Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013396.1 Kokia drynarioides strain JFW-HI SEQ_128420, 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: 52254
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:5242 original size:22 final size:22
Alignment explanation
Indices: 5208--5311 Score: 154
Period size: 22 Copynumber: 4.6 Consensus size: 22
5198 ATGCTAGCGC
*
5208 GCTTACTGATCAGCACTGTGTGT
1 GCTT-CTGTTCAGCACTGTGTGT
5231 GCTTCTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
5253 GCTTCTGATCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
5275 GCTTTTGTTCAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
5297 GCTCTCTGTTTAGCA
1 GCT-TCTGTTCAGCA
5312 TGTTTCGTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
22 61 0.82
23 13 0.18
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.39
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:5334 original size:68 final size:66
Alignment explanation
Indices: 5217--5344 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
5207 CGCTTACTGA
* *
5217 TCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCTTCTGATCAGCACTGTGTGTGCTTTTG
1 TCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTCCCTCTGATCAGCACTGTGTGTGCTTTTG
5282 T
66 T
* * *
5283 TCAGCACTGTGTGTGCTCTCTGTTTAGCA-TGTTTCGTACCCTCTGATCAGCACTTTGTGTGC
1 TCAGCACTGTGTGTGCT-TCTGTTCAGCACTGTGT-GT-CCCTCTGATCAGCACTGTGTGTGC
5345 CCACTTCGTG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
66 21 0.39
67 12 0.22
68 21 0.39
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (66 bp):
TCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTCCCTCTGATCAGCACTGTGTGTGCTTTTG
T
Found at i:7590 original size:18 final size:17
Alignment explanation
Indices: 7567--7610 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
7557 ATACACCTCG
*
7567 TTTCCTTTCATTTTCTAT
1 TTTCCTTTC-CTTTCTAT
7585 TTTCCTCTTCCTTTCTAT
1 TTTCCT-TTCCTTTCTAT
*
7603 TCTCCTTT
1 TTTCCTTT
7611 TCTCACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 18 0.78
19 3 0.13
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCCTTTCCTTTCTAT
Found at i:9747 original size:23 final size:24
Alignment explanation
Indices: 9721--9766 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
9711 AAAAGTGATA
* *
9721 AAAAAAACTAGAGAAA-AAAAAAG
1 AAAAAAACAAGAAAAATAAAAAAG
*
9744 AAAAATACAAGAAAAATAAAAAA
1 AAAAAAACAAGAAAAATAAAAAA
9767 ATTCCATGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (24 bp):
AAAAAAACAAGAAAAATAAAAAAG
Found at i:11388 original size:24 final size:24
Alignment explanation
Indices: 11361--11416 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
11351 GGAGAGTTCT
*
11361 CAAGAGGAAAAAGAAAAAGAAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
* *
11385 CAAGAAGAAAATGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAAAGAAAAA
11409 CAAGAAGA
1 CAAGAAGA
11417 TACCCATACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.71, C:0.05, G:0.20, T:0.04
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAAAGAAAAA
Found at i:13391 original size:21 final size:22
Alignment explanation
Indices: 13359--13400 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
13349 AAAGTAATGT
13359 AAAAAGTAGAGAAAAA-AAAAG
1 AAAAAGTAGAGAAAAAGAAAAG
13380 AAAAA-TACGAGAAAAAGAAAA
1 AAAAAGTA-GAGAAAAAGAAAA
13401 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAAGTAGAGAAAAAGAAAAG
Found at i:15004 original size:12 final size:12
Alignment explanation
Indices: 14987--15028 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
14977 TTCTCAAGAG
14987 GAAAAAGAAAAT
1 GAAAAAGAAAAT
*
14999 GAAAAACAAGAA-
1 GAAAAAGAA-AAT
