Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012261.1 Kokia drynarioides strain JFW-HI SEQ_127262, 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: 29001
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Found at i:3035 original size:30 final size:29
Alignment explanation
Indices: 2970--3107 Score: 93
Period size: 30 Copynumber: 4.6 Consensus size: 29
2960 GCTAAAAAGG
* * *
2970 TAATTTTTGAAAGTTT-CGAGGTCAAAATCA
1 TAATTTTTGGAAGTTTATG-GGTAAAAAT-A
*
3000 AAATTTTTGGAAGTTTATGGGTAAAAAATA
1 TAATTTTTGGAAGTTTATGGGT-AAAAATA
* *
3030 TAATTTTTAGAAGTTT-TGAGGTTAAAAGTA
1 TAATTTTTGGAAGTTTATG-GG-TAAAAATA
* ** *
3060 GAA-TTTTGGATAAGTTTGGGGGTCAAAATA
1 TAATTTTTGG--AAGTTTATGGGTAAAAATA
3090 TAATTTTTGGATAGTTTA
1 TAATTTTTGGA-AGTTTA
3108 GGGACCTCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
29 8 0.09
30 55 0.65
31 21 0.25
32 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (29 bp):
TAATTTTTGGAAGTTTATGGGTAAAAATA
Found at i:3065 original size:60 final size:58
Alignment explanation
Indices: 2970--3098 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 58
2960 GCTAAAAAGG
*
2970 TAATTTTTGAAAGTTTCGAGGTCAAAATCAAAATTTTTGG-AAGTTTATGGGTAAAAAATA
1 TAATTTTTG-AAGTTTCGAGGTCAAAATCAAAA-TTTTGGAAAGTTTAGGGGT-AAAAATA
* * * * *
3030 TAATTTTTAGAAGTTTTGAGGTTAAAAGT-AGAATTTTGGATAAGTTTGGGGGTCAAAATA
1 TAATTTTT-GAAGTTTCGAGGTCAAAA-TCAAAATTTTGGA-AAGTTTAGGGGTAAAAATA
3090 TAATTTTTG
1 TAATTTTTG
3099 GATAGTTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
59 7 0.12
60 40 0.68
61 12 0.20
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (58 bp):
TAATTTTTGAAGTTTCGAGGTCAAAATCAAAATTTTGGAAAGTTTAGGGGTAAAAATA
Found at i:4793 original size:14 final size:15
Alignment explanation
Indices: 4776--4806 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4766 GTTTAGTTTA
4776 GGTC-AATTAGATTT
1 GGTCAAATTAGATTT
4790 GGTCAAATTAGATTT
1 GGTCAAATTAGATTT
4805 GG
1 GG
4807 GGTGCAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (15 bp):
GGTCAAATTAGATTT
Found at i:4962 original size:34 final size:34
Alignment explanation
Indices: 4924--4990 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
4914 TTTTAATTTA
*
4924 AAAATAAATTTAAATTTAAAGTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATCCAAACTC
* * *
4958 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATCCAAACT
4991 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.31
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATCCAAACTC
Found at i:4984 original size:17 final size:17
Alignment explanation
Indices: 4912--4984 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
4902 CCTTTAATTT
*
4912 AATTTTAATTTAAAAATA
1 AATTTAAATTT-AAAATA
*
4930 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
** * * *
4947 AATCCAAACTCAAAATG
1 AATTTAAATTTAAAATA
*
4964 AATTTGAATTTAAAATA
1 AATTTAAATTTAAAATA
4981 AATT
1 AATT
4985 CAAACTTATT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
17 31 0.76
18 10 0.24
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:8487 original size:16 final size:16
Alignment explanation
Indices: 8468--8506 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
8458 GGGTGGCATG
8468 GAAGGAAAAATTGGGT
1 GAAGGAAAAATTGGGT
8484 GAAGGAAAAATTGGGT
1 GAAGGAAAAATTGGGT
8500 GAAGGAA
1 GAAGGAA
8507 GAAAATGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (16 bp):
GAAGGAAAAATTGGGT
Found at i:12529 original size:79 final size:78
Alignment explanation
Indices: 12424--12609 Score: 300
Period size: 79 Copynumber: 2.3 Consensus size: 78
12414 GTGCTGGGCA
12424 CACATTGCGGTTTAATCCGCTAGGCACTGGGTGCTAGGATTTGACGGACATTGTTGGTTAATCCA
1 CACATTGCGGTTTAA-CCGCTAGGCACTGGGTGCTAGGATTTGACGGACATTGTTGGTTAATCCA
12489 ACTAGAGTTAGGCT
65 ACTAGAGTTAGGCT
* *
12503 CATGATTGCGGTTTAACCGCTAGGCACTGGGTGTTAGGATTTGACGGACATTGTTGGTTAATCCA
1 CA-CATTGCGGTTTAACCGCTAGGCACTGGGTGCTAGGATTTGACGGACATTGTTGGTTAATCCA
