Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003785.1 Kokia drynarioides strain JFW-HI SEQ_116765, 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: 37984
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:2465 original size:30 final size:30
Alignment explanation
Indices: 2408--2511 Score: 147
Period size: 30 Copynumber: 3.5 Consensus size: 30
2398 TTAATATAAT
*
2408 ATTTGGTACTTAAATTTGATAATTTTTCTTA
1 ATTTGGTACTTAAATTTGA-CATTTTTCTTA
2439 ATTTGGTACTTAAATTTGACATTTTTCTTA
1 ATTTGGTACTTAAATTTGACATTTTTCTTA
* *
2469 ATTTGGTACCTAAACTTGACATTTTT-TTA
1 ATTTGGTACTTAAATTTGACATTTTTCTTA
* *
2498 AGTTGGCACTTAAA
1 ATTTGGTACTTAAA
2512 CTTTTTGGGA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.21
30 34 0.51
31 19 0.28
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (30 bp):
ATTTGGTACTTAAATTTGACATTTTTCTTA
Found at i:2817 original size:60 final size:59
Alignment explanation
Indices: 2736--2910 Score: 172
Period size: 59 Copynumber: 2.9 Consensus size: 59
2726 AAATTGAATC
* * *
2736 TAAAAAAAGA-TTAGGTACCAAATTAGGAAAAATTGCCAAGTTCAGGAACCAAATTGTG
1 TAAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
** * * * **
2794 TCAAAAAAAAATTTAGGTACCAAATTAAAAAAAAAAGTGTCAAGTTTAGGTACTGAATTGAG
1 T-AAAAAAAAATTTAGGTACCAAATT--AGGAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
* * * * * *
2856 TAAAAAAAAGTTTAGGTATCAAATTAGGAAAAAGTGTCAAATTCATGTACCAAAT
1 TAAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAGGAACCAAAT
2911 GTTATATTAA
Statistics
Matches: 94, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
58 1 0.01
59 31 0.33
60 14 0.15
61 22 0.23
62 26 0.28
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.25
Consensus pattern (59 bp):
TAAAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
Found at i:2864 original size:61 final size:60
Alignment explanation
Indices: 2736--2881 Score: 152
Period size: 62 Copynumber: 2.4 Consensus size: 60
2726 AAATTGAATC
* ** * *
2736 TAAAAAAAGA-TTAGGTACCAAATT-AGGAAAAATTGCCAAGTTCAGGAACCAAATTGTG
1 TAAAAAAAAATTTAGGTACCAAATTAAAAAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
* * * **
2794 TCAAAAAAAAATTTAGGTACCAAATTAAAAAAAAAAGTGTCAAGTTTAGGTACTGAATTGAG
1 T-AAAAAAAAATTTAGGTACCAAATT-AAAAAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
* *
2856 TAAAAAAAAGTTTAGGTATCAAATTA
1 TAAAAAAAAATTTAGGTACCAAATTA
2882 GGAAAAAGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
58 1 0.01
59 8 0.11
60 15 0.21
61 22 0.31
62 26 0.36
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (60 bp):
TAAAAAAAAATTTAGGTACCAAATTAAAAAAAAAGTGCCAAGTTCAGGAACCAAATTGAG
Found at i:2880 original size:28 final size:27
Alignment explanation
Indices: 2835--2888 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
2825 AAAAAGTGTC
* *
2835 AAGTTTAGGTACTGAATTGAGTAAAAAA
1 AAGTTTAGGTACTAAATT-AGGAAAAAA
2863 AAGTTTAGGTA-TCAAATTAGGAAAAA
1 AAGTTTAGGTACT-AAATTAGGAAAAA
2889 GTGTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.48, C:0.04, G:0.20, T:0.28
Consensus pattern (27 bp):
AAGTTTAGGTACTAAATTAGGAAAAAA
Found at i:2888 original size:61 final size:60
Alignment explanation
Indices: 2724--2910 Score: 196
