Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010929.1 Kokia drynarioides strain JFW-HI SEQ_125897, 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: 12697
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Found at i:9646 original size:14 final size:13
Alignment explanation
Indices: 9624--9657 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
9614 CAAAGGGCAT
*
9624 AAAAAAAAAAGTA
1 AAAAAAAAAAATA
9637 AAAAATAAAAAATA
1 AAAAA-AAAAAATA
9651 AAAAAAA
1 AAAAAAA
9658 GGGTTCAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAAATA
Found at i:10842 original size:204 final size:204
Alignment explanation
Indices: 10444--11305 Score: 1340
Period size: 204 Copynumber: 4.2 Consensus size: 204
10434 GATTGCGATT
*
10444 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAATGAGGCTCAA
1 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
* * *
10509 AACGAGCGAAATCTTCGAACCTCGCCTTCCCGATGAG--ACTGAGAAGCAAGTCGAAGCAATAAA
66 AACGAACGAAATCTTCGAACCCCGCCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
* * *
10572 AGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAAGTACAGAGG
131 AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGG
10637 AGCGAATTG
196 AGCGAATTG
* *
10646 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTAAGAAGAAGATCCAAACAAGGCTCAA
1 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
* *
10711 AACGAACGAAATCTTTGAACCCCGCTTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
66 AACGAACGAAATCTTCGAACCCCGCCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
10776 AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGG
131 AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGG
*
10841 AGCAAATTG
196 AGCGAATTG
*
10850 ATCCAAACAGCAATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
1 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
* * * ** * *
10915 AATGAGCGAAATCTTAGAACCCCGCCTTCCTAAAGAGACATTGAGAAGC-GAGTCGAAGCAATAA
66 AACGAACGAAATCTTCGAACCCCGCCTTCCCGATGAGACACTGAGAAGCAG-GTCGAAGCAATAA
* * *
10979 AAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCTTGATGAGGTACAGAG
130 AAGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAG
11044 GAGCGAATTG
195 GAGCGAATTG
** *
11054 AAACAAACAGCGATATGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
1 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
*
11119 AACGAACGAAATCTTCGAACCCCGCCTTCTCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
66 AACGAACGAAATCTTCGAACCCCGCCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
* * * *
11184 AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATGAGATATAGAGA
131 AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGG
*
11249 AGCGAATCG
196 AGCGAATTG
** * **
11258 AAAC-AA-A-TGATGCAATCATCTTCCTGATGAGACACTGAGAAGAAGATC
1 ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATC
11306 AAATCAGTGA
Statistics
Matches: 605, Mismatches: 51, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
201 37 0.06
202 96 0.16
203 3 0.00
204 468 0.77
205 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (204 bp):
ATCCAAACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTCAA
AACGAACGAAATCTTCGAACCCCGCCTTCCCGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
AGGTTAGCTTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGG
AGCGAATTG
Found at i:11399 original size:25 final size:25
Alignment explanation
Indices: 11365--11415 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11355 GCAGAGGTAG
11365 ATGCGGCAAAATCGAACAATTAAAC
1 ATGCGGCAAAATCGAACAATTAAAC
11390 ATGCGGCAAAATCGAACAATTAAAC
1 ATGCGGCAAAATCGAACAATTAAAC
11415 A
1 A
11416 AAGCAGAAAG
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:0.49, C:0.20, G:0.16, T:0.16
Consensus pattern (25 bp):
ATGCGGCAAAATCGAACAATTAAAC
Found at i:11580 original size:11 final size:11
Alignment explanation
Indices: 11561--11616 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
11551 GGTTGGGCCC
*
11561 TTTTTAATTTA
1 TTTTAAATTTA
11572 TTTTAAATTTGA
1 TTTTAAATTT-A
11584 -TTTAAATTTAA
1 TTTTAAATTT-A
* *
11595 ATTTAAATTAA
1 TTTTAAATTTA
*
11606 TCTTAAATTTA
1 TTTTAAATTTA
11617 AATTTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:11594 original size:6 final size:6
Alignment explanation
Indices: 11573--11623 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
11563 TTTAATTTAT
*
11573 TTTAAA TTT-GA TTTAAA TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
11619 TTTAA
1 TTTAA
11624 TTACAAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 2 0.05
5 6 0.15
6 28 0.72
7 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:11605 original size:17 final size:16
