Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015231.1 Kokia drynarioides strain JFW-HI SEQ_130276, 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: 65235
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 228 characters in sequence are not A, C, G, or T
Found at i:9203 original size:31 final size:31
Alignment explanation
Indices: 9159--9220 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
9149 TTAATTATTA
* * *
9159 AATTATTCGAAAGTTTTCATTTAAGTTACTG
1 AATTATTCAAAAGTTTTCATATAAGTCACTG
* *
9190 AATTATTTAAAAGTTTTTATATAAGTCACTG
1 AATTATTCAAAAGTTTTCATATAAGTCACTG
9221 GGCTATTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (31 bp):
AATTATTCAAAAGTTTTCATATAAGTCACTG
Found at i:9648 original size:60 final size:61
Alignment explanation
Indices: 9542--9657 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 61
9532 TAAATGAAAA
* * *
9542 TTTTTGAATAGTTCAGTAATCAAATTGTAACATTTTTTTAATTAAATGACCAAAATAAATT
1 TTTTTGAATAGTTCACTAACCAAATTGTAACATTTTTTTAATTAAATAACCAAAATAAATT
* *
9603 TTTTTGAATAGTTCACTAACCAAATTGTAA-TTTTTTTTAGTTAAATAACCAAAAT
1 TTTTTGAATAGTTCACTAACCAAATTGTAACATTTTTTTAATTAAATAACCAAAAT
9658 GAACATTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 22 0.44
61 28 0.56
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (61 bp):
TTTTTGAATAGTTCACTAACCAAATTGTAACATTTTTTTAATTAAATAACCAAAATAAATT
Found at i:9651 original size:29 final size:29
Alignment explanation
Indices: 9562--9655 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 29
9552 GTTCAGTAAT
* * *
9562 CAAATTGTAACATTTTTTTAATTAAATGAC
1 CAAATTGTAA-TTTTTTTTAGTTAAATAAC
* * * *
9592 CAAAAT-AAATTTTTTTGAATAGTTCACTAAC
1 CAAATTGTAATTTTTTT---TAGTTAAATAAC
9623 CAAATTGTAATTTTTTTTAGTTAAATAAC
1 CAAATTGTAATTTTTTTTAGTTAAATAAC
9652 CAAA
1 CAAA
9656 ATGAACATTT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
28 6 0.12
29 16 0.33
30 5 0.10
31 13 0.27
32 9 0.18
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (29 bp):
CAAATTGTAATTTTTTTTAGTTAAATAAC
Found at i:21453 original size:10 final size:10
Alignment explanation
Indices: 21438--21566 Score: 58
Period size: 10 Copynumber: 13.4 Consensus size: 10
21428 ACATGTGGTA
21438 AAAAAATTAT
1 AAAAAATTAT
*
21448 AAAAAA-AAT
1 AAAAAATTAT
*
21457 -AAAAATCA-
1 AAAAAATTAT
**
21465 ATAAAGGTTAT
1 A-AAAAATTAT
21476 AAAAATATT-T
1 AAAAA-ATTAT
*
21486 -AAAAATTAG
1 AAAAAATTAT
21495 AAAATAATTAT
1 AAAA-AATTAT
*
21506 -AAAAATAAT
1 AAAAAATTAT
*
21515 AAAAAATTGT
1 AAAAAATTAT
* *
21525 ACAAAATTGT
1 AAAAAATTAT
**
21535 AAAATTTTAT
1 AAAAAATTAT
* *
21545 -AAAACTCAT
1 AAAAAATTAT
21554 -AAAAATTAT
1 AAAAAATTAT
21563 AAAA
1 AAAA
21567 TGCATAAAAA
Statistics
Matches: 87, Mismatches: 22, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
8 8 0.09
9 25 0.29
10 46 0.53
11 8 0.09
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:21517 original size:39 final size:40
Alignment explanation
Indices: 21474--21559 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
21464 AATAAAGGTT
21474 ATAAAAATATT-TA-AAAATTAG-AAAATAATTATAAAAATA
1 ATAAAAATATTGTACAAAATT-GTAAAAT-ATTATAAAAATA
* * *
21513 ATAAAAA-ATTGTACAAAATTGTAAAATTTTATAAAACTC
1 ATAAAAATATTGTACAAAATTGTAAAATATTATAAAAATA
