Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010619.1 Kokia drynarioides strain JFW-HI SEQ_125552, 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: 8939
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:505 original size:83 final size:82
Alignment explanation
Indices: 366--532 Score: 316
Period size: 83 Copynumber: 2.0 Consensus size: 82
356 CTGAAGCCGG
366 AGCTTGGCCGGCCACCGAGGGGATTTGAGAGAAAACAGAAAGGAGGGTTTTCATTTTTCTGAAAT
1 AGCTTGGCCGGCCACCGAGGGGATTTGAGAGAAAACAGAAAGGAGGGTTTTCATTTTTCTGAAAT
431 TTGAAAAAAAGGAAGAA
66 TTGAAAAAAAGGAAGAA
*
448 NAGCTTGGCCGGCCACCGAGGGGATTTGAGAGAAAACAGAAAGGGGGGTTTTCATTTTTCTGAAA
1 -AGCTTGGCCGGCCACCGAGGGGATTTGAGAGAAAACAGAAAGGAGGGTTTTCATTTTTCTGAAA
513 TTTGAAAAAAAGGAAGAA
65 TTTGAAAAAAAGGAAGAA
531 AG
1 AG
533 AGCTTTTTTT
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 2 0.02
83 81 0.98
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (82 bp):
AGCTTGGCCGGCCACCGAGGGGATTTGAGAGAAAACAGAAAGGAGGGTTTTCATTTTTCTGAAAT
TTGAAAAAAAGGAAGAA
Found at i:1070 original size:30 final size:29
Alignment explanation
Indices: 1036--1439 Score: 314
Period size: 29 Copynumber: 13.8 Consensus size: 29
1026 GGAGGTCCTT
1036 AAACTTTCCAAAAATTACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* *
1066 AAACTTCCAAAAA-TCCCATTTTTGA-CCTC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* * *
1095 GAACATTCTAAAAATTACCATTTTATCCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* *
1125 GAACTTCCAAAAA-TCCCATTTTTGA-CCCC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
*
1154 AAACTTTCCAAAAAATACCATTTTACCCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCC
* * *
1184 TAATTTCCAAAAA-TCCCATCTTTGA-CCCC
1 AAACTTCCAAAAATTACCAT-TTT-ACCCCC
*
1213 GAACTTTCCAAAAAGTTACCATTTTACCCCC
1 AAAC-TTCCAAAAA-TTACCATTTTACCCCC
* * **
1244 AAA----CAAAAA-TCCCATTTTTGACTCTG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
*
1270 AAACCTTCAAAAAATTACCATTTTACCCCC
1 AAA-CTTCCAAAAATTACCATTTTACCCCC
*
1300 AAACTTCCAAAAATT-CCATTTTTGACCCAC
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
*
1330 AAACTTCCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* * *
1359 AAACTTCCAAAAA-TCCCATTTTTGACTCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCC
* *
1389 AACCTTCCAAAAATTACCATTTTACTCCC
1 AAACTTCCAAAAATTACCATTTTACCCCC
* *
1418 GAACTTCCAAAAA-TCCCATTTT
1 AAACTTCCAAAAATTACCATTTT
1440 TGACCCTAAA
Statistics
Matches: 305, Mismatches: 39, Indels: 62
0.75 0.10 0.15
Matches are distributed among these distances:
24 4 0.01
25 4 0.01
26 12 0.04
28 28 0.09
29 111 0.36
30 104 0.34
31 33 0.11
32 9 0.03
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCC
Found at i:1458 original size:59 final size:57
Alignment explanation
Indices: 1036--1472 Score: 524
Period size: 59 Copynumber: 7.5 Consensus size: 57
1026 GGAGGTCCTT
1036 AAACTTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTC
1 AAAC-TTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACC-C
* * * *
1095 GAACATTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCC
* * * *
1154 AAACTTTCCAAAAAATACCATTTTACCCCCTAATTTCCAAAAATCCCATCTTTGACCCC
1 AAAC-TTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CCC
* *
1213 GAACTTTCCAAAAAGTTACCATTTTACCCCCAAA----CAAAAATCCCATTTTTGACTCTG
1 AAAC-TTCCAAAAA-TTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC-C-C
* *
1270 AAACCTTCAAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCAC
1 AAA-CTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA-CC-C
*
1330 AAACTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACTCC
1 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC-CC
* * *
1388 GAACCTTCCAAAAATTACCATTTTACTCCCGAACTTCCAAAAATCCCATTTTTGACCC
1 -AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCC
* *
1446 TAAATCTACC-AAAATTACCCTTTTACC
1 -AAA-CTTCCAAAAATTACCATTTTACC
1473 TCCGAATGCT
Statistics
Matches: 330, Mismatches: 35, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
55 1 0.00
56 37 0.11
57 10 0.03
58 22 0.07
59 219 0.66
60 40 0.12
61 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.30
Consensus pattern (57 bp):
AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCC
Found at i:2610 original size:22 final size:22
Alignment explanation
Indices: 2585--2638 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
2575 TAAAATTTTG
**
2585 ATTTAATTTTTTAAAAATTACA
1 ATTTAATTTAGTAAAAATTACA
*
2607 ATTTTATTATAGTAAAAATTACA
1 ATTTAATT-TAGTAAAAATTACA
*
2630 TTTTAATTT
1 ATTTAATTT
2639 CAACGTGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTTAATTTAGTAAAAATTACA
Found at i:3545 original size:14 final size:14
Alignment explanation
Indices: 3511--3573 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
3501 AACTAGAATA
* *
3511 AATATAAGATTATT
1 AATATAATATTAAT
* *
3525 AACATAATACTAAT
1 AATATAATATTAAT
3539 AATATAATATTAAT
1 AATATAATATTAAT
* *
3553 AAAATGATATTAAT
1 AATATAATATTAAT
3567 AATATAA
1 AATATAA
3574 CTACACCTAC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (14 bp):
AATATAATATTAAT
Found at i:3550 original size:28 final size:28
Alignment explanation
Indices: 3511--3573 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3501 AACTAGAATA
* *
3511 AATATAAGATTATTAACATAATACTAAT
1 AATATAAGATTAATAAAATAATACTAAT
* * *
3539 AATATAATATTAATAAAATGATATTAAT
1 AATATAAGATTAATAAAATAATACTAAT
3567 AATATAA
1 AATATAA
3574 CTACACCTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (28 bp):
AATATAAGATTAATAAAATAATACTAAT
Found at i:4563 original size:96 final size:96
Alignment explanation
Indices: 4396--4570 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 96
4386 TTTGATTATC
** * *
4396 TCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGATAAGAAA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCGAAGATAAGAAA
4461 ACATTGCCTCGATTAAGGGTATTCGATTACT
66 ACATTGCCTCGATTAAGGGTATTCGATTACT
*
4492 TCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCGAA-ATAA-A
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAA-CCGAAGATAAGA
*
4554 AGAATATTGCCTCGATT
64 A-AACATTGCCTCGATT
4571 TTAAAGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
95 3 0.04
96 63 0.90
97 4 0.06
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCGAAGATAAGAAA
ACATTGCCTCGATTAAGGGTATTCGATTACT
Found at i:4857 original size:30 final size:29
Alignment explanation
Indices: 4801--5332 Score: 532
Period size: 30 Copynumber: 18.0 Consensus size: 29
4791 TGGATGCACG
* * *
4801 GGGGCAAAATGGTAGTTTTGGGGAAGGTTC
1 GGGGTAAAATGGTAATTTT-TGGAAGGTTC
* * *
4831 GGAGTCAAAAATGGGAA-TTTGGGAAGGTTC
1 GGGGT--AAAATGGTAATTTTTGGAAGGTTC
* ** *
4861 GAGAAAAAATGG-GATTTTTGGAA-GTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
4888 ACGGGTAAAATGGTAATTTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
4918 GGGGTTAAAAAT-G-AGATTTTTGGAAGTTTG
1 GGGG-T-AAAATGGTA-ATTTTTGGAAGGTTC
*
4948 GGGGTAAAATGGTAATTTTTAGAAGGTTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
4977 GGGGTTAAAAATGG-GATTTTTGGAA-GTTT
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
5006 GAGGGTAAAATGGTAATTTTTGGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
5036 GGGGTTAAAAATGGT-ATTTTTGGAA-GTTC
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
5065 GAGGGTAAAATGGTAATTTTTGGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
* *
5095 AAGGGTAAAATGTTAATTTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
*
5125 GGGGTTAAAAATGG-GATTTTTGGAA-GTTC
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
*
5154 GAGGGTAAAATGGTAATTTTTGGATGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
5184 GAGGGTAAAATGGTAATTTTTGGAAGGTTC
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTC
* * *
5214 GGGGTTAAAAATGG-GATTTTTGGAAGTTTA
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTC
*
5244 GGGGTAAAATGGTAATTTTTGGAAGGTTT
1 GGGGTAAAATGGTAATTTTTGGAAGGTTC
* *
5273 GGGGTTTAAAATGGGATTTTTTGGAA-GTTC
1 GGGG--TAAAATGGTAATTTTTGGAAGGTTC
5303 GGGGGTAAAATGGTAATTTTTGGAAGGTTC
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTC
5333 ACGGTTAAAA
Statistics
Matches: 423, Mismatches: 45, Indels: 68
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.01
28 56 0.13
29 123 0.29
30 173 0.41
31 58 0.14
32 8 0.02
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTC
