Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014638.1 Kokia drynarioides strain JFW-HI SEQ_129677, 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: 97166
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:11381 original size:23 final size:22
Alignment explanation
Indices: 11329--11381 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
11319 CTTAGTGCTC
*
11329 ATAAATTACTTGAATTTGACTT
1 ATAAATTATTTGAATTTGACTT
11351 A-AAA-TATTTGAATTTGA-TT
1 ATAAATTATTTGAATTTGACTT
11370 CAATAAATTATT
1 --ATAAATTATT
11382 AAAATCTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 12 0.46
21 4 0.15
22 4 0.15
23 4 0.15
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
ATAAATTATTTGAATTTGACTT
Found at i:18318 original size:21 final size:22
Alignment explanation
Indices: 18285--18347 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
18275 AACATATATG
** *
18285 ATTAAAACCTATAATGA-AATT
1 ATTAAAAAATATAATAATAATT
18306 ATTAAAAAATAT-ATAATAATT
1 ATTAAAAAATATAATAATAATT
18327 ATTATAAAAATATAAATAATA
1 ATTA-AAAAATAT-AATAATA
18348 CGAAAAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.51
22 8 0.23
24 6 0.17
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (22 bp):
ATTAAAAAATATAATAATAATT
Found at i:32489 original size:15 final size:17
Alignment explanation
Indices: 32455--32492 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
32445 TTTGTTTTTT
32455 TTTTTATTGTTTAATAAA
1 TTTTTATTGTTT-ATAAA
32473 TTTTTATT-TTT-TAAA
1 TTTTTATTGTTTATAAA
32488 TTTTT
1 TTTTT
32493 TATCTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
17 3 0.15
18 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTATTGTTTATAAA
Found at i:32502 original size:18 final size:17
Alignment explanation
Indices: 32454--32502 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
32444 TTTTGTTTTT
32454 TTTTTTATTGTTTAATAAA
1 TTTTTTATTGTTT--TAAA
32473 -TTTTTATT-TTTTAAA
1 TTTTTTATTGTTTTAAA
32488 TTTTTTATCTGTTTT
1 TTTTTTAT-TGTTTT
32503 TGCAGTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.15
16 7 0.26
17 4 0.15
18 12 0.44
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTTATTGTTTTAAA
Found at i:34060 original size:30 final size:32
Alignment explanation
Indices: 34024--34083 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
34014 GTAATAATGG
**
34024 TTAAATTTCAATTTTAATT-T-TATATTATGT
1 TTAAATTAAAATTTTAATTATATATATTATGT
34054 TTAAATTAAAATTTTAATTATATATATTAT
1 TTAAATTAAAATTTTAATTATATATATTAT
34084 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 17 0.65
31 1 0.04
32 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (32 bp):
TTAAATTAAAATTTTAATTATATATATTATGT
Found at i:34852 original size:23 final size:22
Alignment explanation
Indices: 34809--34882 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
34799 AAATTGAATC
*
34809 TAAAAAAAATTAGATACCAAAT
1 TAAAAAAAATTAAATACCAAAT
* *
34831 TAAAAAATATTAAATTATCAAAT
1 TAAAAAAAATTAAA-TACCAAAT
34854 TGAGTAAAATAAATTTAAATACCAAAT
1 T-A--AAAA-AAA-TTAAATACCAAAT
34881 TA
1 TA
34883 GTAAAATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 12 0.29
23 8 0.20
24 1 0.02
26 5 0.12
27 10 0.24
28 5 0.12
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (22 bp):
TAAAAAAAATTAAATACCAAAT
Found at i:34861 original size:27 final size:26
Alignment explanation
Indices: 34835--34889 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
34825 CCAAATTAAA
*
34835 AAATATTAAATTATCAAATTGAGTAAAAT
1 AAAT-TTAAA-TACCAAATT-AGTAAAAT
34864 AAATTTAAATACCAAATTAGTAAAAT
1 AAATTTAAATACCAAATTAGTAAAAT
34890 TATAAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 8 0.32
28 5 0.20
29 4 0.16
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (26 bp):
AAATTTAAATACCAAATTAGTAAAAT
Found at i:42750 original size:30 final size:30
Alignment explanation
Indices: 42715--42771 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
42705 AATTTTTAGG
*
42715 AGTAAAAAT-TAAATTATATTTTTTTATTAT
1 AGTAAAAATAT-AATTATATTATTTTATTAT
*
42745 AGTAAAAATATAATTTTATTATTTTAT
1 AGTAAAAATATAATTATATTATTTTAT
42772 ATTTTTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
AGTAAAAATATAATTATATTATTTTATTAT
Found at i:43073 original size:2 final size:2
Alignment explanation
Indices: 43066--43107 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
43056 ATTGATTTGG
43066 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
43108 TAAAAGTTGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43496 original size:31 final size:31
Alignment explanation
Indices: 43460--43534 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
43450 TATTTTTTAA
