Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008908.1 Kokia drynarioides strain JFW-HI SEQ_123597, 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: 96854
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:434 original size:26 final size:26
Alignment explanation
Indices: 405--458 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
395 GCAATGAAGT
*
405 TTAAGGTTTTGAAGTGTCAGTTTAAC
1 TTAAGGTTTTGAAGTATCAGTTTAAC
*
431 TTAAGGTTTTGCAGTATCAGTTTAAC
1 TTAAGGTTTTGAAGTATCAGTTTAAC
457 TT
1 TT
459 GAGTGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.44
Consensus pattern (26 bp):
TTAAGGTTTTGAAGTATCAGTTTAAC
Found at i:1343 original size:21 final size:22
Alignment explanation
Indices: 1319--1359 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1309 AAAAAAAAAA
*
1319 AAAACTAAG-TATCAAATTGGT
1 AAAACTAAGTTACCAAATTGGT
*
1340 AAAACTCAGTTACCAAATTG
1 AAAACTAAGTTACCAAATTG
1360 AACATTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (22 bp):
AAAACTAAGTTACCAAATTGGT
Found at i:3911 original size:3 final size:3
Alignment explanation
Indices: 3905--3930 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3895 GTTGTTGTTG
3905 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3931 CTTGTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5674 original size:30 final size:30
Alignment explanation
Indices: 5640--5715 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
5630 CTCTCATTTA
*
5640 TTTTCCCCAAAAACTTCAAAACTCTTTCAC
1 TTTTCCCCTAAAACTTCAAAACTCTTTCAC
** **
5670 TTTTCCCCTAAAACTTTTACTCTCTTTCAC
1 TTTTCCCCTAAAACTTCAAAACTCTTTCAC
5700 TTTTCCCCTAAAACTT
1 TTTTCCCCTAAAACTT
5716 TTACTTCCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCTAAAACTTCAAAACTCTTTCAC
Found at i:5716 original size:30 final size:30
Alignment explanation
Indices: 5661--5720 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5651 AACTTCAAAA
5661 CTCTTTCACTTTTCCCCTAAAACTTTTACT
1 CTCTTTCACTTTTCCCCTAAAACTTTTACT
5691 CTCTTTCACTTTTCCCCTAAAACTTTTACT
1 CTCTTTCACTTTTCCCCTAAAACTTTTACT
5721 TCCCTCCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (30 bp):
CTCTTTCACTTTTCCCCTAAAACTTTTACT
Found at i:10429 original size:2 final size:2
Alignment explanation
Indices: 10422--10475 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
10412 TGGATCTCAT
**
10422 CA CA CA CA TG CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10464 CA CA CA CA CA CA
1 CA CA CA CA CA CA
10476 TATATATCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.48, G:0.02, T:0.02
Consensus pattern (2 bp):
CA
Found at i:25104 original size:22 final size:22
Alignment explanation
Indices: 25057--25105 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
25047 ACCACTTATA
*
25057 CAAA-TTTTCAATTTAATAATT
1 CAAATTTTTCAATTCAATAATT
*
25078 AAAATTTTTCAATTCAA-AATT
1 CAAATTTTTCAATTCAATAATT
25099 CCAAATT
1 -CAAATT
25106 AAATTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (22 bp):
CAAATTTTTCAATTCAATAATT
Found at i:29270 original size:9 final size:9
Alignment explanation
Indices: 29256--29280 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29246 TAGCAATTAA
29256 CTTTTACTC
1 CTTTTACTC
29265 CTTTTACTC
1 CTTTTACTC
29274 CTTTTAC
1 CTTTTAC
29281 AATTTACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (9 bp):
CTTTTACTC
Found at i:43851 original size:133 final size:133
Alignment explanation
Indices: 43613--43904 Score: 566
Period size: 133 Copynumber: 2.2 Consensus size: 133
