Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012190.1 Kokia drynarioides strain JFW-HI SEQ_127191, 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: 10242
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:3653 original size:17 final size:17
Alignment explanation
Indices: 3633--3701 Score: 93
Period size: 17 Copynumber: 4.0 Consensus size: 17
3623 TTAAACCCAA
* *
3633 ATTTTAATTTTTAATTT
1 ATTTTAAATTTAAATTT
*
3650 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
3667 ATTTTAAACTTAAATTT
1 ATTTTAAATTTAAATTT
3684 ATTTTAAATTTGAAATTT
1 ATTTTAAATTT-AAATTT
3702 GAAAGTTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 40 0.87
18 6 0.13
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:5564 original size:30 final size:30
Alignment explanation
Indices: 5530--5800 Score: 180
Period size: 30 Copynumber: 9.2 Consensus size: 30
5520 TAGAAATCAT
* *
5530 ATTTTAACCCCCAAACTTTTCAAAAATTGC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* *
5560 ATTTTAACCCCTAAACTTTTCCAAAATTAT
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* ** * *
5590 ATTTTAA-CCTTCAAACTTCCCAAAAATCAT
1 ATTTTAACCCCT-AAACTTTTCAAAAATTAC
* * *
5620 ATGTTAATCCCTAAAC-TTTCCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* * * *
5649 ATTTTGACCCCTAAACTTTCCAAAAATCAT
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* *
5679 ATTTTAACCCCTAAACTTCTC--AAATCAC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
* * * *
5707 ATTTTTACCTC-GAA-TTTTATAAAAATTAC
1 ATTTTAACCCCTAAACTTTT-CAAAAATTAC
* * * *
5736 ATTTTGA-CCCTCGAACTTCTCCAAAATTAC
1 ATTTTAACCCCT-AAACTTTTCAAAAATTAC
* * * *
5766 ATTTTGACCCCCAAAC-ATACAAAAATTAC
1 ATTTTAACCCCTAAACTTTTCAAAAATTAC
5795 AATTTT
1 -ATTTT
5801 GCCCTCAAAT
Statistics
Matches: 186, Mismatches: 44, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
26 3 0.02
27 2 0.01
28 17 0.09
29 45 0.24
30 110 0.59
31 9 0.05
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTTCAAAAATTAC
Found at i:5660 original size:29 final size:29
Alignment explanation
Indices: 5530--5848 Score: 172
Period size: 30 Copynumber: 10.9 Consensus size: 29
5520 TAGAAATCAT
* * * *
5530 ATTTTAACCCCCAAACTTTTCAAAAATTGC
1 ATTTTGACCCCTAAAC-TTTCCAAAATTAC
* *
5560 ATTTTAACCCCTAAACTTTTCCAAAATTAT
1 ATTTTGACCCCTAAAC-TTTCCAAAATTAC
* * * *
5590 ATTTT-AACCTTCAAACTTCCCAAAAAT-C
1 ATTTTGACCCCT-AAACTTTCCAAAATTAC
* *
5618 ATATGTTAATCCCTAAACTTTCCAAAATTAC
1 AT-T-TTGACCCCTAAACTTTCCAAAATTAC
* *
5649 ATTTTGACCCCTAAACTTTCCAAAAATCAT
1 ATTTTGACCCCTAAACTTTCC-AAAATTAC
* *
5679 ATTTTAACCCCTAAAC-TTCTC-AAATCAC
1 ATTTTGACCCCTAAACTTTC-CAAAATTAC
* * * * **
5707 ATTTTTACCTC-GAATTTTATAAAAATTAC
1 ATTTTGACCCCTAAACTTT-CCAAAATTAC
*
5736 ATTTTGA-CCCTCGAACTTCTCCAAAATTAC
1 ATTTTGACCCCT-AAACTT-TCCAAAATTAC
* * * *
5766 ATTTTGACCCCCAAACATACAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAATTAC
*
5795 AATTTTG--CCCTCAAA-TTTCCAAAAATCAC
1 -ATTTTGACCCCT-AAACTTTCC-AAAATTAC
* *
5824 ATTTTCGACCTC-AAATTTTCCAAAA
1 ATTTT-GACCCCTAAACTTTCCAAAA
5849 GTTCGATTTT
Statistics
Matches: 226, Mismatches: 42, Indels: 43
