI SEQ_119375, 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: 91109
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5087 original size:24 final size:24
Alignment explanation
Indices: 5040--5100 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 24
5030 TTTTTTAAAT
5040 TTAATTTTAGTTAAATTACTTAAAATAA
1 TTAATTTT--TTAAATTAC-T-AAATAA
5068 TTAATTTTTTAAATTA-TAAATAA
1 TTAATTTTTTAAATTACTAAATAA
*
5091 AT-ATTTTTTA
1 TTAATTTTTTA
5101 TATAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.25
23 7 0.22
24 1 0.03
26 8 0.25
28 8 0.25
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTAATTTTTTAAATTACTAAATAA
Found at i:5104 original size:19 final size:19
Alignment explanation
Indices: 5082--5140 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
5072 TTTTTTAAAT
*
5082 TATAAATAAATATTTTTTA
1 TATAAATTAATATTTTTTA
*
5101 TATAAATTTTAATA-TTTTTC
1 TATAAA--TTAATATTTTTTA
*
5121 CATAAATTAATATTTTTTA
1 TATAAATTAATATTTTTTA
5140 T
1 T
5141 TTTTGTGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 10 0.31
21 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAAATTAATATTTTTTA
Found at i:5340 original size:15 final size:15
Alignment explanation
Indices: 5320--5348 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5310 TTCAATGTTT
5320 AAGTTTAGGGTTTAC
1 AAGTTTAGGGTTTAC
5335 AAGTTTAGGGTTTA
1 AAGTTTAGGGTTTA
5349 AGTTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (15 bp):
AAGTTTAGGGTTTAC
Found at i:10653 original size:44 final size:44
Alignment explanation
Indices: 10565--10645 Score: 123
Period size: 41 Copynumber: 1.9 Consensus size: 44
10555 AACCCTAGTC
10565 ATATATATTATATATAACACCAAAACCCATGCATATATATATAA
1 ATATATATTATATATAACACCAAAACCCATGCATATATATATAA
* *
10609 ATATATATTATATAT-A-A-TAAAGCCCATGCATATATAT
1 ATATATATTATATATAACACCAAAACCCATGCATATATAT
10646 TATATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 18 0.51
42 1 0.03
43 1 0.03
44 15 0.43
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.35
Consensus pattern (44 bp):
ATATATATTATATATAACACCAAAACCCATGCATATATATATAA
Found at i:10672 original size:29 final size:29
Alignment explanation
Indices: 10611--10683 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
10601 ATATATAAAT
* ** *
10611 ATATATTATATATAATAAAGCCCATGCAT
1 ATATATTATATAAAATAAAGCCCACACAG
*
10640 ATATATTATATAAAATAAAGCCTACACAG
1 ATATATTATATAAAATAAAGCCCACACAG
10669 ATATTATCTATATAA
1 ATA-TAT-TATATAA
10684 TAAAGTCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.73
30 3 0.08
31 7 0.19
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (29 bp):
ATATATTATATAAAATAAAGCCCACACAG
Found at i:14360 original size:38 final size:38
Alignment explanation
Indices: 14318--14413 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
14308 CGAAGCTTGC
* * *
14318 TAGGCACTAAGCCCAATAAACACTGGCACGAAACTTAT
1 TAGGCACTAAGCCCGATAAACACCGGCACGAAACCTAT
* * *
14356 TAGGCACTAAGGCCGATAAACACCGGCACGAAGCCTGT
1 TAGGCACTAAGCCCGATAAACACCGGCACGAAACCTAT
14394 TAGGCACTAAGCCCGATAAA
1 TAGGCACTAAGCCCGATAAA
14414 TATCGAGGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (38 bp):
TAGGCACTAAGCCCGATAAACACCGGCACGAAACCTAT
Found at i:16714 original size:47 final size:47
Alignment explanation
Indices: 16644--16737 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
16634 ATTCTAATGG
*
16644 CTAAAAACTTAGTTTAAAGGACTAGATATCATTGAAAACTCATAGGA
1 CTAAAAACTTAGTTTAAACGACTAGATATCATTGAAAACTCATAGGA
*
16691 CTAAAAACTTAGTTTAAACGACTAGATATCATTTAAAACTCATAGGA
1 CTAAAAACTTAGTTTAAACGACTAGATATCATTGAAAACTCATAGGA
16738 AAATAATTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.29
Consensus pattern (47 bp):
CTAAAAACTTAGTTTAAACGACTAGATATCATTGAAAACTCATAGGA
