Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005592.1 Kokia drynarioides strain JFW-HI SEQ_119720, 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: 55412
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 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
27 TATCAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:746 original size:18 final size:19
Alignment explanation
Indices: 711--757 Score: 87
Period size: 18 Copynumber: 2.5 Consensus size: 19
701 TGCATACAAC
711 TAAACTAACTATTGAAAAG
1 TAAACTAACTATTGAAAAG
730 TAAACTAACTA-TGAAAAG
1 TAAACTAACTATTGAAAAG
748 TAAACTAACT
1 TAAACTAACT
758 TAGTGTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.26
Consensus pattern (19 bp):
TAAACTAACTATTGAAAAG
Found at i:4184 original size:41 final size:41
Alignment explanation
Indices: 4127--4250 Score: 221
Period size: 41 Copynumber: 3.0 Consensus size: 41
4117 CTTGAACAAG
* *
4127 TATGGCTCATTCCAATGATACTTCGTAGCATCTCGAAGAAA
1 TATGGCTCATTCCAATGATACTTCGCAGCATCCCGAAGAAA
*
4168 TATGGCTCATTCCAATGATAGTTCGCAGCATCCCGAAGAAA
1 TATGGCTCATTCCAATGATACTTCGCAGCATCCCGAAGAAA
4209 TATGGCTCATTCCAATGATACTTCGCAGCATCCCGAAGAAA
1 TATGGCTCATTCCAATGATACTTCGCAGCATCCCGAAGAAA
4250 T
1 T
4251 CTGACCTTCT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 79 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
TATGGCTCATTCCAATGATACTTCGCAGCATCCCGAAGAAA
Found at i:18513 original size:27 final size:27
Alignment explanation
Indices: 18483--18591 Score: 218
Period size: 27 Copynumber: 4.0 Consensus size: 27
18473 TTGTCTAAGC
18483 ATTCAATCCATTGTAATGTCATTTCGT
1 ATTCAATCCATTGTAATGTCATTTCGT
18510 ATTCAATCCATTGTAATGTCATTTCGT
1 ATTCAATCCATTGTAATGTCATTTCGT
18537 ATTCAATCCATTGTAATGTCATTTCGT
1 ATTCAATCCATTGTAATGTCATTTCGT
18564 ATTCAATCCATTGTAATGTCATTTCGT
1 ATTCAATCCATTGTAATGTCATTTCGT
18591 A
1 A
18592 ACCTTGTATT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (27 bp):
ATTCAATCCATTGTAATGTCATTTCGT
Found at i:23507 original size:12 final size:12
Alignment explanation
Indices: 23477--23508 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
23467 TTCCTCAGCT
*
23477 TCTTTTCCTTCC
1 TCTTTTTCTTCC
23489 TCTTTTTCTTCC
1 TCTTTTTCTTCC
23501 TCTTTTTC
1 TCTTTTTC
23509 CACTTGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTTTTCTTCC
Found at i:33493 original size:24 final size:24
Alignment explanation
Indices: 33465--33539 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
33455 ATATACTAAT
* *
33465 TAACCATTCTAGGCTCATAAGTGC
1 TAACCATTCTGGGCTCATAAGAGC
33489 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* * *
33513 TAACCATCCTGGGCTCTTGAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
33537 TAA
1 TAA
33540 TGTTGTCTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:40887 original size:72 final size:72
Alignment explanation
Indices: 40811--40960 Score: 219
Period size: 72 Copynumber: 2.1 Consensus size: 72
40801 AATATAATCA
* *
40811 GTCACATGGCATGAAGAACATACCCACATATTCTCTGTCACATGACATGAAGAACATACCCATAT
1 GTCACATGGAATGAAGAACATACCCACATATTCTCTGTCACATGACATGAAGAACATAACCATAT
*
40876 ATTCTCT
66 ATTCACT
* * * * *
40883 GTCACATGGAATGAAGAACATACTCGCATATTTTCTGTCACATGGCATGAAGAACATAATCATAT
1 GTCACATGGAATGAAGAACATACCCACATATTCTCTGTCACATGACATGAAGAACATAACCATAT
40948 ATTCACT
66 ATTCACT
*
40955 TTCACA
1 GTCACA
40961 ATAGTCATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (72 bp):
GTCACATGGAATGAAGAACATACCCACATATTCTCTGTCACATGACATGAAGAACATAACCATAT
ATTCACT
