Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015664.1 Corchorus capsularis cultivar CVL-1 contig15685, 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: 21887
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:301 original size:2 final size:2
Alignment explanation
Indices: 294--319 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
284 TGACTTCACA
294 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
320 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8805 original size:30 final size:30
Alignment explanation
Indices: 8600--8802 Score: 237
Period size: 30 Copynumber: 6.7 Consensus size: 30
8590 ATAAATCTTC
* *
8600 ATTGACACCAGAAGTTGTCAATGGTGTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
*
8631 ATTGACACCAGAAGTTGTCAATAATCTTACA
1 ATTGACACCAGAAGTTGTC-ATGATCTTACA
* *
8662 AATGACACCAGAAGTTGTCATGGTCTTACA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* * * *
8692 AATGACACTAGAAGTTGTCATGGTCTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
* *
8722 ATTGACACTAGAAGTTGTCATGATTTTGA-A
1 ATTGACACCAGAAGTTGTCATGATCTT-ACA
* * * *
8752 ATTGACACCATAAGTTGTCATCATTTTGCA
1 ATTGACACCAGAAGTTGTCATGATCTTACA
8782 ATTGACACCAGAAGTTGTCAT
1 ATTGACACCAGAAGTTGTCAT
8803 CATGAAGTTG
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
30 107 0.70
31 46 0.30
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
ATTGACACCAGAAGTTGTCATGATCTTACA
Found at i:8811 original size:14 final size:14
Alignment explanation
Indices: 8792--8819 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
8782 ATTGACACCA
8792 GAAGTTGTCATCAT
1 GAAGTTGTCATCAT
8806 GAAGTTGTCATCAT
1 GAAGTTGTCATCAT
8820 TTTGCAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
GAAGTTGTCATCAT
Found at i:8826 original size:44 final size:44
Alignment explanation
Indices: 8763--8849 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
8753 TTGACACCAT
8763 AAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCATG
1 AAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCATG
8807 AAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCAT
1 AAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCAT
8850 TTTGCAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (44 bp):
AAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCATG
Found at i:8842 original size:30 final size:30
Alignment explanation
Indices: 8806--8876 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
8796 TTGTCATCAT
8806 GAAGTTGTCATCATTTTGCAATTGACACCA
1 GAAGTTGTCATCATTTTGCAATTGACACCA
8836 GAAGTTGTCATCATTTTGCAATTGACACCA
1 GAAGTTGTCATCATTTTGCAATTGACACCA
8866 GAAGTTGTCAT
1 GAAGTTGTCAT
8877 ATACACCATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
GAAGTTGTCATCATTTTGCAATTGACACCA
Found at i:8853 original size:74 final size:74
Alignment explanation
Indices: 8732--8876 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 74
8722 ATTGACACTA
* *
8732 GAAGTTGTCATGATTTTGAAATTGACACCATAAGTTGTCATCATTTTGCAATTGACACCAGAAGT
1 GAAGTTGTCATCATTTTGAAATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGT
8797 TGTCATCAT
66 TGTCATCAT
*
8806 GAAGTTGTCATCATTTTGCAATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGT
1 GAAGTTGTCATCATTTTGAAATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGT
8871 TGTCAT
66 TGTCAT
8877 ATACACCATG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (74 bp):
GAAGTTGTCATCATTTTGAAATTGACACCAGAAGTTGTCATCATTTTGCAATTGACACCAGAAGT
TGTCATCAT
Found at i:9142 original size:118 final size:118
Alignment explanation
Indices: 8930--9166 Score: 429
Period size: 118 Copynumber: 2.0 Consensus size: 118
8920 ATAACGAATT
* *
8930 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAGTTACATGTCTAGGCAAATTCTGTCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTATCTAAGGA
*
8995 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCCATCTTTCCTGGGAATTTA
66 GTTGGATTTTAAGTGAGACCGTTTCTGACTCCTCCATCTTTCCTGGGAATTTA
*
9048 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTGTAGGCAAATTCTATCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTATCTAAGGA
*
9113 GTTGGATTTTAAGTGAGATCGTTTCTGACTCCTCCATCTTTCCTGGGAATTTA
66 GTTGGATTTTAAGTGAGACCGTTTCTGACTCCTCCATCTTTCCTGGGAATTTA
9166 C
1 C
9167 TTGGTGTAAT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (118 bp):
CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTATCTAAGGA
GTTGGATTTTAAGTGAGACCGTTTCTGACTCCTCCATCTTTCCTGGGAATTTA
Found at i:14853 original size:19 final size:20
Alignment explanation
Indices: 14807--14854 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
14797 TATCTATATT
14807 ATAT-TAAAAAGTACGTTCA
1 ATATGTAAAAAGTACGTTCA
*
14826 ATATTTAAAAAGTACGTTCA
1 ATATGTAAAAAGTACGTTCA
*
14846 GT-TGTAAAA
1 ATATGTAAAA
14855 CTTTGAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.33
Consensus pattern (20 bp):
ATATGTAAAAAGTACGTTCA
Found at i:19338 original size:29 final size:29
Alignment explanation
Indices: 19306--19379 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
19296 TTTTTAAGAG
19306 TTCAGGGGCTTATTTGGCTGAAATAATAA
1 TTCAGGGGCTTATTTGGCTGAAATAATAA
19335 TTCAGGGGCTTATTTGGCTGAAATAATAA
1 TTCAGGGGCTTATTTGGCTGAAATAATAA
19364 TTCAGGGGCTTATTTG
1 TTCAGGGGCTTATTTG
19380 ACGGTTCGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.36
Consensus pattern (29 bp):
TTCAGGGGCTTATTTGGCTGAAATAATAA
Done.