Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009410.1 Corchorus capsularis cultivar CVL-1 contig09431, 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: 23767
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:163 original size:3 final size:3
Alignment explanation
Indices: 155--183 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
145 ATCCTCCCTC
155 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
184 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:188 original size:3 final size:3
Alignment explanation
Indices: 182--226 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
172 ATAATAATAA
182 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
227 ATAATAGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12317 original size:12 final size:12
Alignment explanation
Indices: 12289--12326 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
12279 AACAACTCAA
*
12289 ACTCAACAAACTG
1 ACTCAA-AAACTC
12302 ACTCAAAAACTC
1 ACTCAAAAACTC
12314 ACTCAAAAACTC
1 ACTCAAAAACTC
12326 A
1 A
12327 AATACCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.50, C:0.32, G:0.03, T:0.16
Consensus pattern (12 bp):
ACTCAAAAACTC
Found at i:12936 original size:2 final size:2
Alignment explanation
Indices: 12929--12979 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12919 GAATGAAAGG
12929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
12971 TA TA TA TA T
1 TA TA TA TA T
12980 TTGGAAGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13561 original size:12 final size:12
Alignment explanation
Indices: 13538--13568 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13528 CTTAAAATAC
13538 AAGGAT-AAAAT
1 AAGGATAAAAAT
13549 AAGGATAAAAAT
1 AAGGATAAAAAT
13561 AAGGATAA
1 AAGGATAA
13569 TTTTAAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (12 bp):
AAGGATAAAAAT
Found at i:15549 original size:7 final size:7
Alignment explanation
Indices: 15538--15572 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
15528 AACATTGGTT
*
15538 TGGCAAT
1 TGGCAAA
15545 TGGCAAA
1 TGGCAAA
15552 TGGCAAA
1 TGGCAAA
15559 TGGCAAA
1 TGGCAAA
15566 TGGCAAA
1 TGGCAAA
15573 CAAATCAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (7 bp):
TGGCAAA
Found at i:17207 original size:63 final size:63
Alignment explanation
Indices: 17107--17243 Score: 177
Period size: 63 Copynumber: 2.2 Consensus size: 63
17097 GTACTTCCTC
* * * * *
17107 TTCTTCTTCTTCCCACCAACGTTACAGCAACACCAACCG-GGGTTATGGTTATGGTTATTCCGG
1 TTCTTCTTCTTCCCACCAACATTACAGCAAAAACAACCGTGGCTT-CGGTTATGGTTATTCCGG
* * *
17170 TTCTTCTTCTTCTCACCAACATTATAGTAAAAACAACCGTGGCTTCGGTTATGGTTATTCCGG
1 TTCTTCTTCTTCCCACCAACATTACAGCAAAAACAACCGTGGCTTCGGTTATGGTTATTCCGG
*
17233 TTCTGCTTCTT
1 TTCTTCTTCTT
17244 ATAACACTAG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 60 0.94
64 4 0.06
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.36
Consensus pattern (63 bp):
TTCTTCTTCTTCCCACCAACATTACAGCAAAAACAACCGTGGCTTCGGTTATGGTTATTCCGG
Found at i:18858 original size:5 final size:5
Alignment explanation
Indices: 18848--18886 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
18838 GGAGGAAAAT
18848 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT
18887 CTGCTACATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:22634 original size:111 final size:111
Alignment explanation
Indices: 22435--22654 Score: 368
Period size: 111 Copynumber: 2.0 Consensus size: 111
22425 TAATAAGCTA
*
22435 TTCACGAAATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGGTAT
1 TTCACGAAATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGGTAC
* *
22500 GGGGCAGACTTGCAATTGATGATCACGATCGCCAACATCTAGTTTC
66 GGCGCAGACTTGCAATTGATGATCACGATCACCAACATCTAGTTTC
* * * * *
22546 TTCAGGAAATCATCATCATCATCAGGGAGAGGGGTATCAACAAGCCCAGCTTGTTCTTCGGTTAC
1 TTCACGAAATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGGTAC
22611 GGCGCAGACTTGCAATTGATGATCACGATCACCAACATCTAGTT
66 GGCGCAGACTTGCAATTGATGATCACGATCACCAACATCTAGTT
22655 CTTTGAAACC
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.25
Consensus pattern (111 bp):
TTCACGAAATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGGTAC
GGCGCAGACTTGCAATTGATGATCACGATCACCAACATCTAGTTTC
Done.