Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014394.1 Kokia drynarioides strain JFW-HI SEQ_129432, 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: 55161
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:634 original size:38 final size:38
Alignment explanation
Indices: 583--658 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
573 AATATAAGAA
583 TTGCTTTACAATAAGCATGTAATTTTATTTGCATCAAG
1 TTGCTTTACAATAAGCATGTAATTTTATTTGCATCAAG
621 TTGCTTTACAATAAGCATGTAATTTTATTTGCATCAAG
1 TTGCTTTACAATAAGCATGTAATTTTATTTGCATCAAG
659 CCAACATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (38 bp):
TTGCTTTACAATAAGCATGTAATTTTATTTGCATCAAG
Found at i:1934 original size:47 final size:47
Alignment explanation
Indices: 1880--1975 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
1870 ATGTAGTGTA
1880 ATCGCCTTAGTGAATACCTATTGAGAGATGACTATAAGAATGATCCC
1 ATCGCCTTAGTGAATACCTATTGAGAGATGACTATAAGAATGATCCC
1927 ATCGCCTTAGTGAATACCTATTGAGAGATGACTATAAGAATGATCCC
1 ATCGCCTTAGTGAATACCTATTGAGAGATGACTATAAGAATGATCCC
1974 AT
1 AT
1976 TTCTCCATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (47 bp):
ATCGCCTTAGTGAATACCTATTGAGAGATGACTATAAGAATGATCCC
Found at i:2975 original size:17 final size:17
Alignment explanation
Indices: 2916--2975 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2906 AAATGGATGT
2916 TCAACCTTCCATCTTCC
1 TCAACCTTCCATCTTCC
* *
2933 TTAACCTCTCC-T-TGACC
1 TCAACCT-TCCATCT-TCC
*
2950 TTTAACCTTCCATCTTCC
1 -TCAACCTTCCATCTTCC
2968 TCAACCTT
1 TCAACCTT
2976 TCATATTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 1 0.03
17 19 0.56
18 13 0.38
19 1 0.03
ACGTcount: A:0.18, C:0.42, G:0.02, T:0.38
Consensus pattern (17 bp):
TCAACCTTCCATCTTCC
Found at i:5543 original size:15 final size:15
Alignment explanation
Indices: 5514--5580 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
5504 GCTACATTTC
*
5514 AAACATAAGTAACTA
1 AAACGTAAGTAACTA
* *
5529 AAATGTAAGTGACTA
1 AAACGTAAGTAACTA
* * *
5544 AAACGTAA-CAATTC
1 AAACGTAAGTAACTA
*
5558 AAACATAAGTAACTA
1 AAACGTAAGTAACTA
*
5573 AAATGTAA
1 AAACGTAA
5581 TATGAGATAA
Statistics
Matches: 37, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
14 9 0.24
15 28 0.76
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.22
Consensus pattern (15 bp):
AAACGTAAGTAACTA
Found at i:5559 original size:44 final size:44
Alignment explanation
Indices: 5494--5580 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
5484 AACGGCTCAA
* *
5494 TGACTAAAATGCTACATTTCAAACATAAGTAACTAAAATGTAAG
1 TGACTAAAACGCTACAATTCAAACATAAGTAACTAAAATGTAAG
5538 TGACTAAAACG-TAACAATTCAAACATAAGTAACTAAAATGTAA
1 TGACTAAAACGCT-ACAATTCAAACATAAGTAACTAAAATGTAA
5581 TATGAGATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (44 bp):
TGACTAAAACGCTACAATTCAAACATAAGTAACTAAAATGTAAG
Found at i:6140 original size:26 final size:27
Alignment explanation
Indices: 6102--6159 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
6092 TTAGGCCCGC
* *
6102 TTATATTATTTTTATTTTTTAA-AATAT
1 TTATATTATTTTTAATATTTAATAAT-T
*
6129 TTATTTTA-TTTTAATATTTAATAATT
1 TTATATTATTTTTAATATTTAATAATT
6155 TTATA
1 TTATA
6160 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATATTATTTTTAATATTTAATAATT
Found at i:6597 original size:11 final size:11
Alignment explanation
Indices: 6581--6606 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6571 ATACATCTTA
6581 ATTAATAAAAT
1 ATTAATAAAAT
6592 ATTAATAAAAT
1 ATTAATAAAAT
6603 ATTA
1 ATTA
6607 TAATATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAATAAAAT
Found at i:21448 original size:20 final size:20
Alignment explanation
