Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023937.1 Corchorus olitorius cultivar O-4 contig23970, 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: 6148
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.28
Found at i:3580 original size:22 final size:23
Alignment explanation
Indices: 3547--3590 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3537 AAGAGGTCGA
3547 AAAAGAAAAAC-TGGACCTAAAAT
1 AAAAGAAAAACTTGG-CCTAAAAT
3570 AAAA-AAAAACTTGGCCTAAAA
1 AAAAGAAAAACTTGGCCTAAAA
3591 CAGAGAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.61, C:0.14, G:0.11, T:0.14
Consensus pattern (23 bp):
AAAAGAAAAACTTGGCCTAAAAT
Found at i:4708 original size:117 final size:116
Alignment explanation
Indices: 4449--4747 Score: 535
Period size: 117 Copynumber: 2.6 Consensus size: 116
4439 CAGTTTAAAA
* *
4449 CAAAATCTTATCTTGTTTTAAAATCCTGCTCGAGGTCTCTGCTAGAGAGTTTTCAACTCAAAATC
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
* *
4514 TTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTACTAGAGAGTTTTCAATT
66 TCATCTTGTTTTAAAATCCTGCTCGAGGTCTCTACTAGAGAGTTTTCAATT
4565 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
*
4630 TCATCTTGTTTTCAAAATCCTGCTCGAGGTCTCTGCTAGAGAGTTTTCAATT
66 TCATCTTGTTTT-AAAATCCTGCTCGAGGTCTCTACTAGAGAGTTTTCAATT
*
4682 TAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
4747 T
66 T
4748 TATTTTGGTC
Statistics
Matches: 176, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
116 74 0.42
117 102 0.58
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (116 bp):
CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATTCAAAATC
TCATCTTGTTTTAAAATCCTGCTCGAGGTCTCTACTAGAGAGTTTTCAATT
Found at i:4769 original size:58 final size:58
Alignment explanation
Indices: 4449--4750 Score: 541
Period size: 58 Copynumber: 5.2 Consensus size: 58
4439 CAGTTTAAAA
* *
4449 CAAAATCTTATCTTGTTTTAAAATCCTGCTCGAGGTCTCTGCTAGAGAGTTTTCAACT
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
*
4507 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTACTAGAGAGTTTTCAATT
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
4565 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
* *
4623 CAAAATCTCATCTTGTTTTCAAAATCCTGCTCGAGGTCTCTGCTAGAGAGTTTTCAATT
1 CAAAATCTTATCTTGTTTT-AAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
*
4682 TAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
1 CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
4740 CAAAATCTTAT
1 CAAAATCTTAT
4751 TTTGGTCGAG
Statistics
Matches: 233, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
58 178 0.76
59 55 0.24
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (58 bp):
CAAAATCTTATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGCTAGAGAGTTTTCAATT
Found at i:5208 original size:89 final size:84
Alignment explanation
Indices: 5009--5300 Score: 277
Period size: 89 Copynumber: 3.3 Consensus size: 84
4999 TTAATTGACC
* * *
5009 TTTTGCGA-ATCCAGGGGCATTTTGGTCATTTTTGA-ACATCTAGGGGCATTTTGGTCA-TTTTG
1 TTTTGC-ACATCCAAGGGCATTTTGGTCA--GTT-ACACATCCA-GGGCATTTTGGTCATTTTTG
*
5071 CACATCCAAGGGCATTTTGGTCAT
61 CACATCCAGGGGCATTTTGGTCAT
* *
5095 TTTTGCACATTC-AGGAGCATTTTGGTCAGTTACGCATATCCAAGGGCATTTTGGTCATTTTTGC
1 TTTTGCACATCCAAGG-GCATTTTGGTCAGTTA--CACATCC-AGGGCATTTTGGTCATTTTTGC
* * *
5159 ACAATTCAGGGGGCATTTTGATCGT
62 AC-ATCCA-GGGGCATTTTGGTCAT
* * *
5184 TTTTCCACATCCAAAGGCATTTTGGTCGTATTTACACATCCAGGGACATTTTGGTCATTTTTTGC
1 TTTTGCACATCCAAGGGCATTTTGGTC--AGTTACACATCCAGGG-CATTTTGGTCA-TTTTTGC
*
5249 ACGTCCAGGGGCATTTTGGTCATT
62 ACATCCAGGGGCATTTTGGTCA-T
* *
5273 TTTTGCACGTCCAGGGGCATTTTGGTCA
1 TTTTGCACATCCAAGGGCATTTTGGTCA
5301 TTTTTTCATA
Statistics
Matches: 169, Mismatches: 22, Indels: 29
0.77 0.10 0.13
Matches are distributed among these distances:
83 1 0.01
84 2 0.01
85 3 0.02
86 39 0.23
87 10 0.06
88 21 0.12
89 78 0.46
90 11 0.07
91 4 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (84 bp):
TTTTGCACATCCAAGGGCATTTTGGTCAGTTACACATCCAGGGCATTTTGGTCATTTTTGCACAT
CCAGGGGCATTTTGGTCAT
Found at i:5306 original size:30 final size:29
Alignment explanation
Indices: 5009--5305 Score: 337
Period size: 29 Copynumber: 10.1 Consensus size: 29
4999 TTAATTGACC
5009 TTTTGCGA-ATCCAGGGGCATTTTGGTCAT
1 TTTTGC-ACATCCAGGGGCATTTTGGTCAT
* *
5038 TTTTGAACATCTAGGGGCATTTTGGTCA-
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
*
5066 TTTTGCACATCCAAGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* * *
5095 TTTTGCACATTCAGGAGCATTTTGGTCAG
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
** * *
5124 TTACGCATATCCAAGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* * *
5153 TTTTGCACAATTCAGGGGGCATTTTGATCGT
1 TTTTGCAC-ATCCA-GGGGCATTTTGGTCAT
* ** *
5184 TTTTCCACATCCAAAGGCATTTTGGTCGT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
* * *
5213 ATTTACACATCCAGGGACATTTTGGTCATT
1 TTTTGCACATCCAGGGGCATTTTGGTCA-T
*
5243 TTTTGCACGTCCAGGGGCATTTTGGTCATT
1 TTTTGCACATCCAGGGGCATTTTGGTCA-T
*
5273 TTTTGCACGTCCAGGGGCATTTTGGTCAT
1 TTTTGCACATCCAGGGGCATTTTGGTCAT
5302 TTTT
1 TTTT
5306 TCATACTCTG
Statistics
Matches: 225, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
28 26 0.12
29 116 0.52
30 63 0.28
31 20 0.09
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (29 bp):
TTTTGCACATCCAGGGGCATTTTGGTCAT
Done.