Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013936.1 Kokia drynarioides strain JFW-HI SEQ_128966, 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: 38283
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Warning! 99 characters in sequence are not A, C, G, or T
Found at i:311 original size:4 final size:4
Alignment explanation
Indices: 304--384 Score: 57
Period size: 4 Copynumber: 21.0 Consensus size: 4
294 TACCTTTTTT
* * *
304 TTTC TTTC --TC TTTC TTCC TCTTC TTCTC CTTC -TTC CTTC -TTC -TTC
1 TTTC TTTC TTTC TTTC TTTC T-TTC TT-TC TTTC TTTC TTTC TTTC TTTC
*
349 TTTC TTTC TTTC TTTC TCTTT TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
385 CTTCAATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
2 2 0.03
3 12 0.19
4 41 0.64
5 9 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:361 original size:25 final size:24
Alignment explanation
Indices: 304--380 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 24
294 TACCTTTTTT
* *
304 TTTCTTTCTCTTTCTTCCTC-TTC
1 TTTCTTTCTCCTTCTTCTTCTTTC
*
327 TTCTCCTTCTTCCTTCTTCTTCTTTC
1 TT-TCTTTC-TCCTTCTTCTTCTTTC
*
353 TTTCTTTCT--TTC-TCTTTTTTC
1 TTTCTTTCTCCTTCTTCTTCTTTC
374 TTTCTTT
1 TTTCTTT
381 TTTCCTTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.33
22 3 0.07
23 2 0.04
24 6 0.13
25 15 0.33
26 5 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTTTCTCCTTCTTCTTCTTTC
Found at i:368 original size:21 final size:19
Alignment explanation
Indices: 304--388 Score: 58
Period size: 17 Copynumber: 4.8 Consensus size: 19
294 TACCTTTTTT
* *
304 TTTCTTTC-TCTTTCTTCC
1 TTTCTTTCTTCCTTCTTTC
322 TCTTC-TTC-TCCTTC-TTC
1 T-TTCTTTCTTCCTTCTTTC
* *
339 CTTC-TTCTTCTTTCTTTC
1 TTTCTTTCTTCCTTCTTTC
*
357 TTTCTTTC-T-CTTTTTTC
1 TTTCTTTCTTCCTTCTTTC
*
374 TTTCTTTTTTCCTTC
1 TTTCTTTCTTCCTTC
389 AATTTTCGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
16 6 0.12
17 20 0.38
18 17 0.33
19 9 0.17
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTCTTCCTTCTTTC
Found at i:379 original size:35 final size:35
Alignment explanation
Indices: 297--380 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
287 AACACATTAC
297 CTTTTTT-TTTCTTTCTCTTTCTTCCTCTTCTTCT
1 CTTTTTTCTTTCTTTCTCTTTCTTCCTCTTCTTCT
* * * *
331 CCTTCTTCCTTC-TTCTTCTTTCTTTCT-TTCTTTCT
1 CTTTTTTCTTTCTTTC-TCTTTCTTCCTCTTC-TTCT
366 CTTTTTTCTTTCTTT
1 CTTTTTTCTTTCTTT
381 TTTCCTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
34 11 0.28
35 26 0.67
36 2 0.05
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (35 bp):
CTTTTTTCTTTCTTTCTCTTTCTTCCTCTTCTTCT
Found at i:11726 original size:2 final size:2
Alignment explanation
Indices: 11719--11744 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11709 CTAAAACCTA
11719 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
11745 CAACCACCTA
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:15024 original size:18 final size:18
Alignment explanation
Indices: 14998--15034 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14988 AAAATTACAC
*
14998 TGAAAATGTAATTTAATA
1 TGAAAATGTAATTCAATA
*
15016 TGAATATGTAATTCAATA
1 TGAAAATGTAATTCAATA
15034 T
1 T
15035 TCATCGTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
TGAAAATGTAATTCAATA
Found at i:20238 original size:15 final size:15
Alignment explanation
Indices: 20218--20246 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20208 TTTTGCCTTT
20218 TAACTTAATAGTTTA
1 TAACTTAATAGTTTA
20233 TAACTTAATAGTTT
1 TAACTTAATAGTTT
20247 TTACTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TAACTTAATAGTTTA
Found at i:20661 original size:81 final size:80
Alignment explanation
Indices: 20558--20719 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 80
20548 TCAAAAGGTT
20558 AACAAGTGTCTTATAAAGGTATAGTAAAATATTTAAAAAAAAAACACATATGACAATTTTTTAAA
1 AACAAGTGTCTTATAAAGGTATAGTAAAATATTTAAAAAAAAAACACATATGACAATTTTTTAAA
20623 GTTGTTTGTAGAATA
66 GTTGTTTGTAGAATA
*
20638 ANACAAGTGTCTTATAAAGGTATAGTAAAATATTTTAAAAAAAAACACATATGACAATTTTTTAA
1 A-ACAAGTGTCTTATAAAGGTATAGTAAAATATTTAAAAAAAAAACACATATGACAATTTTTTAA
20703 AGTTGTTTGTAGAATA
65 AGTTGTTTGTAGAATA
20719 A
1 A
20720 TAAAAAAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
80 1 0.01
81 79 0.99
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (80 bp):
AACAAGTGTCTTATAAAGGTATAGTAAAATATTTAAAAAAAAAACACATATGACAATTTTTTAAA
GTTGTTTGTAGAATA
Found at i:20883 original size:19 final size:20
Alignment explanation
Indices: 20859--20904 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20849 ACAAACAGAA
*
20859 TCAAAAAATTAA-CAAATAT
1 TCAAAAAATTAATAAAATAT
*
20878 TCAAAATA-TAATAAAATAT
1 TCAAAAAATTAATAAAATAT
20897 T-AAAAAAT
1 TCAAAAAAT
20905 GAGAGAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (20 bp):
TCAAAAAATTAATAAAATAT
Found at i:26215 original size:18 final size:18
Alignment explanation
Indices: 26175--26226 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
26165 TTTTCAGTTG
*
26175 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
*
26193 CAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
26211 TAATTAA--AAATTTATT
1 TAATTAATTAAATTTATT
26227 CTCATCCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 7 0.23
18 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Done.