Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015568.1 Corchorus capsularis cultivar CVL-1 contig15589, 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: 11017
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Found at i:1625 original size:75 final size:75
Alignment explanation
Indices: 1467--1618 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
1457 AACTACATAG
1467 ATACATCATCAATAGAATACGTGTAACTAGGCCAAGCTTTATAGCGCAATTAGGGTTAAACTGTT
1 ATACATCATCAATAGAATACGTGTAACTAGGCCAAGCTTTATAGCGCAATTAGGGTTAAACTGTT
1532 GAATGTAAAA
66 GAATGTAAAA
1542 ATACATCATCAATAGAATACGTGTAACTAGGCCAAGCTTTATAGCGCAATTAGGGTTAAACTGTT
1 ATACATCATCAATAGAATACGTGTAACTAGGCCAAGCTTTATAGCGCAATTAGGGTTAAACTGTT
1607 GAATGTAAAA
66 GAATGTAAAA
1617 AT
1 AT
1619 TTATCATTAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (75 bp):
ATACATCATCAATAGAATACGTGTAACTAGGCCAAGCTTTATAGCGCAATTAGGGTTAAACTGTT
GAATGTAAAA
Found at i:2065 original size:2 final size:2
Alignment explanation
Indices: 2058--2129 Score: 68
Period size: 2 Copynumber: 38.5 Consensus size: 2
2048 TCAATAGCAT
*
2058 TA TA TA TA TA TA TA TA TA TA AA TA CTCA TA -A TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA TA TA TA TA
2099 TA TA -A T- TA -A TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2130 TCCATGCAAG
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
1 7 0.12
2 49 0.83
3 2 0.03
4 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2100 original size:19 final size:18
Alignment explanation
Indices: 2059--2129 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 18
2049 CAATAGCATT
2059 ATATATATATATATATATAA
1 ATATATA-ATATATATAT-A
2079 ATACTCATAATATA-ATATA
1 ATA-T-ATAATATATATATA
2098 ATATAATTAATATATATATA
1 ATAT-A-TAATATATATATA
2118 TATATATAATAT
1 -ATATATAATAT
2130 TCCATGCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.04
19 17 0.38
20 13 0.29
21 10 0.22
22 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATAATATATATATA
Found at i:5120 original size:53 final size:51
Alignment explanation
Indices: 4990--5172 Score: 190
Period size: 53 Copynumber: 3.4 Consensus size: 51
4980 CCCAATAATT
* * * *
4990 AAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACATAGGCAAT-TCTATA
1 AAAGTCCTCAAACACAAGGG--TAT-TCA-TCCCTAAACACAAAGGC-ATCTCT-CA
*
5046 TCAAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCACCTCTCTCA
1 --AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAAAGGCA--TCTCTCA
*
5101 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAAAGGCATTTACATC-
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAAAGGCATCT-C-TCA
5153 AAAGTCCTCAAACACAAGGG
1 AAAGTCCTCAAACACAAGGG
5173 CATCTATATT
Statistics
Matches: 114, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
51 2 0.02
52 21 0.18
53 46 0.40
54 16 0.14
55 4 0.04
56 5 0.04
58 20 0.18
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.20
Consensus pattern (51 bp):
AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAAAGGCATCTCTCA
Found at i:5166 original size:30 final size:28
Alignment explanation
Indices: 5127--5228 Score: 80
Period size: 30 Copynumber: 3.4 Consensus size: 28
5117 AGGGTATTCA
5127 TCCCTAAACACAAAGGCATTTACATCAAAG
1 TCCC-AAACACAAAGGCATTTACAT-AAAG
* * *
5157 TCCTCAAACACAAGGGCATCTATATTAAAG
1 TCC-CAAACACAAAGGCATTTACA-TAAAG
* *
5187 TCCCTAAACACAGAGACATCTATAC-TAAAG
1 TCCC-AAACACAAAGGCAT-T-TACATAAAG
5217 TCCCCAAACACA
1 T-CCCAAACACA
5229 TGTAACACAG
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
29 1 0.02
30 50 0.86
31 5 0.09
32 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (28 bp):
TCCCAAACACAAAGGCATTTACATAAAG
Found at i:6113 original size:19 final size:19
Alignment explanation
Indices: 6079--6117 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6069 CATGAACATC
6079 CATCACTTCATACAAGAAT
1 CATCACTTCATACAAGAAT
6098 CATCATCTTCAT-CAAGAAT
1 CATCA-CTTCATACAAGAAT
6117 C
1 C
6118 TCTCAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.28
Consensus pattern (19 bp):
CATCACTTCATACAAGAAT
Done.