Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016839.1 Corchorus olitorius cultivar O-4 contig16872, 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: 19167
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:9308 original size:21 final size:21
Alignment explanation
Indices: 9282--9323 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
9272 TCCTTTGGTG
* *
9282 ATGATCTCTAATGGGCTTCAA
1 ATGATCTCCAATGGCCTTCAA
9303 ATGATCTCCAATGGCCTTCAA
1 ATGATCTCCAATGGCCTTCAA
9324 CTCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
ATGATCTCCAATGGCCTTCAA
Found at i:9463 original size:21 final size:21
Alignment explanation
Indices: 9439--9530 Score: 134
Period size: 21 Copynumber: 4.4 Consensus size: 21
9429 CTTAGGCAAT
*
9439 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
9460 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
*
9481 TCCAATGAACTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
9502 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
9523 TCCAATGA
1 TCCAATGA
9531 ACGCCTAGCA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 3 0.04
21 64 0.96
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:10263 original size:20 final size:21
Alignment explanation
Indices: 10228--10297 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
10218 CTTAGACAAT
10228 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
10249 TCCAATGAG-TTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
10269 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
10290 TCCAATGA
1 TCCAATGA
10298 ACTCCTAGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.06
20 16 0.34
21 28 0.60
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:11714 original size:25 final size:24
Alignment explanation
Indices: 11677--11723 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
11667 CTAGAAAATT
11677 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
11703 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
11724 AATAGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:11733 original size:28 final size:26
Alignment explanation
Indices: 11677--11733 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
11667 CTAGAAAATT
* *
11677 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGAA
11703 TGAAAAACTTGATGATAGATGA-ATAGAA
1 TGAAAAACTT--TGATAGATGAGAT-GAA
11731 TGA
1 TGA
11734 TAGATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 14 0.54
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGAA
Found at i:12459 original size:21 final size:21
Alignment explanation
Indices: 12433--12474 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12423 TCCTTTGGTG
* *
12433 ATGATCTCTAATGGGCTTCAA
1 ATGATCTCCAATGGCCTTCAA
12454 ATGATCTCCAATGGCCTTCAA
1 ATGATCTCCAATGGCCTTCAA
12475 CTCTTCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (21 bp):
ATGATCTCCAATGGCCTTCAA
Found at i:12614 original size:21 final size:21
Alignment explanation
Indices: 12590--12681 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
12580 CTTAGACAAT
*
12590 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
12611 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
*
12632 TCCAATGAACTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
* *
12653 TCTAATGAGTTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
12674 TCCAATGA
1 TCCAATGA
12682 ACTCCTAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 3 0.05
21 61 0.95
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:14944 original size:43 final size:43
Alignment explanation
Indices: 14850--14935 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
14840 AGATCACAAG
14850 ATTCACAAGCAATCAAGTATCACAACTTAATTGTTTGCTAGGA
1 ATTCACAAGCAATCAAGTATCACAACTTAATTGTTTGCTAGGA
14893 ATTCACAAGCAATCAAGTATCACAACTTAATTGTTTGCTAGGA
1 ATTCACAAGCAATCAAGTATCACAACTTAATTGTTTGCTAGGA
14936 CTCTACAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (43 bp):
ATTCACAAGCAATCAAGTATCACAACTTAATTGTTTGCTAGGA
Done.