Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016512.1 Corchorus olitorius cultivar O-4 contig16545, 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: 50743
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11151 original size:17 final size:17
Alignment explanation
Indices: 11129--11163 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11119 GTATAATTAT
11129 TATAGGTATAGTGTAGG
1 TATAGGTATAGTGTAGG
11146 TATAGGTATAGTGTAGG
1 TATAGGTATAGTGTAGG
11163 T
1 T
11164 TGACATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (17 bp):
TATAGGTATAGTGTAGG
Found at i:34388 original size:56 final size:56
Alignment explanation
Indices: 34292--34405 Score: 183
Period size: 56 Copynumber: 2.0 Consensus size: 56
34282 TATCCATTTC
* * ** *
34292 CTTTCACACAATAAATGTTATAATAAATCCTATCTTCCTATCTTTACTTAATTATT
1 CTTTCACACAATAAATGTTAAAATAAATCATATCCCCCTATCTCTACTTAATTATT
34348 CTTTCACACAATAAATGTTAAAATAAATCATATCCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTAAAATAAATCATATCCCCCTATCTCTACTTAATTATT
34404 CT
1 CT
34406 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTAAAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:34530 original size:42 final size:41
Alignment explanation
Indices: 34471--34550 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
34461 TAAGTATCAG
*
34471 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTCAGTTGAGTATTTCTTAA-TTACAAAGAATTTTCTAT
*
34513 GATTTCAGTTGAGTATTTCTTAATTACAGAGAATTTTC
1 GATTTCAGTTGAGTATTTCTTAATTACAAAGAATTTTC
34551 AAGACTTAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 14 0.39
42 22 0.61
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (41 bp):
GATTTCAGTTGAGTATTTCTTAATTACAAAGAATTTTCTAT
Found at i:35339 original size:17 final size:17
Alignment explanation
Indices: 35317--35352 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35307 TTCAAGAAAA
35317 TTATACAAATAGTGGGG
1 TTATACAAATAGTGGGG
35334 TTATACAAATAGTGGGG
1 TTATACAAATAGTGGGG
35351 TT
1 TT
35353 TGAAGAAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (17 bp):
TTATACAAATAGTGGGG
Found at i:39858 original size:16 final size:18
Alignment explanation
Indices: 39825--39861 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
39815 AATCTGCACT
39825 ATCAATCAATCAATAACA
1 ATCAATCAATCAATAACA
39843 ATCAA-CAATC-ATAACA
1 ATCAATCAATCAATAACA
39859 ATC
1 ATC
39862 TCTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 5 0.26
18 5 0.26
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (18 bp):
ATCAATCAATCAATAACA
Found at i:50019 original size:41 final size:42
Alignment explanation
Indices: 49940--50019 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
49930 ATTTGTCCAT
*
49940 GTCATCTGTCCACGTGGCTCAAAAAGCCACGTGGCCAAACCAC
1 GTCATCTGTCCACGTGGC-CAAAAAGCCACGTGACCAAACCAC
49983 GTCATCT-TCCCACGTGG-CAAAAAGCCACGTGACCAAA
1 GTCATCTGT-CCACGTGGCCAAAAAGCCACGTGACCAAA
50020 ATATTGTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
41 19 0.54
42 1 0.03
43 15 0.43
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (42 bp):
GTCATCTGTCCACGTGGCCAAAAAGCCACGTGACCAAACCAC
Done.