Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007899.1 Kokia drynarioides strain JFW-HI SEQ_122540, 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: 37000
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:631 original size:7 final size:7
Alignment explanation
Indices: 619--662 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
609 TCCCCTTTTT
619 TTATTAA
1 TTATTAA
626 TTATTAA
1 TTATTAA
*
633 TTAATAA
1 TTATTAA
640 TTATTAA
1 TTATTAA
647 TATCATT-A
1 T-T-ATTAA
655 TTATTAA
1 TTATTAA
662 T
1 T
663 ATCAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 3 0.09
7 23 0.72
8 3 0.09
9 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (7 bp):
TTATTAA
Found at i:659 original size:15 final size:15
Alignment explanation
Indices: 623--666 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
613 CTTTTTTTAT
*
623 TAATTATTAAT-TAA
1 TAATTATTAATATCA
637 TAATTATTAATATCA
1 TAATTATTAATATCA
*
652 TTATTATTAATATCA
1 TAATTATTAATATCA
667 AAACATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATTAATATCA
Found at i:755 original size:18 final size:19
Alignment explanation
Indices: 734--775 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
724 ATTAGTATTA
*
734 TTATTAATATTAA-AACAG
1 TTATTAATATTAATAAAAG
752 TTATTAATATTAATAAAAG
1 TTATTAATATTAATAAAAG
771 TTATT
1 TTATT
776 GAAACGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TTATTAATATTAATAAAAG
Found at i:763 original size:30 final size:30
Alignment explanation
Indices: 707--763 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
697 AAAAACTTAT
* *
707 TTAATATTAATAAGGTCATTAGTATTATTA
1 TTAATATTAATAAAGTCATTAATATTATTA
*
737 TTAATATTAA-AACAGTTATTAATATTA
1 TTAATATTAATAA-AGTCATTAATATTA
764 ATAAAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
TTAATATTAATAAAGTCATTAATATTATTA
Found at i:1457 original size:35 final size:35
Alignment explanation
Indices: 1417--1490 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
1407 TTTTAAACTA
* *
1417 TAAATTTGAAAATAATTTTAAACTTAAATTAAATT
1 TAAATTTGAAAACAATTTTAAACTTAAAATAAATT
** **
1452 TAAATTTTTAAACAATTTTAATTTTAAAATAAATT
1 TAAATTTGAAAACAATTTTAAACTTAAAATAAATT
1487 TAAA
1 TAAA
1491 GAGAGTATGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (35 bp):
TAAATTTGAAAACAATTTTAAACTTAAAATAAATT
Found at i:1468 original size:17 final size:18
Alignment explanation
Indices: 1417--1490 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 18
1407 TTTTAAACTA
* *
1417 TAAATTTGAAAATAATTT
1 TAAATTTTAAAATAAATT
* *
1435 TAAA-CTTAAATTAAATT
1 TAAATTTTAAAATAAATT
* *
1452 TAAATTTTTAAA-CAATT
1 TAAATTTTAAAATAAATT
*
1469 TTAATTTTAAAATAAATT
1 TAAATTTTAAAATAAATT
1487 TAAA
1 TAAA
1491 GAGAGTATGG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATAAATT
Found at i:2536 original size:31 final size:29
Alignment explanation
Indices: 2501--2561 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
2491 ATGTTAATAG
*
2501 ATGATTAATTTGTTATTTTTTAATAATATTA
1 ATGATTAATTTATTATTTTTTAA-AA-ATTA
*
2532 ATGATTGATTTATTATTTTTTAAAAATTA
1 ATGATTAATTTATTATTTTTTAAAAATTA
2561 A
1 A
2562 ATAACTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.18
30 2 0.07
31 21 0.75
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
ATGATTAATTTATTATTTTTTAAAAATTA
Found at i:2737 original size:20 final size:20
Alignment explanation
Indices: 2699--2739 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2689 ATAAATATCA
* * *
2699 AACATATATTAAGAGTTATT
1 AACAGATATTAACAATTATT
2719 AACAGATATTAACAATTATT
1 AACAGATATTAACAATTATT
2739 A
1 A
