Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002790.1 Kokia drynarioides strain JFW-HI SEQ_115128, 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: 4830
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Found at i:368 original size:4 final size:4
Alignment explanation
Indices: 348--426 Score: 72
Period size: 4 Copynumber: 19.8 Consensus size: 4
338 AAAAATAAAA
* * * * *
348 TTCT TTCC TTC- TTCT TTCT TTCC TTC- TTCT TTTT TTCCT CTCC TTCT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT
*
395 TCCT TTCT TTCT TTCTT TTCT TTCT TTCT TTC
1 TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTC
427 CCGTTTATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 6 0.10
4 49 0.80
5 6 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTCT
Found at i:368 original size:15 final size:15
Alignment explanation
Indices: 348--422 Score: 83
Period size: 15 Copynumber: 5.5 Consensus size: 15
338 AAAAATAAAA
348 TTCTTTCCTTCTTCT
1 TTCTTTCCTTCTTCT
363 TTCTTTCCTTCTTCT
1 TTCTTTCCTTCTTCT
* *
378 TTTTTTCC-TC-TCC
1 TTCTTTCCTTCTTCT
391 TTC-TTCC-T-TTCT
1 TTCTTTCCTTCTTCT
403 TTCTTT-CTT-TTCT
1 TTCTTTCCTTCTTCT
416 TTCTTTC
1 TTCTTTC
423 TTTCCCGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
12 11 0.21
13 17 0.33
14 2 0.04
15 22 0.42
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCTTTCCTTCTTCT
Found at i:401 original size:32 final size:32
Alignment explanation
Indices: 348--424 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
338 AAAAATAAAA
*
348 TTCTTTCCTTCTTCTTTCTTTCCTTC-TTCTT
1 TTCTTTCCTTCTTCTTCCTTTCCTTCTTTCTT
*
379 TT-TTTCCTCTCCTTCTTCCTTTCTTTCTTTCTT
1 TTCTTTCCT-T-CTTCTTCCTTTCCTTCTTTCTT
*
412 TTCTTTCTTTCTT
1 TTCTTTCCTTCTT
425 TCCCGTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 6 0.15
31 3 0.08
32 17 0.44
33 8 0.21
34 5 0.13
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (32 bp):
TTCTTTCCTTCTTCTTCCTTTCCTTCTTTCTT
Found at i:983 original size:5 final size:5
Alignment explanation
Indices: 973--1012 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
963 AAAAACATAA
973 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG -AAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1013 GAAGGGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.35
5 22 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3131 original size:23 final size:23
Alignment explanation
Indices: 3101--3144 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3091 CATAAAAAAT
3101 AAAAAATA-AAAGAAAATTTATCA
1 AAAAAATATAAA-AAAATTTATCA
3124 AAAAAATATAAAAAAATTTAT
1 AAAAAATATAAAAAAATTTAT
3145 TAAATATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAAATATAAAAAAATTTATCA
Found at i:3270 original size:20 final size:19
Alignment explanation
Indices: 3247--3318 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
3237 AAACATATTT
*
3247 AAAATATTTAAAATTTTATA
1 AAAATA-TTAAAATTCTATA
*
3267 AAAACTATTAAAATTCTATT
1 AAAA-TATTAAAATTCTATA
**
3287 AAAATCA-TAAAA-AGTATA
1 AAAAT-ATTAAAATTCTATA
3305 AAAATATTAAAATT
1 AAAATATTAAAATT
3319 GATATAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
17 1 0.02
18 13 0.31
19 6 0.14
20 20 0.48
21 2 0.05
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATATTAAAATTCTATA
Found at i:3277 original size:29 final size:29
Alignment explanation
Indices: 3236--3318 Score: 73
Period size: 29 Copynumber: 2.8 Consensus size: 29
3226 CAAAATTAAT
*
3236 AAAACATATTTAAAATATTTAAAATTTTATA
1 AAAAC-TA-TTAAAATATTTAAAATTTCATA
*
3267 AAAACTATTAAAATTCTATTAAAA--TCATA
1 AAAACTATTAAAA-TAT-TTAAAATTTCATA
* *
3296 AAAAGTATAAAAATA-TTAAAATT
1 AAAACTATTAAAATATTTAAAATT
3319 GATATAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
26 6 0.14
28 1 0.02
29 21 0.49
30 4 0.09
31 11 0.26
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAACTATTAAAATATTTAAAATTTCATA
Found at i:3326 original size:20 final size:18
Alignment explanation
Indices: 3247--3333 Score: 70
Period size: 18 Copynumber: 4.7 Consensus size: 18
3237 AAACATATTT
3247 AAAATATTTAAAATTTTATA
1 AAAATA-TTAAAA-TTTATA
*
3267 AAAACTATTAAAATTCTATT
1 AAAA-TATTAAAATT-TATA
**
3287 AAAATCA-TAAAAAGTATA
1 AAAAT-ATTAAAATTTATA
*
3305 AAAATATTAAAATTGATA
1 AAAATATTAAAATTTATA
*
3323 TAAAT-TTAAAA
1 AAAATATTAAAA
3334 AAATTAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 7 0.13
18 20 0.36
19 8 0.15
20 18 0.33
21 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATATTAAAATTTATA
Found at i:3336 original size:37 final size:38
Alignment explanation
Indices: 3263--3345 Score: 89
Period size: 37 Copynumber: 2.2 Consensus size: 38
3253 TTTAAAATTT
* *
3263 TATAAAAACTATTAAAATTCTATTAAAATCATAAAAAG
1 TATAAAAACTATTAAAATTATATTAAAATCAAAAAAAG
* * *
3301 TATAAAAA-TATTAAAATTGATA-TAAATTTAAAAAAAT
1 TATAAAAACTATTAAAATT-ATATTAAAATCAAAAAAAG
*
3338 TAAAAAAA
1 TATAAAAA
3346 ATAGAACGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 28 0.74
38 10 0.26
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (38 bp):
TATAAAAACTATTAAAATTATATTAAAATCAAAAAAAG
Done.