Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014892.1 Corchorus capsularis cultivar CVL-1 contig14913, 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: 33680
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3247 original size:49 final size:47
Alignment explanation
Indices: 3184--3420 Score: 154
Period size: 45 Copynumber: 5.1 Consensus size: 47
3174 AGCAACCAAG
* *
3184 GGTATCTTCAAGTTTTAA-TGATAATTTGATATGGCACATGCTTTCCAGA
1 GGTATCATCAAG-TTTAATTGATAATTTGACA--GCACATGCTTTCCAGA
* * *
3233 GGTATCATCGAGTTTAATTGAT-A-TGGACAGCACATGCTTTCCGGA
1 GGTATCATCAAGTTTAATTGATAATTTGACAGCACATGCTTTCCAGA
* * * *
3278 GGTAT-ATCAAGTTTCACTGATATATATGGACCA-CACATGCTTTTCAGA
1 GGTATCATCAAGTTTAATTGATA-AT-TTGA-CAGCACATGCTTTCCAGA
* * * ***
3326 GGTATCTTCGAGTTTAATTGAT-A-TGGAGC-GCACATGCTTTATGGA
1 GGTATCATCAAGTTTAATTGATAATTTGA-CAGCACATGCTTTCCAGA
* * * *
3371 GATATCTTCGAGTTTAATTGAT-A-TGGAGC-GCACATGCTTTCCAGA
1 GGTATCATCAAGTTTAATTGATAATTTGA-CAGCACATGCTTTCCAGA
3416 GGTAT
1 GGTAT
3421 TTTCGAGTTT
Statistics
Matches: 157, Mismatches: 23, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
44 13 0.08
45 82 0.52
46 1 0.01
47 5 0.03
48 28 0.18
49 28 0.18
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (47 bp):
GGTATCATCAAGTTTAATTGATAATTTGACAGCACATGCTTTCCAGA
Found at i:3280 original size:45 final size:45
Alignment explanation
Indices: 3217--3685 Score: 505
Period size: 45 Copynumber: 10.4 Consensus size: 45
3207 ATTTGATATG
* *
3217 GCACATGCTTTCCAGAGGTATCATCGAGTTTAATTGATATGGA-C
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * *
3261 AGCACATGCTTTCCGGAGGTAT-ATCAAGTTTCACTGATAT-ATATGGACC
1 -GCACATGCTTTCCGGAGGTATCTTCGAGTTT-A---AT-TGATATGGAGC
* * *
3310 ACACATGCTTTTCAGAGGTATCTTCGAGTTTAATTGATATGGAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
** *
3355 GCACATGCTTTATGGAGATATCTTCGAGTTTAATTGATATGGAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * * * * *
3400 GCACATGCTTTCCAGAGGTATTTTCGAGTTTCACTGATGTGGAGT
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * * * *
3445 GCACATACTTT-CGCAGATATTTTCGAGTTTAATTGATATGGAGT
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * * *
3489 GCACATGCTTTCTGGAGGTATCTTCGAGTTTCACTGATATGAAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * * *
3534 GCACATGCTTTCTGGAGGTATCTTCGAGTTTCACTGATATAGAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* *
3579 GCACATGCTTTCCAGAGATATCTTCGAGTTTAATTGATATGGAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* * * * *
3624 GCATATGCTTCCCGTAGGTATCTTCGAGTTTCACTGATATGGAGC
1 GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
* *
3669 GCACATACTTTTCGGAG
1 GCACATGCTTTCCGGAG
3686 ATCAAACTTT
Statistics
Matches: 357, Mismatches: 58, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
44 46 0.13
45 274 0.77
48 28 0.08
49 9 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (45 bp):
GCACATGCTTTCCGGAGGTATCTTCGAGTTTAATTGATATGGAGC
Found at i:3652 original size:224 final size:225
Alignment explanation
