Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010269.1 Kokia drynarioides strain JFW-HI SEQ_125113, 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: 28556
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:118 original size:20 final size:20
Alignment explanation
Indices: 93--150 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
83 TACCTTTCTT
93 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
*
113 TCCTTCTTCTTTTTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
133 TCCTTCTTCCTTTCTTTC
1 TCCTTCTT-CTTTCTTTC
151 TTTCCCGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:120 original size:17 final size:17
Alignment explanation
Indices: 86--146 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 17
76 AACACATTAC
86 CTTTCTTTCCT-T-CTT
1 CTTTCTTTCCTCTCCTT
101 CTTTCTTTCCTCTCCTTCTT
1 CTTTCTTTCCTCT-C--CTT
*
121 CTTTTTTTCCTCTCCTT
1 CTTTCTTTCCTCTCCTT
*
138 CTTCCTTTC
1 CTTTCTTTC
147 TTTCTTTCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
17 10 0.26
19 1 0.03
20 15 0.39
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (17 bp):
CTTTCTTTCCTCTCCTT
Found at i:2221 original size:7 final size:7
Alignment explanation
Indices: 2191--2215 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2181 GCCTCATGCA
2191 TTTTCTT
1 TTTTCTT
2198 TTTTCTT
1 TTTTCTT
2205 TTTTCTT
1 TTTTCTT
2212 TTTT
1 TTTT
2216 TATTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:9508 original size:19 final size:20
Alignment explanation
Indices: 9477--9514 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9467 AACAATTAAT
9477 TATTTTTTAAAAATAAAAAA
1 TATTTTTTAAAAATAAAAAA
*
9497 TATTTTTTAAAATTAAAA
1 TATTTTTTAAAAATAAAA
9515 TTATTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTTTTAAAAATAAAAAA
Found at i:9512 original size:37 final size:38
Alignment explanation
Indices: 9465--9540 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
9455 CAATGACATA
* * *
9465 TTAACAATTAATTATTTTTTAAAAA-TAAAAAATATTTT
1 TTAACAATTAA-AATTATTAAAAAAGTAAAAAATATTTT
*
9503 TTAA-AATTAAAATTATTAAAAAAGTATAAAATATTTT
1 TTAACAATTAAAATTATTAAAAAAGTAAAAAATATTTT
9540 T
1 T
9541 ATTTTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 10 0.30
37 19 0.58
38 4 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
TTAACAATTAAAATTATTAAAAAAGTAAAAAATATTTT
Found at i:9519 original size:19 final size:20
Alignment explanation
Indices: 9474--9519 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
9464 ATTAACAATT
9474 AATTATTTTTTAAAAATAAA
1 AATTATTTTTTAAAAATAAA
* *
9494 AAATATTTTTT-AAAATTAA
1 AATTATTTTTTAAAAATAAA
9513 AATTATT
1 AATTATT
9520 AAAAAAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTATTTTTTAAAAATAAA
Found at i:9659 original size:24 final size:24
Alignment explanation
Indices: 9618--9664 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
9608 TTTGAGTGAT
*
9618 TTGAAAAAATAAATAAATTTAAATG
1 TTGAAAAAATAAACAAA-TTAAATG
*
9643 TTGAAAAAAT-TACAAATTAAAT
1 TTGAAAAAATAAACAAATTAAAT
9665 AAATGATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (24 bp):
TTGAAAAAATAAACAAATTAAATG
Found at i:12568 original size:30 final size:29
Alignment explanation
Indices: 12534--12685 Score: 118
Period size: 29 Copynumber: 5.2 Consensus size: 29
12524 GCAAAATGGT
*
12534 AATTTTGGGAAAGTTCG-GGATTAAAAATGA
1 AATTTT-GGAAAGTTCGAGG-GTAAAAATGA
*
12564 AATTTTTGAAAGTTCGAGGGTAAAAATGGA
1 AATTTTGGAAAGTTCGAGGGTAAAAAT-GA
* * *
12594 ATTTTTGG-AAGTTTGAGGGTAAAAATGG
1 AATTTTGGAAAGTTCGAGGGTAAAAATGA
* **
12622 ATTTTTGG-AAGTTTTAGGGTCAAAAATGGA
1 AATTTTGGAAAGTTCGAGGGT-AAAAAT-GA
*
12652 ATTTTTGG-AAGTTC-AGGGGTAAAAAT-A
1 AATTTTGGAAAGTTCGA-GGGTAAAAATGA
12679 TAATTTT
1 -AATTTT
12686 CAGATAGTTT
Statistics
Matches: 106, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
27 1 0.01
28 25 0.24
29 46 0.43
30 34 0.32
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AATTTTGGAAAGTTCGAGGGTAAAAATGA
Found at i:12587 original size:29 final size:29
Alignment explanation
Indices: 12555--12685 Score: 151
Period size: 29 Copynumber: 4.5 Consensus size: 29
12545 AGTTCGGGAT
*
12555 TAAAAATGAAATTTTTGAAAGTTCGAGGG
1 TAAAAATGAAATTTTTGGAAGTTCGAGGG
* *
12584 TAAAAATGGAATTTTTGGAAGTTTGAGGG
1 TAAAAATGAAATTTTTGGAAGTTCGAGGG
