Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009342.1 Kokia drynarioides strain JFW-HI SEQ_124049, 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: 27782
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:4261 original size:23 final size:22
Alignment explanation
Indices: 4233--4428 Score: 182
Period size: 23 Copynumber: 8.5 Consensus size: 22
4223 ATGCAAGTGC
4233 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
4256 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTT-GTGT
* *
4279 GCTTACTATTTCGCAACTCGTGT
1 GCTTACTGTTTCGC-ACTTGTGT
4302 GCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTCGCA-CTTGTGT
* *
4325 GCCTACTGATTT-GCACTATGTGC
1 GCTTACTG-TTTCGCACT-TGTGT
* *
4348 GCCTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACT-TGTGT
* *
4370 GCTTGCTGGATT-GCACTGTGTGT
1 GCTTACT-GTTTCGCACT-TGTGT
4393 GCTTACTGTTTCTCCAGCACTTGTGT
1 GCTTACTG-TT-T-C-GCACTTGTGT
4419 GCTTACTGTT
1 GCTTACTGTT
4429 AAATACTTAG
Statistics
Matches: 150, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
22 20 0.13
23 103 0.69
24 7 0.05
25 2 0.01
26 13 0.09
27 5 0.03
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (22 bp):
GCTTACTGTTTCGCACTTGTGT
Found at i:5117 original size:21 final size:20
Alignment explanation
Indices: 5071--5117 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
5061 ATAAACCGGG
5071 TATAAAGGTGTTACATTTTT
1 TATAAAGGTGTTACATTTTT
5091 TATAAAGGTGTTACATTTTT
1 TATAAAGGTGTTACATTTTT
5111 TACTAAA
1 TA-TAAA
5118 TTAATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (20 bp):
TATAAAGGTGTTACATTTTT
Found at i:11374 original size:2 final size:2
Alignment explanation
Indices: 11367--11391 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11357 CTTGAAAGTG
11367 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 A
11392 ATTTTCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16151 original size:15 final size:17
Alignment explanation
Indices: 16131--16164 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
16121 AATCTTGTAA
16131 AAACTA-TAAAAA-TAT
1 AAACTATTAAAAATTAT
16146 AAACTATTAAAAATTAT
1 AAACTATTAAAAATTAT
16163 AA
1 AA
16165 TTAATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAACTATTAAAAATTAT
Found at i:17099 original size:27 final size:28
Alignment explanation
Indices: 17068--17128 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
17058 AATTAGACTT
17068 TTTTGGA-TACCCGGGGGCAAAAT-GTAA
1 TTTTGGACT-CCCGGGGGCAAAATGGTAA
*
17095 TTTTGGACTCTCGGGGGCAAAATGGTAA
1 TTTTGGACTCCCGGGGGCAAAATGGTAA
17123 TTTTGG
1 TTTTGG
17129 GAAAGCTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (28 bp):
TTTTGGACTCCCGGGGGCAAAATGGTAA
Found at i:17244 original size:61 final size:60
Alignment explanation
Indices: 17143--17267 Score: 151
Period size: 61 Copynumber: 2.1 Consensus size: 60
17133 GCTTGGGGTT
* * *
17143 AAAAAATGGAATTTTAGACATTCGGGGGTAAAACAATAATTTTTTAAAAAAATCAGGATA
1 AAAAAACGGAATTTTAGACATCCGGGGGTAAAACAATAATTTTTGAAAAAAATCAGGATA
* *** ** *
17203 AAAAAACGGAAATTTTGGACATCCGGGGGTAAAATGGTAATTTTTGAAAAACTTCAGGGTA
1 AAAAAACGG-AATTTTAGACATCCGGGGGTAAAACAATAATTTTTGAAAAAAATCAGGATA
17264 AAAA
1 AAAA
17268 TGAAATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 8 0.15
61 46 0.85
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (60 bp):
AAAAAACGGAATTTTAGACATCCGGGGGTAAAACAATAATTTTTGAAAAAAATCAGGATA
Found at i:17513 original size:29 final size:30
Alignment explanation
Indices: 17259--17531 Score: 205
Period size: 29 Copynumber: 9.3 Consensus size: 30
17249 AAAAACTTCA
* * *
17259 GGGT-AAAAATGAAATTTTTGGAAG-TTCG
1 GGGTCAAAAATGGAATTTTTGAAAGTTTTG
* * *
17287 TGGAT-AAAAATGGAATTTTGGAAAGTTTCG
1 -GGGTCAAAAATGGAATTTTTGAAAGTTTTG
* * *
17317 AGGTTAAAAAT-GAATTTTTTGGAAA--TTCG
1 GGGTCAAAAATGGAA-TTTTT-GAAAGTTTTG
* *
17346 AGGGT-AAAAGTGGAATTTTGGAAAGTTTTG
1 -GGGTCAAAAATGGAATTTTTGAAAGTTTTG
* *
17376 GGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTCAAAAATGGAATTTTTGAAAGTTTTG
* *
17406 GGGT--AAAATGGTAAATTTT-AGAAGCTTTG
1 GGGTCAAAAATGG-AATTTTTGA-AAGTTTTG
