Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008476.1 Kokia drynarioides strain JFW-HI SEQ_123151, 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: 2585
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:440 original size:30 final size:29
Alignment explanation
Indices: 403--744 Score: 170
Period size: 29 Copynumber: 11.6 Consensus size: 29
393 GACATCCGGT
403 GTAAAAATGTAATTTTTTGAAAGTTTGGG
1 GTAAAAATGTAATTTTTTGAAAGTTTGGG
* * *
432 GTTAAAAATGTAA-TTTTTGGAATTTTAGG
1 G-TAAAAATGTAATTTTTTGAAAGTTTGGG
*
461 GT-AAAATGGTAATTTTTGGAAAGTTTGGG
1 GTAAAAAT-GTAATTTTTTGAAAGTTTGGG
* *
490 GTCAAAAAAAATGGAA-TTTTTGAAAATTTGGG
1 GT----AAAAATGTAATTTTTTGAAAGTTTGGG
* **
522 GT-AAAATGGTAA-TTTTTGGAAGTGAGGGG
1 GTAAAAAT-GTAATTTTTTGAAAGT-TTGGG
* ** * ***
551 GCAAAAATGGGATTTTTGGAAAGTTCAAG
1 GTAAAAATGTAATTTTTTGAAAGTTTGGG
* *
580 GTAAAAAATG--ATATTTTTGGAAGTTCGGGG
1 GT-AAAAATGTAAT-TTTTTGAAAGTT-TGGG
* *
610 GT-AAAATGGTAATTTTTGGAAAGTTTAGG
1 GTAAAAAT-GTAATTTTTTGAAAGTTTGGG
* *
639 GTCAAAAA--TAATATTTTTGGAAGTTCGAGG
1 GT-AAAAATGTAAT-TTTTTGAAAGTTTG-GG
* * *
669 GTGAAAATTTAA-TTTTTGAAAAGGTTGAGG
1 GTAAAAATGTAATTTTTTG-AAAGTTTG-GG
*
699 GT-AAAATGTAATTTTTGTG-AAGTTCGAGG
1 GTAAAAATGTAATTTTT-TGAAAGTTTG-GG
* *
728 GTCAAAATATAATTTTT
1 GTAAAAATGTAATTTTT
745 GGGAAGTTCG
Statistics
Matches: 239, Mismatches: 46, Indels: 55
0.70 0.14 0.16
Matches are distributed among these distances:
27 10 0.04
28 28 0.12
29 90 0.38
30 76 0.32
31 11 0.05
32 16 0.07
33 3 0.01
34 5 0.02
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
GTAAAAATGTAATTTTTTGAAAGTTTGGG
Found at i:446 original size:58 final size:57
Alignment explanation
Indices: 384--746 Score: 185
Period size: 59 Copynumber: 6.2 Consensus size: 57
374 GGCAAAAACA
* * *
384 TAATTTTTGGACA-TCCGGTGTAAAAAT-GTAATTTTTTGAAAGTTTGGGGTTAAAAATG
1 TAATTTTTGGA-ATTCAGG-GT-AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATG
*
442 TAATTTTTGGAATTTTAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAAAAATG
1 TAATTTTTGGAA-TTCAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTC---AAAAATG
* * ** ** *
503 GAATTTTTGAAAATTTGGGGTAAAATGGTAATTTTTGG-AAGTGAGGGGGCAAAAATG
1 TAATTTTTG-GAATTCAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATG
** * * *
560 GGATTTTTGGAAAGTTCAAGGTAAAAAATGAT-ATTTTTGG-AAGTTCGGGGGT--AAAATGG
1 TAATTTTTGG-AA-TTCAGGGT--AAAATGGTAATTTTTGGAAAGTT-TGGGGTCAAAAAT-G
* ** * * *
619 TAATTTTTGGAAAGTTTAGGGTCAAAAATAAT-ATTTTTGG-AAGTTCGAGGGT-GAAAATT
1 TAATTTTTGG-AA-TTCAGGGT--AAAATGGTAATTTTTGGAAAGTTTG-GGGTCAAAAATG
* * * *
678 TAATTTTTGAAAAGGTTGAGGGTAAAAT-GTAATTTTTGTG-AAGTTCGAGGGTC-AAAATA
1 TAATTTTTG-GAA--TTCAGGGTAAAATGGTAATTTTTG-GAAAGTTTG-GGGTCAAAAATG
737 TAATTTTTGG
1 TAATTTTTGG
747 GAAGTTCGAA
Statistics
Matches: 253, Mismatches: 32, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
57 24 0.09
58 58 0.23
59 97 0.38
60 33 0.13
61 39 0.15
62 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
TAATTTTTGGAATTCAGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATG
Found at i:530 original size:61 final size:58
Alignment explanation
Indices: 406--715 Score: 208
Period size: 59 Copynumber: 5.3 Consensus size: 58
396 ATCCGGTGTA
* * * * *
406 AAAAT-GTAATTTTTTGAAAGTTTGGGGTTAAAAATGTAATTTTTGGAATTTTAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTGAAAATTTAGGGT
