Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013158.1 Kokia drynarioides strain JFW-HI SEQ_128177, 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: 72578
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:522 original size:30 final size:30
Alignment explanation
Indices: 481--691 Score: 152
Period size: 30 Copynumber: 7.1 Consensus size: 30
471 GAGGTCCCTA
481 AACTATCCAAAAAGTCCCATTTTTACCCCCG
1 AACT-TCCAAAAAGTCCCATTTTTACCCCCG
512 AACTTCC-AAAAGTCCCATTTTTGA-CCCCG
1 AACTTCCAAAAAGTCCCATTTTT-ACCCCCG
* * **
541 AACCTTCCAAAAAATACCA-TTTTACCCCTA
1 AA-CTTCCAAAAAGTCCCATTTTTACCCCCG
* *
571 AATTTCC-AAAAGTCCCATTTTTGA-CCTCG
1 AACTTCCAAAAAGTCCCATTTTT-ACCCCCG
* * *
600 AACCTTCCTAAAATTACCA-TTTTACCCCCCG
1 AA-CTTCCAAAAAGTCCCATTTTTA-CCCCCG
* * * **
631 AAATTCCAAAAA-TCTCATTTTTAACCCTA
1 AACTTCCAAAAAGTCCCATTTTTACCCCCG
*
660 AACCTTCCAAAAATTACCC--TTTTACCCCCG
1 AA-CTTCCAAAAAGT-CCCATTTTTACCCCCG
690 AA
1 AA
692 TGTTTGAAAT
Statistics
Matches: 140, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
28 8 0.06
29 44 0.31
30 59 0.42
31 27 0.19
32 2 0.01
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (30 bp):
AACTTCCAAAAAGTCCCATTTTTACCCCCG
Found at i:529 original size:29 final size:29
Alignment explanation
Indices: 481--671 Score: 138
Period size: 29 Copynumber: 6.4 Consensus size: 29
471 GAGGTCCCTA
481 AACTATCCAAAAAGTCCCATTTTTACCCCCG
1 AACT-TCC-AAAAGTCCCATTTTTACCCCCG
512 AACTTCCAAAAGTCCCATTTTTGA-CCCCG
1 AACTTCCAAAAGTCCCATTTTT-ACCCCCG
* * **
541 AACCTTCCAAAAAATACCA-TTTTACCCCTA
1 AA-CTTCC-AAAAGTCCCATTTTTACCCCCG
* *
571 AATTTCCAAAAGTCCCATTTTTGA-CCTCG
1 AACTTCCAAAAGTCCCATTTTT-ACCCCCG
* *
600 AACCTTCCTAAAATTACCA-TTTTACCCCCCG
1 AA-CTTCC-AAAAGTCCCATTTTTA-CCCCCG
* * * * **
631 AAATTCCAAAAATCTCATTTTTAACCCTA
1 AACTTCCAAAAGTCCCATTTTTACCCCCG
660 AACCTTCCAAAA
1 AA-CTTCCAAAA
672 ATTACCCTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 25
0.73 0.13 0.14
Matches are distributed among these distances:
28 8 0.06
29 48 0.38
30 44 0.35
31 26 0.21
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (29 bp):
AACTTCCAAAAGTCCCATTTTTACCCCCG
Found at i:666 original size:60 final size:59
Alignment explanation
Indices: 486--691 Score: 254
Period size: 59 Copynumber: 3.5 Consensus size: 59
476 CCCTAAACTA
* * * *
486 TCCAAAAAGTCCCATTTTTACCCCCGAACTTCCAAAAGTCCCATTTTTGACCCCGAACCT
1 TCCAAAAATTACCA-TTTTACCCCCGAAATTCCAAAAGTCCCATTTTTGACCCTGAACCT
* *
546 TCCAAAAAATACCATTTTA-CCCCTAAATTTCCAAAAGTCCCATTTTTGA-CCTCGAACCT
1 TCCAAAAATTACCATTTTACCCCCGAAA-TTCCAAAAGTCCCATTTTTGACCCT-GAACCT
* * * * *
605 TCCTAAAATTACCATTTTACCCCCCGAAATTCCAAAAATCTCATTTTTAACCCTAAACCT
1 TCCAAAAATTACCATTTTA-CCCCCGAAATTCCAAAAGTCCCATTTTTGACCCTGAACCT
*
665 TCCAAAAATTACCCTTTTACCCCCGAA
1 TCCAAAAATTACCATTTTACCCCCGAA
692 TGTTTGAAAT
Statistics
Matches: 127, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.06
59 57 0.45
60 52 0.41
61 10 0.08
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCCCGAAATTCCAAAAGTCCCATTTTTGACCCTGAACCT
Found at i:7710 original size:5 final size:5
Alignment explanation
Indices: 7700--7730 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
7690 TATCAAATAG
7700 TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
7731 GTATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:13388 original size:17 final size:17
Alignment explanation
Indices: 13361--13394 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13351 AGATATTTTG
13361 TCAATTGATT-ATAATT
1 TCAATTGATTAATAATT
13377 TCAATCTGATTAATAATT
1 TCAAT-TGATTAATAATT
13395 AATTCAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (17 bp):
TCAATTGATTAATAATT
Found at i:14430 original size:22 final size:22
Alignment explanation
Indices: 14405--14461 Score: 53
Period size: 22 Copynumber: 2.5 Consensus size: 22
14395 TAAAACTGAC
14405 CAAATTTATTATAAAAAAAAAT
1 CAAATTTATTATAAAAAAAAAT
* **
14427 CAAAATTT-TTATTAAATTAAAT
1 C-AAATTTATTATAAAAAAAAAT
*
14449 TAAATTTAATTAT
1 CAAATTT-ATTAT
14462 TTTATAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 6 0.21
22 12 0.43
23 10 0.36
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
CAAATTTATTATAAAAAAAAAT
Found at i:15961 original size:31 final size:31
Alignment explanation
Indices: 15926--15991 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
15916 TAACAGAGAA