Period size: 60 Copynumber: 3.1 Consensus size: 60
2714 AATTTAGGTG
* * * * *
2724 CCAAATTGAATCTAAAAAAAGATTAGGTACCAAATTAGGAAAAATTGCCAAGTTCAGGAA
1 CCAAATTGAGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGAA
* * ** * *
2784 CCAAATTGTGTCAAAAAAAAATTTAGGTACCAAATTAAAAAAAAAAGTGTCAAGTTTAGGTA
1 CCAAATTGAGTCAAAAAAAAGTTTAGGTACCAAATT--AGGAAAAAGTGTCAAGTTCAGGAA
** * * * *
2846 CTGAATTGAGT-AAAAAAAAGTTTAGGTATCAAATTAGGAAAAAGTGTCAAATTCATGTA
1 CCAAATTGAGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGAA
2905 CCAAAT
1 CCAAAT
2911 GTTATATTAA
Statistics
Matches: 102, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
59 23 0.23
60 31 0.30
61 22 0.22
62 26 0.25
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (60 bp):
CCAAATTGAGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGAA
Found at i:5574 original size:6 final size:6
Alignment explanation
Indices: 5563--5589 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5553 TTTAACCATT
5563 TGAATA TGAATA TGAATA TGAATA TGA
1 TGAATA TGAATA TGAATA TGAATA TGA
5590 TAGGATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (6 bp):
TGAATA
Found at i:10568 original size:18 final size:18
Alignment explanation
Indices: 10545--10585 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10535 GTTCAAGGTG
10545 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
10563 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
10581 TAATT
1 TAATT
10586 TAATACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:12417 original size:27 final size:27
Alignment explanation
Indices: 12377--12549 Score: 118
Period size: 27 Copynumber: 6.3 Consensus size: 27
12367 TTCAGCAATA
** * *
12377 ACAAAATACCGCTCGTTCGATCCAAAT
1 ACAAAATAATGCTCATTCGAGCCAAAT
* *
12404 ACAAAATAATGCTCATTTGAGCCAGAT
1 ACAAAATAATGCTCATTCGAGCCAAAT
*
12431 ACAAAAT-ATCGCTCATTCGAGCCATAT
1 ACAAAATAAT-GCTCATTCGAGCCAAAT
* * *
12458 ACAAATATTTATCACTCATTCGAGCCAGAT
1 ACAAA-A-TAAT-GCTCATTCGAGCCAAAT
* * * *
12488 ACATAAT-ATCGCTTATTCAAGCCAGAT
1 ACAAAATAAT-GCTCATTCGAGCCAAAT
* *
12515 ACAAAAT-ATCACTCATTCAAGCCAAAT
1 ACAAAATAAT-GCTCATTCGAGCCAAAT
*
12542 ACAGAATA
1 ACAAAATA
12550 TATATCGCTC
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.02
27 94 0.77
28 2 0.02
29 2 0.02
30 22 0.18
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.25
Consensus pattern (27 bp):
ACAAAATAATGCTCATTCGAGCCAAAT
Found at i:12444 original size:54 final size:57
Alignment explanation
Indices: 12377--12550 Score: 180
Period size: 54 Copynumber: 3.2 Consensus size: 57
12367 TTCAGCAATA
* * * * *
12377 ACAAAATACCGCTCGTTCGATCCAAATACAAA-A-TAAT-GCTCATTTGAGCCAGAT
1 ACAAAATATCGCTCATTCGAGCCAAATACAAATATTAATCACTCATTCGAGCCAGAT
* *
12431 ACAAAATATCGCTCATTCGAGCCATATACAAATATTTATCACTCATTCGAGCCAGAT
1 ACAAAATATCGCTCATTCGAGCCAAATACAAATATTAATCACTCATTCGAGCCAGAT
* * * * * *
12488 ACATAATATCGCTTATTCAAGCCAGATACAAA-A-T-ATCACTCATTCAAGCCAAAT
1 ACAAAATATCGCTCATTCGAGCCAAATACAAATATTAATCACTCATTCGAGCCAGAT
*
12542 ACAGAATAT
1 ACAAAATAT
12551 ATATCGCTCA
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
54 54 0.52
55 2 0.02
56 4 0.04
57 43 0.42
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (57 bp):
