Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002257.1 Kokia drynarioides strain JFW-HI SEQ_114270, 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: 2928
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.30
Warning! 85 characters in sequence are not A, C, G, or T
Found at i:577 original size:17 final size:16
Alignment explanation
Indices: 552--633 Score: 101
Period size: 17 Copynumber: 4.9 Consensus size: 16
542 CTGGGCCCAA
552 TAAATTTAAATTTATT
1 TAAATTTAAATTTATT
* *
568 GTAAAATTAAGTTTATTT
1 -TAAATTTAAATTTA-TT
*
586 TAAATTTAAATCTATT
1 TAAATTTAAATTTATT
602 TGAAATTTAAATTTATT
1 T-AAATTTAAATTTATT
619 ATAAATTTAAATTTA
1 -TAAATTTAAATTTA
634 AAATCTATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.05
17 50 0.89
18 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (16 bp):
TAAATTTAAATTTATT
Found at i:595 original size:34 final size:34
Alignment explanation
Indices: 551--633 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
541 TCTGGGCCCA
*
551 ATAAATTTAAATTTA-TTGTAAAATTAAGTTTATT
1 ATAAATTTAAATTTATTTG-AAAATTAAATTTATT
* * *
585 TTAAATTTAAATCTATTTGAAATTTAAATTTATT
1 ATAAATTTAAATTTATTTGAAAATTAAATTTATT
619 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
634 AAATCTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 39 0.93
35 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (34 bp):
ATAAATTTAAATTTATTTGAAAATTAAATTTATT
Found at i:609 original size:7 final size:6
Alignment explanation
Indices: 552--635 Score: 56
Period size: 6 Copynumber: 14.7 Consensus size: 6
542 CTGGGCCCAA
* * * *
552 TAAATT TAAATT T--ATT GTAAAAT TAAGTT T-ATTT TAAATT TAAATC
1 TAAATT TAAATT TAAATT -TAAATT TAAATT TAAATT TAAATT TAAATT
598 T--ATT TGAAATT TAAATT T--ATT ATAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT TAAA
636 ATCTATTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
4 9 0.15
5 6 0.10
6 37 0.61
7 9 0.15
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:610 original size:23 final size:22
Alignment explanation
Indices: 584--647 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
574 TTAAGTTTAT
584 TTTAAATTTAAATCTATTTGAAA
1 TTTAAATTTAAATCTATTT-AAA
607 TTTAAATTT--AT-TA--TAAA
1 TTTAAATTTAAATCTATTTAAA
624 TTTAAATTTAAAATCTATTTAAA
1 TTTAAATTT-AAATCTATTTAAA
647 T
1 T
648 AATGTCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
17 12 0.34
18 1 0.03
20 4 0.11
21 4 0.11
23 14 0.40
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (22 bp):
TTTAAATTTAAATCTATTTAAA
Found at i:1393 original size:21 final size:21
Alignment explanation
Indices: 1356--1399 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1346 ACGTTTCAAT
* *
1356 AATAATAATAGATATTAATAA
1 AATAATAATAAAAATTAATAA
*
1377 AATAATAATAAAAATTATTAA
1 AATAATAATAAAAATTAATAA
1398 AA
1 AA
1400 AAAAGGGAAA
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:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AATAATAATAAAAATTAATAA
Found at i:1395 original size:24 final size:24
Alignment explanation
Indices: 1353--1402 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1343 AGAACGTTTC
* *
1353 AATAATAATAATAGATATTAATAA