Indices: 21423--21460 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
21413 ATTATTTTAG
21423 AATTTGTATAATTTTTTATA
1 AATTTGTATAATTTTTTATA
21443 AATTTGTATAATTTTTTA
1 AATTTGTATAATTTTTTA
21461 AAAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTGTATAATTTTTTATA
Found at i:21478 original size:22 final size:23
Alignment explanation
Indices: 21442--21484 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
21432 AATTTTTTAT
*
21442 AAATTTGTATAATTTTTTAAAAA
1 AAATTTATATAATTTTTTAAAAA
21465 AAATTTATAT-ATTTTTTAAA
1 AAATTTATATAATTTTTTAAA
21485 TAATACTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTTATATAATTTTTTAAAAA
Found at i:31927 original size:14 final size:14
Alignment explanation
Indices: 31908--31953 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
31898 TCCTAAATTC
*
31908 TCAATCTTCAATCT
1 TCAATCCTCAATCT
* *
31922 TCAATCCCCAATTT
1 TCAATCCTCAATCT
*
31936 TCAATCCTCAATCC
1 TCAATCCTCAATCT
31950 TCAA
1 TCAA
31954 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (14 bp):
TCAATCCTCAATCT
Found at i:31933 original size:21 final size:21
Alignment explanation
Indices: 31909--31949 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31899 CCTAAATTCT
*
31909 CAATCTTCAATCTTCAATCCC
1 CAATCTTCAATCCTCAATCCC
*
31930 CAATTTTCAATCCTCAATCC
1 CAATCTTCAATCCTCAATCC
31950 TCAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (21 bp):
CAATCTTCAATCCTCAATCCC
Found at i:34528 original size:33 final size:34
Alignment explanation
Indices: 34463--34540 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
34453 TCATCCTTTT
*
34463 TATAAATATTATTATTTCTTAAAATATAAAATTCA
1 TATAAAT-TTATTATTTCTAAAAATATAAAATTCA
*
34498 TATATAATTTATTATTT-TAAAAATAT-AAATTTA
1 TATA-AATTTATTATTTCTAAAAATATAAAATTCA
34531 TATACAATTT
1 TATA-AATTT
34541 TTTTCATCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 15 0.38
34 8 0.21
35 13 0.33
36 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (34 bp):
TATAAATTTATTATTTCTAAAAATATAAAATTCA
Found at i:51066 original size:40 final size:41
Alignment explanation
Indices: 51003--51084 Score: 123
Period size: 40 Copynumber: 2.0 Consensus size: 41
50993 ATCTGACACA
* *
51003 TTGCAGTGTTTATAGTTTCACTGCCAGTTCAGT-GATATTC
1 TTGCAGTGTTTACAGTTTCACTGCCAGTTCAGTAAATATTC
51043 TTGCAGTGTTTACAGTGTT-ACTGCCAGTTCAGTAAATATTC
1 TTGCAGTGTTTACAGT-TTCACTGCCAGTTCAGTAAATATTC
51084 T
1 T
51085 CAAATGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 29 0.76
41 9 0.24
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (41 bp):
TTGCAGTGTTTACAGTTTCACTGCCAGTTCAGTAAATATTC
Found at i:51404 original size:17 final size:17
Alignment explanation
Indices: 51374--51465 Score: 98
Period size: 17 Copynumber: 5.5 Consensus size: 17
51364 CAAGTCCAAC
*
51374 TTTT-AATTTTAATTTA
1 TTTTAAATTTAAATTTA
*
51390 TTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
*
51407 TTTTTAAATTTAAATTCA
1 -TTTTAAATTTAAATTTA
* *
51425 -TTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
* *
51441 CTTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
51458 TTTTAAAT
1 TTTTAAAT
51466 GAAAATTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
16 17 0.27
17 31 0.49
18 15 0.24
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:51592 original size:15 final size:15
Alignment explanation
Indices: 51574--51608 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51564 AAACAAAAGG
51574 CCCAATTACAAATAA
1 CCCAATTACAAATAA
**
51589 CCCAATTACACTTAA
1 CCCAATTACAAATAA
51604 CCCAA
1 CCCAA
51609 ACCCTCAGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
CCCAATTACAAATAA
Done.