Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015248.1 Corchorus olitorius cultivar O-4 contig15281, 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: 42028
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2028 original size:11 final size:11
Alignment explanation
Indices: 2012--2037 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2002 AGATAATTTC
2012 TTTTCTTCTAG
1 TTTTCTTCTAG
2023 TTTTCTTCTAG
1 TTTTCTTCTAG
2034 TTTT
1 TTTT
2038 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:2826 original size:14 final size:16
Alignment explanation
Indices: 2797--2829 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2787 TTACTTTGCT
2797 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
2813 TTGTTTT-T-GTTTAA
1 TTGTTTTCTAGTTTAA
2827 TTG
1 TTG
2830 CCTTCTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:4482 original size:19 final size:18
Alignment explanation
Indices: 4449--4484 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4439 TTGAAATTAT
4449 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
4467 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
4485 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:8238 original size:19 final size:19
Alignment explanation
Indices: 8213--8252 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8203 TCAGGGTGAA
8213 ATTTTTTT-AT-TTGTTTTG
1 ATTTTTTTAATATT-TTTTG
8231 ATTTTTTTAATATTTTTTG
1 ATTTTTTTAATATTTTTTG
8250 ATT
1 ATT
8253 AAACCCTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 10 0.50
20 2 0.10
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (19 bp):
ATTTTTTTAATATTTTTTG
Found at i:14967 original size:29 final size:30
Alignment explanation
Indices: 14915--14974 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
14905 GAAGTTCGTG
*
14915 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGACT-ATTGAAGACTTATTTCAAGA
*
14946 TTTGAAGACT-TTGAAGATTTATTTCAAGA
1 TTTGAAGACTATTGAAGACTTATTTCAAGA
14975 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (30 bp):
TTTGAAGACTATTGAAGACTTATTTCAAGA
Found at i:21581 original size:21 final size:21
Alignment explanation
Indices: 21555--21609 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
21545 ATCCATCGTG
21555 CCACCACCGGTTAAACCCGTA
1 CCACCACCGGTTAAACCCGTA
*
21576 CCACCACCGTTTAAACCCGTA
1 CCACCACCGGTTAAACCCGTA
21597 CCACCACCGGTTA
1 CCACCACCGGTTA
21610 TGCCTGTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.27, C:0.44, G:0.13, T:0.16
Consensus pattern (21 bp):
CCACCACCGGTTAAACCCGTA
Found at i:24859 original size:5 final size:6
Alignment explanation
Indices: 24848--24872 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
24838 CAAATCAAAT
24848 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
24873 TAATACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:26366 original size:22 final size:21
Alignment explanation
Indices: 26314--26368 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
26304 TGCTTCTTGA
26314 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
26335 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
26354 AATAAGTCTTCAAAT
1 AATAA-TCTTCAAAT
26369 ACGAACTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 2 0.07
21 2 0.07
22 9 0.31
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:32774 original size:19 final size:19
Alignment explanation
Indices: 32752--32802 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
32742 GTGCTGAAAT
32752 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
32771 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
32790 TAATT-ATTATTAA
1 TAATTAATTATTAA
32803 AAATCTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:38345 original size:12 final size:13
Alignment explanation
Indices: 38323--38352 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
38313 ACTAGCAATT
38323 AAAATCAATCAAG
1 AAAATCAATCAAG
38336 AAAA-CAATCAAG
1 AAAATCAATCAAG
38348 AAAAT
1 AAAAT
38353 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:40296 original size:32 final size:32
Alignment explanation
Indices: 40272--40370 Score: 180
Period size: 32 Copynumber: 3.1 Consensus size: 32
40262 ATAGAGGTCG
* *
40272 TTTGGTCTGTAGACGCCGCTAAATAAGGGCGT
1 TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
40304 TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
1 TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
40336 TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
1 TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
40368 TTT
1 TTT
40371 CTATTCACAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (32 bp):
TTTGTTCTATAGACGCCGCTAAATAAGGGCGT
Found at i:41920 original size:17 final size:17
Alignment explanation
Indices: 41895--41929 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41885 TGCATAATGT
41895 TAATATACCAACAAGAA
1 TAATATACCAACAAGAA
*
41912 TAATGTACCAACAAGAA
1 TAATATACCAACAAGAA
41929 T
1 T
41930 GCATTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (17 bp):
TAATATACCAACAAGAA
Done.