* **
12613 TAAAAATG-GATTTTTGGAAGTTTTAGGG
1 TAAAAATGAAATTTTTGGAAGTTCGAGGG
*
12641 TCAAAAATGGAATTTTTGGAAGTTC-AGGGG
1 T-AAAAATGAAATTTTTGGAAGTTCGA-GGG
12671 TAAAAAT-ATAATTTT
1 TAAAAATGA-AATTTT
12686 CAGATAGTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.21
29 54 0.60
30 17 0.19
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TAAAAATGAAATTTTTGGAAGTTCGAGGG
Found at i:12647 original size:58 final size:58
Alignment explanation
Indices: 12526--12685 Score: 175
Period size: 58 Copynumber: 2.7 Consensus size: 58
12516 TTGGAGGGGC
* *
12526 AAAATGGTAATTTTGGGAAAGTTC-GGGATTAAAAATGAAATTTTTGAAAGTTCGAGGGTA
1 AAAATGG-AATTTTTGG-AAGTTCAGGG-GTAAAAATGAAATTTTTGAAAGTTCGAGGGTA
* * * **
12586 AAAATGGAATTTTTGGAAGTT-TGAGGGTAAAAATG-GATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCAG-GGGTAAAAATGAAATTTTTGAAAGTTCGAGGGT-A
12644 AAAATGGAATTTTTGGAAGTTCAGGGGTAAAAAT-ATAATTTT
1 AAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGA-AATTTT
12686 CAGATAGTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 13
0.80 0.07 0.12
Matches are distributed among these distances:
57 17 0.20
58 46 0.53
59 16 0.19
60 7 0.08
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTCAGGGGTAAAAATGAAATTTTTGAAAGTTCGAGGGTA
Found at i:13702 original size:3 final size:3
Alignment explanation
Indices: 13694--13783 Score: 101
Period size: 3 Copynumber: 29.7 Consensus size: 3
13684 TCGATTTTAT
* * * * * *
13694 TTA TTA TTA TTA ATA ATA TTAA TTA ATA TTA TCA TTA TTA -CA ATA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
13739 TTTA TTA 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 TTA TTA TT
13784 GTTGTTGTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.01
3 69 0.92
4 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:13788 original size:3 final size:3
Alignment explanation
Indices: 13782--13810 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13772 ATTATTATTA
13782 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
13811 ATTAATGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:14553 original size:19 final size:19
Alignment explanation
Indices: 14518--14573 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
14508 CAAGATTGTA
14518 ATTTGGAC-TTTATATTTGTT
1 ATTTGGACTTTTA-ATTT-TT
14538 -TTTGGACTTTTAATTTTT
1 ATTTGGACTTTTAATTTTT
*
14556 ATTTGGGCTTTTAATTTT
1 ATTTGGACTTTTAATTTT
14574 AATATTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 2 0.06
19 27 0.82
20 4 0.12
ACGTcount: A:0.18, C:0.05, G:0.14, T:0.62
Consensus pattern (19 bp):
ATTTGGACTTTTAATTTTT
Found at i:14650 original size:20 final size:20
Alignment explanation
Indices: 14609--14672 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
14599 AATTTGATTT
*
14609 AATTTAAATTT--AAAG-CA
1 AATTTAAATTTAAAAAGATA
14626 AATTTAAATTTAAAAAGATA
1 AATTTAAATTTAAAAAGATA
14646 AATTTAAATTTAAAAA-ATA
1 AATTTAAATTTAAAAAGATA
14665 AATTTAAA
1 AATTTAAA
14673 CTAATTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 11 0.26
19 15 0.35
20 17 0.40
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (20 bp):
AATTTAAATTTAAAAAGATA
Found at i:14660 original size:19 final size:19
Alignment explanation
Indices: 14609--14672 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
14599 AATTTGATTT
*
14609 AATTTAAATTT-AAAG-CA
1 AATTTAAATTTAAAAGATA
14626 AATTTAAATTTAAAAAGATA
1 AATTTAAATTT-AAAAGATA
*
14646 AATTTAAATTTAAAAAATA
1 AATTTAAATTTAAAAGATA
14665 AATTTAAA
1 AATTTAAA
14673 CTAATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.26
19 19 0.45
20 12 0.29
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
AATTTAAATTTAAAAGATA
Found at i:15127 original size:37 final size:37
Alignment explanation
Indices: 15085--15183 Score: 171
Period size: 37 Copynumber: 2.7 Consensus size: 37
15075 TATTTTGATC
* *
15085 CACTTCTCTGTGTTTCATCAGGAAGATGGTTTTGGTT
1 CACTTCCCCGTGTTTCATCAGGAAGATGGTTTTGGTT
15122 CACTTCCCCGTGTTTCATCAGGAAGATGGTTTTGGTT
1 CACTTCCCCGTGTTTCATCAGGAAGATGGTTTTGGTT
*
15159 CACTTCCCCGTATTTCATCAGGAAG
1 CACTTCCCCGTGTTTCATCAGGAAG
15184 CTAACCGTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (37 bp):
CACTTCCCCGTGTTTCATCAGGAAGATGGTTTTGGTT
Found at i:15501 original size:205 final size:205