0.73 0.14 0.14
Matches are distributed among these distances:
27 2 0.01
28 31 0.14
29 72 0.32
30 108 0.48
31 13 0.06
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTTGACCCCTAAACTTTCCAAAATTAC
Found at i:5672 original size:59 final size:57
Alignment explanation
Indices: 5530--5696 Score: 192
Period size: 59 Copynumber: 2.8 Consensus size: 57
5520 TAGAAATCAT
* * *
5530 ATTTTAACCCCCAAACTTTTCAAAAATTGCAT-TTTAACCCCTAAACTTTTCCAAAATTAT
1 ATTTT-ACCCCTAAACTTTCCAAAAA-T-CATATTTAACCCCTAAAC-TTTCCAAAATTAC
* * * *
5590 ATTTTAACCTTCAAACTTCCCAAAAATCATATGTTAATCCCTAAACTTTCCAAAATTAC
1 ATTTTACCCCT-AAACTTTCCAAAAATCATAT-TTAACCCCTAAACTTTCCAAAATTAC
5649 ATTTTGACCCCTAAACTTTCCAAAAATCATATTTTAACCCCTAAACTT
1 ATTTT-ACCCCTAAACTTTCCAAAAATCATA-TTTAACCCCTAAACTT
5697 CTCAAATCAC
Statistics
Matches: 91, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
58 3 0.03
59 54 0.59
60 34 0.37
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (57 bp):
ATTTTACCCCTAAACTTTCCAAAAATCATATTTAACCCCTAAACTTTCCAAAATTAC
Found at i:5695 original size:89 final size:90
Alignment explanation
Indices: 5523--5702 Score: 240
Period size: 89 Copynumber: 2.0 Consensus size: 90
5513 AATTTTCTAG
* * *
5523 AAATCATATTTTAACCCCCAAACTTTTCAAAAATTGCATTTTAACCCCTAAACTTTTCCAAAATT
1 AAATCATATGTTAACCCCCAAACTTTTCAAAAATTACATTTTAACCCCTAAACTTTTCCAAAATC
*
5588 ATATTTTAACCTTCAAACTTCCCAA
66 ATATTTTAACCCTCAAACTTCCCAA
* * * *
5613 AAATCATATGTTAATCCCTAAAC-TTTCCAAAATTACATTTTGACCCCTAAAC-TTTCCAAAAAT
1 AAATCATATGTTAACCCCCAAACTTTTCAAAAATTACATTTTAACCCCTAAACTTTTCC-AAAAT
*
5676 CATATTTTAACCC-CTAAACTTCTCAA
65 CATATTTTAACCCTC-AAACTTCCCAA
5702 A
1 A
5703 TCACATTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
88 6 0.08
89 53 0.67
90 20 0.25
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (90 bp):
AAATCATATGTTAACCCCCAAACTTTTCAAAAATTACATTTTAACCCCTAAACTTTTCCAAAATC
ATATTTTAACCCTCAAACTTCCCAA
Found at i:5791 original size:59 final size:57
Alignment explanation
Indices: 5523--5833 Score: 187
Period size: 59 Copynumber: 5.3 Consensus size: 57
5513 AATTTTCTAG
* * * * * *
5523 AAATCATATTTTAACCCCCAAACTTTTCAAAAATTGCATTTTAACCCCTAAACTTTTCCA
1 AAATCACATTTTGACCCCCAAAC-TTACAAAAATTACATTTTGA-CCCTCAAC-TTTCCA
* * * ** * * * * * *
5583 AAATTATATTTTAACCTTCAAACTTCCCAAAAATCATATGTTAATCCCTAAACTTTCCA
1 AAATCACATTTTGACCCCCAAACTT-ACAAAAATTACATTTTGA-CCCTCAACTTTCCA
* * * * * * *
5642 AAATTACATTTTGACCCCTAAACTTTCCAAAAATCATATTTTAACCCCTAAAC-TTCTC-
1 AAATCACATTTTGACCCCCAAAC-TTACAAAAATTACATTTTGA-CCCTCAACTTTC-CA
* * * ** *
5700 AAATCACATTTTTACCTCGAATTTTATAAAAATTACATTTTGACCCTCGAACTTCTCCA
1 AAATCACATTTTGACCCCCAAACTTACAAAAATTACATTTTGACCCTC-AACTT-TCCA
* * *
5759 AAATTACATTTTGACCCCCAAACATACAAAAATTACAATTTTG-CCCTCAAATTTCCAA
1 AAATCACATTTTGACCCCCAAACTTACAAAAATTAC-ATTTTGACCCTCAACTTTCC-A
5817 AAATCACATTTTCGACC
1 AAATCACATTTT-GACC
5834 TCAAATTTTC
Statistics
Matches: 203, Mismatches: 38, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
56 4 0.02
57 21 0.10
58 38 0.19
59 91 0.45
60 49 0.24
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (57 bp):
