Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013409.1 Kokia drynarioides strain JFW-HI SEQ_128434, 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: 12202
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Found at i:26 original size:2 final size:2
Alignment explanation
Indices: 19--51 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9 GAAAAGTAAA
19 AT 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 AT A
52 AAAAGATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:960 original size:30 final size:30
Alignment explanation
Indices: 923--1223 Score: 264
Period size: 30 Copynumber: 10.1 Consensus size: 30
913 TTACCCCGAG
*
923 CTTTCTAAAAATTCATTTTTGACCCCTAAA
1 CTTTCTAAAATTTCATTTTTGACCCCTAAA
* * * *
953 TTTTCTAAAATTTCATCTTCGA-CCCTCGAA
1 CTTTCTAAAATTTCATTTTTGACCCCT-AAA
*
983 CTTTCTAAAATTTCATTTTTGACCCTTAAA
1 CTTTCTAAAATTTCATTTTTGACCCCTAAA
* * *
1013 CTTTCTAGAATTTCATTTTT-AACCCTCGAA
1 CTTTCTAAAATTTCATTTTTGACCCCT-AAA
* * *
1043 CTTTCTAAAATTTCATTTGTGAACTCC-GAA
1 CTTTCTAAAATTTCATTTTTG-ACCCCTAAA
1073 CTTTCTAAAATTTCA-TTTTGACCCCTAAA
1 CTTTCTAAAATTTCATTTTTGACCCCTAAA
1102 CTTTCTAAAAATTTCA-TTTTGACCCCTAAA
1 CTTTCT-AAAATTTCATTTTTGACCCCTAAA
* *
1132 CTTTTTGAAAATTTCA-TTTT-AACCCTCAAA
1 CTTTCT-AAAATTTCATTTTTGACCCCT-AAA
* * * * *
1162 CTTTTTGAACATTTCA-TTTTAACCCTTGAA
1 CTTTCT-AAAATTTCATTTTTGACCCCTAAA
* *
1192 CTTT-TAAAATTGCA-CTTTGA-CCCTCAAA
1 CTTTCTAAAATTTCATTTTTGACCCCT-AAA
1220 CTTT
1 CTTT
1224 TTGAAAAATT
Statistics
Matches: 227, Mismatches: 34, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.01
28 21 0.09
29 26 0.11
30 167 0.74
31 7 0.03
32 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (30 bp):
CTTTCTAAAATTTCATTTTTGACCCCTAAA
Found at i:998 original size:60 final size:59
Alignment explanation
Indices: 923--1223 Score: 324
Period size: 60 Copynumber: 5.1 Consensus size: 59
913 TTACCCCGAG
* * * *
923 CTTTCTAAAAATTCATTTTTGACCCCTAAATTTTCTAAAATTTCATCTTCGACCCTCGAA
1 CTTTCTAAAATTTCATTTTTGACCCCTAAACTTTCTAAAATTTCAT-TTTGACCCTCAAA
* * * *
983 CTTTCTAAAATTTCATTTTTGACCCTTAAACTTTCTAGAATTTCATTTTTAACCCTCGAA
1 CTTTCTAAAATTTCATTTTTGACCCCTAAACTTTCTAAAATTTCA-TTTTGACCCTCAAA
* * *
1043 CTTTCTAAAATTTCATTTGTGAACTCC-GAACTTTCTAAAATTTCATTTTGACCC-CTAAA
1 CTTTCTAAAATTTCATTTTTG-ACCCCTAAACTTTCTAAAATTTCATTTTGACCCTC-AAA
* *
1102 CTTTCTAAAAATTTCA-TTTTGACCCCTAAACTTTTTGAAAATTTCATTTTAACCCTCAAA
1 CTTTCT-AAAATTTCATTTTTGACCCCTAAACTTTCT-AAAATTTCATTTTGACCCTCAAA
* * * * * * *
1162 CTTTTTGAACATTTCA-TTTTAACCCTTGAACTTT-TAAAATTGCACTTTGACCCTCAAA
1 CTTTCT-AAAATTTCATTTTTGACCCCTAAACTTTCTAAAATTTCATTTTGACCCTCAAA
1220 CTTT
1 CTTT
1224 TTGAAAAATT
Statistics
Matches: 207, Mismatches: 27, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
58 29 0.14
59 28 0.14
60 145 0.70
61 5 0.02
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (59 bp):
CTTTCTAAAATTTCATTTTTGACCCCTAAACTTTCTAAAATTTCATTTTGACCCTCAAA
Found at i:1028 original size:90 final size:88
Alignment explanation
