Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011236.1 Kokia drynarioides strain JFW-HI SEQ_126214, 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: 63331
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--33 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AA
3 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34 AATTTGGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6724 original size:11 final size:12
Alignment explanation
Indices: 6702--6737 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6692 ATTTTTTTGT
6702 TTTTTAATTTAA
1 TTTTTAATTTAA
6714 TTTTTAA-TTAA
1 TTTTTAATTTAA
*
6725 TTTTTTATTTAA
1 TTTTTAATTTAA
6737 T
1 T
6738 GTTGTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:6853 original size:20 final size:21
Alignment explanation
Indices: 6812--6853 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6802 TAATTTACTT
6812 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
6833 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
6853 T
1 T
6854 GGTAGTAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:7159 original size:16 final size:16
Alignment explanation
Indices: 7114--7163 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
7104 TAAACCTAGC
*
7114 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
7130 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
7144 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
7160 TAAT
1 TAAT
7164 ATCTCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:7231 original size:15 final size:15
Alignment explanation
Indices: 7211--7244 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
7201 AATATTTATT
7211 TTTTATTTTGTACCA
1 TTTTATTTTGTACCA
7226 TTTTATTTTGTACCA
1 TTTTATTTTGTACCA
7241 TTTT
1 TTTT
7245 GGTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTATTTTGTACCA
Found at i:9198 original size:44 final size:45
Alignment explanation
Indices: 9132--9257 Score: 166
Period size: 44 Copynumber: 2.8 Consensus size: 45
9122 GCATAGTTTA
*
9132 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCG-AATAC
1 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGTAATAC
**
9176 TCAAGCCAAGGATATCAACCTCAAATTGACGAGCCACCGTAATAC
1 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGTAATAC
* * * *
9221 TCAAAG-GAAGGATATCAAACTGAGTTTAACGAGCCAC
1 TC-AAGCCAAGGATATCAACCTCAGTTTGACGAGCCAC
9258 TACGATACTC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
44 36 0.51
45 32 0.45
46 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGTAATAC
Found at i:9586 original size:28 final size:28
Alignment explanation
Indices: 9529--9611 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
9519 TATTAAACCC
* * * *
9529 TAAAACC-TAAATTATAAACCCTAAACT
1 TAAAACCTTAAATCATAAACACTAGATT
*
9556 TAAAACCTTAAATCATAAACAATAGATT
1 TAAAACCTTAAATCATAAACACTAGATT
* *
9584 TAAAA-CTCTAAACCGTAAACACTAGATT
1 TAAAACCT-TAAATCATAAACACTAGATT
9612 GATTAATGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 9 0.20
28 37 0.80
ACGTcount: A:0.51, C:0.19, G:0.04, T:0.27
Consensus pattern (28 bp):
TAAAACCTTAAATCATAAACACTAGATT
Found at i:12622 original size:19 final size:19
Alignment explanation
Indices: 12576--12623 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
12566 AATAAATCTG
*
12576 TTAAAAATTAAATAAAATT
1 TTAAAAATAAAATAAAATT
**
12595 TTAATAAATAAAATACGATT
1 TTAA-AAATAAAATAAAATT
12615 TTAAAAATA
1 TTAAAAATA
12624 TATCATACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAATAAAATT
Found at i:12669 original size:4 final size:4
Alignment explanation
Indices: 12660--12751 Score: 105
Period size: 4 Copynumber: 22.5 Consensus size: 4
12650 AAACACATTA
* * * *
12660 TCTT TCTT TCTT TC-T TCTT TCTT TCCTC TCCT TCTT CCTT TCTTT TCTC
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TC-TT TCTT
*
12709 TCTT TCTT CCTT TCTT TCTT TCTT TCTTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TC
12752 CTATTTTATA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.04
4 60 0.81
5 11 0.15
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TCTT
Found at i:12742 original size:21 final size:20
Alignment explanation
Indices: 12660--12751 Score: 114
Period size: 21 Copynumber: 4.5 Consensus size: 20
12650 AAACACATTA
12660 TCTTTCTTTCTTTCTT-CTT
1 TCTTTCTTTCTTTCTTCCTT
* *
12679 TCTTTCCTCTCCTTCTTCCTT
1 TCTTT-CTTTCTTTCTTCCTT
*
12700 TCTTTTCTCTCTTTCTTCCTT
1 TC-TTTCTTTCTTTCTTCCTT
*
12721 TCTTTCTTTCTTTCTTTTCTT
1 TCTTTCTTTCTTTC-TTCCTT
12742 TCTTTCTTTC
1 TCTTTCTTTC
12752 CTATTTTATA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
19 5 0.08
20 20 0.31
21 36 0.56
22 3 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTTTCTTTCTTTCTTCCTT
Found at i:23173 original size:12 final size:12
Alignment explanation
Indices: 23152--23181 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23142 GGGAGAAGAA
*
23152 AAAGAAAGAAAG
1 AAAGATAGAAAG
23164 AAAGATAGAAAG
1 AAAGATAGAAAG
23176 AAAGAT
1 AAAGAT
23182 GGGTTCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (12 bp):
AAAGATAGAAAG
Found at i:39888 original size:23 final size:22
Alignment explanation
Indices: 39841--39892 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
39831 AATTGATCCT
* *
39841 AAAATATTGAAAATATCCCATA
1 AAAATTTTGAAAATATCCCACA
*
39863 AAAATTTTGAAAATCAT-CCACC
1 AAAATTTTGAAAAT-ATCCCACA
39885 AAAATTTT
1 AAAATTTT
39893 ATGAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATTTTGAAAATATCCCACA
Found at i:46375 original size:25 final size:25
Alignment explanation
Indices: 46342--46415 Score: 139
Period size: 25 Copynumber: 3.0 Consensus size: 25
46332 TAAAAATGAG
46342 AAAATATTTTTTTATAAATTTTTAA
1 AAAATATTTTTTTATAAATTTTTAA
46367 AAAATATTTTTTTATAAATTTTTAA
1 AAAATATTTTTTTATAAATTTTTAA
*
46392 AAAATATTTTTTTATAAAATTTTA
1 AAAATATTTTTTTATAAATTTTTA
46416 TAGTTTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AAAATATTTTTTTATAAATTTTTAA
Found at i:47167 original size:14 final size:13
Alignment explanation
Indices: 47127--47167 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
47117 AAAATACATT
47127 TTTATTAAAAATA
1 TTTATTAAAAATA
* *
47140 TTTATTTAATATA
1 TTTATTAAAAATA
47153 TTTCATTAAAAATA
1 TTT-ATTAAAAATA
47167 T
1 T
47168 AATCTAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TTTATTAAAAATA
Found at i:54654 original size:2 final size:2
Alignment explanation
Indices: 54647--54674 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54637 CATTTAAGAA
54647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54675 TTAAGTTTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62437 original size:3 final size:3
Alignment explanation
Indices: 62387--62417 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
62377 GAGCCTACAT
*
62387 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
62418 AAATAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:62565 original size:24 final size:24
Alignment explanation
Indices: 62537--62584 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
62527 AAATTGAGAG
62537 TACTAAATCTGTTCAAGTGAGAAA
1 TACTAAATCTGTTCAAGTGAGAAA
62561 TACTAAATCTGTTCAAGTGAGAAA
1 TACTAAATCTGTTCAAGTGAGAAA
62585 CTTTTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (24 bp):
TACTAAATCTGTTCAAGTGAGAAA
Done.