Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011183.1 Kokia drynarioides strain JFW-HI SEQ_126159, 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: 57833
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:1634 original size:114 final size:114
Alignment explanation
Indices: 1442--1709 Score: 419
Period size: 114 Copynumber: 2.4 Consensus size: 114
1432 GAATAGTAGT
* * *
1442 TATTAAACTCTCAATTTGGGCCAGTAAAATAAATAAATTCTAGTAACATAATTCAACTCACACTA
1 TATTAAACTCTCAATTTGAGCCAATAAAATAAATAAATTTTAGTAACATAATTCAACTCACACTA
* *
1507 GAATTTTACAATGAATAAAATAAAATTACTGCATGTAAATTATAGTAAA
66 AAATTTTACAATGAATAAAATAAAATAACTGCATGTAAATTATAGTAAA
* * *
1556 TATTAAACTCTCAATTTGAACCAATAAAATAAATAAATTTTAGTAACCTAATTCTACTCACACTA
1 TATTAAACTCTCAATTTGAGCCAATAAAATAAATAAATTTTAGTAACATAATTCAACTCACACTA
* * *
1621 AAATTTTACAATGAATAAAATAAAATAAGTTCATGTAAATTCTAGTAAA
66 AAATTTTACAATGAATAAAATAAAATAACTGCATGTAAATTATAGTAAA
* *
1670 TACTAAATTCTCAATTTGAGCCAATAAAATAAATAAATTT
1 TATTAAACTCTCAATTTGAGCCAATAAAATAAATAAATTT
1710 CATCACTCTA
Statistics
Matches: 140, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 140 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (114 bp):
TATTAAACTCTCAATTTGAGCCAATAAAATAAATAAATTTTAGTAACATAATTCAACTCACACTA
AAATTTTACAATGAATAAAATAAAATAACTGCATGTAAATTATAGTAAA
Found at i:4643 original size:114 final size:112
Alignment explanation
Indices: 4427--4647 Score: 320
Period size: 114 Copynumber: 2.0 Consensus size: 112
4417 CGTACTAAAT
* * * *
4427 GTAATCTAATTCTATTGATACTAAGATTTTACAATGAATAAAATAAAATAGGTGCATGTAAATTC
1 GTAACCTAATTCTACTGACACTAAGATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTC
**
4492 TAATAAATACTAAACTCTCAATTTAGGTGAATAAAATAAATAAATTCTA
66 TAATAAATACTAAACTCT--ATTTAGGCCAATAAAATAAATAAATTCTA
*
4541 GTAACCTAATTCTACTGACACTAGGATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTC
1 GTAACCTAATTCTACTGACACTAAGATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTC
* * *
4606 TAGTAAATATTAAACTCT-TTTGGGCCAAT-AAATAAATAAATT
66 TAATAAATACTAAACTCTATTTAGGCCAATAAAATAAATAAATT
4648 TCATCTCTCC
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
110 13 0.13
111 8 0.08
114 76 0.78
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.33
Consensus pattern (112 bp):
GTAACCTAATTCTACTGACACTAAGATTTTACAATGAATAAAATAAAATAAGTGCATGTAAATTC
TAATAAATACTAAACTCTATTTAGGCCAATAAAATAAATAAATTCTA
Found at i:17604 original size:63 final size:63
Alignment explanation
Indices: 17485--17615 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 63
17475 ATGCACTTAA
* * * *
17485 AAAATTGGCATGAACAAATCAATACCTAAATCCCACTTCGACCTGACTTTCAAAAATTATCTT
1 AAAATCGGCATGAACAAATCAACACCTAAATCCAACTTCGACCTAACTTTCAAAAATTATCTT
* * *
17548 AAAATCGGCATGAATAAATCAACACTTAACATCCAACTTCGACAC-AAC-TTCCAAAATTATCTT
1 AAAATCGGCATGAACAAATCAACACCTAA-ATCCAACTTCGAC-CTAACTTTCAAAAATTATCTT
*
17611 GAAAT
1 AAAAT
17616 TTGTTGACCG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 43 0.74
64 14 0.24
65 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.27
Consensus pattern (63 bp):
AAAATCGGCATGAACAAATCAACACCTAAATCCAACTTCGACCTAACTTTCAAAAATTATCTT
Found at i:26394 original size:26 final size:26
Alignment explanation
Indices: 26358--26422 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
26348 AATTAGATTA
*
26358 AATTATTTTTTATTAAAAAATAAATT
1 AATTAATTTTTATTAAAAAATAAATT
26384 AATTAATTTTTATTAAAAAATAAATT
1 AATTAATTTTTATTAAAAAATAAATT
26410 AATTAATTTTTAT
1 AATTAATTTTTAT
26423 ATGTTAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AATTAATTTTTATTAAAAAATAAATT
Found at i:33653 original size:25 final size:25
Alignment explanation
Indices: 33623--33673 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
33613 ATCAAATAAG
33623 TCTAAATTATAAAAGAGGGGTTAAT
1 TCTAAATTATAAAAGAGGGGTTAAT
33648 TCTAAATTATAAAAGAGGGGTTAAT
1 TCTAAATTATAAAAGAGGGGTTAAT
33673 T
1 T
33674 TGATCCAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (25 bp):
TCTAAATTATAAAAGAGGGGTTAAT
Found at i:40851 original size:31 final size:31
Alignment explanation
Indices: 40809--40876 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
40799 TTACAAAATG
* *
40809 GTTATTGAACTATTTGAAAATTTTCATTGAA
1 GTTATTAAACTATTTGAAAATTTTCATTCAA
* * *
40840 TTTATTAAACTATTTTAAAGTTTTCATTCAA
1 GTTATTAAACTATTTGAAAATTTTCATTCAA
