Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011913.1 Corchorus capsularis cultivar CVL-1 contig11934, 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: 28120
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1762 original size:28 final size:28
Alignment explanation
Indices: 1722--1778 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1712 CCGGGAAGGC
1722 TTAAAGGCATGGGCCGGCCTGACCCAAT
1 TTAAAGGCATGGGCCGGCCTGACCCAAT
1750 TTAAAGGCATGGGCCGGCCTGACCCAAT
1 TTAAAGGCATGGGCCGGCCTGACCCAAT
1778 T
1 T
1779 CGTACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (28 bp):
TTAAAGGCATGGGCCGGCCTGACCCAAT
Found at i:2922 original size:11 final size:11
Alignment explanation
Indices: 2908--2945 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2898 ATTCATAACA
2908 AATTTATAATT
1 AATTTATAATT
2919 AATTTATAATT
1 AATTTATAATT
2930 -ATTTGATAATT
1 AATTT-ATAATT
*
2941 TATTT
1 AATTT
2946 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:11937 original size:32 final size:32
Alignment explanation
Indices: 11876--11937 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
11866 TAATACCAGA
*
11876 TTAATAGACACGTTTTTGGTTTTTTTTTTTTT
1 TTAATAGACACGTTTTTCGTTTTTTTTTTTTT
*
11908 TTAA-AGACACGTTTTTCGTTTTTTCTTTTT
1 TTAATAGACACGTTTTTCGTTTTTTTTTTTT
11938 AATTGAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.16, C:0.10, G:0.11, T:0.63
Consensus pattern (32 bp):
TTAATAGACACGTTTTTCGTTTTTTTTTTTTT
Found at i:12327 original size:88 final size:88
Alignment explanation
Indices: 12173--12348 Score: 325
Period size: 88 Copynumber: 2.0 Consensus size: 88
12163 TACCTGGAGC
* *
12173 TGGGCTTTAAATCTTTATCCTTCTTTCTTCCTTCGGCTGTTCCTCTTTAATTGTAATGTTCCAAT
1 TGGGCTTTAAATCTTTATCCTTCTTTCTTCCTTCGACTATTCCTCTTTAATTGTAATGTTCCAAT
12238 GTTATAAAAAATAATAAACAATT
66 GTTATAAAAAATAATAAACAATT
*
12261 TGGGTTTTAAATCTTTATCCTTCTTTCTTCCTTCGACTATTCCTCTTTAATTGTAATGTTCCAAT
1 TGGGCTTTAAATCTTTATCCTTCTTTCTTCCTTCGACTATTCCTCTTTAATTGTAATGTTCCAAT
12326 GTTATAAAAAATAATAAACAATT
66 GTTATAAAAAATAATAAACAATT
12349 AATATATTTA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (88 bp):
TGGGCTTTAAATCTTTATCCTTCTTTCTTCCTTCGACTATTCCTCTTTAATTGTAATGTTCCAAT
GTTATAAAAAATAATAAACAATT
Found at i:14470 original size:24 final size:24
Alignment explanation
Indices: 14443--14492 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
14433 GTTGTTGCGG
14443 AATTGGAGGTGCAACAGCATGTTC
1 AATTGGAGGTGCAACAGCATGTTC
*
14467 AATTGGAGGTGCAACAGTATGTTC
1 AATTGGAGGTGCAACAGCATGTTC
14491 AA
1 AA
14493 ACCCTGATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (24 bp):
AATTGGAGGTGCAACAGCATGTTC
Found at i:15432 original size:2 final size:2
Alignment explanation
Indices: 15417--15548 Score: 63
Period size: 2 Copynumber: 71.0 Consensus size: 2
15407 ACCGACCGAT
* *
15417 TA TA T- TA T- TA TA TA TA -A AA TA TA TT TA TGA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * *
15456 AA TA TA TA TA -A TA TA TT TA -A T- TA TT TA TGA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * * *
15496 -A AA TA TA TG TA -A AA TA TA TA AA T- TA TA TT TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
15534 TA TA -A AA TA TA TA TA
1 TA TA TA TA TA TA TA TA
15549 ATAAATTATT
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
1 12 0.12
2 83 0.84
3 4 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:15546 original size:11 final size:11
Alignment explanation
Indices: 15425--15549 Score: 98
Period size: 11 Copynumber: 11.8 Consensus size: 11
15415 ATTATATTAT
15425 TATATATAAAA
1 TATATATAAAA
* **
15436 TATATTTATGA
1 TATATATAAAA
15447 TATATATAAAA
1 TATATATAAAA
15458 TATATAT--AA
1 TATATATAAAA
* *
15467 TATAT-TTAAT
1 TATATATAAAA
* * *
15477 TATTTATGATA
1 TATATATAAAA
15488 TATATATAAAA
1 TATATATAAAA
*
15499 TATATGT-AAA
1 TATATATAAAA
*
15509 -ATATATAAAT