1 AATAATAATAATAAATATTAAAAA
1377 AATAATAATAA-AAATTATTAAAAA
1 AATAATAATAATAAA-TATTAAAAA
1401 AA
1 AA
1403 AGGGAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAATAATAAATATTAAAAA
Found at i:2363 original size:30 final size:29
Alignment explanation
Indices: 2322--2552 Score: 241
Period size: 29 Copynumber: 7.8 Consensus size: 29
2312 GAGGTCCCTA
* *
2322 AACTGTCCAAAAATCTCATTTTCACCCCACG
1 AACT-TCCAAAAATCCCATTTTTACCCC-CG
* * **
2353 AACTTCCAAAAATCCCATTTTTAATCGCAA
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* *
2383 AACTTCCAAAAATCCCATTTTTATCCTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* * *
2412 AACTTTCAAAAATCCCATTTTCACCCCTG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
*
2441 AACTTCCAAAAATCCCATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* *
2470 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
**
2499 AAACTTCCAAAAATTTCATTTTTACCCCC-
1 -AACTTCCAAAAATCCCATTTTTACCCCCG
2528 ATACTTCCAAAAATCTCCATTTTTA
1 A-ACTTCCAAAAATC-CCATTTTTA
2553 ACCTCAAAAC
Statistics
Matches: 168, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.01
29 89 0.53
30 71 0.42
31 7 0.04
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCCG
Found at i:2426 original size:59 final size:59
Alignment explanation
Indices: 2321--2611 Score: 288
Period size: 59 Copynumber: 4.9 Consensus size: 59
2311 GGAGGTCCCT
* * * *
2321 AAACTGTCCAAAAATCTCATTTTCACCCCACGAACTTCCAAAAATCCCATTTTTAATCGCA
1 AAACT-TCCAAAAATCCCATTTTTACCCC-CGAACTTCCAAAAATCCCATTTTTAACCTCA
* * * * * *
2382 AAACTTCCAAAAATCCCATTTTTATCCTCGAACTTTCAAAAATCCCA-TTTTCACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
* * * * *
2440 GAACTTCCAAAAATCCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
**
2499 AAACTTCCAAAAATTTCATTTTTACCCCC-ATACTTCCAAAAATCTCCATTTTTAACCTCA
1 AAACTTCCAAAAATCCCATTTTTACCCCCGA-ACTTCCAAAAATC-CCATTTTTAACCTCA
* * * *
2559 AAAC-TCTCAAAATTACCC--TTTTACCCCCGAA-TGACTAAAAATTCCATTTTTAA
1 AAACTTC-CAAAAAT-CCCATTTTTACCCCCGAACT-TCCAAAAATCCCATTTTTAA
2612 ACCCTAAATT
Statistics
Matches: 193, Mismatches: 30, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
58 60 0.31
59 84 0.44
60 43 0.22
61 6 0.03
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCA
Found at i:2659 original size:60 final size:61
Alignment explanation
Indices: 2474--2676 Score: 149
Period size: 60 Copynumber: 3.4 Consensus size: 61
2464 CCCCCAAACT
* * * *
2474 TCCAAAAATTCCATTTTT-GA-CCTCGAAACTTCCAAAAATT-TCATTTTTACCCCC--AT-A
1 TCCAAAAATTCCATTTTTAAACCCTCAAAAC-TCCCAAAATTACCA-TTTTACCCCCGAATGA
* *
2531 CTTCCAAAAATCTCCATTTTT-AA-CCTCAAAACTCTCAAAATTACCCTTTTACCCCCGAATGA
1 --TCCAAAAAT-TCCATTTTTAAACCCTCAAAACTCCCAAAATTACCATTTTACCCCCGAATGA
* ** * *
2593 -CTAAAAATTCCATTTTTAAACCCT-AAATTTTCCCAAAATTACCATTTTGCCCCCGAGT-A
1 TCCAAAAATTCCATTTTTAAACCCTCAAA-ACTCCCAAAATTACCATTTTACCCCCGAATGA
* *
2652 TCCAAAAAGTCTCATTTTCAAACCC
1 TCCAAAAATTC-CATTTTTAAACCC
2677 GATCGCATCC
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
58 9 0.08
59 40 0.34
60 54 0.46
61 14 0.12
62 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (61 bp):
TCCAAAAATTCCATTTTTAAACCCTCAAAACTCCCAAAATTACCATTTTACCCCCGAATGA
Done.