21552 ATAAAAAT
1 ATAAAAAT
21560 TATAAAATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 3 0.08
39 26 0.65
40 11 0.28
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (40 bp):
ATAAAAATATTGTACAAAATTGTAAAATATTATAAAAATA
Found at i:21522 original size:19 final size:19
Alignment explanation
Indices: 21438--21566 Score: 84
Period size: 19 Copynumber: 6.7 Consensus size: 19
21428 ACATGTGGTA
**
21438 AAAAAATTATAAAAAAAAT
1 AAAAAATTATAAAAATTAT
* **
21457 -AAAAATCAATAAAGGTTAT
1 AAAAAAT-TATAAAAATTAT
*
21476 AAAAATATT-TAAAAATTAG
1 AAAAA-ATTATAAAAATTAT
*
21495 AAAATAATTATAAAAATAAT
1 AAAA-AATTATAAAAATTAT
* *
21515 AAAAAATTGTACAAAATTGT
1 AAAAAATTATA-AAAATTAT
** * *
21535 AAAATTTTATAAAACTCAT
1 AAAAAATTATAAAAATTAT
21554 -AAAAATTATAAAA
1 AAAAAATTATAAAA
21567 TGCATAAAAA
Statistics
Matches: 82, Mismatches: 22, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
18 17 0.21
19 32 0.39
20 31 0.38
21 2 0.02
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAT
Found at i:21562 original size:18 final size:18
Alignment explanation
Indices: 21541--21576 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21531 TTGTAAAATT
21541 TTATAAAACT-CATAAAAA
1 TTATAAAA-TGCATAAAAA
21559 TTATAAAATGCATAAAAA
1 TTATAAAATGCATAAAAA
21577 AGATCCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 16 0.94
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.28
Consensus pattern (18 bp):
TTATAAAATGCATAAAAA
Found at i:21824 original size:18 final size:18
Alignment explanation
Indices: 21801--21844 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21791 TTTATAATTT
*
21801 TTTTATGACTTTATAAAA
1 TTTTATAACTTTATAAAA
* *
21819 TTTTATAATTTTTTAAAA
1 TTTTATAACTTTATAAAA
21837 TTTTATAA
1 TTTTATAA
21845 TTTTTTTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATAACTTTATAAAA
Found at i:21845 original size:18 final size:18
Alignment explanation
Indices: 21814--21850 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
21804 TATGACTTTA
21814 TAAAATTTTATAATTTTT
1 TAAAATTTTATAATTTTT
21832 TAAAATTTTATAATTTTT
1 TAAAATTTTATAATTTTT
21850 T
1 T
21851 TCCTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAAAATTTTATAATTTTT
Found at i:22181 original size:93 final size:94
Alignment explanation
Indices: 22005--22181 Score: 231
Period size: 92 Copynumber: 1.9 Consensus size: 94
21995 AAAACAAAGG
* *
22005 CTTAATTGCTTTTTTAAAAAAACTTTGAAGATTTTTTTTATACATTTTGAAAGTTTAAATATCTA
1 CTTAATTGATTTTTTAAAAAAACTTTGAAGATTTTTTTTATACATTTTGAAAGTTTAAACATCTA
* *
22070 ATTTAGTTGAAAAAAAAAAAAAGGTAAGAT
66 AATGAG-TGAAAAAAAAAAAAAGGTAAGAT
22100 CTTAATT-ATTTTTTAAAAAAA-TTTG-AGAGTTTTTTTTATA-ATTTTGAAAGTTTAAACA-CT
1 CTTAATTGATTTTTTAAAAAAACTTTGAAGA-TTTTTTTTATACATTTTGAAAGTTTAAACATC-
* *
22160 TAAATGAG-GAAAACAAGAAAAA
64 TAAATGAGTGAAAAAAAAAAAAA
22182 TAGTGACAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
90 12 0.16
91 1 0.01
92 26 0.35
93 15 0.20
94 13 0.18
95 7 0.09
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (94 bp):
CTTAATTGATTTTTTAAAAAAACTTTGAAGATTTTTTTTATACATTTTGAAAGTTTAAACATCTA
AATGAGTGAAAAAAAAAAAAAGGTAAGAT
Found at i:29289 original size:18 final size:18
Alignment explanation