AAATCACATTTTGACCCCCAAACTTACAAAAATTACATTTTGACCCTCAACTTTCCA
Found at i:5801 original size:30 final size:30
Alignment explanation
Indices: 5727--5838 Score: 106
Period size: 29 Copynumber: 3.8 Consensus size: 30
5717 CGAATTTTAT
* * *
5727 AAAAATTACATTTTGACCCTCGAACTTCTC
1 AAAAATTACATTTTGACCCTCAAACATCAC
* *
5757 CAAAATTACATTTTGACCCCCAAACAT-AC
1 AAAAATTACATTTTGACCCTCAAACATCAC
**
5786 AAAAATTACAATTTTG-CCCTCAAATTTC-C
1 AAAAATTAC-ATTTTGACCCTCAAACATCAC
*
5815 AAAAATCACATTTTCGA-CCTCAAA
1 AAAAATTACATTTT-GACCCTCAAA
5839 TTTTCCAAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
28 5 0.07
29 34 0.50
30 29 0.43
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCAAACATCAC
Found at i:5848 original size:59 final size:59
Alignment explanation
Indices: 5638--5848 Score: 166
Period size: 58 Copynumber: 3.6 Consensus size: 59
5628 CCCTAAACTT
* * * * * * * *
5638 TCCAAAATTACATTTTGACCCCTAAACTTTCCAAAAATCATATTTTAACCC-CTAAACTTC
1 TCCAAAATCACATTTTGACCTC-AAATTTTACAAAAATTACATTTTGACCCTCGAAA-TTC
* * * *
5698 T-C-AAATCACATTTTTACCTCGAATTTTATAAAAATTACATTTTGACCCTCGAACTTC
1 TCCAAAATCACATTTTGACCTCAAATTTTACAAAAATTACATTTTGACCCTCGAAATTC
* * **
5755 TCCAAAATTACATTTTGACCCCCAAA-CATACAAAAATTACAATTTTG-CCCTC-AAATT-
1 TCCAAAATCACATTTTGA-CCTCAAATTTTACAAAAATTAC-ATTTTGACCCTCGAAATTC
*
5812 TCCAAAAATCACATTTTCGACCTCAAATTTTCCAAAA
1 TCC-AAAATCACATTTT-GACCTCAAATTTTACAAAA
5849 GTTCGATTTT
Statistics
Matches: 118, Mismatches: 25, Indels: 17
0.74 0.16 0.11
Matches are distributed among these distances:
57 28 0.24
58 41 0.35
59 37 0.31
60 12 0.10
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCAAAATCACATTTTGACCTCAAATTTTACAAAAATTACATTTTGACCCTCGAAATTC
Found at i:8282 original size:49 final size:46
Alignment explanation
Indices: 8209--8307 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 46
8199 ATACGCAGGC
* *
8209 TTATATATATATATAGATAGACATACAT-TCTGATTTTATTCTTTATT
1 TTATATATATATATAGATAAACATACATAT-TGATTTCATT-TTTATT
*
8256 TTATATATATATATATATGCAAACATACATATTGATTTCATTTTTATT
1 TTATATATATATATAGAT--AAACATACATATTGATTTCATTTTTATT
8304 TTAT
1 TTAT
8308 TCATATACAC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
47 17 0.37
48 10 0.22
49 18 0.39
50 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (46 bp):
TTATATATATATATAGATAAACATACATATTGATTTCATTTTTATT
Found at i:9380 original size:28 final size:28
Alignment explanation
Indices: 9341--9476 Score: 89
Period size: 28 Copynumber: 4.8 Consensus size: 28
9331 TTCGGAATCA
9341 AAAATAGG-AATTTTAGCAA-CTCGAGGG-T
1 AAAAT-GGTAATTTT-GCAAGCTCG-GGGAT
* *
9369 AAAATGGTAATTTTGGAAGTTCGGGGAT
1 AAAATGGTAATTTTGCAAGCTCGGGGAT
* * *
9397 AAAATGGTAATTTTTGGAAGATTCGGGGTT
1 AAAATGGTAA-TTTTGCAAG-CTCGGGGAT
* * * * *
9427 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 -AAAATGGTAATTTTGCAAGCTCGGGGAT
* *
9456 AAGATGGTAATTTTGGAAGCT
1 AAAATGGTAATTTTGCAAGCT
9477 TCGAGGTCAA
Statistics
Matches: 92, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
27 8 0.09
28 42 0.46
29 17 0.18
30 17 0.18
31 8 0.09
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGCAAGCTCGGGGAT
