Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012096.1 Corchorus olitorius cultivar O-4 contig12129, 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: 43387
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1523 original size:19 final size:18
Alignment explanation
Indices: 1490--1525 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1480 TGAAAATAAT
1490 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1508 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1526 TAAGTCTTCA
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:17338 original size:2 final size:2
Alignment explanation
Indices: 17331--17376 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
17321 AAGCACTCAT
17331 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17372 TA TA T
1 TA TA T
17377 TGTGGAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18556 original size:6 final size:6
Alignment explanation
Indices: 18545--18574 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
18535 GAACATGATC
18545 CTTGAA CTTGAA CTTGAA CTTGAA CTTGAA
1 CTTGAA CTTGAA CTTGAA CTTGAA CTTGAA
18575 GATGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (6 bp):
CTTGAA
Found at i:18580 original size:18 final size:18
Alignment explanation
Indices: 18535--18580 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
18525 AAGAAAAGGA
*
18535 GAACATGATCCTTGAACTT
1 GAACATGA-ACTTGAACTT
*
18554 GAACTTGAACTTGAACTT
1 GAACATGAACTTGAACTT
*
18572 GAAGATGAA
1 GAACATGAA
18581 GAAGACTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (18 bp):
GAACATGAACTTGAACTT
Found at i:29290 original size:28 final size:27
Alignment explanation
Indices: 29259--29333 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
29249 AGGATCAACT
29259 AGGGGCATTTTGGTCATTTTCAAAATCC
1 AGGGGCATTTTGGTCATTTTC-AAATCC
* * ** *
29287 AGGGGCATTTTAGTCATTTGCACGTCT
1 AGGGGCATTTTGGTCATTTTCAAATCC
*
29314 AAGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
29334 AGGTTCATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCAAATCC
Found at i:29666 original size:20 final size:20
Alignment explanation
Indices: 29641--29681 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
29631 TCCTTGGTCA
29641 TAATTTTGCATTAGCAATTT
1 TAATTTTGCATTAGCAATTT
*
29661 TAATTTTGTATTAGCAATTT
1 TAATTTTGCATTAGCAATTT
29681 T
1 T
29682 TAGTTGGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (20 bp):
TAATTTTGCATTAGCAATTT
Found at i:39625 original size:76 final size:76
Alignment explanation
Indices: 39474--39618 Score: 179
Period size: 76 Copynumber: 1.9 Consensus size: 76
39464 ACAAGGGCCC
* * *
39474 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTACCTGAGCACCCAGGT
39539 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * *
39550 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCACCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-ACCTGAGCACCCA
39612 GGTGGGC
63 GGTGGGC
39619 TATGTCATAG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 49 0.83
77 6 0.10
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTACCTGAGCACCCAGGT
GGGCAGTGTCA
Found at i:42023 original size:15 final size:16
Alignment explanation
Indices: 41990--42029 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
41980 TTACTTTGTT
41990 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
42006 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
42021 TTGTTTTCT
1 TTGTTTTCT
42030 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Done.