Indices: 3240--3679 Score: 629
Period size: 224 Copynumber: 2.0 Consensus size: 225
3230 AGAGGTATCA
3240 TCGAGTTTAATTGATATGGACAGCACATGCTTTCCGGAGGTATATCAAGTTTCACTGATATATAT
1 TCGAGTTTAATTGATATGGACAGCACATGCTTTCCGGAGGTATATCAAGTTTCACTGATATATA-
* * **
3305 GGACCACACATGCTTTTCAGAGGTATCTTCGAGTTTAATTGATATGGAGCGCACATGCTTTATGG
65 GGA-CACACATGCTTTTCAGAGGTATCTTCGAGTTTAACTGATATAGAGCGCACATGCTTTACAG
*
3370 AGATATCTTCGAGTTTAATTGATATGGAGCGCACATGCTTTCCAGAGGTATTTTCGAGTTTCACT
129 AGATATCTTCGAGTTTAATTGATATGGAGCGCACATGCTTTCCAGAGGTATCTTCGAGTTTCACT
* *
3435 GATGTGGAGTGCACATACTTTCGCAGATATTT
194 GATATGGAGCGCACATACTTTCGCAGATATTT
** * * *
3467 TCGAGTTTAATTGATATGGAGTGCACATGCTTTCTGGAGGTATCTTCGAGTTTCACTGATATGA-
1 TCGAGTTTAATTGATATGGACAGCACATGCTTTCCGGAGGTAT-ATCAAGTTTCACTGATAT-AT
* * * *
3531 A-G-CGCACATGC-TTTCTGGAGGTATCTTCGAGTTTCACTGATATAGAGCGCACATGCTTTCCA
64 AGGACACACATGCTTTTC-AGAGGTATCTTCGAGTTTAACTGATATAGAGCGCACATGCTTTACA
* *
3593 GAGATATCTTCGAGTTTAATTGATATGGAGCGCATATGC-TTCCCGTAGGTATCTTCGAGTTTCA
128 GAGATATCTTCGAGTTTAATTGATATGGAGCGCACATGCTTTCCAG-AGGTATCTTCGAGTTTCA
3657 CTGATATGGAGCGCACATACTTT
192 CTGATATGGAGCGCACATACTTT
3680 TCGGAGATCA
Statistics
Matches: 191, Mismatches: 18, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
223 9 0.05
224 123 0.64
226 1 0.01
227 40 0.21
228 17 0.09
229 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (225 bp):
TCGAGTTTAATTGATATGGACAGCACATGCTTTCCGGAGGTATATCAAGTTTCACTGATATATAG
GACACACATGCTTTTCAGAGGTATCTTCGAGTTTAACTGATATAGAGCGCACATGCTTTACAGAG
ATATCTTCGAGTTTAATTGATATGGAGCGCACATGCTTTCCAGAGGTATCTTCGAGTTTCACTGA
TATGGAGCGCACATACTTTCGCAGATATTT
Found at i:4978 original size:16 final size:17
Alignment explanation
Indices: 4957--5000 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
4947 TATGTAAATG
*
4957 CATGTATGCAT-ATGTA
1 CATGTATGCATGATGAA
4973 CATGTATG-ATGATGAA
1 CATGTATGCATGATGAA
*
4989 CATATATGCATG
1 CATGTATGCATG
5001 TCTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 19 0.79
17 3 0.12
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (17 bp):
CATGTATGCATGATGAA
Found at i:7502 original size:2 final size:2
Alignment explanation
Indices: 7495--7540 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
7485 TATGTAGTAC
*
7495 AT AT AT AT GAT AT AT AT AT AT AT AT CA- AC AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
7538 AT A
1 AT A
7541 GCAAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
1 1 0.03
2 36 0.90
3 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:7503 original size:15 final size:15
Alignment explanation
Indices: 7483--7536 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
7473 ATTCTAGGCC
7483 TATATG-TAGTACATA
1 TATATGATA-TACATA
*
7498 TATATGATATATATA
1 TATATGATATACATA
7513 TATAT-ATCA-ACATA
1 TATATGAT-ATACATA
7527 TATAT-ATATA
1 TATATGATATA
7537 TATAGCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 14 0.41
15 17 0.50
16 2 0.06
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (15 bp):
TATATGATATACATA
Done.