Indices: 29268--29311 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29258 AAATTAAAAC
* *
29268 AATACTATAATATTTTTA
1 AATACTATAATAATTATA
*
29286 AATACAATAATAATTATA
1 AATACTATAATAATTATA
29304 AATA-TATA
1 AATACTATA
29312 CTTAAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AATACTATAATAATTATA
Found at i:31511 original size:22 final size:21
Alignment explanation
Indices: 31478--31522 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
31468 ATTTTTACAA
31478 TTTTTTATATTTTATAATTTT
1 TTTTTTATATTTTATAATTTT
*
31499 TTTTTTGTAATTTTATAATTTT
1 TTTTTTAT-ATTTTATAATTTT
31521 TT
1 TT
31523 CTATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTATATTTTATAATTTT
Found at i:31715 original size:31 final size:30
Alignment explanation
Indices: 31680--31749 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
31670 AAGTCCAAAG
* *
31680 ATTAAATCAAGAATATTTGATAACGTTAGAT
1 ATTAAATCAA-AATATTTGATAACATTAGAC
* *
31711 ATTAAACTGAAAATGTTTGATAACATTAGAC
1 ATTAAA-TCAAAATATTTGATAACATTAGAC
31742 ATTGAAAT
1 ATT-AAAT
31750 GGACAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (30 bp):
ATTAAATCAAAATATTTGATAACATTAGAC
Found at i:36494 original size:11 final size:12
Alignment explanation
Indices: 36466--36536 Score: 54
Period size: 12 Copynumber: 6.0 Consensus size: 12
36456 GTTCGTGAAC
36466 ATGTTCGTTTAT
1 ATGTTCGTTTAT
36478 ATGTTCGTTTA-
1 ATGTTCGTTTAT
*** *
36489 ATGTTCGCGAAC
1 ATGTTCGTTTAT
36501 ATGTTCGTTTAT
1 ATGTTCGTTTAT
** ** *
36513 GCGTTCGTGAAC
1 ATGTTCGTTTAT
36525 ATGTTCGTTTAT
1 ATGTTCGTTTAT
36537 GTTAACTATC
Statistics
Matches: 41, Mismatches: 17, Indels: 2
0.68 0.28 0.03
Matches are distributed among these distances:
11 8 0.20
12 33 0.80
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.46
Consensus pattern (12 bp):
ATGTTCGTTTAT
Found at i:36524 original size:24 final size:23
Alignment explanation
Indices: 36478--36537 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
36468 GTTCGTTTAT
36478 ATGTTCGTTTAAT-GTTCGCGAAC
1 ATGTTCGTTT-ATGGTTCGCGAAC
*
36501 ATGTTCGTTTATGCGTTCGTGAAC
1 ATGTTCGTTTATG-GTTCGCGAAC
36525 ATGTTCGTTTATG
1 ATGTTCGTTTATG
36538 TTAACTATCC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 2 0.06
23 10 0.29
24 22 0.65
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.43
Consensus pattern (23 bp):
ATGTTCGTTTATGGTTCGCGAAC
Found at i:37806 original size:20 final size:17
Alignment explanation
Indices: 37781--37819 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
37771 ATCATGTATG
37781 AAATTAAATAACATAAATGA
1 AAATTAAA-AA-AT-AATGA
37801 AAATTAAAAAATAATGA
1 AAATTAAAAAATAATGA
37818 AA
1 AA
37820 TAAAACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 2 0.11
20 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAATAATGA
Found at i:40874 original size:23 final size:23
Alignment explanation
Indices: 40844--40920 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
40834 ATGGGTCTAA
*
40844 TAAACGAGCTTATAAACGGGCTT
1 TAAACGAGCTTATAAACGAGCTT
40867 TAAACGAGCTTATAAACGAGCTT
1 TAAACGAGCTTATAAACGAGCTT
* * *
40890 TATACGAGCTAATAAACGAGCTAA
1 TAAACGAGCTTATAAACGAGCT-T
40914 TAAACGA
1 TAAACGA