*
15926 TGACCAAAATAGAAACGATCTAAAACATGAG
1 TGACCAAAACAGAAACGATCTAAAACATGAG
* * * * *
15957 TGACCTAAACATAAATGATCTAAAGCATTAG
1 TGACCAAAACAGAAACGATCTAAAACATGAG
15988 TGAC
1 TGAC
15992 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (31 bp):
TGACCAAAACAGAAACGATCTAAAACATGAG
Found at i:19612 original size:18 final size:19
Alignment explanation
Indices: 19589--19627 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19579 TATATTTATT
*
19589 AATTTAAAATTTTAAA-AA
1 AATTTAAAAGTTTAAATAA
19607 AATTTAAAAGTTTAAATAA
1 AATTTAAAAGTTTAAATAA
19626 AA
1 AA
19628 AATTTTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTTAAAAGTTTAAATAA
Found at i:24618 original size:28 final size:28
Alignment explanation
Indices: 24578--24633 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
24568 GATTATTTAT
24578 GGTCTTGGTTGTTGAAAAAGTCGAAAAC
1 GGTCTTGGTTGTTGAAAAAGTCGAAAAC
24606 GGTCTTGGTTGTTGAAAAAGTCGAAAAC
1 GGTCTTGGTTGTTGAAAAAGTCGAAAAC
24634 CCGAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (28 bp):
GGTCTTGGTTGTTGAAAAAGTCGAAAAC
Found at i:53810 original size:3 final size:3
Alignment explanation
Indices: 53802--53839 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
53792 TGGCTCCCTT
53802 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
53840 GTAACACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54694 original size:12 final size:12
Alignment explanation
Indices: 54677--54709 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
54667 GGGTTGATCG
54677 ACCCGTTAATCA
1 ACCCGTTAATCA
54689 ACCCGTTAATCA
1 ACCCGTTAATCA
*
54701 ACCAGTTAA
1 ACCCGTTAA
54710 CCGACCCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.24
Consensus pattern (12 bp):
ACCCGTTAATCA
Found at i:61884 original size:24 final size:24
Alignment explanation
Indices: 61857--61903 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
61847 GAGTTGACCG
*
61857 ACCCATTAACCGACCTGTTAACCT
1 ACCCACTAACCGACCTGTTAACCT
* * *
61881 ACCCGCTGACCGACTTGTTAACC
1 ACCCACTAACCGACCTGTTAACC
61904 GTTGATCATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.38, G:0.13, T:0.23
Consensus pattern (24 bp):
ACCCACTAACCGACCTGTTAACCT
Found at i:61947 original size:13 final size:13
Alignment explanation
Indices: 61926--61955 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
61916 CTATTAATAG
*
61926 TTGATCGTTGACT
1 TTGACCGTTGACT
61939 TTGACCGTTGACT
1 TTGACCGTTGACT
61952 TTGA
1 TTGA
61956 TCCAGAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:62831 original size:43 final size:43
Alignment explanation
Indices: 62783--62868 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
62773 TTTCACTGTG
62783 TTGGTGTGTTGGAGTATGAGTGCATTGTATTGTGCTTGTGATT
1 TTGGTGTGTTGGAGTATGAGTGCATTGTATTGTGCTTGTGATT
*
62826 TTGGTGTGTTGGAGTATGGGTGCATTGTATTGTGCTTGTGATT
1 TTGGTGTGTTGGAGTATGAGTGCATTGTATTGTGCTTGTGATT
62869 GAAATATGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.13, C:0.05, G:0.36, T:0.47
Consensus pattern (43 bp):
TTGGTGTGTTGGAGTATGAGTGCATTGTATTGTGCTTGTGATT
Found at i:63308 original size:3 final size:3
Alignment explanation
Indices: 63302--63336 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
63292 ATTATTATTA
63302 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
63337 TGTTAGACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:64436 original size:31 final size:33
Alignment explanation
Indices: 64396--64467 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
64386 AACTTTTATG
64396 AAATAATTTTA-A-GAAATC-TGCCAAACAACAGA
1 AAAT-ATTTTACACGAAATCAT-CCAAACAACAGA
*
64428 AAATATTTTACACGGAATCATCCAAACAACAGA
1 AAATATTTTACACGAAATCATCCAAACAACAGA
*
64461 AAGTATT
1 AAATATT
64468 AACTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 6 0.17
32 5 0.14
33 23 0.66
34 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (33 bp):
AAATATTTTACACGAAATCATCCAAACAACAGA
Found at i:71526 original size:17 final size:17
Alignment explanation
Indices: 71474--71534 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
71464 TCCAATTTTT
* *
71474 AATTTTAATTTACTTTA
1 AATTTAAATTTACTCTA
* * **
71491 AGTTTGAATTTGTTCTA
1 AATTTAAATTTACTCTA
*
71508 AATTTAAATTTACTGTA
1 AATTTAAATTTACTCTA
*
71525 AATTAAAATT
1 AATTTAAATT
71535 AATTAAAAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTACTCTA
Done.