*
12568 ACTAGAGTTGGGCT
65 ACTAGAGTTAGGCT
* *
12582 CACATTTGCGGTTTATCCGCTAAGCACT
1 CACA-TTGCGGTTTAACCGCTAGGCACT
12610 AGGTACCATA
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
78 1 0.01
79 86 0.87
80 12 0.12
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (78 bp):
CACATTGCGGTTTAACCGCTAGGCACTGGGTGCTAGGATTTGACGGACATTGTTGGTTAATCCAA
CTAGAGTTAGGCT
Found at i:15062 original size:18 final size:18
Alignment explanation
Indices: 15041--15078 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15031 AAAACTATAA
15041 TATTATTATAATT-ATCGT
1 TATTATTAT-ATTAATCGT
*
15059 TATTTTTATATTAATCGT
1 TATTATTATATTAATCGT
15077 TA
1 TA
15079 ATAAACACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TATTATTATATTAATCGT
Found at i:16149 original size:17 final size:18
Alignment explanation
Indices: 16127--16163 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
16117 TTTAATCTTT
16127 ATAATTTAATTTTGA-AA
1 ATAATTTAATTTTGAGAA
16144 ATAATTTAATTTTGAGAA
1 ATAATTTAATTTTGAGAA
16162 AT
1 AT
16164 TCAATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (18 bp):
ATAATTTAATTTTGAGAA
Found at i:16993 original size:22 final size:22
Alignment explanation
Indices: 16965--17014 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
16955 CTTATTTTGA
16965 TTGTTTAATCGATG-TTGTTGTT
1 TTGTTTAATCGA-GATTGTTGTT
16987 TTGTTTAATCGAGATTGTTGTT
1 TTGTTTAATCGAGATTGTTGTT
17009 TTGTTT
1 TTGTTT
17015 TTTATTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.14, C:0.04, G:0.22, T:0.60
Consensus pattern (22 bp):
TTGTTTAATCGAGATTGTTGTT
Found at i:17018 original size:25 final size:24
Alignment explanation
Indices: 16950--17016 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 24
16940 GTTTTTTTGT
*
16950 TGTTGCTTATTTTGATTGTTTAATCGA
1 TGTTG-TTGTTTTG-TT-TTTAATCGA
16977 TGTTGTTGTTTTG--TTTAATCGA
1 TGTTGTTGTTTTGTTTTTAATCGA
16999 -GATTGTTGTTTTGTTTTT
1 TG-TTGTTGTTTTGTTTTT
17017 TATTCCCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
21 1 0.03
22 20 0.56
24 3 0.08
26 7 0.19
27 5 0.14
ACGTcount: A:0.13, C:0.04, G:0.21, T:0.61
Consensus pattern (24 bp):
TGTTGTTGTTTTGTTTTTAATCGA
Found at i:19236 original size:52 final size:52
Alignment explanation
Indices: 19148--19325 Score: 277
Period size: 52 Copynumber: 3.4 Consensus size: 52
19138 ATTTCATTTC
* * * * *
19148 ATTCATATACTCACGATGACACACAACCA-CTAGACCTCATAATCCATAAAGG
1 ATTCATATACTCACGATGACACATAGCCATC-GGACCTCATAATCCGTAAAAG
19200 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAAG
* *
19252 ATTCATATACTCACAATGACACATAGCCATCGGACCTCATAATACGTAAAAG
1 ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAAG
19304 ATTCATATACTCACGATGACAC
1 ATTCATATACTCACGATGACAC
19326 TTAATCATCA
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 116 0.99
53 1 0.01
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGCCATCGGACCTCATAATCCGTAAAAG
Found at i:22609 original size:160 final size:160
Alignment explanation
Indices: 22173--22610 Score: 594
Period size: 160 Copynumber: 2.7 Consensus size: 160
22163 TTTTGGCTTC
* * * * * * **
22173 TAGTTCTCATACTCGTACCAAACTGAGA-ACAACAATCAGAACCCAAATTAGATTTAAATAATTT
1 TAGTTCTCATACTCGTACCAGACTAAGACACAAAAATAAAAACCGAAATTAGATTTTTATAATTT
* * *
22237 GGAACTGACAATGAGAAAGTGTTTACGATATACCTGTGATCCAGTTGTGTTAAGCTGAATGCATG
66 GGAATTGACAATGAGAAAGTGTTTACGATATACCTGTGTTCCAGTTGTGTTAGGCTGAATGCATG
* * *
22302 GTCGTGTTTTGTCATTCTTTTTTTGGGTTG
131 GTCGTGTTCTATCATTCTTTTTTTAGGTTG
** * * * *
22332 TAGTTCTCATACTCGTAGTAGAATAAGACATAAAAATAAAAATCGAAATTAGATTATTATAATTT
1 TAGTTCTCATACTCGTACCAGACTAAGACACAAAAATAAAAACCGAAATTAGATTTTTATAATTT
* *
22397 GGAATTGACAATGAGAAAGTGTTTACGATATTCCTGTGATT-CAGTTGTGTTAGGTTGAATGCAT
66 GGAATTGACAATGAGAAAGTGTTTACGATATACCTGTG-TTCCAGTTGTGTTAGGCTGAATGCAT
* *
22461 GGTGGTGTTCTATCGTTCTTTTTTTAGGTTG
130 GGTCGTGTTCTATCATTCTTTTTTTAGGTTG
*
