Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018390.1 Corchorus olitorius cultivar O-4 contig18423, 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: 23099
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:196 original size:29 final size:29
Alignment explanation
Indices: 163--221 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
153 TTGAGTGTGG
163 TATGGAAGGCGTAGAGCCAGATTAATAAA
1 TATGGAAGGCGTAGAGCCAGATTAATAAA
*
192 TATGGAAGGTGTAGAGCCAGATTAATAAA
1 TATGGAAGGCGTAGAGCCAGATTAATAAA
221 T
1 T
222 GTATGCCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (29 bp):
TATGGAAGGCGTAGAGCCAGATTAATAAA
Found at i:5204 original size:29 final size:29
Alignment explanation
Indices: 5162--5251 Score: 135
Period size: 29 Copynumber: 3.1 Consensus size: 29
5152 TGTTGAGTGT
*
5162 AATATGGAAGGTGTAGAGCCAAATTAATA
1 AATATGGAAGGTGTAGAGCCAGATTAATA
*
5191 AATACGGAAGGTGTAGAGCCAGATTAATA
1 AATATGGAAGGTGTAGAGCCAGATTAATA
* * *
5220 AAAATAGAAGATGTAGAGCCAGATTAATA
1 AATATGGAAGGTGTAGAGCCAGATTAATA
5249 AAT
1 AAT
5252 GTATGCCTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.47, C:0.08, G:0.23, T:0.22
Consensus pattern (29 bp):
AATATGGAAGGTGTAGAGCCAGATTAATA
Found at i:6538 original size:37 final size:37
Alignment explanation
Indices: 6489--6598 Score: 193
Period size: 37 Copynumber: 3.0 Consensus size: 37
6479 AAATAGATAC
*
6489 ATGTATTTTCACAAGACAACTCTTGATTCATGAATAG
1 ATGTCTTTTCACAAGACAACTCTTGATTCATGAATAG
*
6526 ATGTCTTTTCACAAGACAACTCTTGATTCATGAATAT
1 ATGTCTTTTCACAAGACAACTCTTGATTCATGAATAG
*
6563 ATGTCTTTTCACAAGACCACTCTTGATTCATGAATA
1 ATGTCTTTTCACAAGACAACTCTTGATTCATGAATA
6599 ATCACATTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (37 bp):
ATGTCTTTTCACAAGACAACTCTTGATTCATGAATAG
Found at i:9914 original size:2 final size:2
Alignment explanation
Indices: 9907--9931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9897 AAGCATGAAT
9907 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
9932 GTACTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11458 original size:37 final size:37
Alignment explanation
Indices: 11410--11486 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
11400 TATTAAATAG
*
11410 ATAGATGTCTTTTCACAAGACAACTCTTGATTCATGA
1 ATAGATATCTTTTCACAAGACAACTCTTGATTCATGA
*
11447 ATAGATATCTTTTCACAAGACCACTCTTGATTCATGA
1 ATAGATATCTTTTCACAAGACAACTCTTGATTCATGA
11484 ATA
1 ATA
11487 ATCACTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (37 bp):
ATAGATATCTTTTCACAAGACAACTCTTGATTCATGA
Found at i:12404 original size:13 final size:13
Alignment explanation
Indices: 12386--12410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12376 AAACAATGAC
12386 ATTTAAAAAATAT
1 ATTTAAAAAATAT
12399 ATTTAAAAAATA
1 ATTTAAAAAATA
12411 AGGATATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:17777 original size:12 final size:12
Alignment explanation
Indices: 17760--17820 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
17750 CCGTTTAATA
17760 ATTATATATATT
1 ATTATATATATT
17772 ATTATATATA--
1 ATTATATATATT
17782 ATTATATAGTA-T
1 ATTATATA-TATT
*
17794 ATAATATATATTT
1 ATTATATATA-TT
*
17807 AATCATATATATT
1 -ATTATATATATT
17820 A
1 A
17821 CTAAACGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 8 0.19
11 4 0.10
12 18 0.43
13 3 0.07
14 9 0.21
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (12 bp):
ATTATATATATT
Found at i:17785 original size:22 final size:23
Alignment explanation
Indices: 17757--17820 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 23
17747 AGACCGTTTA
17757 ATAATTATATATATTAT-TATAT
1 ATAATTATATATATTATATATAT
17779 ATAATTATATAGTATATAATATATAT
1 ATAATTATATA-TAT-T-ATATATAT
* *
17805 TTAATCATATATATTA
1 ATAATTATATATATTA
17821 CTAAACGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 11 0.31
23 4 0.11
24 2 0.06
25 5 0.14
26 14 0.39
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAATTATATATATTATATATAT
Found at i:23063 original size:14 final size:13
Alignment explanation
Indices: 23041--23076 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
23031 CATTTTTTGT
23041 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
23054 AAAAAGAAAAAGAA
1 AAAAA-AAAAAGAA
23068 AAGAAAAAA
1 AA-AAAAAA
23077 GAATAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 13 0.62
15 3 0.14
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Done.