43603 AAAATAGTAG
**
43613 GGGTAAAACTATAATTTCCCAAAAAGGACTAAATTGTGTTGGATGACTAAATTATGTAATTTAAT
1 GGGTAAAACTGCAATTTCCCAAAAAGGACTAAATTGTGTTGGATGACTAAATTATGTAATTTAAT
43678 GTGAAAATTGAATGAGTTGTGAATGTAGATTACGATTGTACTACCGACCGTGGAAAAGGGAAATT
66 GTGAAAATTGAATGAGTTGTGAATGTAGATTACGATTGTACTACCGACCGTGGAAAAGGGAAATT
43743 AAC
131 AAC
43746 GGGTAAAACTGCAATTTCCCAAAAAGGACTAAATTGTGTTGGATGACTAAATTATGTAATTTAAT
1 GGGTAAAACTGCAATTTCCCAAAAAGGACTAAATTGTGTTGGATGACTAAATTATGTAATTTAAT
43811 GTGAAAATTGAATGAGTTGTGAATGTAGATTACGATTGTACTACCGACCGTGGAAAAGGGAAATT
66 GTGAAAATTGAATGAGTTGTGAATGTAGATTACGATTGTACTACCGACCGTGGAAAAGGGAAATT
43876 AAC
131 AAC
43879 GGGTAAAACTGCAATTTCCCAAAAAG
1 GGGTAAAACTGCAATTTCCCAAAAAG
43905 TCTTTCCAAA
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 157 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (133 bp):
GGGTAAAACTGCAATTTCCCAAAAAGGACTAAATTGTGTTGGATGACTAAATTATGTAATTTAAT
GTGAAAATTGAATGAGTTGTGAATGTAGATTACGATTGTACTACCGACCGTGGAAAAGGGAAATT
AAC
Found at i:62514 original size:16 final size:16
Alignment explanation
Indices: 62493--62540 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
62483 ATCGAGCAAC
62493 TTCAAGAAGACGTGTA
1 TTCAAGAAGACGTGTA
62509 TTCAAGAAGACGTGTA
1 TTCAAGAAGACGTGTA
62525 TTCAAGAAGACGTGTA
1 TTCAAGAAGACGTGTA
62541 GTCGGAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (16 bp):
TTCAAGAAGACGTGTA
Found at i:66683 original size:24 final size:24
Alignment explanation
Indices: 66651--66701 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
66641 CATGTTTGTG
66651 ATTAGCACTTTGGTGC-TTGTGATT
1 ATTAGCACTTTGGTGCTTTGTG-TT
*
66675 ATTAGCACTTTTGTGCTTTGTGTT
1 ATTAGCACTTTGGTGCTTTGTGTT
66699 ATT
1 ATT
66702 TTGTGTATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.16, C:0.12, G:0.22, T:0.51
Consensus pattern (24 bp):
ATTAGCACTTTGGTGCTTTGTGTT
Found at i:72463 original size:23 final size:23
Alignment explanation
Indices: 72426--72819 Score: 409
Period size: 23 Copynumber: 17.2 Consensus size: 23
72416 AATTCTTTGC
72426 GCACAAATCACATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* * * *
72449 TCATAAATCATATTAATATTTGA
1 GCACAAATCACATTAATATTTAA
* *
72472 -CTACAAATCATACTAATATTTAA
1 GC-ACAAATCACATTAATATTTAA
72495 GCACAAATCACATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* * *
72518 TCATAAATCATATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
*
72541 GCGCAAATCACATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
72564 GCACAAATCACATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* * *
72587 GTATAAATCACATTAATATTTGA
1 GCACAAATCACATTAATATTTAA
**
72610 GCACAAATCATTTTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* * *
72633 GTATAAATCACATTAATATTTGA
1 GCACAAATCACATTAATATTTAA
**
72656 GCACAAATCATTTTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* ** *
72679 GTATGAATCACATTAATACTTAA
1 GCACAAATCACATTAATATTTAA
72702 GCACAAATCACATTAATATTTAA
1 GCACAAATCACATTAATATTTAA
* * * *
72725 TCATAAATCATATTATTATTTAA
1 GCACAAATCACATTAATATTTAA
* ** *
72748 GCATAAATTGCATTAATACTTAA
1 GCACAAATCACATTAATATTTAA
* **
72771 GCACAAATTATGTTAATA--TAA
1 GCACAAATCACATTAATATTTAA
* *
72792 GCATAGATCACATTAATACTTT-A
1 GCACAAATCACATTAATA-TTTAA
72815 GCACA
1 GCACA
72820 TGTTTCACAT
Statistics
Matches: 301, Mismatches: 65, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
21 16 0.05
22 1 0.00
23 282 0.94
24 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.36
Consensus pattern (23 bp):
GCACAAATCACATTAATATTTAA