Found at i:40960 original size:36 final size:36
Alignment explanation
Indices: 40811--40940 Score: 206
Period size: 36 Copynumber: 3.6 Consensus size: 36
40801 AATATAATCA
40811 GTCACATGGCATGAAGAACATACCCACATATTCTCT
1 GTCACATGGCATGAAGAACATACCCACATATTCTCT
* *
40847 GTCACATGACATGAAGAACATACCCATATATTCTCT
1 GTCACATGGCATGAAGAACATACCCACATATTCTCT
* * * *
40883 GTCACATGGAATGAAGAACATACTCGCATATTTTCT
1 GTCACATGGCATGAAGAACATACCCACATATTCTCT
40919 GTCACATGGCATGAAGAACATA
1 GTCACATGGCATGAAGAACATA
40941 ATCATATATT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 85 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (36 bp):
GTCACATGGCATGAAGAACATACCCACATATTCTCT
Found at i:41112 original size:69 final size:69
Alignment explanation
Indices: 41030--41266 Score: 332
Period size: 69 Copynumber: 3.4 Consensus size: 69
41020 ATCTCAATTC
* * * * * *
41030 TTTAAGCACAAATCATATTAATATTTAATC-CAAAATCATATTAATGTTTAAGCACAAATCAAAT
1 TTTAAGCATAAATCACATTAATATTTAAGCAC-AAATCATATTAATATTTAAGCAAAAATCACAT
41094 TAATA
65 TAATA
* ** *
41099 TTTAAGCATAAATCACATTAATATTTGAGCACAAGCCATATTAATATTTAAGCATAAATCACATT
1 TTTAAGCATAAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCAAAAATCACATT
41164 AATA
66 AATA
*
41168 TTTAAGCATAAATCACATTAATATTTGAGCACAAATCATATTAATATTTAAGCAAAAATCACATT
1 TTTAAGCATAAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCAAAAATCACATT
41233 AATA
66 AATA
* * *
41237 CTTAAGCATAAATTAAATTAATATTTAAGC
1 TTTAAGCATAAATCACATTAATATTTAAGC
41267 TTAAATTCAT
Statistics
Matches: 151, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
69 150 0.99
70 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (69 bp):
TTTAAGCATAAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCAAAAATCACATT
AATA
Found at i:41273 original size:23 final size:23
Alignment explanation
Indices: 41030--41272 Score: 290
Period size: 23 Copynumber: 10.6 Consensus size: 23
41020 ATCTCAATTC
* *
41030 TTTAAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
41053 TTTAATCCA-AAATCATATTAATG
1 TTTAA-GCATAAATCACATTAATA
* *
41076 TTTAAGCACAAATCAAATTAATA
1 TTTAAGCATAAATCACATTAATA
41099 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * ** *
41122 TTTGAGCACAAGCCATATTAATA
1 TTTAAGCATAAATCACATTAATA
41145 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
41168 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
41191 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
41214 TTTAAGCAAAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
41237 CTTAAGCATAAATTAAATTAATA
1 TTTAAGCATAAATCACATTAATA
*
41260 TTTAAGCTTAAAT
1 TTTAAGCATAAAT
41273 TCATTAAAAC
Statistics
Matches: 189, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
22 2 0.01
23 185 0.98
24 2 0.01
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.35
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:43722 original size:41 final size:43
Alignment explanation
Indices: 43602--43723 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 43
43592 GAACCACTTG
* * * * *
43602 ATGTATAAATGGAAGACTCATATCTCGGGATGAGCGTGAGATT
1 ATGTATAAATGGAAGACTCATGTCTCGGAAAGAGCATGAGACT
* * *
43645 ATGTATAAATGGAAGACTCTTGACTCGGAAAAAGCATGAGACT
1 ATGTATAAATGGAAGACTCATGTCTCGGAAAGAGCATGAGACT
* *
43688 ATGT-TAAA-GGAAGACACATGTCTCGGAAGGAGCATG
1 ATGTATAAATGGAAGACTCATGTCTCGGAAAGAGCATG
43724 GGGAGACTCA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
41 23 0.35
42 4 0.06
43 39 0.59
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (43 bp):
ATGTATAAATGGAAGACTCATGTCTCGGAAAGAGCATGAGACT