Found at i:9440 original size:29 final size:29
Alignment explanation
Indices: 9368--9771 Score: 229
Period size: 29 Copynumber: 13.8 Consensus size: 29
9358 AACTCGAGGG
*
9368 TAAAATGGTAATTTTGGAAG-TTCGGGGA
1 TAAAATGGTAATTTTGGAAGATTCGGGGT
9396 TAAAATGGTAATTTTTGGAAGATTCGGGGT
1 TAAAATGGTAA-TTTTGGAAGATTCGGGGT
* * *
9426 TAAAAATGGGATTTTTGGAAG-TTCGGGGG
1 T-AAAATGGTAATTTTGGAAGATTCGGGGT
* * *
9455 TAAGATGGTAATTTTGGAAGCTTCGAGGT
1 TAAAATGGTAATTTTGGAAGATTCGGGGT
* * * *
9484 CAAAAAATGGGATTTTTTGGGA-ATTCAGGGG-
1 --TAAAATGGTA-ATTTTGGAAGATTC-GGGGT
* * * **
9515 TAAAATGGTAATTTCGAAAGCTTTAGGGT
1 TAAAATGGTAATTTTGGAAGATTCGGGGT
* * * * *
9544 TAAAAATGG-GATTTTTGAAAATTTGGGGG
1 T-AAAATGGTAATTTTGGAAGATTCGGGGT
*
9573 TAAAATGGTAATTTTGGAAGCTTCGGGGT
1 TAAAATGGTAATTTTGGAAGATTCGGGGT
* *
9602 TAAAATTGG-ATTTTTGGAA-ATTCGGGGG
1 TAAAA-TGGTAATTTTGGAAGATTCGGGGT
* * * *
9630 TAAAACGGTAATTTTTGGTAGCTTCGAGGT
1 TAAAATGGTAA-TTTTGGAAGATTCGGGGT
* * * *
9660 CAAAAGTGGGATTTTTGGGA-ATTCGAGGG-
1 TAAAA-TGGTAATTTTGGAAGATTCG-GGGT
* * *
9689 TAAAACGGTAATTTTTGAAAGCTTCGGGGT
1 TAAAATGGTAA-TTTTGGAAGATTCGGGGT
* * *
9719 CAAAAATAGG-ATTTTTGGGA-ATTCGAGGG-
1 -TAAAAT-GGTAATTTTGGAAGATTCG-GGGT
*
9748 TAAAACGGTAATTTTTGGAAGATT
1 TAAAATGGTAA-TTTTGGAAGATT
9772 TAAGGACCTC
Statistics
Matches: 277, Mismatches: 72, Indels: 52
0.69 0.18 0.13
Matches are distributed among these distances:
27 4 0.01
28 63 0.23
29 110 0.40
30 62 0.22
31 26 0.09
32 12 0.04
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTGGAAGATTCGGGGT
Found at i:9442 original size:59 final size:57
Alignment explanation
Indices: 9369--9768 Score: 421
Period size: 59 Copynumber: 6.8 Consensus size: 57
9359 ACTCGAGGGT
* * *
9369 AAAATGGTAATTTTGGAAGTTCGGGGATAAAATGGTAATTTTTGGAAGATTCGGGGTTA
1 AAAATGGGATTTTTGGAA-TTCGGGG-TAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
* * *
9428 AAAATGGGATTTTTGGAAGTTCGGGGGTAAGATGGTAA-TTTTGGAAGCTTCGAGGTCAA
1 AAAATGGGATTTTTGGAA-TTC-GGGGTAAAATGGTAATTTTTGGAAGCTTCGGGGT-TA
* * **
9487 AAAATGGGATTTTTTGGGAATTCAGGGGTAAAATGGTAA-TTTCGAAAGCTTTAGGGTTA
1 AAAATGGGA-TTTTT-GGAATTC-GGGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
* *
9546 AAAATGGGATTTTTGAAAATTTGGGGGTAAAATGGTAA-TTTTGGAAGCTTCGGGGTT-
1 AAAATGGGATTTTTG-GAA-TTCGGGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
* * * * *
9603 AAAATTGGATTTTTGGAAATTCGGGGGTAAAACGGTAATTTTTGGTAGCTTCGAGGTCA
1 AAAATGGGATTTTTGG-AATTC-GGGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
* * * *
9662 AAAGTGGGATTTTTGGGAATTCGAGGGTAAAACGGTAATTTTTGAAAGCTTCGGGGTCA
1 AAAATGGGATTTTT-GGAATTCG-GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
* *
9721 AAAATAGGATTTTTGGGAATTCGAGGGTAAAACGGTAATTTTTGGAAG
1 AAAATGGGATTTTT-GGAATTCG-GGGTAAAATGGTAATTTTTGGAAG
9769 ATTTAAGGAC
Statistics
Matches: 294, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
56 2 0.01
57 31 0.11
58 70 0.24
59 146 0.50
60 41 0.14
61 4 0.01
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.33
Consensus pattern (57 bp):
AAAATGGGATTTTTGGAATTCGGGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTTA
Done.