Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011493.1 Corchorus capsularis cultivar CVL-1 contig11514, 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: 38978
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3433 original size:85 final size:85
Alignment explanation
Indices: 3277--3465 Score: 247
Period size: 85 Copynumber: 2.2 Consensus size: 85
3267 GAAAATTGAT
** * **
3277 TGAAATCAAGCCTCAATCGATTTAATGGTAGAATCGTAAATACTGTTGAAGTCTCTGTAACAATG
1 TGAAATCAAGATTCAATCGATTTAATGGCAGAATCGTAAATACTGTTGAAGTCTCTGTAACAAAC
* **
3342 GCTGAAGCTGGTCAATCGAC
66 ACTGAAGCTGCACAATCGAC
3362 TGAAATCAAGATTCAATCGATTTAATGGCAGAATCGTAAATACTGTTGAAGTCTCTGTAA-AGAA
1 TGAAATCAAGATTCAATCGATTTAATGGCAGAATCGTAAATACTGTTGAAGTCTCTGTAACA-AA
* *
3426 CATTGAAGCTGCACAATCGAT
65 CACTGAAGCTGCACAATCGAC
*
3447 TGAAAAT-AAGTTTCAATCG
1 TG-AAATCAAGATTCAATCG
3466 GTTCCACTAG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 86 0.95
86 4 0.04
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (85 bp):
TGAAATCAAGATTCAATCGATTTAATGGCAGAATCGTAAATACTGTTGAAGTCTCTGTAACAAAC
ACTGAAGCTGCACAATCGAC
Found at i:5907 original size:3 final size:3
Alignment explanation
Indices: 5901--5933 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5891 GCCGCCGCCG
*
5901 CCA CCA CCA CCA CCA CCA CCT CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
5934 AAGTCCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.67, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:8239 original size:21 final size:22
Alignment explanation
Indices: 8200--8240 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
8190 TAACTAAAAA
*
8200 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCACTATGATT
*
8222 TTTTGAT-ACCTCATTATGA
1 TTTTGATAACCTCACTATGA
8241 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGATT
Found at i:8314 original size:22 final size:21
Alignment explanation
Indices: 8057--8314 Score: 134
Period size: 22 Copynumber: 12.0 Consensus size: 21
8047 TAATTTTTTT
* *
8057 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCCTATGAAATTTTGA
* *
8079 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
*
8101 -AGACCTCAATATGAAATTTTGA
1 TA-ACCTC-CTATGAAATTTTGA
* * *
8123 TAACTTCCCAATAAAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
* * *
8145 TAACCAACACTATGAGATGTTGA
1 TAACC-TC-CTATGAAATTTTGA
* * *
8168 TAACTTTCTTATGAAATCTTGA
1 TAAC-CTCCTATGAAATTTTGA
*
8190 TAA----CTA-AAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
8206 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
* *
8228 T-ACCTCATTATGAAATTTTGT
1 TAACCTC-CTATGAAATTTTGA
*
8249 TAATCTTCCTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
* * *
8271 TCTACATACTATGAAATTTTGA
1 T-AACCTCCTATGAAATTTTGA
*
8293 TAACCCTCTTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
8315 AAACTAAACT
Statistics
Matches: 175, Mismatches: 42, Indels: 38
0.69 0.16 0.15
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
20 1 0.01
21 22 0.13
22 118 0.67
23 21 0.12
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:18547 original size:12 final size:12
Alignment explanation
Indices: 18530--18563 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
18520 GAGATCTTTT
18530 AAAACCCACTTC
1 AAAACCCACTTC
18542 AAAACCCACTTC
1 AAAACCCACTTC
18554 AAAACCCACT
1 AAAACCCACT
18564 CCAATTGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACCCACTTC
Found at i:19574 original size:11 final size:11
Alignment explanation
Indices: 19531--19568 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19521 TTCCTATATA
*
19531 AAATAAATTAT
1 AAATTAATTAT
19542 CAAA-TAATTAT
1 -AAATTAATTAT
19553 AAATTAATTAT
1 AAATTAATTAT
19564 AAATT
1 AAATT
19569 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:24075 original size:21 final size:21
Alignment explanation
Indices: 24051--24090 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24041 AGCTCGAGCT
*
24051 CGAGCTCG-ACTCGACTTTTTC
1 CGAGC-CGAACTCGAATTTTTC
24072 CGAGCCGAACTCGAATTTT
1 CGAGCCGAACTCGAATTTT
24091 CCTCGAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
CGAGCCGAACTCGAATTTTTC
Found at i:27667 original size:27 final size:27
Alignment explanation
Indices: 27631--27724 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
27621 GCTCAGCCCT
27631 TTACTATGATGGGGCAGCTCAGCCGGG
1 TTACTATGATGGGGCAGCTCAGCCGGG
*
27658 TTACTATGATGTGG-ATGCTCAGCCGGG
1 TTACTATGATGGGGCA-GCTCAGCCGGG
* * * *
27685 TCACTATGATGGGGCTGTTCAGCCAGG
1 TTACTATGATGGGGCAGCTCAGCCGGG
*
27712 TTATTATGATGGG
1 TTACTATGATGGG
27725 CCCGAGGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 56 0.98
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (27 bp):
TTACTATGATGGGGCAGCTCAGCCGGG
Found at i:30517 original size:21 final size:21
Alignment explanation
Indices: 30491--30534 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
30481 CAAACGTGTA
*
30491 AAAAAAGGGGTGGTGTTTAGC
1 AAAAAAGGGGCGGTGTTTAGC
30512 AAAAAAGGGGCGGTGTTTAGC
1 AAAAAAGGGGCGGTGTTTAGC
30533 AA
1 AA
30535 TACCCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.20
Consensus pattern (21 bp):
AAAAAAGGGGCGGTGTTTAGC
Found at i:37496 original size:70 final size:70
Alignment explanation
Indices: 37419--37549 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
37409 AAAAAGAAAT
* *
37419 ATCTAAAATGTATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAAGTTTGATTATAA
1 ATCTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAACTTTGATTATAA
37484 AAAAG
66 AAAAG
*
37489 ATCTAAAATATATCTTCTTAAACTTTTATTTAAATTCAACTTTTAAACTTTAACTTTGATT
1 ATCTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAACTTTGATT
37550 GGCCAAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (70 bp):
ATCTAAAATATATCTTCTTAAACATTTATTTAAATTCAACTTTTAAACTTTAACTTTGATTATAA
AAAAG
Found at i:38266 original size:16 final size:16
Alignment explanation
Indices: 38247--38279 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38237 TTTAGATTTT
38247 AAAAAATCCCTATTAA
1 AAAAAATCCCTATTAA
*
38263 AAAAAATCCCTCTTAA
1 AAAAAATCCCTATTAA
38279 A
1 A
38280 TATCCCCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAATCCCTATTAA
Done.