Found at i:34386 original size:13 final size:13
Alignment explanation
Indices: 34378--34444 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
34368 GGTATGAATC
34378 AGTTATATGGAAAT
1 AGTTATAT-GAAAT
*
34392 AGATATATGAAAT
1 AGTTATATGAAAT
*
34405 GGTTATATG-AAT
1 AGTTATATGAAAT
34417 CAGTTATATGGAAAT
1 -AGTTATAT-GAAAT
*
34432 AGATATATGAAAT
1 AGTTATATGAAAT
34445 GGAACATTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
12 3 0.07
13 24 0.53
14 15 0.33
15 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.19, T:0.34
Consensus pattern (13 bp):
AGTTATATGAAAT
Found at i:34424 original size:40 final size:40
Alignment explanation
Indices: 34370--34446 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
34360 AATGAAATGG
34370 TATGAATCAGTTATATGGAAATAGATATATGAAATGGTTA
1 TATGAATCAGTTATATGGAAATAGATATATGAAATGGTTA
34410 TATGAATCAGTTATATGGAAATAGATATATGAAATGG
1 TATGAATCAGTTATATGGAAATAGATATATGAAATGG
34447 AACATTGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.34
Consensus pattern (40 bp):
TATGAATCAGTTATATGGAAATAGATATATGAAATGGTTA
Found at i:34448 original size:19 final size:19
Alignment explanation
Indices: 34384--34448 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
34374 AATCAGTTAT
34384 ATGGAAATAGATATATGAA
1 ATGGAAATAGATATATGAA
** * *
34403 ATGGTTATATGA-ATCAGTTAT
1 ATGGAAATA-GATAT-A-TGAA
34424 ATGGAAATAGATATATGAA
1 ATGGAAATAGATATATGAA
34443 ATGGAA
1 ATGGAA
34449 CATTGGATAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 17 0.50
20 6 0.18
21 11 0.32
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.31
Consensus pattern (19 bp):
ATGGAAATAGATATATGAA
Found at i:44060 original size:18 final size:18
Alignment explanation
Indices: 44037--44084 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
44027 GTCCTTGCAT
*
44037 TTGTGGCTGCAAGCTTGA
1 TTGTGGCTGCAAGCATGA
* * *
44055 TTGTGGCGGTAATCATGA
1 TTGTGGCTGCAAGCATGA
*
44073 TTGTGGTTGCAA
1 TTGTGGCTGCAA
44085 TTGACTATGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.33, T:0.35
Consensus pattern (18 bp):
TTGTGGCTGCAAGCATGA
Found at i:48766 original size:2 final size:2
Alignment explanation
Indices: 48759--48784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48749 GTATAGTGAG
48759 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
48785 CACACACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67458 original size:97 final size:97
Alignment explanation
Indices: 67345--67734 Score: 392
Period size: 97 Copynumber: 4.0 Consensus size: 97
67335 ATCATAGAGT
* * * * *
67345 TTGAAGAGGGATAGGTTAAAGTCACAACGACAGACTTAACACCCTAAAACCAAAGAGGGAAGGTT
1 TTGAAGAGGGATAGGTTAAAGTCGCAACAACGGACCTAACACCCTAAAACCAAAGAGGGAAGATT
*
67410 GAAGCCGCAACGACAAACCATACACCTTAAAA
66 GAAGCCGCAACGACAAACCTTACACCTTAAAA
* * * * * ** * *
67442 TTGAAGAGGAATAGGTTAAAGCCGCGACGACGGATCTAA-TGCCTTAAACTAAAGAGGGATAGAT
1 TTGAAGAGGGATAGGTTAAAGTCGCAACAACGGACCTAACACCCTAAAACCAAAGAGGGA-AGAT
* * *
67506 TAAAGTCGCAAC-AGTAAACC-TAGCACCTTAAAA
65 TGAAGCCGCAACGA-CAAACCTTA-CACCTTAAAA
* * * *
67539 CTGAAGAGGGATAGGTTGAAGTCGCAACAACGGACCTAACACCCTAAAA-CTAAGAAGGGAAGGT
1 TTGAAGAGGGATAGGTTAAAGTCGCAACAACGGACCTAACACCCTAAAACCAAAG-AGGGAAGAT
*
67603 TGAAGCCGCAACGACGAACCTTACACCTTAAAA
65 TGAAGCCGCAACGACAAACCTTACACCTTAAAA
** * * * * *
67636 TAAAAGAGGGATAGGTTGAAGTCGCAACAATGGACCTAACACCTTAAAAACCAAAAAGGGAAATA
1 TTGAAGAGGGATAGGTTAAAGTCGCAACAACGGACCTAACACCCT-AAAACCAAAGAGGG-AAGA
* * * *
67701 TTGAAGTCGTAACGACAGATCTTACACCTTAAAA
64 TTGAAGCCGCAACGACAAACCTTACACCTTAAAA
67735 CAAAAGAGGA
Statistics
Matches: 237, Mismatches: 46, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
96 19 0.08
97 162 0.68
98 22 0.09
99 34 0.14