Alignment explanation
Indices: 11563--11625 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
11553 TTGGGCCCTT
* *
11563 TTTAATTTATTTTAAA
1 TTTAAATTAATTTAAA
* *
11579 TTTGATTTAAATTTAAA
1 TTTAAATT-AATTTAAA
11596 TTTAAATTAATCTTAAA
1 TTTAAATTAAT-TTAAA
11613 TTTAAATTTAATT
1 TTTAAA-TTAATT
11626 ACAAAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 10 0.25
17 25 0.62
18 5 0.12
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:11883 original size:23 final size:23
Alignment explanation
Indices: 11857--11918 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 23
11847 TCATCAGCAG
*
11857 CTTGTCACCATCTTCGGCCCCAA
1 CTTGTCACCATCTTCGACCCCAA
*
11880 CTTGCACTGTCACCATCTTCGACCCCAG
1 C-T----TGTCACCATCTTCGACCCCAA
11908 CTTGTCACCAT
1 CTTGTCACCAT
11919 TTTCCATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
23 10 0.31
24 1 0.03
27 1 0.03
28 20 0.62
ACGTcount: A:0.18, C:0.42, G:0.13, T:0.27
Consensus pattern (23 bp):
CTTGTCACCATCTTCGACCCCAA
Found at i:12055 original size:29 final size:29
Alignment explanation
Indices: 12023--12300 Score: 225
Period size: 30 Copynumber: 9.5 Consensus size: 29
12013 AAATTATTTG
* *
12023 AAAATTACCATTTTACCCTCGAACTTCTA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* *
12052 AAAA-TCCCATTTTTAACCCTAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTCAAACTTCCA
* * *
12082 AAAAATACCATTTTACCCCCGAACTTCCA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* *
12111 AAAGTCA-CATTTTTAACCC-CAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTC-AAACTTCCA
*
12141 AAAATTACCA-TTTAGCCCTCGAACTTCCA
1 AAAATTACCATTTTA-CCCTCAAACTTCCA
*
12170 AAAA-TCCCATTTTTGACCC-CAAAACTTCCA
1 AAAATTACCA-TTTT-ACCCTC-AAACTTCCA
12200 AAAATTACCATTTTACCC-CTAAACTTCCA
1 AAAATTACCATTTTACCCTC-AAACTTCCA
*
12229 AAAA-TCCCATTTTTTA-CCTCGAAACTTCCA
1 AAAATTACCA--TTTTACCCTC-AAACTTCCA
* *
12259 AGAATTACCATTTTACCCCCAAACTT-CA
1 AAAATTACCATTTTACCCTCAAACTTCCA
* *
12287 AAAAGTCCCATTTT
1 AAAATTACCATTTT
12301 TAACCCCGAA
Statistics
Matches: 203, Mismatches: 27, Indels: 39
0.75 0.10 0.14
Matches are distributed among these distances:
28 28 0.14
29 79 0.39
30 81 0.40
31 15 0.07
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCAAACTTCCA
Found at i:12105 original size:59 final size:59
Alignment explanation
Indices: 12023--12307 Score: 403
Period size: 59 Copynumber: 4.8 Consensus size: 59
12013 AAATTATTTG
* * *
12023 AAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTAACCCTAAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
* * *
12082 AAAAATACCATTTTACCCCCGAACTTCCAAAAGTCACATTTTTAACCCCAAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
* *
12141 AAAATTACCA-TTTAGCCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
1 AAAATTACCATTTTA-CCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
** * * *
12200 AAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTTACCTCGAAACTTCCA
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
* *
12259 AGAATTACCATTTTACCCCCAAACTT-CAAAAAGTCCCATTTTTAACCCC
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAA-TCCCATTTTTAACCCC
12308 GAATTTTCTC
Statistics
Matches: 202, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
58 10 0.05
59 188 0.93
60 4 0.02
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.29
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCA
Found at i:12301 original size:29 final size:29
Alignment explanation
Indices: 12033--12307 Score: 229
Period size: 29 Copynumber: 9.3 Consensus size: 29
12023 AAAATTACCA
* * *
12033 TTTTACCCTCGAACTTCTAAAAATCCCAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
** *
12062 TTTTAACCCTAAAACTTCCAAAAAATACCA-
1 TTTT-ACCCCCAAACTTCC-AAAAATCCCAT
* * *
12092 TTTTACCCCCGAACTTCCAAAAGTCACAT
1 TTTTACCCCCAAACTTCCAAAAATCCCAT
* *
12121 TTTTAACCCCAAAACTTCCAAAAATTACCA-
1 TTTT-ACCCCCAAACTTCCAAAAA-TCCCAT
* *
12151 -TTTAGCCCTCGAACTTCCAAAAATCCCAT
1 TTTTA-CCCCCAAACTTCCAAAAATCCCAT
* *
12180 TTTTGACCCCAAAACTTCCAAAAATTACCA-
1 TTTT-ACCCCCAAACTTCCAAAAA-TCCCAT
*
12210 TTTTACCCCTAAACTTCCAAAAATCCCATT
1 TTTTACCCCCAAACTTCCAAAAATCCCA-T
* * * *
12240 TTTTACCTCGAAACTTCCAAGAATTACCA-
1 TTTTACCCCCAAACTTCCAA-AAATCCCAT
12269 TTTTACCCCCAAACTT-CAAAAAGTCCCAT
1 TTTTACCCCCAAACTTCCAAAAA-TCCCAT
*
12298 TTTTAACCCC
1 TTTTACCCCC
12308 GAATTTTCTC
Statistics
Matches: 197, Mismatches: 34, Indels: 30
0.75 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 23 0.12
29 78 0.40
30 71 0.36
31 23 0.12
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.29
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCAAAAATCCCAT
Done.