Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011030.1 Kokia drynarioides strain JFW-HI SEQ_126001, 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: 12405
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Found at i:1020 original size:22 final size:22
Alignment explanation
Indices: 977--1052 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
967 CACTTTATGT
* *
977 GCCTACTGATTTGCGCTATGTGC
1 GCCTACTGA-TTGCACTGTGTGC
* *
1000 GCCTACTTATTGCACTGTGTGT
1 GCCTACTGATTGCACTGTGTGC
*
1022 GCCTACTGGATTGCACTGTGTGT
1 GCCTACT-GATTGCACTGTGTGC
*
1045 GCTTACTG
1 GCCTACTG
1053 TTTCTCAGCA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.39
23 28 0.61
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37
Consensus pattern (22 bp):
GCCTACTGATTGCACTGTGTGC
Found at i:2069 original size:3 final size:3
Alignment explanation
Indices: 2001--2052 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
1991 ACATTTTTAT
* *
2001 TAA TAA TAG CAA TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2047 TAA TAA
1 TAA TAA
2053 ATGTAGCTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3303 original size:59 final size:58
Alignment explanation
Indices: 3190--3390 Score: 235
Period size: 59 Copynumber: 3.4 Consensus size: 58
3180 TAGAGGTCCT
* * * * *
3190 TAAATTGTCAAGAAATTATATTTTAACCCCCGAACTTCTCCAAAATT-ATATTTTGACCC
1 TAAATTTTCAAAAAATTATATTTTAACCCTCGAACTT-TCCAAAATTCCTTTTTTGA-CC
* * *
3249 TAAACTTTTC-AAAAATTACATTTTGACCCTCAAACTTTCCAAAATTCCTTTTTTGACC
1 TAAA-TTTTCAAAAAATTATATTTTAACCCTCGAACTTTCCAAAATTCCTTTTTTGACC
* * * *
3307 TCAAATTTTCAAAAAATTATATTTTTACCCTCGAACATTCTAAAACTCCTTTTTTGACC
1 T-AAATTTTCAAAAAATTATATTTTAACCCTCGAACTTTCCAAAATTCCTTTTTTGACC
3366 TAAAATTTTCAAAAAATTATATTTT
1 T-AAATTTTCAAAAAATTATATTTT
3391 TAGCCCCTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
58 17 0.14
59 102 0.83
60 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (58 bp):
TAAATTTTCAAAAAATTATATTTTAACCCTCGAACTTTCCAAAATTCCTTTTTTGACC
Found at i:3432 original size:29 final size:29
Alignment explanation
Indices: 3202--3535 Score: 166
Period size: 29 Copynumber: 11.4 Consensus size: 29
3192 AATTGTCAAG
* * * * *
3202 AAATTATATTTTAACCCCCGAACTTCTCCA
1 AAATTACATTTTTACCCTCAAACTTC-CAA
* * *
3232 AAATTATATTTTGACCCT-AAACTTTTCAA
1 AAATTACATTTTTACCCTCAAAC-TTCCAA
*
3261 AAATTACATTTTGACCCTCAAACTTTCC-A
1 AAATTACATTTTTACCCTCAAAC-TTCCAA
* * * *
3290 AAATTCCTTTTTTGA-CCTCAAATTTTCAAA
1 AAATTACATTTTT-ACCCTCAAA-CTTCCAA
* * *
3320 AAATTATATTTTTACCCTCGAACATT-CTA
1 AAATTACATTTTTACCCTCAAAC-TTCCAA
* * * * * *
3349 AAACTCCTTTTTTGA-CCTAAAATTTTCAAA
1 AAATTACATTTTT-ACCCTCAAA-CTTCCAA
*
3379 AAATTATATTTTTAGCCC-CTAAACTTCCAA
1 AAATTACATTTTTA-CCCTC-AAACTTCCAA
* *
3409 AAATTACATTTTTACCCTCGAACTTCCTA
1 AAATTACATTTTTACCCTCAAACTTCCAA
* * * ***
3438 AAATTCCATTTTTTACCTTGATTTTTCCAA
1 AAATTACA-TTTTTACCCTCAAACTTCCAA
*
3468 AAATTAC-TATTTTACCCTCGAACTTCCAA
1 AAATTACAT-TTTTACCCTCAAACTTCCAA
** * *
3497 ATGTTACGTTTTT-CCC-CAAACTTCCTA
1 AAATTACATTTTTACCCTCAAACTTCCAA
3524 AAATT-CATTTTT
1 AAATTACATTTTT
3536 TGACCCCGTT
Statistics
Matches: 227, Mismatches: 60, Indels: 38
0.70 0.18 0.12
Matches are distributed among these distances:
26 6 0.03
27 12 0.05
28 4 0.02
29 103 0.45
30 97 0.43
31 5 0.02
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTTACCCTCAAACTTCCAA
Found at i:3441 original size:59 final size:56
Alignment explanation
Indices: 3378--3535 Score: 137
Period size: 59 Copynumber: 2.8 Consensus size: 56
3368 AAATTTTCAA
3378 AAAATTATATTTTTAGCCCCTAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCC
1 AAAATTAT-TTTTTA-CCCCTAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCC
* ***
3436 TAAAATTCCATTTTTTA-CCTTGATTTTTCCAAAAATTAC-TATTTTACCCTCGAACTTCC
1 -AAAATT--ATTTTTTACCCCT-AAACTTCCAAAAATTACAT-TTTTACCCTCGAACTTCC
* * *
3495 AAATGTTACGTTTTT-CCCC-AAACTTCCTAAAATT-CATTTTT
1 AAA-ATTA-TTTTTTACCCCTAAACTTCCAAAAATTACATTTTT
3536 TGACCCCGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
55 5 0.06
56 12 0.15
57 1 0.01
58 14 0.17
59 40 0.50
60 6 0.08
61 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (56 bp):
AAAATTATTTTTTACCCCTAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCC
Found at i:3549 original size:86 final size:87
Alignment explanation
Indices: 3318--3594 Score: 242
Period size: 89 Copynumber: 3.2 Consensus size: 87
3308 CAAATTTTCA
* * * *** * *
3318 AAAAATTATATTTTTACCCTCGAACATT-CTAAAACTCC-TTTTTTGACCTAAAATTTTCAAAAA
1 AAAAATTACATTTTTACCCTCAAAC-TTCCTAAAATTCCATTTTTT-ACCCCGATTTTTCCAAAA
* *
3381 ATTA-TATTTTTAGCCCCTAAACTTCC
64 ATTACCA--TTTA-CCCCCAAACTTCC
* **
3407 AAAAATTACATTTTTACCCTCGAACTTCCTAAAATTCCATTTTTTACCTTGATTTTTCCAAAAAT
1 AAAAATTACATTTTTACCCTCAAACTTCCTAAAATTCCATTTTTTACCCCGATTTTTCCAAAAAT
* * *
3472 TACTATTTTACCCTCGAACTTCC
66 TACCA-TTTACCCCCAAACTTCC
** * * *
3495 AAATGTTACGTTTTT-CCC-CAAACTTCCTAAAATT-CATTTTTTGACCCCGTTTTTTCCCAAAA
1 AAAAATTACATTTTTACCCTCAAACTTCCTAAAATTCCATTTTTT-ACCCCGATTTTTCCAAAAA
3557 TTACCATTTACCCCCAAACTTCC
65 TTACCATTTACCCCCAAACTTCC
* *
3580 AAAAGTTTCATTTTT
1 AAAAATTACATTTTT
3595 TATCCCAATT
Statistics
Matches: 161, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
85 35 0.22
86 35 0.22
87 3 0.02
88 24 0.15
89 56 0.35
90 8 0.05
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (87 bp):
AAAAATTACATTTTTACCCTCAAACTTCCTAAAATTCCATTTTTTACCCCGATTTTTCCAAAAAT
TACCATTTACCCCCAAACTTCC
Found at i:3595 original size:86 final size:88
Alignment explanation
Indices: 3371--3595 Score: 244
Period size: 86 Copynumber: 2.6 Consensus size: 88
3361 TGACCTAAAA
* * * * * *
3371 TTTTCAAAAAATTA-TATTTTTAGCCCCTAAACTTCCAAAAATTACATTTTTACCCTCGAACTTC
1 TTTTCCAAAAATTACCA-TTTTA-CCCCCAAACTTCCAAAAGTTACATTTTTTCCCTCAAACTTC
**
3435 CTAAAATTCCATTTTTTACCTTGAT
64 CTAAAATTCCATTTTTTACCCCGAT
* * * * *
3460 TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAATGTTAC-GTTTTTCCC-CAAACTTCCT
1 TTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAGTTACATTTTTTCCCTCAAACTTCCT
*
3523 AAAATT-CATTTTTTGACCCCGTT
66 AAAATTCCATTTTTT-ACCCCGAT
* *
3546 TTTTCCCAAAATTACCA-TTTACCCCCAAACTTCCAAAAGTTTCATTTTTT
1 TTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAGTTACATTTTTT
3596 ATCCCAATTT
Statistics
Matches: 114, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
85 30 0.26
86 40 0.35
87 7 0.06
88 17 0.15
89 18 0.16
90 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (88 bp):
TTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAGTTACATTTTTTCCCTCAAACTTCCT
AAAATTCCATTTTTTACCCCGAT
Found at i:3627 original size:59 final size:58
Alignment explanation
Indices: 3510--3623 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 58
3500 TTACGTTTTT
