Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002611.1 Kokia drynarioides strain JFW-HI SEQ_114826, 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: 57316
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:1571 original size:29 final size:29
Alignment explanation
Indices: 1526--1581 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1516 TGATCTAATT
** * *
1526 TGTAATTTTATGTATGAACTTTTATTTTG
1 TGTAATTTTATACATGAAATTTGATTTTG
1555 TGTAATTTTATACATGAAATTTGATTT
1 TGTAATTTTATACATGAAATTTGATTT
1582 GATTCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (29 bp):
TGTAATTTTATACATGAAATTTGATTTTG
Found at i:3980 original size:21 final size:21
Alignment explanation
Indices: 3936--3980 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3926 TAAGGTTCAA
* * * *
3936 GTTTTGAGTTTTATATTTTGG
1 GTTTTGAGTTTGAGATTCTAG
3957 GTTTTGAGTTTGAGATTCTAG
1 GTTTTGAGTTTGAGATTCTAG
3978 GTT
1 GTT
3981 CATGGTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.56
Consensus pattern (21 bp):
GTTTTGAGTTTGAGATTCTAG
Found at i:21439 original size:31 final size:33
Alignment explanation
Indices: 21364--21439 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
21354 AATCTGCTTC
*
21364 AAGTCCTTA-TTTTATTTTATTTTTATAAATTTG
1 AAGT-CTTAGTTTTATTTTATTTTCATAAATTTG
21397 AAGT-TTAGTTTTATTTTATTTTCATAAATTT-
1 AAGTCTTAGTTTTATTTTATTTTCATAAATTTG
*
21428 TA-TCTTAGTTTT
1 AAGTCTTAGTTTT
21440 TAAATTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 1 0.03
31 12 0.31
32 22 0.56
33 4 0.10
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (33 bp):
AAGTCTTAGTTTTATTTTATTTTCATAAATTTG
Found at i:28586 original size:6 final size:6
Alignment explanation
Indices: 28575--28608 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
28565 TCTCTTATAT
*
28575 CGCAAA CGCAAA CGCAAA CGCAAA CGCAAG CGCA
1 CGCAAA CGCAAA CGCAAA CGCAAA CGCAAA CGCA
28609 TGCCAATGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.35, G:0.21, T:0.00
Consensus pattern (6 bp):
CGCAAA
Found at i:29305 original size:29 final size:29
Alignment explanation
Indices: 29273--29334 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
29263 TATTCCATGT
29273 AATAATTTAAAAATTACAATATTTTT-TAA
1 AATAATTTAAAAA-TACAATATTTTTATAA
* **
29302 AATACTTTTTAAATACAATATTTTTATAA
1 AATAATTTAAAAATACAATATTTTTATAA
29331 AATA
1 AATA
29335 CTTATTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAATTTAAAAATACAATATTTTTATAA
Found at i:31378 original size:2 final size:2
Alignment explanation
Indices: 31373--31398 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31363 AAAAAAAAAA
31373 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
31399 GTAACACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32393 original size:18 final size:18
Alignment explanation
Indices: 32352--32394 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
32342 AAATATTTTT
*
32352 TATTTAAATTATTGAATA
1 TATTAAAATTATTGAATA
32370 TAATTAAAATATATT-AATA
1 T-ATTAAAAT-TATTGAATA
32389 TATTAA
1 TATTAA
32395 TTTATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 12 0.55
20 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TATTAAAATTATTGAATA
Found at i:33592 original size:22 final size:22
Alignment explanation
Indices: 33531--33597 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
33521 TAAATAACTC
* *
33531 TAAAATAATTACAAAATTAATAA
1 TAAAATAATAACAATA-TAATAA
* ***
33554 TAAAATAAGAGTTATATAATAA
1 TAAAATAATAACAATATAATAA
33576 TAAAATAATAACAATATAATAA
1 TAAAATAATAACAATATAATAA
33598 CGAAACGATA
Statistics
Matches: 34, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 24 0.71
23 10 0.29
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAATAATAACAATATAATAA
Found at i:40915 original size:17 final size:17
Alignment explanation
Indices: 40893--40932 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
40883 ATAATATTTT
*
40893 TATTAAAAAAAGTATAA
1 TATTAAAAAAAGTAGAA
*
40910 TATTAAAAAAATTAGAA
1 TATTAAAAAAAGTAGAA
40927 TATTAA
1 TATTAA
40933 TCATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TATTAAAAAAAGTAGAA
Found at i:43410 original size:2 final size:2
Alignment explanation
Indices: 43405--43436 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43395 AAATGTAAAT
43405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43437 ATTTTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43461 original size:11 final size:11
Alignment explanation
Indices: 43441--43497 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 11
43431 TATATAATTT
43441 TAATAAATAAA
1 TAATAAATAAA
*
43452 TAATACATAAA
1 TAATAAATAAA
*
43463 -ATTAAAT-AA
1 TAATAAATAAA
43472 TAATAAATTAAA
1 TAATAAA-TAAA
*
43484 AAATAATATAAA
1 TAATAA-ATAAA
43496 TA
1 TA
43498 TTTTCATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
9 2 0.06
10 10 0.28
11 11 0.31
12 12 0.33
13 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:43479 original size:15 final size:15
Alignment explanation
Indices: 43441--43491 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
43431 TATATAATTT
43441 TAATAAA-TAAATAA
1 TAATAAATTAAATAA
43455 TACATAAAATTAAATAA
1 TA-AT-AAATTAAATAA
*
43472 TAATAAATTAAAAAA
1 TAATAAATTAAATAA
43487 TAATA
1 TAATA
43492 TAAATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 2 0.06
15 17 0.52
16 5 0.15
17 9 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATAAATTAAATAA
Found at i:43483 original size:21 final size:21
Alignment explanation
Indices: 43444--43484 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
43434 ATAATTTTAA
*
43444 TAAATAAATAATACATAAAAT
1 TAAATAAATAATAAATAAAAT
43465 TAAAT-AATAATAAATTAAAA
1 TAAATAAATAATAAA-TAAAA
43485 AATAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATAAATAATAAATAAAAT
Found at i:46265 original size:19 final size:19
Alignment explanation
Indices: 46227--46268 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
46217 AGTAATTTAA
*
46227 TTTAATTTTTTTTATGTTT
1 TTTAATTTTTTTTATATTT
46246 TTTAATTTTTTCTT-TATTT
1 TTTAATTTTTT-TTATATTT
46265 TTTA
1 TTTA
46269 TTATATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTAATTTTTTTTATATTT
Found at i:46272 original size:10 final size:9
Alignment explanation
Indices: 46231--46304 Score: 53
Period size: 10 Copynumber: 7.9 Consensus size: 9
46221 ATTTAATTTA
46231 ATTTTTTTT
1 ATTTTTTTT
*
46240 ATGTTTTTTA
1 AT-TTTTTTT
46250 ATTTTTTCTT
1 ATTTTTT-TT
*
46260 -TATTTTTT
1 ATTTTTTTT
* *
46268 ATTATATATT
1 ATT-TTTTTT
46278 ATTTCTTTTT
1 ATTT-TTTTT
46288 -TTTTTTTT
1 ATTTTTTTT
46296 CATTTTTTT
1 -ATTTTTTT
46305 AACATAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
8 7 0.14
9 17 0.34
10 26 0.52
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.80
Consensus pattern (9 bp):
ATTTTTTTT
Done.