*
463 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAAAAATGGAATTTTTGAAAATTTGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGT---AAAAAATGGAATTTTTGAAAATTTAGGGT
** ** * * * *
524 AAAATGGTAATTTTTGG-AAGTGAGGGGGCAAAAATGGGATTTTTGGAAAGTTCAAGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTT-GAAAATTTAGGGT
* * *
582 AAAAAATGAT-ATTTTTGG-AAGTTCGGGGGT--AAAATGGTAATTTTTGGAAAGTTTAGGGT
1 --AAAATGGTAATTTTTGGAAAGTT-TGGGGTAAAAAATGG-AATTTTT-GAAAATTTAGGGT
** * * ** *
641 CAAAAATAAT-ATTTTTGG-AAGTTCGAGGGT-GAAAATTTAATTTTTGAAAAGGTTGAGGGT
1 --AAAATGGTAATTTTTGGAAAGTTTG-GGGTAAAAAATGGAATTTTTGAAAA--TTTAGGGT
701 AAAAT-GTAATTTTTG
1 AAAATGGTAATTTTTG
716 TGAAGTTCGA
Statistics
Matches: 209, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
57 20 0.10
58 55 0.26
59 62 0.30
60 31 0.15
61 41 0.20
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAGTTTGGGGTAAAAAATGGAATTTTTGAAAATTTAGGGT
Found at i:663 original size:59 final size:57
Alignment explanation
Indices: 562--753 Score: 208
Period size: 59 Copynumber: 3.3 Consensus size: 57
552 CAAAAATGGG
* *
562 ATTTTTGGAAAGTTCAAGGTAAAAAATGATATTTTTGGAAGTTCGGGGGT-AAAATGGTA
1 ATTTTTGGAAAGTTCAGGGT-AAAAAT-ATATTTTTGGAAGTTCGAGGGTCAAAAT-GTA
* * *
621 ATTTTTGGAAAGTTTAGGGTCAAAAATAATATTTTTGGAAGTTCGAGGGTGAAAATTTA
1 ATTTTTGGAAAGTTCAGGGT-AAAAAT-ATATTTTTGGAAGTTCGAGGGTCAAAATGTA
* * * *
680 ATTTTTGAAAAGGTTGAGGGT-AAAATGTAATTTTTGTGAAGTTCGAGGGTCAAAATATA
1 ATTTTTGGAAA-GTTCAGGGTAAAAATAT-ATTTTTG-GAAGTTCGAGGGTCAAAATGTA
*
739 ATTTTTGGGAAGTTC
1 ATTTTTGGAAAGTTC
754 GAAGGTTAAA
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 15 0.13
59 86 0.75
60 13 0.11
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (57 bp):
ATTTTTGGAAAGTTCAGGGTAAAAATATATTTTTGGAAGTTCGAGGGTCAAAATGTA
Found at i:745 original size:30 final size:28
Alignment explanation
Indices: 562--764 Score: 162
Period size: 30 Copynumber: 6.9 Consensus size: 28
552 CAAAAATGGG
* *
562 ATTTTTGGAAAGTTC-AAGGTAAAAAATGA
1 ATTTTTGG-AAGTTCGAGGGTAAAATAT-A
* *
591 TATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCGAGGGTAAAAT-ATA
*
621 ATTTTTGGAAAGTT-TAGGGTCAAAA-ATAA
1 ATTTTTGG-AAGTTCGAGGGT-AAAATAT-A
*
650 TATTTTTGGAAGTTCGAGGGTGAAAATTTA
1 -ATTTTTGGAAGTTCGAGGGT-AAAATATA
* *
680 ATTTTTGAAAAGGTT-GAGGGTAAAATGTA
1 ATTTTTG-GAA-GTTCGAGGGTAAAATATA
709 ATTTTTGTGAAGTTCGAGGGTCAAAATATA
1 ATTTTTG-GAAGTTCGAGGGT-AAAATATA
*
739 ATTTTTGGGAAGTTCGAAGGTTAAAA
1 ATTTTT-GGAAGTTCG-AGGGTAAAA
765 AGTGATTTTT
Statistics
Matches: 143, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.03
29 53 0.37
30 76 0.53
31 10 0.07
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGAGGGTAAAATATA
Found at i:2465 original size:17 final size:16
Alignment explanation
Indices: 2426--2519 Score: 64
Period size: 17 Copynumber: 5.6 Consensus size: 16
2416 GAATATTATT
*
2426 AATTTAAA-TAAAATTA
1 AATTTAAATTTAAA-TA
*
2442 AACTTAAATTTATAATA
1 AATTTAAATTTA-AATA
* *
2459 AATTTAAATTCCAAATG
1 AATTTAAATT-TAAATA
* * *
2476 GATTTAAACTGAATATA
1 AATTTAAATTTAA-ATA
*
2493 AACTTAAATTTAAAATA
1 AATTTAAATTT-AAATA
2510 AATTTAAATT
1 AATTTAAATT
2520 CTATTGGGCC
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.15
17 45 0.76
18 5 0.08
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Done.