Found at i:44396 original size:24 final size:24
Alignment explanation
Indices: 44364--44414 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
44354 AACTTGAGTT
44364 GTATCGGTAGTTCTATTCATAGAA
1 GTATCGGTAGTTCTATTCATAGAA
44388 GTATCGGTAGTTCTATTCATAGAA
1 GTATCGGTAGTTCTATTCATAGAA
44412 GTA
1 GTA
44415 CTAGTAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (24 bp):
GTATCGGTAGTTCTATTCATAGAA
Found at i:44421 original size:24 final size:24
Alignment explanation
Indices: 44364--44422 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
44354 AACTTGAGTT
*
44364 GTATCGGTAGTTCTATTCATAGAA
1 GTATCAGTAGTTCTATTCATAGAA
*
44388 GTATCGGTAGTTCTATTCATAGAA
1 GTATCAGTAGTTCTATTCATAGAA
44412 GTA-CTAGTAGT
1 GTATC-AGTAGT
44423 CTGATTGCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (24 bp):
GTATCAGTAGTTCTATTCATAGAA
Found at i:44535 original size:21 final size:21
Alignment explanation
Indices: 44483--44536 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
44473 AGAGTTTCTA
*
44483 GTATCGGTAAAAGCATGACTT
1 GTATCGGTAGAAGCATGACTT
* *
44504 GTATCGATAGAAGTTAT-ACTT
1 GTATCGGTAGAAG-CATGACTT
44525 GTATCGGTAGAA
1 GTATCGGTAGAA
44537 TTAGCACAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACTT
Found at i:50887 original size:41 final size:40
Alignment explanation
Indices: 50799--50996 Score: 184
Period size: 41 Copynumber: 4.8 Consensus size: 40
50789 GGGATAAGCG
* * **
50799 TGAGATTATGTATAAATGGAATACTTGTGACTCGGAAAGAGCA
1 TGAGACTATGT-TAAA-GGAAGACTCATGACTC-GAAAGAGCA
*
50842 TGAGACTATGTTAAAGGAAGACTCATGTCTCGAAAGGAGCA
1 TGAGACTATGTTAAAGGAAGACTCATGACTCGAAA-GAGCA
*
50883 TGAGACTATGTTAAAGGAAGACTCATGACTCAGAAAGAGCG
1 TGAGACTATGTTAAAGGAAGACTCATGACTC-GAAAGAGCA
* * * * *
50924 TGGGATTATGTTTAAAGGAAGACTTATGTCT-TAATAGAGCA
1 TGAGACTATG-TTAAAGGAAGACTCATGACTCGAA-AGAGCA
* * *
50965 TAAGATTAT-TTGAAAGGAAGACTTATGACTCG
1 TGAGACTATGTT-AAAGGAAGACTCATGACTCG
50997 GTGTAGAATA
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 2 0.02
40 23 0.17
41 71 0.54
42 26 0.20
43 10 0.08
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (40 bp):
TGAGACTATGTTAAAGGAAGACTCATGACTCGAAAGAGCA
Found at i:50964 original size:82 final size:82
Alignment explanation
Indices: 50799--50995 Score: 229
Period size: 82 Copynumber: 2.4 Consensus size: 82
50789 GGGATAAGCG
* * *
50799 TGAGATTATGTATAAATGGAATACTTGTGACTCGGAAAGAGCATGAGACTATGTTAAAGGAAGAC
1 TGAGATTATGT-TAAA-GGAAGACTTATGACTCAGAAAGAGCATGAGACTATGTTAAAGGAAGAC
50864 TCATGTCTCGAAAGGAGCA
64 TCATGTCTCGAAAGGAGCA
* * * * *
50883 TGAGACTATGTTAAAGGAAGACTCATGACTCAGAAAGAGCGTGGGATTATGTTTAAAGGAAGACT
1 TGAGATTATGTTAAAGGAAGACTTATGACTCAGAAAGAGCATGAGACTATG-TTAAAGGAAGACT
* *
50948 TATGTCT-TAATA-GAGCA
65 CATGTCTCGAA-AGGAGCA
*
50965 TAAGATTAT-TTGAAAGGAAGACTTATGACTC
1 TGAGATTATGTT-AAAGGAAGACTTATGACTC
50996 GGTGTAGAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
81 2 0.02
82 61 0.63
83 24 0.25
84 10 0.10
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (82 bp):
TGAGATTATGTTAAAGGAAGACTTATGACTCAGAAAGAGCATGAGACTATGTTAAAGGAAGACTC
ATGTCTCGAAAGGAGCA
Found at i:51559 original size:24 final size:24
Alignment explanation
Indices: 51532--51590 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
51522 GACTTGAGTT
* * *
51532 GTATCGGTAGTTTTGTTCATAGAA
1 GTATCGGTAGTTCTATTCATAAAA
*
51556 GTATCAGTAGTTCTATTCATAAAA
1 GTATCGGTAGTTCTATTCATAAAA
51580 GTATCGGTAGT
1 GTATCGGTAGT
51591 CTGAATGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTCTATTCATAAAA
Done.