40921 ACCATAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 42 0.88
24 6 0.12
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (23 bp):
TAAACGAGCTTATAAACGAGCTT
Found at i:40889 original size:35 final size:35
Alignment explanation
Indices: 40840--40920 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
40830 TCTGATGGGT
* *
40840 CTAATAAACGAGCTTATAAACGGGCT-TTAAACGAG
1 CTAATAAACGAGCTT-TAAACGAGCTAATAAACGAG
* *
40875 CTTATAAACGAGCTTTATACGAGCTAATAAACGAG
1 CTAATAAACGAGCTTTAAACGAGCTAATAAACGAG
40910 CTAATAAACGA
1 CTAATAAACGA
40921 ACCATAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 8 0.20
35 32 0.80
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (35 bp):
CTAATAAACGAGCTTTAAACGAGCTAATAAACGAG
Found at i:40896 original size:11 final size:12
Alignment explanation
Indices: 40843--40920 Score: 106
Period size: 12 Copynumber: 6.7 Consensus size: 12
40833 GATGGGTCTA
40843 ATAAACGAGCTT
1 ATAAACGAGCTT
*
40855 ATAAACGGGCTT
1 ATAAACGAGCTT
40867 -TAAACGAGCTT
1 ATAAACGAGCTT
40878 ATAAACGAGCTT
1 ATAAACGAGCTT
* *
40890 -TATACGAGCTA
1 ATAAACGAGCTT
*
40901 ATAAACGAGCTA
1 ATAAACGAGCTT
40913 ATAAACGA
1 ATAAACGA
40921 ACCATAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
11 19 0.32
12 40 0.68
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:44204 original size:121 final size:118
Alignment explanation
Indices: 44075--44317 Score: 423
Period size: 121 Copynumber: 2.0 Consensus size: 118
44065 GGTTAATAGC
44075 TTATTTGGTTTATGAGCTAAAGTTAAAAATTTATTTTTGATATTTTTTAAATTTTCTTAACAATA
1 TTATTTGGTTTATGAGCTAAAGTTAAAAATTTATTTTTGATATTTTTTAAATTTTCTTAACAATA
* *
44140 ATTGTAAAAAAATAAAAAAAAAACCATTTTGATATAGTCATTGATGGTAGAAATTT
66 ATTGTAAAAAAAT---AAAAAAACCATTTTGATAGAGTCATTGATGGTAAAAATTT
*
44196 TTATTTGGTTTATGAGCTAAAGTTAAAATTTTATTTTTGATATTTTTTAAATTTTCTTAACAATA
1 TTATTTGGTTTATGAGCTAAAGTTAAAAATTTATTTTTGATATTTTTTAAATTTTCTTAACAATA
*
44261 ATTGTAAAAAAATAAAAAAATCATTTTGATAGAGTCATTGATGGTAAAAATTT
66 ATTGTAAAAAAATAAAAAAACCATTTTGATAGAGTCATTGATGGTAAAAATTT
44314 TTAT
1 TTAT
44318 GACTCTCAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
118 41 0.35
121 77 0.65
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (118 bp):
TTATTTGGTTTATGAGCTAAAGTTAAAAATTTATTTTTGATATTTTTTAAATTTTCTTAACAATA
ATTGTAAAAAAATAAAAAAACCATTTTGATAGAGTCATTGATGGTAAAAATTT
Found at i:54841 original size:27 final size:27
Alignment explanation
Indices: 54811--54890 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
54801 ACAAATTTTT
* *
54811 CCGTGTTTATTGTATCGGCGAACTATC
1 CCGTGTTTATTGTACCGACGAACTATC
* * * *
54838 CCGTGTTCATTGTCCCGACGGATTATC
1 CCGTGTTTATTGTACCGACGAACTATC
* * *
54865 CCATGTTTATTGTCCCAACGAACTAT
1 CCGTGTTTATTGTACCGACGAACTAT
54891 TTATGATGTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (27 bp):
CCGTGTTTATTGTACCGACGAACTATC
Found at i:64633 original size:24 final size:24
Alignment explanation
Indices: 64590--64636 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
64580 AAACAGAGTT
64590 AAAAATATAAAATAAGAAATAAGC
1 AAAAATATAAAATAAGAAATAAGC
*
64614 AAAAATA-AAAATAGGAAAATAAG
1 AAAAATATAAAATAAG-AAATAAG
64637 GTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (24 bp):
AAAAATATAAAATAAGAAATAAGC
Done.