Found at i:72504 original size:69 final size:69
Alignment explanation
Indices: 72426--72778 Score: 467
Period size: 69 Copynumber: 5.1 Consensus size: 69
72416 AATTCTTTGC
* * *
72426 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTGA-CTACAAATCATACTAATA
1 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGC-ACAAATCACATTAATA
72490 TTTAA
65 TTTAA
*
72495 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCGCAAATCACATTAATAT
1 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATTAATAT
72560 TTAA
66 TTAA
* * **
72564 GCACAAATCACATTAATATTTAAGT-ATAAATCACATTAATATTTGAGCACAAATCATTTTAATA
1 GCACAAATCACATTAATATTTAA-TCATAAATCATATTAATATTTAAGCACAAATCACATTAATA
72628 TTTAA
65 TTTAA
* * * * * * * ** *
72633 GTATAAATCACATTAATATTTGAGCACAAATCATTTTAATATTTAAGTATGAATCACATTAATAC
1 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATTAATAT
72698 TTAA
66 TTAA
* * ** *
72702 GCACAAATCACATTAATATTTAATCATAAATCATATTATTATTTAAGCATAAATTGCATTAATAC
1 GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATTAATAT
72767 TTAA
66 TTAA
72771 GCACAAAT
1 GCACAAAT
72779 TATGTTAATA
Statistics
Matches: 247, Mismatches: 34, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
69 245 0.99
70 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (69 bp):
GCACAAATCACATTAATATTTAATCATAAATCATATTAATATTTAAGCACAAATCACATTAATAT
TTAA
Found at i:75677 original size:36 final size:36
Alignment explanation
Indices: 75625--75757 Score: 196
Period size: 36 Copynumber: 3.7 Consensus size: 36
75615 TCGTTATTCG
*
75625 TTTTACTCCCTGTTGACCAAAAGGTCACGATGTTCA
1 TTTTACTCCCTATTGACCAAAAGGTCACGATGTTCA
75661 TTTTACTCCCTATTGACCAAAAGGTCACGATGTTCA
1 TTTTACTCCCTATTGACCAAAAGGTCACGATGTTCA
** * *
75697 TTTTACTCCCCGTTGACCCAAAA-GTCATGATGCTCA
1 TTTTACTCCCTATTGA-CCAAAAGGTCACGATGTTCA
*
75733 TTTTACTCCCTATTGACCCAAAGGT
1 TTTTACTCCCTATTGACCAAAAGGT
75758 TATGCCTATT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
35 5 0.06
36 76 0.87
37 6 0.07
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (36 bp):
TTTTACTCCCTATTGACCAAAAGGTCACGATGTTCA
Found at i:77186 original size:52 final size:52
Alignment explanation
Indices: 77114--77393 Score: 373
Period size: 52 Copynumber: 5.4 Consensus size: 52
77104 ATAGGTCTGC
77114 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
* * * * * *
77166 CGACTATGTGTCATCATGAGTATATGAATCCTTGATGGACTATGAGATCCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
* * *
77218 TGACTATGTGTCATCGTGCGTATATGAATCCTTGACGGATTATGAGGTTCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
* * *
77270 TGACTATGTGTCATCATGAGTATATGAATTCTTTATGGATTATGAGGTCCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
* * * *
77322 TGACTATGTGTCATCGTGAGTATATGATTCCCATTACGGATTA-AAGGTCCAA
1 TGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATGAGGTCCGA
* * *
77374 TAACTCTGTGTCTTCGTGAG
1 TGACTATGTGTCATCGTGAG
77394 AATCAAATAT
Statistics
Matches: 198, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
52 188 0.95
53 10 0.05
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (52 bp):
TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGA
Found at i:89666 original size:17 final size:17
Alignment explanation
Indices: 89646--89681 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
89636 AGTATAAATT
89646 ATTCAAAAATAAAAAAA
1 ATTCAAAAATAAAAAAA
* *
89663 ATTCAAAATTCAAAAAA
1 ATTCAAAAATAAAAAAA
89680 AT
1 AT
89682 ATAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (17 bp):
ATTCAAAAATAAAAAAA
Done.