*
15011 GAGAAAGAAAAT
1 GAAAAAGAAAAT
15023 GAAAAA
1 GAAAAA
15029 CAAGAAGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (12 bp):
GAAAAAGAAAAT
Found at i:15008 original size:24 final size:24
Alignment explanation
Indices: 14981--15036 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
14971 GGAGAGTTCT
*
14981 CAAGAGGAAAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
*
15005 CAAGAAGAGAAAGAAAATGAAAAA
1 CAAGAAGAAAAAGAAAATGAAAAA
15029 CAAGAAGA
1 CAAGAAGA
15037 TACCCATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.70, C:0.05, G:0.21, T:0.04
Consensus pattern (24 bp):
CAAGAAGAAAAAGAAAATGAAAAA
Found at i:19016 original size:79 final size:80
Alignment explanation
Indices: 18890--19078 Score: 301
Period size: 79 Copynumber: 2.4 Consensus size: 80
18880 AATTTAACTG
* * *
18890 ACTAGAGTTGGGCTCAC-TTTCACGATTTATCCACTAGGCACTGGGTGCTAGGATTTGACAGATA
1 ACTAGAGCTGGGCTCACATTT-GCGATTTATCCACTAGGCACTAGGTGCTAGGATTTGACAGATA
18954 TTTGTTGGTTAAACCA
65 TTTGTTGGTTAAACCA
*
18970 ACTAGAGCTGGGCTCACATTTGC-ATTTATCCACTAGGCACTAGGTGCTAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACATTTGCGATTTATCCACTAGGCACTAGGTGCTAGGATTTGACAGATAT
19034 TTGTTGGTTAAACCA
66 TTGTTGGTTAAACCA
* *
19049 ACTAGAGCTGGGCTCAAATTTGCGGTTTAT
1 ACTAGAGCTGGGCTCACATTTGCGATTTAT
19079 TGGTTAGGCA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
79 76 0.75
80 22 0.22
81 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACATTTGCGATTTATCCACTAGGCACTAGGTGCTAGGATTTGACAGATAT
TTGTTGGTTAAACCA
Found at i:20730 original size:15 final size:15
Alignment explanation
Indices: 20712--20743 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20702 AGCATGTACC
20712 TTGCGAGCACTAATG
1 TTGCGAGCACTAATG
*
20727 TTGCGAGCACTTATG
1 TTGCGAGCACTAATG
20742 TT
1 TT
20744 ATGAACACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (15 bp):
TTGCGAGCACTAATG
Found at i:23155 original size:24 final size:23
Alignment explanation
Indices: 23123--23179 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
23113 AAGAAATGAG
23123 AGAAAAAGAAATTGAAAGAGAAAA
1 AGAAAAAGAAATTGAAAGA-AAAA
*
23147 AGAAAAAGAACTTGAAAGAAAAA
1 AGAAAAAGAAATTGAAAGAAAAA
23170 AGAAAGAAGA
1 AGAAA-AAGA
23180 GTTGTTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 9 0.29
24 22 0.71
ACGTcount: A:0.70, C:0.02, G:0.21, T:0.07
Consensus pattern (23 bp):
AGAAAAAGAAATTGAAAGAAAAA
Found at i:29210 original size:15 final size:15
Alignment explanation
Indices: 29190--29245 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
29180 TTTAGATGTC
*
29190 AAACTATAGATTTTG
1 AAACTATAGATTATG
*
29205 AAACTATAAAATTATG
1 AAACTAT-AGATTATG
*
29221 AAAACTAT-GAGTTGTG
1 -AAACTATAGA-TTATG
29237 AAACTATAG
1 AAACTATAG
29246 GAAACTATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 15 0.45
16 11 0.33
17 7 0.21
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (15 bp):
AAACTATAGATTATG
Found at i:36698 original size:51 final size:51
Alignment explanation
Indices: 36626--36738 Score: 226
Period size: 51 Copynumber: 2.2 Consensus size: 51
36616 ACTATCTTAT
36626 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
1 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
36677 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
1 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
36728 GTTAAGAGGGT
1 GTTAAGAGGGT
36739 GAATTTGCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (51 bp):
GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
Found at i:36771 original size:51 final size:51
Alignment explanation
Indices: 36626--36771 Score: 161
Period size: 51 Copynumber: 2.9 Consensus size: 51
