Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002914.1 Kokia drynarioides strain JFW-HI SEQ_115345, 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: 17989
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Found at i:3444 original size:50 final size:50
Alignment explanation
Indices: 3317--3444 Score: 175
Period size: 50 Copynumber: 2.6 Consensus size: 50
3307 ATCTTTTACC
* * *
3317 CCTAAAGCTATAAAGGTGCAGATTGAAACCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAAGGCAAATCTCATACA
* * * * *
3367 CCTAAAGCTGTAAAGGGGTAGAATGAAGTCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAAGGCAAATCTCATACA
*
3417 CCTAAAGCTGTAGAGGGGCAGATTGAAG
1 CCTAAAGCTGTAAAGGGGCAGATTGAAG
3445 ACACAAGGAC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAAAGGGGCAGATTGAAGCCGCAAAGGCAAATCTCATACA
Found at i:3458 original size:50 final size:49
Alignment explanation
Indices: 3317--3465 Score: 174
Period size: 50 Copynumber: 3.0 Consensus size: 49
3307 ATCTTTTACC
* *
3317 CCTAAAGCTATAAAGGTGCAGATTGAA-ACCGCAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGA-CGC-AAGGCAAATCTCATACA
* * * *
3367 CCTAAAGCTGTAAAGGGGTAGAATGAAGTCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGACGCAA-GGCAAATCTCATACA
* * *
3417 CCTAAAGCTGTAGAGGGGCAGATTGAAGACACAAGGACAAATCTTATAC
1 CCTAAAGCTGTAAAGGGGCAGATTGAAGACGCAAGG-CAAATCTCATAC
3466 TCTTGAGGCT
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 4 0.05
50 79 0.95
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (49 bp):
CCTAAAGCTGTAAAGGGGCAGATTGAAGACGCAAGGCAAATCTCATACA
Found at i:3544 original size:40 final size:41
Alignment explanation
Indices: 3498--3672 Score: 171
Period size: 40 Copynumber: 4.4 Consensus size: 41
3488 AGTTACAACC
* *
3498 TCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGACCA
1 TCCAATCTTTTACCCCAACCATGAGGGCAGATTGAAGACAA
* ** * *
3538 TCCAATCTTTTACCCTAATTA-GAGGGTAGATTGAAGAAAA
1 TCCAATCTTTTACCCCAACCATGAGGGCAGATTGAAGACAA
* * *
3578 TCAAATCTCTTACCCCAACCATGA-GGCAGATTAAAGACAA
1 TCCAATCTTTTACCCCAACCATGAGGGCAGATTGAAGACAA
* * * ** *
3618 TCTAATCTCTTACCCCGACCATG-GAACGGATTGAA-ACAA
1 TCCAATCTTTTACCCCAACCATGAGGGCAGATTGAAGACAA
3657 TCCAATCTTTTACCCC
1 TCCAATCTTTTACCCC
3673 TAAAGTTACG
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
39 18 0.16
40 92 0.82
41 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (41 bp):
TCCAATCTTTTACCCCAACCATGAGGGCAGATTGAAGACAA
Found at i:3721 original size:50 final size:51
Alignment explanation
Indices: 3660--3826 Score: 259
Period size: 50 Copynumber: 3.3 Consensus size: 51
3650 GAAACAATCC
* *
3660 AATCTTTTACCCCTAAAGTTAC-GAAGAGGCAGATTGAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAAGAGGCAGATTAAAGCTACAAAAGCA
* *
3710 AATCTTATACCCCTAAAGTTACAGAAG-GGTAGATTAAACCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAAGAGGCAGATTAAAGCTACAAAAGCA
* *
3760 AATTTTATACCCCTATAGTTACAGAA-AGGCAGATTAAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAAGAGGCAGATTAAAGCTACAAAAGCA
3810 AATCTTATACCCCTAAA
1 AATCTTATACCCCTAAA
3827 AGTATTGAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
50 101 0.96
51 4 0.04
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (51 bp):
AATCTTATACCCCTAAAGTTACAGAAGAGGCAGATTAAAGCTACAAAAGCA
Found at i:4276 original size:12 final size:12
Alignment explanation
Indices: 4259--4284 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4249 TTTATTTATT
4259 AAATAAATAAAC
1 AAATAAATAAAC
4271 AAATAAATAAAC
1 AAATAAATAAAC
4283 AA
1 AA
4285 TAGAATTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:5526 original size:30 final size:30
Alignment explanation
Indices: 5485--5660 Score: 194
Period size: 30 Copynumber: 5.8 Consensus size: 30
5475 GCTCCCAAAG
* *
5485 TTTTCAAAAATTCAAATTTGACCCCTAATT
1 TTTTCAAAAATTCAAATTTAACCCCTAAAT
* *
5515 TTTTAAAAAATTCAAATTTCACCACC-AAAT
1 TTTTCAAAAATTCAAATTTAACC-CCTAAAT
* * * *
5545 TTTCCAAAAAATTCAAATTCAATCACC-AAAG
1 TTTTC-AAAAATTCAAATTTAA-CCCCTAAAT
*
5576 TTTTCAAAAATTCAAATTTGACCCCTAAAT
1 TTTTCAAAAATTCAAATTTAACCCCTAAAT
* *
5606 TTTCCAAAAATTCAAATTTAACCCCTAAAG
1 TTTTCAAAAATTCAAATTTAACCCCTAAAT
* *
5636 TTTTCAAAAATTAAAATCTAACCCC
1 TTTTCAAAAATTCAAATTTAACCCC
