Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005640.1 Corchorus capsularis cultivar CVL-1 contig05658, 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: 7531
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:4218 original size:3 final size:3
Alignment explanation
Indices: 4210--4250 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
4200 ATTTGCATTA
4210 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4251 AAGGATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4950 original size:8 final size:9
Alignment explanation
Indices: 4937--4980 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
4927 AATGAAAAAT
4937 GAAAAAGAG
1 GAAAAAGAG
4946 GAAAAAGAG
1 GAAAAAGAG
*
4955 GAAAAAGAAA
1 GAAAAAG-AG
4965 GAAAAA-AG
1 GAAAAAGAG
4973 AGAAAAAG
1 -GAAAAAG
4981 CAACGATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 1 0.03
9 22 0.73
10 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
GAAAAAGAG
Found at i:4968 original size:19 final size:18
Alignment explanation
Indices: 4937--4980 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
4927 AATGAAAAAT
*
4937 GAAAAAG-AGGAAAAAGA
1 GAAAAAGAAGAAAAAAGA
4954 GGAAAAAGAAAGAAAAAAGA
1 -GAAAAAG-AAGAAAAAAGA
4974 GAAAAAG
1 GAAAAAG
4981 CAACGATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 7 0.30
20 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAGAAAAAAGA
Found at i:6309 original size:51 final size:50
Alignment explanation
Indices: 6254--6412 Score: 160
Period size: 51 Copynumber: 3.1 Consensus size: 50
6244 CAGGTTTGAT
* * * * * **
6254 TATAAAAATCGAACCTTTAGGTAATATTGATGAGTTTTTGGTAATTTTGTC
1 TATAAAAATTGAATCTTTAGGTAATAATGATAAG-ATTTGGTAATTTCATC
*
6305 TATAAAAATTGAATCTTTAGGTCATAATGATAAGATTTGGTAATTTCATC
1 TATAAAAATTGAATCTTTAGGTAATAATGATAAGATTTGGTAATTTCATC
* * *
6355 AATAAAAATTGAATCTTTAAGTAGCA-AATGACAA-ATTTTGGTAATTTCATC
1 TATAAAAATTGAATCTTTAGGTA--ATAATGATAAGA-TTTGGTAATTTCATC
*
6406 AATAAAA
1 TATAAAA
6413 TCGGATCTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
50 34 0.37
51 58 0.62
52 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (50 bp):
TATAAAAATTGAATCTTTAGGTAATAATGATAAGATTTGGTAATTTCATC
Found at i:6361 original size:50 final size:48
Alignment explanation
Indices: 6290--6530 Score: 189
Period size: 51 Copynumber: 4.8 Consensus size: 48
6280 TTGATGAGTT
** * * *
6290 TTTGGTAATTTTGTCTATAAAAATTGAATCTTTAGGTCATAATGATAAGA
1 TTTGGTAATTTCATCAATAAAAATCGAATCTTTAGGTCA-AATGACAA-A
* *
6340 TTTGGTAATTTCATCAATAAAAATTGAATCTTTAAGTAGCAAATGACAAA
1 TTTGGTAATTTCATCAATAAAAATCGAATCTTTAGGT--CAAATGACAAA
*
6390 TTTTGGTAATTTCATCAAT-AAAATCGGATCTTTAAAGAAG-CAAATGACAAA
1 -TTTGGTAATTTCATCAATAAAAATCGAATCTTT--AG--GTCAAATGACAAA
* * * ** * *
6441 TTTTGATAATTTCATCAATAAAACTCGGATCTCAAAGTAGCAAAATGACAATT
1 -TTTGGTAATTTCATCAATAAAAATCGAATCTTTAGGT--C-AAATGACAA-A
* *
6494 TTTGGTAATTTTATCAATAAAAATTGAATCTTTAGGT
1 TTTGGTAATTTCATCAATAAAAATCGAATCTTTAGGT
6531 GGTAAGTATT
Statistics
Matches: 156, Mismatches: 22, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
48 1 0.01
50 47 0.30
51 55 0.35
52 52 0.33
54 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (48 bp):
TTTGGTAATTTCATCAATAAAAATCGAATCTTTAGGTCAAATGACAAA
Found at i:6432 original size:51 final size:51
Alignment explanation
Indices: 6340--6515 Score: 248
Period size: 51 Copynumber: 3.4 Consensus size: 51
6330 AATGATAAGA
* *
6340 TTTGGTAATTTCATCAATAAAAATTGAATCTTT-AAGTAGCAAATGACAAAT
1 TTTGGTAATTTCATCAAT-AAAATCGGATCTTTAAAGTAGCAAATGACAAAT
*
6391 TTTGGTAATTTCATCAATAAAATCGGATCTTTAAAGAAGCAAATGACAAAT
1 TTTGGTAATTTCATCAATAAAATCGGATCTTTAAAGTAGCAAATGACAAAT
* * *
6442 TTTGATAATTTCATCAATAAAACTCGGATC-TCAAAGTAGCAAAATGACAATT
1 TTTGGTAATTTCATCAATAAAA-TCGGATCTTTAAAGTAGC-AAATGACAAAT
*
6494 TTTGGTAATTTTATCAATAAAA
1 TTTGGTAATTTCATCAATAAAA
6516 ATTGAATCTT
Statistics
Matches: 113, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
50 12 0.11
51 64 0.57
52 37 0.33
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (51 bp):
TTTGGTAATTTCATCAATAAAATCGGATCTTTAAAGTAGCAAATGACAAAT
Found at i:7462 original size:30 final size:30
Alignment explanation
Indices: 7411--7478 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
7401 TAAAAGGGAG
*
7411 ATCAGTAATTAAGTTCAATAAGA-AATAGTA
1 ATCAGTAATTAAGTTCAATAAGAGAA-AGCA
* * *
7441 ATCAGTGATTAGGTTCGATAAGAGAAAGCA
1 ATCAGTAATTAAGTTCAATAAGAGAAAGCA
7471 ATCAGTAA
1 ATCAGTAA
7479 AGAGTAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCAGTAATTAAGTTCAATAAGAGAAAGCA
Done.