2740 GATAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
AACAGATATTAACAATTATT
Found at i:7649 original size:17 final size:18
Alignment explanation
Indices: 7600--7650 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 18
7590 AAAATACTAA
*
7600 AAAAAACATAGAAAATTAG
1 AAAAAA-ATATAAAATTAG
*
7619 AAAAAAGTAT-AAATT-G
1 AAAAAAATATAAAATTAG
7635 AAAAAAATATAAAATT
1 AAAAAAATATAAAATT
7651 TGAGGACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.36
17 10 0.36
18 2 0.07
19 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (18 bp):
AAAAAAATATAAAATTAG
Found at i:8506 original size:15 final size:15
Alignment explanation
Indices: 8469--8507 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
8459 GGTCTGTAGT
8469 TATTTTTTTGGTTGA
1 TATTTTTTTGGTTGA
*
8484 TTTTTTTTTGG-TGA
1 TATTTTTTTGGTTGA
8498 TATTCTTTTT
1 TATT-TTTTT
8508 ACTGGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (15 bp):
TATTTTTTTGGTTGA
Found at i:11655 original size:53 final size:53
Alignment explanation
Indices: 11575--11681 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
11565 TTTGATTAAT
11575 TATTAGAAGGACACTATGAAACTGAAGTCTTCTATGTTTATATTACTTTTATG
1 TATTAGAAGGACACTATGAAACTGAAGTCTTCTATGTTTATATTACTTTTATG
*
11628 TATTATAAGGACACTATGAAACTGAAGTCTTCTATGTTTATATTACTTTTATG
1 TATTAGAAGGACACTATGAAACTGAAGTCTTCTATGTTTATATTACTTTTATG
11681 T
1 T
11682 CTTGATCTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (53 bp):
TATTAGAAGGACACTATGAAACTGAAGTCTTCTATGTTTATATTACTTTTATG
Found at i:25228 original size:18 final size:19
Alignment explanation
Indices: 25187--25229 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
25177 AGGCTATATT
25187 TTTTATATTTAAAATATAA
1 TTTTATATTTAAAATATAA
* *
25206 -CTTATATTTAAATTA-AA
1 TTTTATATTTAAAATATAA
25223 TTTTATA
1 TTTTATA
25230 AATAATTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATATTTAAAATATAA
Found at i:25406 original size:21 final size:22
Alignment explanation
Indices: 25382--25440 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
25372 ATAACAACAT
*
25382 TTATCATTATAAAATT-TTTAA
1 TTATCATTATAAAATTATATAA
*
25403 TTAT-TTTATTTAAATATTATATAA
1 TTATCATTA--TAAA-ATTATATAA
25427 TTATCATT-TAAAAT
1 TTATCATTATAAAAT
25441 AAATAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 3 0.10
21 6 0.20
22 8 0.27
23 3 0.10
24 8 0.27
25 2 0.07
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATCATTATAAAATTATATAA
Found at i:25790 original size:9 final size:10
Alignment explanation
Indices: 25765--25789 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25755 GTATTTTATT
25765 TTTTTTAAAA
1 TTTTTTAAAA
25775 TTTTTTAAAA
1 TTTTTTAAAA
25785 TTTTT
1 TTTTT
25790 ATTTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:25821 original size:18 final size:17
Alignment explanation
Indices: 25776--25824 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
25766 TTTTTAAAAT
*
25776 TTTTTAA-A-ATTTTTA
1 TTTTTAATATATTTATA
25791 TTTTTAATATATTTATA
1 TTTTTAATATATTTATA
*
25808 TTTTTAAATTTATTTAT
1 TTTTT-AATATATTTAT
25825 TGATGTGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 1 0.03
17 11 0.38
18 10 0.34
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATATATTTATA
Found at i:32113 original size:18 final size:19
Alignment explanation
Indices: 32066--32113 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
32056 AATTCTTTAT
*
32066 TATAATATTTT-AATTAAA
1 TATAATATTTTAAATAAAA
* *
32084 TTTAATAATTTAAATAAAA
1 TATAATATTTTAAATAAAA
32103 TAT-ATATTTTA
1 TATAATATTTTA
32114 TTTTAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATAATATTTTAAATAAAA
Done.