Found at i:4936 original size:59 final size:59
Alignment explanation
Indices: 4865--5353 Score: 629
Period size: 59 Copynumber: 8.3 Consensus size: 59
4855 AGGTTCGAGA
*
4865 AAAAATGGGATTTTTGGAAGTTCACGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
* ** *
4924 AAAAATGAGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
*
4983 AAAAATGGGATTTTTGGAAGTT-TGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCAG-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
* *
5042 AAAAATGGTATTTTTGGAAGTTC-GAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGG-T
1 AAAAATGGGATTTTTGGAAGTTCAG-GGGTAAAATGGTAATTTTTGGAAGGTTC-GGGGTT
** *
5101 -AAAATGTTAATTTTTGGAAGGTTC-GGGGTTAAAAATGG-GATTTTTGGAA-GTTCGAGGG-T
1 AAAAATG-GGATTTTTGGAA-GTTCAGGGG-T-AAAATGGTAATTTTTGGAAGGTTCG-GGGTT
* *
5160 -AAAATGGTAATTTTTGGATGGTTC-GAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
1 AAAAATGG-GATTTTTGGA-AGTTCAG-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
* *
5220 AAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
* * **
5279 TAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCACGGTT
1 AAAAATGGGA-TTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
5339 AAAAATGGGATTTTT
1 AAAAATGGGATTTTT
5354 TAAAGTTTAG
Statistics
Matches: 385, Mismatches: 28, Indels: 34
0.86 0.06 0.08
Matches are distributed among these distances:
58 14 0.04
59 266 0.69
60 91 0.24
61 14 0.04
ACGTcount: A:0.29, C:0.03, G:0.32, T:0.36
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
Found at i:5055 original size:89 final size:89
Alignment explanation
Indices: 4801--5332 Score: 576
Period size: 89 Copynumber: 6.0 Consensus size: 89
4791 TGGATGCACG
* * * * * * *
4801 GGGGCAAAATGGTAGTTTTGGGGAAGGTTCG-GAGTCAAAAATGGGAA-TTTGGGAAGGTTC-GA
1 GGGGTAAAATGGTAATTTT-TGGAAGGTTCGAGGGT--AAAATGGTAATTTTTGGAAGGTTCGGG
* *
4863 G-AAAAAATGGGATTTTTGGAA-GTTC
63 GTTAAAAATGGTATTTTTGGAAGGTTC
* *
4888 ACGGGTAAAATGGTAATTTTTGGAAGGTTCG-GGGTTAAAAAT-G-AGATTTTTGGAA-GTTTGG
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGG-T-AAAATGGTA-ATTTTTGGAAGGTTCGG
* *
4949 GGGT-AAAATGGTAATTTTTAGAAGGTTC
62 GGTTAAAAATGGT-ATTTTTGGAAGGTTC
* *
4977 GGGGTTAAAAATGG-GATTTTTGGAA-GTTTGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGG
1 GGGG-T-AAAATGGTAATTTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGG
5040 TTAAAAATGGTATTTTTGGAA-GTTC
64 TTAAAAATGGTATTTTTGGAAGGTTC
* *
5065 GAGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGGTAAAATGTTAATTTTTGGAAGGTTCGGGGT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT
*
5130 TAAAAATGGGATTTTTGGAA-GTTC
65 TAAAAATGGTATTTTTGGAAGGTTC
*
5154 GAGGGTAAAATGGTAATTTTTGGATGGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT
1 G-GGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT
* * *
5219 TAAAAATGGGATTTTTGGAAGTTTA
65 TAAAAATGGTATTTTTGGAAGGTTC
* * *
5244 GGGGTAAAATGGTAATTTTTGGAAGGTTTG-GGGTTTAAAATGGGATTTTTTGGAA-GTTCGGGG
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGG--TAAAATGGTAATTTTTGGAAGGTTCGGGG
*
5307 GT-AAAATGGTAATTTTTGGAAGGTTC
64 TTAAAAATGGT-ATTTTTGGAAGGTTC
5333 ACGGTTAAAA
Statistics
Matches: 388, Mismatches: 35, Indels: 41
0.84 0.08 0.09
Matches are distributed among these distances:
85 1 0.00
86 5 0.01
87 46 0.12
88 71 0.18
89 229 0.59
90 36 0.09
ACGTcount: A:0.29, C:0.03, G:0.33, T:0.34
Consensus pattern (89 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT
AAAAATGGTATTTTTGGAAGGTTC
Found at i:6422 original size:12 final size:12
Alignment explanation
Indices: 6389--6431 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
6379 TCGAATGCCT
6389 TTTTTATTATTAA
1 TTTTTATTATT-A
*
6402 TTATTATTATTA
1 TTTTTATTATTA
6414 TTTTTATTATTA
1 TTTTTATTATTA
6426 TTTTTA
1 TTTTTA
6432 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:6446 original size:3 final size:3
Alignment explanation
Indices: 6392--6427 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
6382 AATGCCTTTT
*
6392 TTA TTA TTAA TTA TTA TTA TTA TTT TTA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT
6428 TTTAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.