36616 ACTATCTTAT
* * * *
36626 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
1 GTTAAGAGGGTAAAGTTACCACATCCTAATGTCTTAAAATAATTTAATTAA
* * * *
36677 GTTAAGAGGGTAAAGTTATCACATCCTAATTTCTTTAATTAATTTAATTAA
1 GTTAAGAGGGTAAAGTTACCACATCCTAATGTCTTAAAATAATTTAATTAA
* * *
36728 GTTAAGAGGGTGAATTTGCCAGC-TCCT-ATGTCTTAAAAATAATT
1 GTTAAGAGGGTAAAGTTACCA-CATCCTAATGTCTT-AAAATAATT
36772 GTGAAATTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
50 6 0.07
51 79 0.92
52 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (51 bp):
GTTAAGAGGGTAAAGTTACCACATCCTAATGTCTTAAAATAATTTAATTAA
Found at i:37110 original size:24 final size:24
Alignment explanation
Indices: 37083--37141 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
37073 TGTGAACCAC
* **
37083 GCATTGCGAATTCTTGTGAGTTAT
1 GCATTGCGAACTCTTGCAAGTTAT
* *
37107 GCATTGTGAGCTCTTGCAAGTTAT
1 GCATTGCGAACTCTTGCAAGTTAT
*
37131 GCATTTCGAAC
1 GCATTGCGAAC
37142 ACCTTCGTGC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (24 bp):
GCATTGCGAACTCTTGCAAGTTAT
Found at i:39791 original size:35 final size:36
Alignment explanation
Indices: 39728--39796 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
39718 AATGATCGTT
* *
39728 GTTCATTTTACTCCCTGTTGACTCTAAGGTCATGAC
1 GTTCATTTTACTCCCTATTGACTCTAAGGCCATGAC
39764 GTTCA-TTTACTCCCTATTGAC-CATAAGGCCATG
1 GTTCATTTTACTCCCTATTGACTC-TAAGGCCATG
39797 CCTGTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 1 0.03
35 24 0.80
36 5 0.17
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (36 bp):
GTTCATTTTACTCCCTATTGACTCTAAGGCCATGAC
Found at i:46404 original size:51 final size:50
Alignment explanation
Indices: 46322--46549 Score: 289
Period size: 50 Copynumber: 4.5 Consensus size: 50
46312 ATGAACTAAT
* *
46322 GAGTTAC-TAAATGCATGAC-TTGATTTAATGATGCAAACTTTAATTAACATGG
1 GAGTTACAT-AATGCATGACATT-ATTT-ATGATGCAAAC-TTAACTAACATGA
* *
46374 GAGTTACATAATGCATGACATAATTTATGATGCAATCTTAACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCAAACTTAACTAACATGA
* * *
46424 GAGTTACATAATGCATGTCATTATTTATGATGAAAATTTAACTAATCATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCAAACTTAACTAA-CATGA
* * *
46475 GAGTTACATAATACATGTCATTATTTATGATGCATACTTAACTAACATGA
1 GAGTTACATAATGCATGACATTATTTATGATGCAAACTTAACTAACATGA
* *
46525 AAGTTACATAATGCATGACTTTATT
1 GAGTTACATAATGCATGACATTATT
46550 AAATGTAGAG
Statistics
Matches: 156, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
50 77 0.49
51 56 0.36
52 21 0.13
53 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (50 bp):
GAGTTACATAATGCATGACATTATTTATGATGCAAACTTAACTAACATGA
Found at i:46505 original size:101 final size:102
Alignment explanation
Indices: 46322--46554 Score: 305
Period size: 101 Copynumber: 2.3 Consensus size: 102
46312 ATGAACTAAT
* * *
46322 GAGTTAC-TAAATGCATGACTTGATTTAATGATGCAAACTTTAATTAACATGGGAGTTACATAAT
1 GAGTTACAT-AATGCATGACTTGATTTAATGATGCAAAATTTAACTAACATGAGAGTTACATAAT
*
46386 GCATGACATAATTTATGATGCA-ATCTTAACTAACATGA
65 ACATGACATAATTTATGATGCATA-CTTAACTAACATGA
*
46424 GAGTTACATAATGCATGTCATT-ATTT-ATGATG-AAAATTTAACTAATCATGAGAGTTACATAA
1 GAGTTACATAATGCATGAC-TTGATTTAATGATGCAAAATTTAACTAA-CATGAGAGTTACATAA
* *
46486 TACATGTCATTATTTATGATGCATACTTAACTAACATGA
64 TACATGACATAATTTATGATGCATACTTAACTAACATGA
* * *
46525 AAGTTACATAATGCATGACTTTATTAAATG
1 GAGTTACATAATGCATGACTTGATTTAATG
46555 TAGAGCACAT
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
100 13 0.11
101 75 0.65
102 24 0.21
103 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (102 bp):
GAGTTACATAATGCATGACTTGATTTAATGATGCAAAATTTAACTAACATGAGAGTTACATAATA
CATGACATAATTTATGATGCATACTTAACTAACATGA
Done.