Indices: 923--1202 Score: 318
Period size: 90 Copynumber: 3.1 Consensus size: 88
913 TTACCCCGAG
* *
923 CTTTCTAAAAATTCATTTTTGACCCCTAAATTTTCTAAAATTTCATCTTCGACCCTCGAACTTTC
1 CTTTCTAAAATTTCATTTTTGACCCCTAAATTTTCTAAAATTTCAT-TTTGACCCTCGAACTTTC
988 TAAAATTTCATTTTTGACCCTTAAA
65 TAAAATTTCA-TTTTGACCCTTAAA
* * * * *
1013 CTTTCTAGAATTTCATTTTT-AACCCTCGAACTTTCTAAAATTTCATTTGTGA-ACTCCGAACTT
1 CTTTCTAAAATTTCATTTTTGACCCCT-AAATTTTCTAAAATTTCATTT-TGACCCT-CGAACTT
*
1076 TCTAAAATTTCATTTTGACCCCTAAA
63 TCTAAAATTTCATTTTGACCCTTAAA
* *
1102 CTTTCTAAAAATTTCA-TTTTGACCCCTAAACTTTT-TGAAAATTTCATTTTAACCCTCAAACTT
1 CTTTCT-AAAATTTCATTTTTGACCCCTAAA-TTTTCT-AAAATTTCATTTTGACCCTCGAACTT
* * * *
1165 TTTGAACATTTCATTTTAACCCTTGAA
63 TCT-AAAATTTCATTTTGACCCTTAAA
1192 CTTT-TAAAATT
1 CTTTCTAAAATT
1203 GCACTTTGAC
Statistics
Matches: 161, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
88 6 0.04
89 46 0.29
90 109 0.68
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (88 bp):
CTTTCTAAAATTTCATTTTTGACCCCTAAATTTTCTAAAATTTCATTTTGACCCTCGAACTTTCT
AAAATTTCATTTTGACCCTTAAA
Found at i:3753 original size:40 final size:41
Alignment explanation
Indices: 3672--3759 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 41
3662 ATTTTATCTG
* *
3672 AATTTTTGTAAATATTTTGTAGTGTTAATTATAATTTTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATTATAATTCTTAT
* *
3713 -ATTTTTGTGAATATTTTGTATTATTAATTATAGA-TCTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATTATA-ATTCTTAT
3753 AATTTTT
1 AATTTTT
3760 TTCTATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 34 0.83
41 7 0.17
ACGTcount: A:0.31, C:0.01, G:0.09, T:0.59
Consensus pattern (41 bp):
AATTTTTGTAAATATTTTGTAGTATTAATTATAATTCTTAT
Found at i:6316 original size:40 final size:40
Alignment explanation
Indices: 6261--6341 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
6251 CCAATACAAG
6261 TGCCTTCTCTTTTGCATCCACATATGATCGCTGGCTTTGA
1 TGCCTTCTCTTTTGCATCCACATATGATCGCTGGCTTTGA
*
6301 TGCCTTCTCTTTTGCATCCACATATGATTGCTGGCTTTGA
1 TGCCTTCTCTTTTGCATCCACATATGATCGCTGGCTTTGA
6341 T
1 T
6342 AGTTGCTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.42
Consensus pattern (40 bp):
TGCCTTCTCTTTTGCATCCACATATGATCGCTGGCTTTGA
Found at i:6570 original size:31 final size:31
Alignment explanation
Indices: 6532--6595 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
6522 AGATATCCTT
6532 TTCCACCCATCACACATAATGGTCACCCCTC
1 TTCCACCCATCACACATAATGGTCACCCCTC
6563 TTCCACCCATCACACATAATGGTCACCCCTC
1 TTCCACCCATCACACATAATGGTCACCCCTC
6594 TT
1 TT
6596 TCTTCCCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.44, G:0.06, T:0.25
Consensus pattern (31 bp):
TTCCACCCATCACACATAATGGTCACCCCTC
Found at i:6703 original size:50 final size:50
Alignment explanation
Indices: 6645--6746 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
6635 ATCTCATTAT
6645 ACTTATCTTCCAAATACACTCCCATCACTTCATAAACTGAAGGAACCTTA
1 ACTTATCTTCCAAATACACTCCCATCACTTCATAAACTGAAGGAACCTTA