40871 GTTATT
1 GTTATT
40877 GGATTACAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (31 bp):
GTTATTAAACTATTTGAAAATTTTCATTCAA
Found at i:41032 original size:201 final size:201
Alignment explanation
Indices: 40683--41084 Score: 759
Period size: 201 Copynumber: 2.0 Consensus size: 201
40673 TAGTGTAAAA
40683 AATTGAATCTACATTTTTAAATTCAAACAGTAAATTGATTAAATTGTTAGGTAAAATACACCTAA
1 AATTGAATCTACATTTTTAAATTCAAACAGTAAATTGATTAAATTGTTAGGTAAAATACACCTAA
40748 GGTCACTAAAGTATTAATAAGTTTACGTTTTGGTCACTCAACTTTAAAAAATTACAAAATGGTTA
66 GGTCACTAAAGTATTAATAAGTTTACGTTTTGGTCACTCAACTTTAAAAAATTACAAAATGGTTA
*
40813 TTGAACTATTTGAAAATTTTCATTGAATTTATTAAACTATTTTAAAGTTTTCATTCAAGTTATTG
131 TTGAACTATTTAAAAATTTTCATTGAATTTATTAAACTATTTTAAAGTTTTCATTCAAGTTATTG
40878 GATTAC
196 GATTAC
* *
40884 AATTGAATCTACATTTTTAAGTTCAAACAGTAAATTTATTAAATTGTTAGGTAAAATACACCTAA
1 AATTGAATCTACATTTTTAAATTCAAACAGTAAATTGATTAAATTGTTAGGTAAAATACACCTAA
40949 GGTCACTAAAGTATTAATAAGTTTACGTTTTGGTCACTCAACTTTAAAAAATTACAAAATGGTTA
66 GGTCACTAAAGTATTAATAAGTTTACGTTTTGGTCACTCAACTTTAAAAAATTACAAAATGGTTA
* *
41014 TTGAACTATTTAAAAATTTTCTTTGAATTTATTAAACTATTTTAAAGTTTTCATTTAAGTTATTG
131 TTGAACTATTTAAAAATTTTCATTGAATTTATTAAACTATTTTAAAGTTTTCATTCAAGTTATTG
41079 GATTAC
196 GATTAC
41085 TCGAAAGTTT
Statistics
Matches: 196, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
201 196 1.00
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (201 bp):
AATTGAATCTACATTTTTAAATTCAAACAGTAAATTGATTAAATTGTTAGGTAAAATACACCTAA
GGTCACTAAAGTATTAATAAGTTTACGTTTTGGTCACTCAACTTTAAAAAATTACAAAATGGTTA
TTGAACTATTTAAAAATTTTCATTGAATTTATTAAACTATTTTAAAGTTTTCATTCAAGTTATTG
GATTAC
Found at i:41046 original size:31 final size:31
Alignment explanation
Indices: 41010--41078 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
41000 TTACAAAATG
41010 GTTATTGAACTATTTAAAAATTTTC-TTTGAA
1 GTTATTGAACTATTTAAAAATTTTCATTT-AA
* * * *
41041 TTTATTAAACTATTTTAAAGTTTTCATTTAA
1 GTTATTGAACTATTTAAAAATTTTCATTTAA
41072 GTTATTG
1 GTTATTG
41079 GATTACTCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (31 bp):
GTTATTGAACTATTTAAAAATTTTCATTTAA
Found at i:57739 original size:4 final size:4
Alignment explanation
Indices: 57732--57797 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
57722 AAATAAACGG
* * * *
57732 GAAA GAAA GAAA GGAAA TAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
57782 G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA G
57798 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:57753 original size:9 final size:9
Alignment explanation
Indices: 57732--57798 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
57722 AAATAAACGG
57732 GAAA-GAAA
1 GAAAGGAAA
57740 GAAAGGAAA
1 GAAAGGAAA
*
57749 TAAA-GAAA
1 GAAAGGAAA
57757 GAAAGG-AA
1 GAAAGGAAA
*
57765 G-AAGGAGAG
1 GAAAGGA-AA
57774 GAAA-GAAA
1 GAAAGGAAA
57782 GAAGAAGGAAA
1 G-A-AAGGAAA
57793 GAAAGG
1 GAAAGG
57799 TAATGTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
7 4 0.09
8 16 0.34
9 17 0.36
10 5 0.11
11 5 0.11
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.01
Consensus pattern (9 bp):
GAAAGGAAA
Found at i:57776 original size:29 final size:27
Alignment explanation
Indices: 57734--57797 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
57724 ATAAACGGGA
*
57734 AAGAAAGAAAGGAAATAAAGAAAGAAAGG
1 AAGAAAGAAAGGAAAGAAAG-AAG-AAGG
* *
57763 AAGAAGGAGAGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGGAAAGAAAGAAGAAGG
57790 AAAGAAAG
1 -AAGAAAG
57798 GTAATGTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 9 0.30
29 17 0.57
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (27 bp):
AAGAAAGAAAGGAAAGAAAGAAGAAGG
Found at i:57777 original size:17 final size:15
Alignment explanation
Indices: 57731--57797 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 15
57721 CAAATAAACG
57731 GGAAAGAAAG-A-AA
1 GGAAAGAAAGAAGAA
*
57744 GGAAATAAAG-A-AA
1 GGAAAGAAAGAAGAA
*
57757 -GAAAGGAAGAAGGAGA
1 GGAAAGAAAGAA-GA-A
57773 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAGAA
57788 GGAAAGAAAG
1 GGAAAGAAAG
57798 GTAATGTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.16
13 13 0.29
15 12 0.27
16 3 0.07
17 10 0.22
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.01
Consensus pattern (15 bp):
GGAAAGAAAGAAGAA
Done.