Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014961.1 Kokia drynarioides strain JFW-HI SEQ_130005, 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: 9654
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:130 original size:13 final size:13
Alignment explanation
Indices: 112--137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
102 CAGCAGTTCT
112 AAATTCTATAAGG
1 AAATTCTATAAGG
125 AAATTCTATAAGG
1 AAATTCTATAAGG
138 TTAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
AAATTCTATAAGG
Found at i:668 original size:11 final size:11
Alignment explanation
Indices: 652--677 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
642 AACAAATTTG
652 ATTTCATTTTT
1 ATTTCATTTTT
663 ATTTCATTTTT
1 ATTTCATTTTT
674 ATTT
1 ATTT
678 TATTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTCATTTTT
Found at i:697 original size:7 final size:7
Alignment explanation
Indices: 685--794 Score: 130
Period size: 7 Copynumber: 15.7 Consensus size: 7
675 TTTTATTAAA
685 TAAATAT
1 TAAATAT
692 TAAATAT
1 TAAATAT
699 TAAATAT
1 TAAATAT
706 TAAATAT
1 TAAATAT
713 TAAATAT
1 TAAATAT
720 TAAATAT
1 TAAATAT
727 TAAATAT
1 TAAATAT
***
734 TAAANNN
1 TAAATAT
*******
741 NNNNNNN
1 TAAATAT
748 TAAATAT
1 TAAATAT
755 TAAATAT
1 TAAATAT
762 TAAATAT
1 TAAATAT
769 TAAATAT
1 TAAATAT
776 TAAATAT
1 TAAATAT
783 TAAATAT
1 TAAATAT
790 TAAAT
1 TAAAT
795 TAAGGCTCCA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 89 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAAATAT
Found at i:4187 original size:19 final size:20
Alignment explanation
Indices: 4153--4193 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4143 ATGAAAAGAA
*
4153 AATAATAAAATCGAAATCAT
1 AATAAAAAAATCGAAATCAT
*
4173 AATAAAAAAAT-GAAATTAT
1 AATAAAAAAATCGAAATCAT
4192 AA
1 AA
4194 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAAAAAAATCGAAATCAT
Found at i:4313 original size:17 final size:17
Alignment explanation
Indices: 4262--4325 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
4252 TTTTTCTATT
4262 TAAAT-TAAATAATAA-
1 TAAATATAAATAATAAC
* *
4277 TAAATTCTAAAT-A-GAC
1 TAAA-TATAAATAATAAC
4293 TAAATATAAATAATAAC
1 TAAATATAAATAATAAC
*
4310 TAAATAGAAATAATAA
1 TAAATATAAATAATAA
4326 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.28
16 7 0.17
17 22 0.55
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (17 bp):
TAAATATAAATAATAAC
Found at i:4341 original size:11 final size:12
Alignment explanation
Indices: 4317--4345 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4307 AACTAAATAG
4317 AAATAATAATTT
1 AAATAATAATTT
4329 AAATAAT-ATTT
1 AAATAATAATTT
4340 AAATAA
1 AAATAA
4346 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:4352 original size:3 final size:3
Alignment explanation
Indices: 4341--4411 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
4331 ATAATATTTA
* *
4341 AAT AA- AAT AAT AAT ATAT AAT AAT -AT TAT AAG AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4384 AAT AGAT -AG AAT AAT AA- AAT AAAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT -AAT AAT A
4412 TAGAAATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
2 9 0.16
3 38 0.69
4 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4383 original size:32 final size:28
Alignment explanation
Indices: 4295--4387 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 28
4285 AAATAGACTA
**
4295 AATATAAATAATAACTAAATAGAAATAAT
1 AATATAAATAATATTTAAATA-AAATAAT
*
4324 AATTTAAATAATATTTAAATAAAATAAT
1 AATATAAATAATATTTAAATAAAATAAT
*
4352 AATATATAATAATATTATAAGAATAATATAAT
1 AATATA-AATAATATT-T-A-AATAAAATAAT
4384 AATA
1 AATA
4388 GATAGAATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.22
29 27 0.49
30 1 0.02
31 1 0.02
32 14 0.25
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (28 bp):
AATATAAATAATATTTAAATAAAATAAT
Found at i:4396 original size:20 final size:22
Alignment explanation
Indices: 4347--4405 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
4337 TTTAAATAAA
* *
4347 ATAATAAT-ATATAATAATATT
1 ATAAGAATAATATAATAATATG
4368 ATAAGAATAATATAATAATA-G
1 ATAAGAATAATATAATAATATG
*
4389 AT-AGAATAATAAAATAA
1 ATAAGAATAATATAATAA
4406 ATAATATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.41
21 9 0.26
22 11 0.32
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (22 bp):
ATAAGAATAATATAATAATATG
Found at i:4461 original size:17 final size:17
Alignment explanation
Indices: 4439--4471 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4429 AACTCGAAAT
4439 ATATTAATATAAATATA
1 ATATTAATATAAATATA
4456 ATATTAATATAAATAT
1 ATATTAATATAAATAT
4472 TATTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTAATATAAATATA
Found at i:4473 original size:29 final size:29
Alignment explanation
Indices: 4439--4518 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
4429 AACTCGAAAT
4439 ATATTAATATAAATATAATATTAATATA-A
1 ATATTAATATAAATATAATATTAATA-ACA
*
4468 ATATT-AT-TAATTACTTAATATTAATAACA
1 ATATTAATATAAATA--TAATATTAATAACA
*
4497 A-A-TAATATAAAT-TAATAATAAT
1 ATATTAATATAAATATAATATTAAT
4519 TGATAATAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
26 9 0.21
27 6 0.14
28 6 0.14
29 22 0.51
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
ATATTAATATAAATATAATATTAATAACA
Found at i:4477 original size:15 final size:15
Alignment explanation
Indices: 4435--4478 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 15
4425 TTCTAACTCG
4435 AAATA-TATTAATAT
1 AAATATTATTAATAT
4449 AAATATAATATTAATAT
1 AAATAT--TATTAATAT
4466 AAATATTATTAAT
1 AAATATTATTAAT
4479 TACTTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
17 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATATTATTAATAT
Found at i:4597 original size:20 final size:20
Alignment explanation
Indices: 4572--4609 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4562 GTTATATAAT
4572 TTCGATTGTTAATTGGTTAA
1 TTCGATTGTTAATTGGTTAA
4592 TTCGATTGTTAATTGGTT
1 TTCGATTGTTAATTGGTT
4610 TAGTTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (20 bp):
TTCGATTGTTAATTGGTTAA
Found at i:9344 original size:22 final size:23
Alignment explanation
Indices: 9319--9375 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
9309 GTTCAGCGTG
9319 ATATAA-AAAAATATTCATATTT
1 ATATAATAAAAATATTCATATTT
*
9341 ATATAATTAAAATATTCATATTT
1 ATATAATAAAAATATTCATATTT
9364 -TATAATATAAAA
1 ATATAATA-AAAA
9376 CATTTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAATAAAAATATTCATATTT
Found at i:9356 original size:23 final size:23
Alignment explanation
Indices: 9326--9375 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
9316 GTGATATAAA
9326 AAAATATTCATATTTATATAAT-T
1 AAAATATTCATATTT-TATAATAT
9349 AAAATATTCATATTTTATAATAT
1 AAAATATTCATATTTTATAATAT
9372 AAAA
1 AAAA
9376 CATTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AAAATATTCATATTTTATAATAT
Done.