1 TATATATAAAA
* **
15519 TATATTTATTA
1 TATATATAAAA
15530 TATATATAAAA
1 TATATATAAAA
15541 TATATATAA
1 TATATATAA
15550 TAAATTATTT
Statistics
Matches: 85, Mismatches: 24, Indels: 10
0.71 0.20 0.08
Matches are distributed among these distances:
8 1 0.01
9 12 0.14
10 10 0.12
11 62 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
TATATATAAAA
Found at i:15554 original size:13 final size:13
Alignment explanation
Indices: 15485--15553 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
15475 ATTATTTATG
15485 ATATATATATAAA
1 ATATATATATAAA
*
15498 ATATATGTA-AAA
1 ATATATATATAAA
**
15510 TATATAAATTATATTTA
1 -ATAT--A-TATATAAA
*
15527 TTATATATATAAA
1 ATATATATATAAA
15540 ATATATATAATAAA
1 ATATATAT-ATAAA
15554 TTATTTTTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
12 3 0.07
13 25 0.60
14 6 0.14
15 1 0.02
16 6 0.14
17 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (13 bp):
ATATATATATAAA
Found at i:18468 original size:2 final size:2
Alignment explanation
Indices: 18461--18495 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
18451 ATTGAAAAGT
18461 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18496 AAAACTATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18946 original size:20 final size:20
Alignment explanation
Indices: 18921--18958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18911 GCTAAGAAAC
18921 TTTTAAAATTAAACTATTAT
1 TTTTAAAATTAAACTATTAT
* *
18941 TTTTAAATTTAAATTATT
1 TTTTAAAATTAAACTATT
18959 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTAAACTATTAT
Found at i:19028 original size:26 final size:24
Alignment explanation
Indices: 18960--19025 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
18950 TAAATTATTT
18960 AAAAAATATATATTTTATTTCACC
1 AAAAAATATATATTTTATTTCACC
18984 AAAAAATATATATTTTATTTCACC
1 AAAAAATATATATTTTATTTCACC
19008 AAAAAATATATATTTTAT
1 AAAAAATATATATTTTAT
19026 ATTAAAATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (24 bp):
AAAAAATATATATTTTATTTCACC
Found at i:19476 original size:6 final size:7
Alignment explanation
Indices: 19458--19484 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
19448 TAAAATAAAG
19458 TAAAAAT
1 TAAAAAT
19465 TAAAAAT
1 TAAAAAT
19472 TAAAAAT
1 TAAAAAT
19479 TAAAAA
1 TAAAAA
19485 AGAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:20353 original size:41 final size:41
Alignment explanation
Indices: 20296--20378 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
20286 AGAGTTATAA
*
20296 CTGTTCAATTCTATTTAAACTACTCTTGTCATAACCAATTT
1 CTGTTCAATTCTATTTAAACTACTCTTGCCATAACCAATTT
*
20337 CTGTTCAATTCTATTTAAACTACTCTTGCCATAACTAATTT
1 CTGTTCAATTCTATTTAAACTACTCTTGCCATAACCAATTT
20378 C
1 C
20379 ACAATTCTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.43
Consensus pattern (41 bp):
CTGTTCAATTCTATTTAAACTACTCTTGCCATAACCAATTT
Found at i:21956 original size:20 final size:20
Alignment explanation
Indices: 21926--21984 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 20
21916 TCAATCTTTC
*
21926 CAGATCCGGTTCCTCTTGCT
1 CAGATCTGGTTCCTCTTGCT
*
21946 CGGATCTGGTTCCTCAATCTTGCT
1 CAGATCTGGTT-C-C--TCTTGCT
21970 CAGATCTGGTTCCTC
1 CAGATCTGGTTCCTC
21985 AATCTCTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 11 0.34
21 1 0.03
22 2 0.06
23 1 0.03
24 17 0.53
ACGTcount: A:0.12, C:0.32, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGATCTGGTTCCTCTTGCT
Found at i:21975 original size:24 final size:24
Alignment explanation
Indices: 21939--21989 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
21929 ATCCGGTTCC
*
21939 TCTTGCTCGGATCTGGTTCCTCAA
1 TCTTGCTCAGATCTGGTTCCTCAA
21963 TCTTGCTCAGATCTGGTTCCTCAA
1 TCTTGCTCAGATCTGGTTCCTCAA
21987 TCT
1 TCT
21990 CTCGTGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.39
Consensus pattern (24 bp):
TCTTGCTCAGATCTGGTTCCTCAA
Done.