Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019392.1 Corchorus olitorius cultivar O-4 contig19425, 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: 51543
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Found at i:10557 original size:1 final size:1
Alignment explanation
Indices: 10553--10578 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
10543 TTGTTTTTTT
10553 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
10579 TCAATTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:13865 original size:6 final size:6
Alignment explanation
Indices: 13856--13882 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13846 GATGGGACTG
13856 GGATTT GGATTT GGATTT GGATTT GGA
1 GGATTT GGATTT GGATTT GGATTT GGA
13883 AAAACGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (6 bp):
GGATTT
Found at i:18196 original size:67 final size:69
Alignment explanation
Indices: 18036--18206 Score: 256
Period size: 67 Copynumber: 2.5 Consensus size: 69
18026 GATCTCAAAA
* *
18036 AAGGTAATAGACGTATATTTGTGATTTCTCATTGAATTGATTGAGATATTTGTTGATAACGTTAT
1 AAGGTAGTAGACGTATATTTGTGATTTCTCATTGAATTGACTGAGATA-TTGTTGATAACGTTAT
*
18101 TCATT
65 TAATT
* * *
18106 CAGGTAGCAGACGTATATTTGTGATTTCTCATTGAATTGACTGAGATA-T-TTGATAACTTTATT
1 AAGGTAGTAGACGTATATTTGTGATTTCTCATTGAATTGACTGAGATATTGTTGATAACGTTATT
18169 AATT
66 AATT
*
18173 AAGGTAGTAGACGTTTATTTGTGATTTCTCATTG
1 AAGGTAGTAGACGTATATTTGTGATTTCTCATTG
18207 CCCATCTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
67 47 0.51
68 1 0.01
70 44 0.48
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (69 bp):
AAGGTAGTAGACGTATATTTGTGATTTCTCATTGAATTGACTGAGATATTGTTGATAACGTTATT
AATT
Found at i:18332 original size:35 final size:34
Alignment explanation
Indices: 18293--18360 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
18283 GAAACAAACC
18293 TAATTTTCTTTAACAAATATTTGATTTGAGTCTTT
1 TAATTTTCTTTAACAAA-ATTTGATTTGAGTCTTT
* ** * *
18328 TAATTTTTTTTTGCCAAATTTGATTTGGGTCTT
1 TAATTTTCTTTAACAAAATTTGATTTGAGTCTT
18361 CAAAATTACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (34 bp):
TAATTTTCTTTAACAAAATTTGATTTGAGTCTTT
Found at i:25704 original size:24 final size:23
Alignment explanation
Indices: 25667--25728 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
25657 TGTGGTCACG
25667 AGTGGTCGAGCGCC-GCGTTATGGA
1 AGTGGTCGAGCGCCAG-GTT-TGGA
25691 AGTGGTCG-GTCGCCAGGTTTGGA
1 AGTGGTCGAG-CGCCAGGTTTGGA
25714 AGTGGTC-AGGCGCCA
1 AGTGGTCGA-GCGCCA
25729 AGCAATTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
23 17 0.50
24 16 0.47
25 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.42, T:0.21
Consensus pattern (23 bp):
AGTGGTCGAGCGCCAGGTTTGGA
Found at i:32744 original size:127 final size:127
Alignment explanation
Indices: 32572--33007 Score: 791
Period size: 127 Copynumber: 3.4 Consensus size: 127
32562 TTTGCGCCCC
* *
32572 GGTTGGATCTTTGTCGATCGCCCTGCCTGCTGGCGTTGAGTCCTTTGCGGGCGTTCATTATTTTC
1 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTC
* * *
32637 CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGTACACGTCGAAGGCCATGCTAAGTCAG
66 CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
32699 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTC
1 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTC
32764 CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
66 CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
* * *
32826 GGTTGGATCTTCGTCGATCGCCCTGCTTACTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTT
1 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTC
*
32891 CGTACTTGTGTAGGAATCACTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
66 CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
32953 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTT
1 GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTT
33008 GTTAAGCCTA
Statistics
Matches: 298, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 298 1.00
ACGTcount: A:0.14, C:0.25, G:0.29, T:0.31
Consensus pattern (127 bp):
GGTTGGATCTTCGTCGATCGCCCTGCCTGCTGGCGTTGAGCCCTTTGCGGGCGTTCATTATTTTC
CGTACTTGTGTAGGAATCGCTTCTTGGCGACCATGCACAAGTCGGAGGCCATGCTAAGTCAG
Found at i:40119 original size:23 final size:23
Alignment explanation
Indices: 40079--40161 Score: 132
Period size: 23 Copynumber: 3.6 Consensus size: 23
40069 CGCGTTATGA
*
40079 AAGTGGTC-GGTCGTTAGGTTTGG
1 AAGTGGTCAGG-CGCTAGGTTTGG
*
40102 AAATGGTCAGGCGCTAGGTTTGG
1 AAGTGGTCAGGCGCTAGGTTTGG
40125 AAGTGGTCAGGCGCTAGGTTTGG
1 AAGTGGTCAGGCGCTAGGTTTGG
40148 AAGTGGTCAGGCGC
1 AAGTGGTCAGGCGC
40162 CAAGCAATTG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 54 0.96
24 2 0.04
ACGTcount: A:0.18, C:0.13, G:0.42, T:0.27
Consensus pattern (23 bp):
AAGTGGTCAGGCGCTAGGTTTGG
Found at i:40468 original size:125 final size:128
Alignment explanation
Indices: 40330--40586 Score: 389
Period size: 125 Copynumber: 2.0 Consensus size: 128
40320 CGATTATTAA
*
40330 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T-TA
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
40391 -TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATTAGAATTTTTTAAATAT
66 TTGATTTTTACCATTTTACTATTTTAATTAAAAAAC-T-TATATATATTAGAATTTTTTAAATAT
*
40455 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTAT--C
* * *
40520 TATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
64 TA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
40585 T
128 T
40586 A
1 A
40587 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
125 54 0.45
126 1 0.01
127 1 0.01
128 1 0.01
131 29 0.24
132 1 0.01
133 32 0.27
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (128 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATCTA
TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:40608 original size:14 final size:13
Alignment explanation
Indices: 40572--40610 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
40562 TATATATTAG
40572 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
40585 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
40599 AATTTTTTAAAT
1 AATTTTTTAAAT
40611 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:47049 original size:17 final size:16
Alignment explanation
Indices: 47009--47059 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
46999 CATGTAATCT
*
47009 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
47025 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
47042 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
47059 T
1 T
47060 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Done.