22492 TAGTTCTCACACTCGTACCAGACTAAGACACAAAAA-ATAAAACCGAAATTAGATTTTTATAATT
1 TAGTTCTCATACTCGTACCAGACTAAGACACAAAAATA-AAAACCGAAATTAGATTTTTATAATT
* *
22556 TGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCGTTGTGTTAGG
65 TGGAATTGACAATGAGAAAGTGTTTACGATATACCTGTGTTCCAGTTGTGTTAGG
22611 ATCTTGTTTG
Statistics
Matches: 241, Mismatches: 34, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
159 26 0.11
160 214 0.89
161 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (160 bp):
TAGTTCTCATACTCGTACCAGACTAAGACACAAAAATAAAAACCGAAATTAGATTTTTATAATTT
GGAATTGACAATGAGAAAGTGTTTACGATATACCTGTGTTCCAGTTGTGTTAGGCTGAATGCATG
GTCGTGTTCTATCATTCTTTTTTTAGGTTG
Found at i:23574 original size:36 final size:36
Alignment explanation
Indices: 23533--23623 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 36
23523 GAGACCCTGC
**
23533 AATTTAAATTAAAAAACATAAGTAAGTCTGTTGTCA
1 AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
23569 AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
1 AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
23605 AATTTAAATTAAAAAACAT
1 AATTTAAATTAAAAAACAT
23624 CTCATATGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (36 bp):
AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
Found at i:26156 original size:18 final size:18
Alignment explanation
Indices: 26125--26182 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
26115 CCACCTCCCT
26125 CACC-CTCAACACCCTCAC
1 CACCTCTCAA-ACCCTCAC
* *
26143 C-CTTACTCGAACCCTCAC
1 CACCT-CTCAAACCCTCAC
26161 CACCTCTCAAACCCTCAC
1 CACCTCTCAAACCCTCAC
26179 CACC
1 CACC
26183 CTTACTTCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 1 0.03
18 26 0.79
19 6 0.18
ACGTcount: A:0.26, C:0.57, G:0.02, T:0.16
Consensus pattern (18 bp):
CACCTCTCAAACCCTCAC
Found at i:26275 original size:6 final size:6
Alignment explanation
Indices: 26246--26302 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
26236 CCTCAGCTTT
* * * *
26246 ACCCTT ACCCTT ACCCTC ACCCTC ACCCTC ACCAC-C ACCATC ACCATC
1 ACCCTC ACCCTC ACCCTC ACCCTC ACCCTC ACC-CTC ACCCTC ACCCTC
26294 ACCCTC ACC
1 ACCCTC ACC
26303 ACCTTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
6 45 0.98
7 1 0.02
ACGTcount: A:0.23, C:0.60, G:0.00, T:0.18
Consensus pattern (6 bp):
ACCCTC
Found at i:27417 original size:23 final size:23
Alignment explanation
Indices: 27344--27517 Score: 158
Period size: 23 Copynumber: 7.5 Consensus size: 23
27334 TATATGGAAC
* *
27344 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
27366 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
27387 GGGCAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
27413 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
27436 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
27459 AATCAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
27482 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
27507 AAACAGAGAGC
1 AAACAGAGAGC
27518 GCGCTAGTGT
Statistics
Matches: 126, Mismatches: 17, Indels: 17
0.79 0.11 0.11
Matches are distributed among these distances:
21 17 0.13
23 71 0.56
24 2 0.02
25 29 0.23
26 7 0.06
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:27466 original size:69 final size:67
Alignment explanation
Indices: 27344--27493 Score: 196
Period size: 69 Copynumber: 2.1 Consensus size: 67
27334 TATATGGAAC
*
27344 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAG
27409 TGCT-
63 TGCTA
*
27413 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACATA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACA
27477 GTGCTA
62 GTGCTA
27483 ATAACAGAGAG
1 A-AACAGAGAG
27494 CACGAGACGT
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
68 2 0.03
69 32 0.44
70 12 0.16
71 20 0.27
72 7 0.10
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (67 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGC
TA
Done.