Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013864.1 Corchorus capsularis cultivar CVL-1 contig13885, 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: 16617
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:5276 original size:2 final size:2
Alignment explanation
Indices: 5269--5299 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5259 ATCCCTCCTC
5269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5300 CATAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5404 original size:14 final size:14
Alignment explanation
Indices: 5385--5411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5375 AAAAAAAAAC
5385 TGTTAAGGATAGTG
1 TGTTAAGGATAGTG
5399 TGTTAAGGATAGT
1 TGTTAAGGATAGT
5412 TTTGGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (14 bp):
TGTTAAGGATAGTG
Found at i:7918 original size:26 final size:26
Alignment explanation
Indices: 7882--7939 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
7872 ATATTATTAG
7882 AAATATAATTGAGTTTGTTCACGAAC
1 AAATATAATTGAGTTTGTTCACGAAC
*
7908 AAATATAATTGAGTTTGTTTACGAAC
1 AAATATAATTGAGTTTGTTCACGAAC
7934 AAATAT
1 AAATAT
7940 TATTAGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (26 bp):
AAATATAATTGAGTTTGTTCACGAAC
Found at i:11180 original size:16 final size:16
Alignment explanation
Indices: 11159--11211 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
11149 TATAATAGTA
11159 AATATATATTTATTAT
1 AATATATATTTATTAT
11175 AATATATA---ATTAT
1 AATATATATTTATTAT
11188 AAT-TATAATTTA-TAT
1 AATATAT-ATTTATTAT
*
11203 AATAAATAT
1 AATATATAT
11212 ATATAAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
12 3 0.10
13 9 0.29
15 8 0.26
16 11 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATATATTTATTAT
Found at i:11203 original size:39 final size:40
Alignment explanation
Indices: 11160--11291 Score: 102
Period size: 39 Copynumber: 3.4 Consensus size: 40
11150 ATAATAGTAA
11160 ATATATATTTAT-TATAATATATAATTATAATTATAATTT
1 ATATATATTTATATATAATATATAATTATAATTATAATTT
** *
11199 ATATAATAAATATATATAA-AGTA-AATATATAA-T-TACTTT
1 ATAT-ATATTTATATATAATA-TATAAT-TATAATTATAATTT
*
11238 ATATATATTATATATATAAAGTAAATACA-TATAATTATAA--T
1 ATATATATT-TATATAT-AA-TATATA-ATTATAATTATAATTT
11279 ATATA-ATTTATAT
1 ATATATATTTATAT
11292 TTATTATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
38 3 0.04
39 25 0.34
40 16 0.22
41 24 0.32
42 3 0.04
43 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (40 bp):
ATATATATTTATATATAATATATAATTATAATTATAATTT
Found at i:11216 original size:28 final size:28
Alignment explanation
Indices: 11172--11283 Score: 92
Period size: 28 Copynumber: 4.1 Consensus size: 28
11162 ATATATTTAT
* *
11172 TATAATATATAAT-TATAATTATAATTTA
1 TATAATAAAT-ATATATAATTATAATATA
11200 TATAATAAATATATATAA--AGTAA-ATA
1 TATAATAAATATATATAATTA-TAATATA
* * *
11226 TATAATTACTTTATATATATTAT-ATATA
1 TATAATAAATATATATA-ATTATAATATA
*
11254 TA-AAGTAAATACATATAATTATAATATA
1 TATAA-TAAATATATATAATTATAATATA
11282 TA
1 TA
11284 ATTTATATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
26 17 0.25
27 14 0.21
28 35 0.52
29 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (28 bp):
TATAATAAATATATATAATTATAATATA
Found at i:11217 original size:41 final size:41
Alignment explanation
Indices: 11172--11291 Score: 100
Period size: 43 Copynumber: 2.8 Consensus size: 41
11162 ATATATTTAT
11172 TATAATATATAATTATAATTATAATTTATATAATAAATATA
1 TATAATATATAATTATAATTATAATTTATATAATAAATATA
* * * *
11213 TATAA-AGTA-AATATATAATTACTTTATATATATTATATATATA
1 TATAATA-TATAAT-TATAATTA--TAATTTATATAATAAATATA
*
11256 AAGTAAATACATATAATTATAATATATAATTTATAT
1 TA-T-AAT--ATATAATTATAAT-TATAATTTATAT
11292 TTATTATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
40 4 0.07
41 15 0.25
43 17 0.28
44 1 0.02
45 2 0.03
46 8 0.13
47 8 0.13
48 6 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (41 bp):
TATAATATATAATTATAATTATAATTTATATAATAAATATA
Found at i:11291 original size:11 final size:13
Alignment explanation
Indices: 11170--11286 Score: 81
Period size: 13 Copynumber: 9.2 Consensus size: 13
11160 ATATATATTT
11170 ATTATAATATATA
1 ATTATAATATATA
11183 ATTATAAT-TATA
1 ATTATAATATATA
11195 ATT-T-ATATAATA
1 ATTATAATAT-ATA
*
11207 AATAT-ATATA-A
1 ATTATAATATATA
*
11218 AGTA-AATATATA
1 ATTATAATATATA
*
11230 ATTACT-TTATATA
1 ATTA-TAATATATA
11243 TATTAT-ATATATAA
1 -ATTATAATATAT-A
*
11257 AGTA-AATACATATA
1 ATTATAAT--ATATA
11271 ATTATAATATATA
1 ATTATAATATATA
11284 ATT
1 ATT
11287 TATATTTATT
Statistics
Matches: 84, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
10 2 0.02
11 11 0.13
12 17 0.20
13 38 0.45
14 9 0.11
15 7 0.08
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (13 bp):
ATTATAATATATA
Found at i:16597 original size:14 final size:15
Alignment explanation
Indices: 16570--16598 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16560 CCTTCAAACT
16570 TTCAAAACTCAATCA
1 TTCAAAACTCAATCA
16585 TTCAAAA-TCAATCA
1 TTCAAAACTCAATCA
16599 AGTAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCAAAACTCAATCA
Done.