**
43460 ATGTATATAATTGAATTAAAATTAAAATTTC
1 ATGTATATAATTGAACCAAAATTAAAATTTC
* * * *
43491 ATGTATACATTTGAACCACAATTAAAATTTT
1 ATGTATATAATTGAACCAAAATTAAAATTTC
**
43522 ACATATATAATTG
1 ATGTATATAATTG
43535 CATCGAATCA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
ATGTATATAATTGAACCAAAATTAAAATTTC
Found at i:57354 original size:31 final size:31
Alignment explanation
Indices: 57316--57387 Score: 135
Period size: 31 Copynumber: 2.3 Consensus size: 31
57306 AAATCAAAAT
57316 TTCATGTATAAAATTGCACATTAAACCATAA
1 TTCATGTATAAAATTGCACATTAAACCATAA
*
57347 TTCATGTATACAATTGCACATTAAACCATAA
1 TTCATGTATAAAATTGCACATTAAACCATAA
57378 TTCATGTATA
1 TTCATGTATA
57388 GTTTTAAGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TTCATGTATAAAATTGCACATTAAACCATAA
Found at i:64769 original size:14 final size:15
Alignment explanation
Indices: 64745--64773 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
64735 AGTTTAAGAA
64745 ATTTGTGTATTTTGT
1 ATTTGTGTATTTTGT
64760 ATTT-TGTATTTTGT
1 ATTTGTGTATTTTGT
64774 TATCTTAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (15 bp):
ATTTGTGTATTTTGT
Found at i:67891 original size:23 final size:23
Alignment explanation
Indices: 67817--67984 Score: 120
Period size: 23 Copynumber: 7.5 Consensus size: 23
67807 TAAACGGAAC
* * *
67817 AAACAGAGAGTACA-GAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
67839 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
67861 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
67887 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
67907 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
67926 AATCAGAGAGCACGCGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
67949 AATAACAGAGAGCACACGAAGTGCT
1 -A-AACAGAGAGCACACAAAGTGCT
*
67974 AATCAGAGAGC
1 AAACAGAGAGC
67985 GCGCTAGTGT
Statistics
Matches: 117, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 19 0.16
23 39 0.33
24 2 0.02
25 33 0.28
26 7 0.06
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:68231 original size:30 final size:31
Alignment explanation
Indices: 68197--68277 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
68187 TATAACTAAA
* * *
68197 CACATAATATTTTAT-ATATACATTGTTCAT
1 CACATAATATATCATCATATACATCGTTCAT
*
68227 CACAT-ATATATCATCATATACGTCGTTCAT
1 CACATAATATATCATCATATACATCGTTCAT
68257 CACAT-ATATATCATCATATAC
1 CACATAATATATCATCATATAC
68278 CTCTTTACTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 7 0.15
30 39 0.85
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.40
Consensus pattern (31 bp):
CACATAATATATCATCATATACATCGTTCAT
Found at i:82097 original size:2 final size:2
Alignment explanation
Indices: 82090--82120 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
82080 AGCTGAACAC
82090 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
82121 ATTGAAAACT
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:90366 original size:184 final size:184
Alignment explanation
Indices: 90057--90425 Score: 702
Period size: 184 Copynumber: 2.0 Consensus size: 184
90047 TCTATAAAAA
90057 TTTAAACTCTTTTATTAATTATTTATATCCTATTAATTTAATTAATTAAAGATAAAATAATTCTT
1 TTTAAACTCTTTTATTAATTATTTATATCCTATTAATTTAATTAATTAAAGATAAAATAATTCTT
*
90122 AGAAAATATAATTTCTTTATAAGAGAATTTTAAAATGATTTTATTTCCTTATTTATCTCTTTATT
66 AGAAAATATAATTTCTTTATAAAAGAATTTTAAAATGATTTTATTTCCTTATTTATCTCTTTATT
*
90187 AATAAATTTTAATTTAATTAGAAATAAACATTAATGAGAGATGATGAACTTTGG
131 AATAAAATTTAATTTAATTAGAAATAAACATTAATGAGAGATGATGAACTTTGG
*
90241 TTTAAACTCTTTTATTAATTATTTATATCCTATTAATTTAATTAATTAAAGATAAAATAGTTCTT
1 TTTAAACTCTTTTATTAATTATTTATATCCTATTAATTTAATTAATTAAAGATAAAATAATTCTT
*
90306 AGAAAATATAATTTCTTTATAAAAGAATTTTAAAATGATTTTATTTCCTTTTTTATCTCTTTATT
66 AGAAAATATAATTTCTTTATAAAAGAATTTTAAAATGATTTTATTTCCTTATTTATCTCTTTATT
90371 AATAAAATTTAATTTAATTAGAAATAAACATTAATGAGAGATGATGAACTTTGG
131 AATAAAATTTAATTTAATTAGAAATAAACATTAATGAGAGATGATGAACTTTGG
90425 T
1 T
90426 CAAAAAATTC
Statistics
Matches: 181, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 181 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (184 bp):
TTTAAACTCTTTTATTAATTATTTATATCCTATTAATTTAATTAATTAAAGATAAAATAATTCTT
AGAAAATATAATTTCTTTATAAAAGAATTTTAAAATGATTTTATTTCCTTATTTATCTCTTTATT
AATAAAATTTAATTTAATTAGAAATAAACATTAATGAGAGATGATGAACTTTGG
Found at i:95634 original size:8 final size:7
Alignment explanation
Indices: 95605--95632 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
95595 CTTTTAATTT
95605 TAAAAAA
1 TAAAAAA
95612 TAAAAAA
1 TAAAAAA
95619 TAAAAAA
1 TAAAAAA
95626 TAAAAAA
1 TAAAAAA
95633 ATGGGGCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Done.