**
3510 CCCCAAACTTCCTAAAATTCATTTTTTGACCCCGTTTTTTCCCAAAATTACCATTTAC
1 CCCCAAACTTCCTAAAATTCATTTTTTGACCCAATTTTTTCCCAAAATTACCATTTAC
* *
3568 CCCCAAACTTCC-AAAAGTTTCATTTTTT-ATCCCAATTTTTT-TCAAAATTATCATTT
1 CCCCAAACTTCCTAAAA--TTCATTTTTTGA-CCCAATTTTTTCCCAAAATTACCATTT
3624 TACCTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
57 4 0.08
58 26 0.53
59 19 0.39
ACGTcount: A:0.29, C:0.27, G:0.03, T:0.41
Consensus pattern (58 bp):
CCCCAAACTTCCTAAAATTCATTTTTTGACCCAATTTTTTCCCAAAATTACCATTTAC
Found at i:4112 original size:97 final size:98
Alignment explanation
Indices: 3924--4120 Score: 240
Period size: 97 Copynumber: 2.0 Consensus size: 98
3914 CATAAAAACT
* * *
3924 TTAAAATCGAGGCAATATTCTTTTATTTCGAATTTGGAAAATTTGTACCTTAACTTACTAGGCAC
1 TTAAAATCGAGGCAATATTCTCTTATCTCGAATTTGGAAAATTTGTACCTAAACTTACTAGGCAC
* *
3989 AATTTTTCTTCACATCGGAATAATCGAATATCC
66 AATTTTTCTTCAAATCGGAATAATCGAACATCC
* * **
4022 TTAAAA-CGAGGCAATGTT-TCTTATCTCTG-ATTTTGAAAATTTGTACCTAAACTTACTAGGTG
1 TTAAAATCGAGGCAATATTCTCTTATCTC-GAATTTGGAAAATTTGTACCTAAACTTACTAGGCA
* *
4084 CGACTTTTTCTTTAAATC-GAGATAATCGAACATCC
65 C-AATTTTTCTTCAAATCGGA-ATAATCGAACATCC
4119 TT
1 TT
4121 TTCAAAAGTG
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
96 39 0.46
97 40 0.47
98 6 0.07
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (98 bp):
TTAAAATCGAGGCAATATTCTCTTATCTCGAATTTGGAAAATTTGTACCTAAACTTACTAGGCAC
AATTTTTCTTCAAATCGGAATAATCGAACATCC
Found at i:5010 original size:16 final size:17
Alignment explanation
Indices: 4985--5018 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4975 TTATTTCAGT
*
4985 ATTTTAAAATTTTTAAA
1 ATTTTAAAATTATTAAA
5002 ATTTT-AAATTATTAAA
1 ATTTTAAAATTATTAAA
5018 A
1 A
5019 GTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTTAAAATTATTAAA
Found at i:5224 original size:21 final size:21
Alignment explanation
Indices: 5186--5225 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5176 GCATATAGTA
**
5186 TTAATATATGTTGTTGAAATT
1 TTAATATATGTTAATGAAATT
*
5207 TTAATGTATGTTAATGAAA
1 TTAATATATGTTAATGAAA
5226 AATTAATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (21 bp):
TTAATATATGTTAATGAAATT
Found at i:7065 original size:6 final size:6
Alignment explanation
Indices: 7031--7086 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
7021 TAATAGGGAT
* * * *
7031 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
7078 TTTCAA TTT
1 TTTCAA TTT
7087 TGATCACAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 34 0.83
7 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:7073 original size:18 final size:18
Alignment explanation
Indices: 7050--7086 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
7040 ACAATTCATA
7050 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
*
7068 TCACTTTCACTTTCAATT
1 TCACTTTCAATTTCAATT
7086 T
1 T
7087 TGATCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:10036 original size:24 final size:24
Alignment explanation
Indices: 9974--10037 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
9964 CTAGACTAAT
*
9974 AAGAGTTTAATTCAAACAAATAAA
1 AAGAGTTTAATTGAAACAAATAAA
9998 AAGAGTTTAATTGAAACAAATAAA
1 AAGAGTTTAATTGAAACAAATAAA
* *
10022 CAGAGTTTAACTGAAA
1 AAGAGTTTAATTGAAA
10038 GATTATTTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.25
Consensus pattern (24 bp):
AAGAGTTTAATTGAAACAAATAAA
Done.