ACAAAATATCGCTCATTCGAGCCAAATACAAATATTAATCACTCATTCGAGCCAGAT
Found at i:12550 original size:27 final size:27
Alignment explanation
Indices: 12423--12550 Score: 148
Period size: 27 Copynumber: 4.6 Consensus size: 27
12413 TGCTCATTTG
* *
12423 AGCCAGATACAAAATATCGCTCATTCG
1 AGCCAGATACAAAATATCACTCATTCA
* *
12450 AGCCATATACAAATATTTATCACTCATTCG
1 AGCCAGATACAAA-A--TATCACTCATTCA
* * *
12480 AGCCAGATACATAATATCGCTTATTCA
1 AGCCAGATACAAAATATCACTCATTCA
12507 AGCCAGATACAAAATATCACTCATTCA
1 AGCCAGATACAAAATATCACTCATTCA
* *
12534 AGCCAAATACAGAATAT
1 AGCCAGATACAAAATAT
12551 ATATCGCTCA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
27 61 0.71
28 1 0.01
29 1 0.01
30 23 0.27
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (27 bp):
AGCCAGATACAAAATATCACTCATTCA
Found at i:16506 original size:14 final size:15
Alignment explanation
Indices: 16489--16517 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16479 AAAACCAAAC
16489 CAAAAAAT-AATAAA
1 CAAAAAATAAATAAA
16503 CAAAAAATAAATAAA
1 CAAAAAATAAATAAA
16518 AATATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (15 bp):
CAAAAAATAAATAAA
Found at i:20140 original size:24 final size:24
Alignment explanation
Indices: 20111--20157 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
20101 TAAAAAAGTT
*
20111 AAGAAT-TAAAACTGTCAGCGCAAC
1 AAGAATGTAAAA-TGTCAGAGCAAC
*
20135 AAGAATGTCAAATGTCAGAGCAA
1 AAGAATGTAAAATGTCAGAGCAA
20158 TTAGGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (24 bp):
AAGAATGTAAAATGTCAGAGCAAC
Found at i:31251 original size:29 final size:29
Alignment explanation
Indices: 31191--31278 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
31181 TAATAAATAT
* * * * * *
31191 AGTCATGTCATAGATATAGCTACAAATAC
1 AGTCATGTCACAAATACAGTTACAGATGC
*
31220 AGTCATGTCACAAATACAGTTACGGATGC
1 AGTCATGTCACAAATACAGTTACAGATGC
*
31249 AGTCATGTCACAGATACAGTTACAGATGC
1 AGTCATGTCACAAATACAGTTACAGATGC
31278 A
1 A
31279 AACATGATAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (29 bp):
AGTCATGTCACAAATACAGTTACAGATGC
Found at i:31284 original size:29 final size:29
Alignment explanation
Indices: 31223--31307 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
31213 CAAATACAGT
* **
31223 CATGTCACAAATACAGTTACGGATGCAGT
1 CATGTCACAAATACAGTTACAGATGCAAA
*
31252 CATGTCACAGATACAGTTACAGATGCAAA
1 CATGTCACAAATACAGTTACAGATGCAAA
* * *
31281 CATGAT-ACATATATAGTTACAAATGCA
1 CATG-TCACAAATACAGTTACAGATGCA
31308 GACGTGATAC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 47 0.98
30 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (29 bp):
CATGTCACAAATACAGTTACAGATGCAAA
Found at i:31507 original size:40 final size:40
Alignment explanation
Indices: 31384--31565 Score: 159
Period size: 40 Copynumber: 4.6 Consensus size: 40
31374 GACATGTTGT
* * * * *
31384 AGTGTTTATAGTGTCACT-ACAGTTTAGTGGTAACCTTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTGCTAACCTTGC
* * *** ** **
31423 AATGTTTACAGTGTCACTACTGGTTCAGTTATAATATTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTGCTAACCTTGC
* * * **
31463 AGTGTCTACAGTGTCACTTCCAATTTAGTGCTAACCTTTT
1 AGTGTTTACAGTGTCACTGCCAATTCAGTGCTAACCTTGC
* * *