6695 ACTTATCTTCCAAATACACTCCCATCACTTCATAAACTGAAGGAACCTTA
1 ACTTATCTTCCAAATACACTCCCATCACTTCATAAACTGAAGGAACCTTA
6745 AC
1 AC
6747 CAATTTTCTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.36, C:0.30, G:0.06, T:0.27
Consensus pattern (50 bp):
ACTTATCTTCCAAATACACTCCCATCACTTCATAAACTGAAGGAACCTTA
Found at i:7649 original size:51 final size:51
Alignment explanation
Indices: 7559--7668 Score: 154
Period size: 51 Copynumber: 2.1 Consensus size: 51
7549 ACTTGAGTTC
*
7559 AAACTAACTAATAAAATATTCATAAAAATGAAAAAAAAAATGAT-AAGACTTA
1 AAACTAACTAATAAAATATTCACAAAAATG-AAAAAAAAATGATAAAG-CTTA
7611 AAACTAAC-AATAAAAAATATTCACAAAAATG-AAAAAAAATGATAAAGCTTA
1 AAACTAACTAAT--AAAATATTCACAAAAATGAAAAAAAAATGATAAAGCTTA
7662 AAACTAA
1 AAACTAA
7669 AAAATGAAAC
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
51 26 0.48
52 11 0.20
53 17 0.31
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (51 bp):
AAACTAACTAATAAAATATTCACAAAAATGAAAAAAAAATGATAAAGCTTA
Found at i:7677 original size:33 final size:35
Alignment explanation
Indices: 7635--7724 Score: 141
Period size: 34 Copynumber: 2.7 Consensus size: 35
7625 AAATATTCAC
*
7635 AAAAATGAAA-AAAAATGATAAAG-CTTAAAACTA
1 AAAAATGAAACAAAAATAATAAAGACTTAAAACTA
7668 AAAAATGAAACAAAAATAAT-AAGACTTAAAACTA
1 AAAAATGAAACAAAAATAATAAAGACTTAAAACTA
*
7702 CAAAATGAAACAAAAATAATAAA
1 AAAAATGAAACAAAAATAATAAA
7725 ACTCTAACAG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 13 0.25
34 37 0.71
35 2 0.04
ACGTcount: A:0.69, C:0.08, G:0.07, T:0.17
Consensus pattern (35 bp):
AAAAATGAAACAAAAATAATAAAGACTTAAAACTA
Found at i:7923 original size:21 final size:21
Alignment explanation
Indices: 7899--7938 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7889 TAATTATTAA
*
7899 TTAAATATGTAAAAATAATAT
1 TTAAATATATAAAAATAATAT
* *
7920 TTAAGTATATAAATATAAT
1 TTAAATATATAAAAATAAT
7939 TAATTATTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TTAAATATATAAAAATAATAT
Found at i:10190 original size:29 final size:29
Alignment explanation
Indices: 10143--10201 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
10133 TTATAAAAAA
* * *
10143 AAATTATTAATGATTAAAATGGTATTTTT
1 AAATTATTAATGATCAAAATGATATGTTT
* *
10172 AAATTATTATTTATCAAAATGATATGTTT
1 AAATTATTAATGATCAAAATGATATGTTT
10201 A
1 A
10202 GTTAAGTGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (29 bp):
AAATTATTAATGATCAAAATGATATGTTT
Found at i:10627 original size:4 final size:4
Alignment explanation
Indices: 10614--10688 Score: 59
Period size: 4 Copynumber: 19.0 Consensus size: 4
10604 AAAATTGAAG
*
10614 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA G-AA G-AA G-AA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA
* * *
10659 GGAA GAAG GAAAA GAAA GGGAA GAAA GAAA
1 GAAA GAAA G-AAA GAAA -GAAA GAAA GAAA
10689 AAGAAAAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
3 12 0.20
4 38 0.64
5 9 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:10631 original size:13 final size:13
Alignment explanation