5661 GTTTTAATAT
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
29 3 0.02
30 93 0.76
31 25 0.20
32 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (30 bp):
TTTTCAAAAATTCAAATTTAACCCCTAAAT
Found at i:5561 original size:61 final size:60
Alignment explanation
Indices: 5485--5652 Score: 216
Period size: 61 Copynumber: 2.8 Consensus size: 60
5475 GCTCCCAAAG
* ** *
5485 TTTT-CAAAAATTCAAATTTGACCCCTAATTTTTTAAAAAATTCAAATTTCACCACC-AAA
1 TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTCACC-CCTAAA
* * *
5544 TTTTCCAAAAAATTCAAATTCAATCACC-AAAGTTTTCAAAAATTCAAATTTGACCCCTAAA
1 TTTTCC-AAAAATTCAAATTTAA-CCCCTAAAGTTTTCAAAAATTCAAATTTCACCCCTAAA
*
5605 TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTAAAAT
1 TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAAT
5653 CTAACCCCGT
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 7 0.07
60 38 0.40
61 46 0.49
62 3 0.03
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.34
Consensus pattern (60 bp):
TTTTCCAAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAATTCAAATTTCACCCCTAAA
Found at i:5579 original size:91 final size:91
Alignment explanation
Indices: 5479--5645 Score: 266
Period size: 91 Copynumber: 1.8 Consensus size: 91
5469 TTTTTTGCTC
* * *
5479 CCAAAGTTTTCAAAAATTCAAATTTGACCCCTAATTTTTTAAAAAATTCAAATTTCACCACC-AA
1 CCAAAGTTTTCAAAAATTCAAATTTGACCCCTAAATTTTCAAAAAATTCAAATTTAACC-CCTAA
5543 A-TTTTCCAAAAAATTCAAATTCAATCA
65 AGTTTT-CAAAAAATTCAAATTCAATCA
*
5570 CCAAAGTTTTCAAAAATTCAAATTTGACCCCTAAATTTTCCAAAAATTCAAATTTAACCCCTAAA
1 CCAAAGTTTTCAAAAATTCAAATTTGACCCCTAAATTTTCAAAAAATTCAAATTTAACCCCTAAA
5635 GTTTTCAAAAA
66 GTTTTCAAAAA
5646 TTAAAATCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
90 2 0.03
91 64 0.91
92 4 0.06
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (91 bp):
CCAAAGTTTTCAAAAATTCAAATTTGACCCCTAAATTTTCAAAAAATTCAAATTTAACCCCTAAA
GTTTTCAAAAAATTCAAATTCAATCA
Found at i:6749 original size:25 final size:25
Alignment explanation
Indices: 6690--6750 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
6680 TTTTCATATA
6690 ATTTAAAATTTTAAAACTTAATAAT
1 ATTTAAAATTTTAAAACTTAATAAT
** *
6715 AAATACAATTTTATAAA-TT-ATAATT
1 ATTTAAAATTTTA-AAACTTAATAA-T
6740 ATTTAAAATTT
1 ATTTAAAATTT
6751 AATCATAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
24 4 0.14
25 21 0.75
26 3 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAAAATTTTAAAACTTAATAAT
Found at i:11686 original size:18 final size:19
Alignment explanation
Indices: 11651--11687 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
11641 TAGTGCTATC
*
11651 ATAATCAGGGAAATAGATG
1 ATAATCAGGGAAAGAGATG
11670 ATAATCA-GGAAAGAGATG
1 ATAATCAGGGAAAGAGATG
11688 CAATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.19
Consensus pattern (19 bp):
ATAATCAGGGAAAGAGATG
Found at i:13695 original size:21 final size:21
Alignment explanation
Indices: 13671--13821 Score: 133
Period size: 21 Copynumber: 7.2 Consensus size: 21
13661 ATTAGTAAGA
*
13671 GTTGGCGTACCTCTGATTGTT
1 GTTGGCGTACCTCTGATAGTT
* *
13692 GTTGGCGTGCCTCTGATAATT
1 GTTGGCGTACCTCTGATAGTT
*
13713 CTTGGCGTACCTCTGATAGTT
1 GTTGGCGTACCTCTGATAGTT
* * *
13734 GTCGGCATACCTCTGATTGTT
1 GTTGGCGTACCTCTGATAGTT
* * * * *
13755 GTAGACATAACTCTGATTGTT
1 GTTGGCGTACCTCTGATAGTT
* * * *
13776 GTCGGCGTACTTTTGGTAGTT
1 GTTGGCGTACCTCTGATAGTT
*
13797 -TTCGGCGTACCTCTGATAGTA
1 GTT-GGCGTACCTCTGATAGTT
13818 GTTG
1 GTTG
13822 TAGGCATTCC
Statistics
Matches: 102, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 1 0.01
21 99 0.97
22 2 0.02
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.39
Consensus pattern (21 bp):
GTTGGCGTACCTCTGATAGTT
Found at i:14468 original size:15 final size:17
Alignment explanation
Indices: 14448--14495 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
14438 AGTTATCCCA
14448 ATTCAAAACAAAA-A-T
1 ATTCAAAACAAAACAGT
*
14463 ATTCAAAAGAAAACAGT
1 ATTCAAAACAAAACAGT
14480 ATTCAAAATCAAAACA
1 ATTCAAAA-CAAAACA
14496 AGATGTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 1 0.04
17 9 0.32
18 6 0.21
ACGTcount: A:0.62, C:0.15, G:0.04, T:0.19
Consensus pattern (17 bp):
ATTCAAAACAAAACAGT
Done.