Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016787.1 Corchorus olitorius cultivar O-4 contig16820, 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: 32795
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43 T
1 T
44 TGTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:93 original size:19 final size:19
Alignment explanation
Indices: 69--114 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
59 CGGATCGGGT
*
69 CAAACCGGTTCGGTCCGAC
1 CAAACCGGTTCGGACCGAC
*
88 CAAACCGGTTCGGACCGGC
1 CAAACCGGTTCGGACCGAC
*
107 CAAGCCGG
1 CAAACCGG
115 CTCATGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.37, G:0.30, T:0.11
Consensus pattern (19 bp):
CAAACCGGTTCGGACCGAC
Found at i:3071 original size:21 final size:22
Alignment explanation
Indices: 3047--3090 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3037 AAAAGTTTTC
3047 TTCTTTTTGCG-AAAAAAAAAT
1 TTCTTTTTGCGTAAAAAAAAAT
* *
3068 TTCTTTTTGTGTTAAAAAAAAT
1 TTCTTTTTGCGTAAAAAAAAAT
3090 T
1 T
3091 ATTTTCTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (22 bp):
TTCTTTTTGCGTAAAAAAAAAT
Found at i:6498 original size:14 final size:14
Alignment explanation
Indices: 6479--6512 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6469 CTAACCCTTA
6479 ATTTTTCTTTTTTT
1 ATTTTTCTTTTTTT
6493 ATTTTTCTTTTTTT
1 ATTTTTCTTTTTTT
*
6507 CTTTTT
1 ATTTTT
6513 AGGATTTCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (14 bp):
ATTTTTCTTTTTTT
Found at i:8659 original size:19 final size:19
Alignment explanation
Indices: 8635--8671 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8625 ACCTTATGTA
*
8635 ACACAAATCACAATCACAC
1 ACACAAATCACAAACACAC
*
8654 ACACAATTCACAAACACA
1 ACACAAATCACAAACACA
8672 ATTCTAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.35, G:0.00, T:0.11
Consensus pattern (19 bp):
ACACAAATCACAAACACAC
Found at i:8664 original size:13 final size:13
Alignment explanation
Indices: 8636--8675 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
8626 CCTTATGTAA
8636 CACAAATCACAA-T
1 CACAAA-CACAATT
*
8649 CACACACACAATT
1 CACAAACACAATT
8662 CACAAACACAATT
1 CACAAACACAATT
8675 C
1 C
8676 TAGATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (13 bp):
CACAAACACAATT
Found at i:10373 original size:5 final size:5
Alignment explanation
Indices: 10363--10396 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
10353 GATTTTGGTC
10363 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
10397 ATGGTGAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:11227 original size:13 final size:13
Alignment explanation
Indices: 11202--11242 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
11192 TAGCCAAAAT
11202 AAAATATTAATAA
1 AAAATATTAATAA
* *
11215 AAAATTTTTATAA
1 AAAATATTAATAA
*
11228 TAAATATTAATAA
1 AAAATATTAATAA
11241 AA
1 AA
11243 GTCAAGAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATTAATAA
Found at i:18618 original size:21 final size:21
Alignment explanation
Indices: 18592--18638 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
18582 AATTATTGTG
*
18592 TAAAAACTGAAATAACAAAAAC
1 TAAAAACAGAAATAAC-AAAAC
18614 TAAAAACAGAAATAACAAAAC
1 TAAAAACAGAAATAACAAAAC
18635 TAAA
1 TAAA
18639 CCCGCATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.70, C:0.13, G:0.04, T:0.13
Consensus pattern (21 bp):
TAAAAACAGAAATAACAAAAC
Found at i:18946 original size:11 final size:11
Alignment explanation
Indices: 18930--18954 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18920 CTATATATTG
18930 AAAAAAAAAGA
1 AAAAAAAAAGA
18941 AAAAAAAAAGA
1 AAAAAAAAAGA
18952 AAA
1 AAA
18955 GATGAGAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:21681 original size:24 final size:24
Alignment explanation
Indices: 21653--21701 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21643 CCTCCAGAGA
21653 TGCTTCTGTTGTTAGAACAAGATG
1 TGCTTCTGTTGTTAGAACAAGATG
21677 TGCTTCTGTTGTTAGAACAAGATG
1 TGCTTCTGTTGTTAGAACAAGATG
21701 T
1 T
21702 TAATGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (24 bp):
TGCTTCTGTTGTTAGAACAAGATG
Found at i:26511 original size:11 final size:9
Alignment explanation
Indices: 26487--26515 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
26477 AAAACTCAAG
26487 TAGAGAGAC
1 TAGAGAGAC
26496 TAGAGAGAC
1 TAGAGAGAC
26505 TAGAGAGAC
1 TAGAGAGAC
26514 TA
1 TA
26516 ATTTGACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.31, T:0.14
Consensus pattern (9 bp):
TAGAGAGAC
Found at i:30410 original size:25 final size:25
Alignment explanation
Indices: 30376--30427 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
30366 ATGGAGATCA
30376 TTCCTAACCCAAAGGTATATATTCT
1 TTCCTAACCCAAAGGTATATATTCT
* *
30401 TTCCTAACCCAAAGGTTTGTATTCT
1 TTCCTAACCCAAAGGTATATATTCT
30426 TT
1 TT
30428 ATTTCTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (25 bp):
TTCCTAACCCAAAGGTATATATTCT
Done.