Indices: 10615--10700 Score: 59
Period size: 13 Copynumber: 6.5 Consensus size: 13
10605 AAATTGAAGG
10615 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
*
10628 AAAAGAGAAAG-A
1 AAAAAAGAAAGAA
*
10640 AAGAAAGAAAGAA
1 AAAAAAGAAAGAA
* * *
10653 GAAGAAGGAAGAA
1 AAAAAAGAAAGAA
**
10666 GGAAAAGAAAGGGAA
1 AAAAAAGAAA--GAA
*
10681 GAAAGAA-AAAGAA
1 -AAAAAAGAAAGAA
10694 AAAAAAG
1 AAAAAAG
10701 TAATGTGTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
12 15 0.28
13 30 0.56
15 6 0.11
16 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:10664 original size:25 final size:25
Alignment explanation
Indices: 10610--10694 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
10600 AACGAAAATT
*
10610 GAAGGAAAAAAGAAAG-AA-AA-AA
1 GAAGGAAGAAAGAAAGAAAGAAGAA
*
10632 G-AGAAAGAAAGAAAGAAAGAAGAA
1 GAAGGAAGAAAGAAAGAAAGAAGAA
* *
10656 GAAGGAAGAAGGAAAAGAAAG-GGAA
1 GAAGGAAGAAAG-AAAGAAAGAAGAA
*
10681 GAAAGAA-AAAGAAA
1 GAAGGAAGAAAGAAA
10695 AAAAAGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
21 12 0.24
22 3 0.06
23 5 0.10
24 6 0.12
25 17 0.33
26 8 0.16
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (25 bp):
GAAGGAAGAAAGAAAGAAAGAAGAA
Found at i:11374 original size:157 final size:156
Alignment explanation
Indices: 11085--11403 Score: 570
Period size: 157 Copynumber: 2.0 Consensus size: 156
11075 TTAGTAGTAG
11085 TAAG-TAAAAAATATTGTTTATATTTATTGATTTAAAATTTAATAATTTTAAATTTTGTTAGTTA
1 TAAGTTAAAAAATATTGTTTATATTTATTGATTTAAAATTTAATAATTTTAAATTTTGTTAGTTA
*
11149 ATAATTTTATTATACAAGTCATAAGATTGTTTAATAAAATGTGAAAGAAAACTATTACAAGTGTT
66 ATAATTTTATTATACAAGTCATAAGATTGTTTAATAAAATGTGAAAGAAAAATATTACAAGTGTT
11214 TAATAAAATAAATAATAATCCATTTT
131 TAATAAAATAAATAATAATCCATTTT
11240 TAAGTTAAAAAATATTGTTTATATTTATTGATTTAAAATTTAATAATGTTTAAATTTTGTTAGTT
1 TAAGTTAAAAAATATTGTTTATATTTATTGATTTAAAATTTAATAAT-TTTAAATTTTGTTAGTT
* *
11305 AGTAACTTTT-TTATACAAGTCATAAGATTGTTTAATAAAATGTGAAAGAAAAATATTATAAGTG
65 AATAA-TTTTATTATACAAGTCATAAGATTGTTTAATAAAATGTGAAAGAAAAATATTACAAGTG
*
11369 TTTAATAAAATAAATAATAATTCATTTT
129 TTTAATAAAATAAATAATAATCCATTTT
11397 TAAGTTA
1 TAAGTTA
11404 TAATTAAAAT
Statistics
Matches: 157, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
155 4 0.03
156 42 0.27
157 107 0.68
158 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (156 bp):
TAAGTTAAAAAATATTGTTTATATTTATTGATTTAAAATTTAATAATTTTAAATTTTGTTAGTTA
ATAATTTTATTATACAAGTCATAAGATTGTTTAATAAAATGTGAAAGAAAAATATTACAAGTGTT
TAATAAAATAAATAATAATCCATTTT
Found at i:11543 original size:16 final size:16
Alignment explanation
Indices: 11496--11545 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
11486 TAAACCTAAC
*
11496 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
11512 TAA--AA-TATAAAAAA
1 TAATTAATTAT-CAAAA
11526 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
11542 TAAT
1 TAAT
11546 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 9 0.33
16 13 0.48
17 3 0.11
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Done.