Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021767.1 Corchorus olitorius cultivar O-4 contig21800, 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: 16590
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:2050 original size:24 final size:24
Alignment explanation
Indices: 2013--2071 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
2003 CTTGGCTGTC
*
2013 GTTGCAATCCTGGATTTGATTGAG
1 GTTGCAATCCTGGATTTGACTGAG
**
2037 GTTGCAATTTTGGATTTGACTGAG
1 GTTGCAATCCTGGATTTGACTGAG
*
2061 GTTGGAATCCT
1 GTTGCAATCCT
2072 CTACTTGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (24 bp):
GTTGCAATCCTGGATTTGACTGAG
Found at i:2304 original size:24 final size:24
Alignment explanation
Indices: 2272--2352 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
2262 AACCAAGCAA
2272 ATTTCAAGTGATGAGTCTAGCTAG
1 ATTTCAAGTGATGAGTCTAGCTAG
**
2296 ATTTCAAGTGTACCAG-C-AGC-AG
1 ATTTCAAGTG-ATGAGTCTAGCTAG
**
2318 CA-GCCAAAGTGATGAGTCTAGCTAG
1 -ATTTC-AAGTGATGAGTCTAGCTAG
2343 ATTTCAAGTG
1 ATTTCAAGTG
2353 TACCAGCAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
22 6 0.14
23 10 0.24
24 20 0.48
25 6 0.14
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (24 bp):
ATTTCAAGTGATGAGTCTAGCTAG
Found at i:2929 original size:2 final size:2
Alignment explanation
Indices: 2922--2956 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2912 CCAGGACACC
2922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2957 ATTAAAGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3309 original size:2 final size:2
Alignment explanation
Indices: 3302--3326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3292 TATTAATAAC
3302 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3327 CTCAGAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3900 original size:7 final size:7
Alignment explanation
Indices: 3888--3918 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3878 TGGAGTTTGA
3888 GAGAAGG
1 GAGAAGG
3895 GAGAAGG
1 GAGAAGG
3902 GAGAAGG
1 GAGAAGG
3909 GAGAAGG
1 GAGAAGG
3916 GAG
1 GAG
3919 GCATCAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
GAGAAGG
Found at i:4069 original size:51 final size:51
Alignment explanation
Indices: 4006--4109 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
3996 GAGGATGATA
*
4006 TCTGAATGGAGAGAAGCCGGGAGAGAAGAGAGAAGAGAGGAGTGAGATTTG
1 TCTGAATGGAGAGAAGCCGGGAGAGAAGAGAGAAAAGAGGAGTGAGATTTG
*
4057 TCTGACTGGAGAGAAGCCGGGAGAGAAGAGAGAAAAGAGGAGTGAGATTTG
1 TCTGAATGGAGAGAAGCCGGGAGAGAAGAGAGAAAAGAGGAGTGAGATTTG
4108 TC
1 TC
4110 AAATTCTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.08, G:0.41, T:0.14
Consensus pattern (51 bp):
TCTGAATGGAGAGAAGCCGGGAGAGAAGAGAGAAAAGAGGAGTGAGATTTG
Found at i:5982 original size:9 final size:9
Alignment explanation
Indices: 5968--6005 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
5958 GGATTTTCAT
5968 ATCAACCCC
1 ATCAACCCC
5977 ATCAACCCC
1 ATCAACCCC
5986 ATCAACCCC
1 ATCAACCCC
5995 ATCAACCCC
1 ATCAACCCC
6004 AT
1 AT
6006 ACTAGAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.34, C:0.53, G:0.00, T:0.13
Consensus pattern (9 bp):
ATCAACCCC
Found at i:15836 original size:14 final size:14
Alignment explanation
Indices: 15797--15837 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
15787 TTATAGGCAT
*
15797 ACATGTTAAAATGG
1 ACATGTTAAAATGA
15811 ACATAAGTTAAAATGA
1 ACAT--GTTAAAATGA
15827 ACATGTTAAAA
1 ACATGTTAAAA
15838 CAAGGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (14 bp):
ACATGTTAAAATGA
Done.