* * *
17435 TGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTCAAAAATGGAATTTTTGAAAGTTTTG
*
17465 AGGT--AAAATGGTAATTTTTGAAAGTTTTG
1 GGGTCAAAAATGG-AATTTTTGAAAGTTTTG
17494 GGGTCAAAAATGGAA-TTTTGAAAG-TTTG
1 GGGTCAAAAATGGAATTTTTGAAAGTTTTG
17522 AGGGTCAAAA
1 -GGGTCAAAA
17532 CATAATTTTT
Statistics
Matches: 198, Mismatches: 28, Indels: 36
0.76 0.11 0.14
Matches are distributed among these distances:
28 22 0.11
29 93 0.47
30 65 0.33
31 18 0.09
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
GGGTCAAAAATGGAATTTTTGAAAGTTTTG
Found at i:17550 original size:59 final size:59
Alignment explanation
Indices: 17229--17550 Score: 297
Period size: 59 Copynumber: 5.5 Consensus size: 59
17219 GGACATCCGG
* ** ** *
17229 GGGTAAAATGGTAATTTTTGAAAAACTTCAGGGT-AAAAATGAAATTTTTGGAAGTTCGT-
1 GGGTAAAATGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT--TA
* * * * * *
17288 GGATAAAAATGG-AA-TTTTGGAAAGTTTCGAGGTTAAAAAT-GAATTTTTTGGAAATTCGA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAA-TTTTTGGAAGTT-TA
17347 GGGTAAAAGTGG-AA-TTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
1 GGGTAAAA-TGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
* * * *
17405 GGGGTAAAATGGTAAATTTTAG-AAGCTTTGTGGTCAAAAATGGAATTTTTGGAAGTTTA
1 -GGGTAAAATGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
*
17464 GAGGTAAAATGGTAATTTTT-GAAAGTTTTGGGGTCAAAAATGGAA-TTTTGAAAGTTTGA
1 G-GGTAAAATGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTT-A
** *
17523 GGGTCAAAA-CATAATTTTTGGACAGTTT
1 GGGT-AAAATGGTAATTTTTGGAAAGTTT
17551 AGGGACCTCT
Statistics
Matches: 223, Mismatches: 26, Indels: 28
0.81 0.09 0.10
Matches are distributed among these distances:
58 48 0.22
59 160 0.72
60 15 0.07
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
Found at i:17554 original size:29 final size:27
Alignment explanation
Indices: 17359--17554 Score: 96
Period size: 29 Copynumber: 6.7 Consensus size: 27
17349 GTAAAAGTGG
* *
17359 AATTTTGGAAAGTTTTGGGGTCAAAAAT
1 AATTTTTGAAAG-TTTAGGGTCAAAAAT
* *
17387 GGAATTTTTGGAAGTTTAGGGGT-AAAATGGT
1 --AATTTTTGAAAGTTTA-GGGTCAAAA--AT
*
17418 AAATTTT-AGAAGCTTT-GTGGTCAAAAAT
1 AATTTTTGA-AAG-TTTAG-GGTCAAAAAT
* *
17446 GGAATTTTTGGAAGTTTAGAGGT-AAAATGGT
1 --AATTTTTGAAAGTTTAG-GGTCAAAA--AT
*
17477 AATTTTTGAAAGTTTTGGGGTCAAAAAT
1 AATTTTTGAAAG-TTTAGGGTCAAAAAT
17505 GGAA-TTTTGAAAGTTTGAGGGTCAAAACAT
1 --AATTTTTGAAAGTTT-AGGGTCAAAA-AT
*
17535 AATTTTTGGACAGTTTAGGG
1 AATTTTT-GAAAGTTTAGGG
17555 ACCTCTAAGG
Statistics
Matches: 129, Mismatches: 16, Indels: 43
0.69 0.09 0.23
Matches are distributed among these distances:
28 8 0.06
29 66 0.51
30 53 0.41
31 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (27 bp):
AATTTTTGAAAGTTTAGGGTCAAAAAT
Found at i:21014 original size:30 final size:30
Alignment explanation
Indices: 20975--21051 Score: 136
Period size: 30 Copynumber: 2.5 Consensus size: 30
20965 AATAAATCTG
20975 TAAACTGAAAAGAAGAAGAAGACGTGTGTAA
1 TAAA-TGAAAAGAAGAAGAAGACGTGTGTAA
21006 TAAATGAAAAGAAGAAGAAGACGTGTGTAA
1 TAAATGAAAAGAAGAAGAAGACGTGTGTAA
*
21036 TAAGTGAAAAGAAGAA
1 TAAATGAAAAGAAGAA
21052 AAAAAAAAGG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 41 0.91
31 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.26, T:0.16
Consensus pattern (30 bp):
TAAATGAAAAGAAGAAGAAGACGTGTGTAA
Found at i:23058 original size:14 final size:14
Alignment explanation
Indices: 23025--23058 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
23015 GATTCAAGTA
23025 TAGGGTTTAGGATT
1 TAGGGTTTAGGATT
*
23039 TA-GGTTTATGATT
1 TAGGGTTTAGGATT
23052 TAGGGTT
1 TAGGGTT
23059 AACGTTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
TAGGGTTTAGGATT
Found at i:23395 original size:17 final size:17
Alignment explanation
Indices: 23373--23406 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23363 AGTGTGTTTT
23373 CCTTTTTCTCTCTTTAA
1 CCTTTTTCTCTCTTTAA
*
23390 CCTTTTTCTTTCTTTAA
1 CCTTTTTCTCTCTTTAA
23407 AAGAGCTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (17 bp):
CCTTTTTCTCTCTTTAA
Done.