31503 AGTGTTTACAATGTCACTGCCAGTTCAGTGGTAACCTTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTGCTAACCTTGC
31543 AGTGTTTACAGTGTCACTGCCAA
1 AGTGTTTACAGTGTCACTGCCAA
31566 CTCAATAAAT
Statistics
Matches: 109, Mismatches: 33, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
39 16 0.15
40 93 0.85
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (40 bp):
AGTGTTTACAGTGTCACTGCCAATTCAGTGCTAACCTTGC
Found at i:31518 original size:80 final size:80
Alignment explanation
Indices: 31384--31565 Score: 204
Period size: 80 Copynumber: 2.3 Consensus size: 80
31374 GACATGTTGT
* * * * * **
31384 AGTGTTTATAGTGTCAC-TACAGTTTAGTGGTAACCTTGCAATGTTTACAGTGTCACTACTGGTT
1 AGTGTTTACAGTGTCACTTCCAATTTAGTGCTAACCTTGCAATGTTTACAATGTCACTACCAGTT
* *
31448 CAGTTATAATATTGC
66 CAGTGATAACATTGC
* ** * *
31463 AGTGTCTACAGTGTCACTTCCAATTTAGTGCTAACCTTTTAGTGTTTACAATGTCACTGCCAGTT
1 AGTGTTTACAGTGTCACTTCCAATTTAGTGCTAACCTTGCAATGTTTACAATGTCACTACCAGTT
* *
31528 CAGTGGTAACCTTGC
66 CAGTGATAACATTGC
*
31543 AGTGTTTACAGTGTCACTGCCAA
1 AGTGTTTACAGTGTCACTTCCAA
31566 CTCAATAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
79 15 0.18
80 69 0.82
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (80 bp):
AGTGTTTACAGTGTCACTTCCAATTTAGTGCTAACCTTGCAATGTTTACAATGTCACTACCAGTT
CAGTGATAACATTGC
Found at i:32168 original size:43 final size:41
Alignment explanation
Indices: 32079--32168 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 41
32069 TGTCATCTCG
* * *
32079 TGTGCCCCAGAATAGTATAGACACACCTTGACCCACGCCCG
1 TGTGCCCCAGAATAGTATAGACACACCTAGACACACGCCCA
*
32120 TGTGCCTCCA-AATAGTATAGACACACATCCTAGACACAC-CCTA
1 TGTGCC-CCAGAATAGTATAG--ACACA-CCTAGACACACGCCCA
32163 TGTGCC
1 TGTGCC
32169 AGTTCATGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
41 16 0.39
42 3 0.07
43 13 0.32
44 9 0.22
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (41 bp):
TGTGCCCCAGAATAGTATAGACACACCTAGACACACGCCCA
Found at i:32184 original size:55 final size:55
Alignment explanation
Indices: 32120--32334 Score: 283
Period size: 56 Copynumber: 3.9 Consensus size: 55
32110 CCCACGCCCG
* * *
32120 TGTGCCTCCAAATAGTATAGACACACATCCTAGACACACCCTATGTGCCAGTTCA
1 TGTGCCTCCAAACAGTATAGACACACACCCTAGACACACCCCATGTGCCAGTTCA
32175 TGTGCCTCCAAACAGTATAGACACACACCCTA-ACACACCCCATGTGCCAGCTT-A
1 TGTGCCTCCAAACAGTATAGACACACACCCTAGACACACCCCATGTGCCAG-TTCA
* * ** *
32229 TGTGCCTCCAAACAGTATAGACACACACCCTTGACACACCCCCGTGTGCCAGCCCG
1 TGTGCCTCCAAACAGTATAGACACACACCCTAGACACA-CCCCATGTGCCAGTTCA
* *
32285 TGTGCCTCCAAACATTATAAACACACACCCT-GAACACACCGCCATGTGCC
1 TGTGCCTCCAAACAGTATAGACACACACCCTAG-ACACACC-CCATGTGCC
32335 TTCGAAAAAC
Statistics
Matches: 143, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
54 49 0.34
55 40 0.28
56 54 0.38
ACGTcount: A:0.30, C:0.37, G:0.14, T:0.19
Consensus pattern (55 bp):
TGTGCCTCCAAACAGTATAGACACACACCCTAGACACACCCCATGTGCCAGTTCA
Found at i:34371 original size:2 final size:2
Alignment explanation
Indices: 34364--34405 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
34354 TCCCTACTTA
34364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34406 TAAATATCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.