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (97 bp):
TTGAAGAGGGATAGGTTAAAGTCGCAACAACGGACCTAACACCCTAAAACCAAAGAGGGAAGATT
GAAGCCGCAACGACAAACCTTACACCTTAAAA
Found at i:67549 original size:49 final size:49
Alignment explanation
Indices: 67348--67755 Score: 261
Period size: 49 Copynumber: 8.4 Consensus size: 49
67338 ATAGAGTTTG
* * * * * * * *
67348 AAGAGGGATAGGTTAAAGTCACAACGACAGACTTAACACCCTAAAACCA
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
* * * * *
67397 AAGAGGGA-AGGTTGAAGCCGCAACGACAAACC-ATACACCTTAAAATTG
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTA-ACACCTTAAAACTA
* * * * * *** * **
67445 AAGAGGAATAGGTTAAAGCCGCGACGACGGATCTAATGCCTT-AAACTA
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
* * * * *
67493 AAGAGGGATAGATTAAAGTCGCAACAGTAAACCTAGCACCTTAAAACTG
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
*** *
67542 AAGAGGGATAGGTTGAAGTCGCAACAACGGACCTAACACCCTAAAACT-
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
* * ** *
67590 AAGAAGGGA-AGGTTGAAGCCGCAACGACGAACCTTACACCTTAAAA-TAA
1 AAG-AGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACT-A
** *
67639 AAGAGGGATAGGTTGAAGTCGCAACAATGGACCTAACACCTTAAAAACCA
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTT-AAAACTA
* * ** * * * * * * *
67689 AAAAGGGAAATATTGAAGTCGTAACGACAGATCTTACACCTTAAAACAA
1 AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
*
67738 AAGAGGAATAGGTTGAAG
1 AAGAGGGATAGGTTGAAG
67756 CCGCGATGGC
Statistics
Matches: 281, Mismatches: 68, Indels: 20
0.76 0.18 0.05
Matches are distributed among these distances:
47 2 0.01
48 109 0.39
49 132 0.47
50 38 0.14
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.16
Consensus pattern (49 bp):
AAGAGGGATAGGTTGAAGTCGCAACAATAAACCTAACACCTTAAAACTA
Found at i:78454 original size:21 final size:20
Alignment explanation
Indices: 78425--78493 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
78415 TTTTTTAAAT
*
78425 TAAATAAATTCATAAATTTTC
1 TAAAAAAATTCATAAA-TTTC
**
78446 TAAAAAAATAGA-AAATTTC
1 TAAAAAAATTCATAAATTTC
78465 T--AAAAATTGGCATAAATTTC
1 TAAAAAAATT--CATAAATTTC
78485 -AAAAAAATT
1 TAAAAAAATT
78494 ACAAAATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 6 0.16
19 6 0.16
20 10 0.26
21 16 0.42
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAAAATTCATAAATTTC
Found at i:78500 original size:19 final size:19
Alignment explanation
Indices: 78442--78500 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
78432 ATTCATAAAT
*
78442 TTTCTAAAAAAA-TAGAAAA
1 TTTC-AAAAAAATTACAAAA
* *
78461 TTTC-TAAAAATTGGCATAAA
1 TTTCAAAAAAATT-ACA-AAA
78481 TTTCAAAAAAATTACAAAA
1 TTTCAAAAAAATTACAAAA
78500 T
1 T
78501 AAAACTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 9 0.29
20 9 0.29
21 7 0.23
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (19 bp):
TTTCAAAAAAATTACAAAA
Found at i:82294 original size:27 final size:27
Alignment explanation
Indices: 82264--82322 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
82254 ATAGGGTTTG
* *
82264 CACATGGGCTC-TCACAAATAGGGGGTT
1 CACATAGGCTCGT-ACAAACAGGGGGTT
* *
82291 CACACAGGCTCGTACATACAGGGGGTT
1 CACATAGGCTCGTACAAACAGGGGGTT
82318 CACAT
1 CACAT
82323 TACATGGGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.20
Consensus pattern (27 bp):
CACATAGGCTCGTACAAACAGGGGGTT
Found at i:85797 original size:19 final size:19
Alignment explanation
Indices: 85757--85799 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
85747 TTAATGTCGA
*
85757 AAAATATTAATTTATTTAT
1 AAAATATTAATTTATGTAT
*
85776 AAAATAATTAATTTGTGT-T
1 AAAAT-ATTAATTTATGTAT
85795 AAAAT
1 AAAAT
85800 TACCAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AAAATATTAATTTATGTAT
Done.