Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010591.1 Corchorus capsularis cultivar CVL-1 contig10612, 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: 123224
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:15364 original size:1 final size:1
Alignment explanation
Indices: 15358--15389 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
15348 ACCACTTGAA
15358 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15390 GCCAACAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16673 original size:15 final size:15
Alignment explanation
Indices: 16653--16682 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16643 AAATATCAGT
16653 AGTGTAGTGTGCTGC
1 AGTGTAGTGTGCTGC
16668 AGTGTAGTGTGCTGC
1 AGTGTAGTGTGCTGC
16683 GGGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.40, T:0.33
Consensus pattern (15 bp):
AGTGTAGTGTGCTGC
Found at i:22340 original size:3 final size:3
Alignment explanation
Indices: 22334--22382 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
22324 ATAATAATAT
22334 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22382 T
1 T
22383 CATCATCATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:53783 original size:29 final size:31
Alignment explanation
Indices: 53750--53814 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
53740 ACACATGGTG
* *
53750 TGCCATGTGTC-CTTTTT-GTACATGTGACA
1 TGCCATGTGGCACTTTTTGGTACACGTGACA
*
53779 TGCCATGTGGCATTTTTTGGTACACGTGACA
1 TGCCATGTGGCACTTTTTGGTACACGTGACA
53810 TGCCA
1 TGCCA
53815 CGTCGGATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 10 0.32
30 5 0.16
31 16 0.52
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (31 bp):
TGCCATGTGGCACTTTTTGGTACACGTGACA
Found at i:84546 original size:73 final size:73
Alignment explanation
Indices: 84427--84573 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
84417 GTTAACTGTA
84427 CATACTTTGCATCTTGTACGGAGCTTGGGCAAAGTTCAGCCGCATATTTGACAAGCTCACTGAGG
1 CATACTTTGCATCTTGTACGGAGCTTGGGCAAAGTTCAGCCGCATATTTGACAAGCTCACTGAGG
84492 CACCTTGC
66 CACCTTGC
84500 CATACTTTGCATCTTGTACGGAGCTTGGGCAAAGTTCAGCCGCATATTTGACAAGCTCACTGAGG
1 CATACTTTGCATCTTGTACGGAGCTTGGGCAAAGTTCAGCCGCATATTTGACAAGCTCACTGAGG
84565 CACCTTGC
66 CACCTTGC
84573 C
1 C
84574 CAAGTTCAGC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (73 bp):
CATACTTTGCATCTTGTACGGAGCTTGGGCAAAGTTCAGCCGCATATTTGACAAGCTCACTGAGG
CACCTTGC
Found at i:84594 original size:44 final size:44
Alignment explanation
Indices: 84531--84619 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
84521 AGCTTGGGCA
84531 AAGTTCAGCCGCATATTTGACAAGCTCACTGAGGCACCTTGCCC
1 AAGTTCAGCCGCATATTTGACAAGCTCACTGAGGCACCTTGCCC
84575 AAGTTCAGCCGCATATTTGACAAGCTCACTGAGGCACCTTGCCC
1 AAGTTCAGCCGCATATTTGACAAGCTCACTGAGGCACCTTGCCC
84619 A
1 A
84620 CCTGTTCTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.22
Consensus pattern (44 bp):
AAGTTCAGCCGCATATTTGACAAGCTCACTGAGGCACCTTGCCC
Found at i:97758 original size:39 final size:37
Alignment explanation
Indices: 97712--97806 Score: 126
Period size: 33 Copynumber: 2.6 Consensus size: 37
97702 GGAACCTGCA
97712 GGAATTAGAATGCCTGGAGATGGGCATGGGAATCCTCCG
1 GGAATTAGAATGCCTGGAGAT-GG-ATGGGAATCCTCCG
*
97751 GGAATTAGAATGCCTGG-GA---ATGGGATTCCTCCG
1 GGAATTAGAATGCCTGGAGATGGATGGGAATCCTCCG
*
97784 GGAATTAGAATGCCTGGAAATGG
1 GGAATTAGAATGCCTGGAGATGG
97807 TGGTGACCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
33 30 0.60
34 1 0.02
38 2 0.04
39 17 0.34
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (37 bp):
GGAATTAGAATGCCTGGAGATGGATGGGAATCCTCCG
Found at i:97771 original size:16 final size:16
Alignment explanation
Indices: 97750--97800 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
97740 GGAATCCTCC
97750 GGGAATTAGAATGCCT
1 GGGAATTAGAATGCCT
* * *
97766 GGGAA-TGGGATTCCT
1 GGGAATTAGAATGCCT
97781 CCGGGAATTAGAATGCCT
1 --GGGAATTAGAATGCCT
97799 GG
1 GG
97801 AAATGGTGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 5 0.19
18 7 0.27
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (16 bp):
GGGAATTAGAATGCCT
Found at i:109242 original size:12 final size:12
Alignment explanation
Indices: 109227--109255 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
109217 TGAACCTGAA
109227 GGTGTTGCTGTT
1 GGTGTTGCTGTT
109239 GGTGTTGCTGTT
1 GGTGTTGCTGTT
109251 -GTGTT
1 GGTGTT
109256 TTGTGAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.00, C:0.07, G:0.41, T:0.52
Consensus pattern (12 bp):
GGTGTTGCTGTT
Found at i:122148 original size:6 final size:6
Alignment explanation
Indices: 122137--122193 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
122127 AAATCAAGAG
* * * * *
122137 GAGGAA GAGGAA CG-CGAA GAGGTA GAGGAA GATGAA GATGAA GATGAA
1 GAGGAA GAGGAA -GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
122185 GAGGAA GAG
1 GAGGAA GAG
122194 TTTTCTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
5 1 0.02
6 41 0.95
7 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.44, T:0.07
Consensus pattern (6 bp):
GAGGAA
Done.