Alignment explanation
Indices: 15136--15934 Score: 1181
Period size: 205 Copynumber: 3.9 Consensus size: 205
15126 TCCCCGTGTT
* ** * * * *
15136 TCATCAGGAAGATGGTTTTGGTTCACTTCCCCGTATTTCATCAGGAAGCTAACCGTTTTATTACT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTACT
* * ** * *
15201 TCGACTTGCTTCTCCTTATCTCATCAGGAAGCTG-GGCTCGAAGATTTGCTCACATCGAGCGTGG
65 TCGACCTACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGG
* * *
15265 GTTTGATTTGGTCTTC-TCTTCTGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCT
130 GTTTGATTTGGTCTTCTTC-TCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCG
15329 CTTCTCTGTATC
194 CTTCTCTGTATC
15341 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTT
* * *
15406 CGACCTGCTTCTTAGTGTCTCATCAGGAAGCTAAGGTTCGAAGATTTGCTCACA-CTGAGCGTGG
66 CGACCTACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATC-GAGCGTGG
* *
15470 GTTTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGAACGCGTCGTTTGTTTCAATTCGC
130 GTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGC
*
15535 TTTTCTGTATC
195 TTCTCTGTATC
* * *
15546 TCTTCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTGCTT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTT
* * *
15611 CGACCCACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAGGATTTGCTCACATCGAGCGTGTG
66 CGACCTACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGG
* * * *
15676 TTTGATTTGGTATTCTTCTCAGTATCTCATCAGAAAGATGACCGTGTCATTTGTTTCAATTCGCT
131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCT
*
15741 TCTCTGTATT
196 TCTCTGTATC
* *
15751 TCATCAGGAAGACGAATTTGGTCAACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTT
1 TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTT
* * * * *
15816 CGACCTACTTCTCAATGTCTCATCAAGAAGCTGGGGTTCAAAAATTTGCTCACATCGAGCGTGGG
66 CGACCTACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGG
*
15881 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCGTCGTTTGT
131 TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
15935 GGATAATCGC
Statistics
Matches: 537, Mismatches: 53, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
204 39 0.07
205 495 0.92
206 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (205 bp):
TCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTT
CGACCTACTTCTCAGTGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCGTGGG
TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCT
TCTCTGTATC
Found at i:27365 original size:15 final size:15
Alignment explanation
Indices: 27345--27375 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27335 TGAAGAAAGG
*
27345 TTGCACCTAGTGAGT
1 TTGCACCTAGTAAGT
27360 TTGCACCTAGTAAGT
1 TTGCACCTAGTAAGT
27375 T
1 T
27376 AAGGCACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (15 bp):
TTGCACCTAGTAAGT
Found at i:28036 original size:29 final size:29
Alignment explanation
Indices: 27667--28022 Score: 427
Period size: 29 Copynumber: 12.2 Consensus size: 29
27657 GCAAAATGTT
* * * *
27667 AATTTTGGGAAGTTCG-GGATTGAAAATGG
1 AATTTTTGGAAGTTCGAGG-GTAAAAATGA
*
27696 AATTTTTGGAAGTTC-AGGGGTAAAAATGG
1 AATTTTTGGAAGTTCGA-GGGTAAAAATGA
27725 AATTTTTGGAAGTTCGAGGGTAAAAATGA
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
* ** *
27754 AAATTTTCAAAGTTTCG-GAGTAAAAATGA
1 AATTTTTGGAAG-TTCGAGGGTAAAAATGA
*
27783 AATTTTTGGAAGTTCGAAGGTAAAAATGA
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
27812 AATTTTTGGAAGTTCGAGGGTAAAAATGA
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
* *
27841 AATTTTTGGAAGTTCAAGGGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
*
27870 AATTTTTGGAAGTTTC-AGGGTTAAAATGGA
1 AATTTTTGGAAG-TTCGAGGGTAAAAAT-GA
*
27900 AA-TTTTGGAAGTTTGAGGGTAAAAATGA
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
*
27928 AATTTTTGGAAGTTCGAGGGTCAAAAATGC
1 AATTTTTGGAAGTTCGAGGGT-AAAAATGA
* * *
27958 AATTATTGTAAGTTTCGA-GGTAAAAAATGG
1 AATTTTTGGAAG-TTCGAGGGT-AAAAATGA
*
27988 AATTTTTGGAAGTTCGAGGGTAAAAATGT
1 AATTTTTGGAAGTTCGAGGGTAAAAATGA
28017 AATTTT
1 AATTTT
28023 CGAACAGTTT
Statistics
Matches: 286, Mismatches: 29, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
28 10 0.03
29 218 0.76
30 53 0.19
31 5 0.02
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGA
Done.