Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015473.1 Corchorus capsularis cultivar CVL-1 contig15494, 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: 27640
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:579 original size:21 final size:21
Alignment explanation
Indices: 555--594 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
545 TTTTTTCTCA
555 TTTTT-ATTTTTATTTTTATG
1 TTTTTCATTTTTATTTTTATG
* *
575 TTTTTCGTTTTTGTTTTTAT
1 TTTTTCATTTTTATTTTTAT
595 TTTAATATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTTCATTTTTATTTTTATG
Found at i:5245 original size:37 final size:37
Alignment explanation
Indices: 5195--5269 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5185 TGTCACTTGT
5195 TCCTCTTAAGCAAGGTCTTGAGTTCGAGTTTTATGAA
1 TCCTCTTAAGCAAGGTCTTGAGTTCGAGTTTTATGAA
*
5232 TCCTCTTAAGCAAGGTCTTGGGTTCGAGTTTTATGAA
1 TCCTCTTAAGCAAGGTCTTGAGTTCGAGTTTTATGAA
5269 T
1 T
5270 GGAGAAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (37 bp):
TCCTCTTAAGCAAGGTCTTGAGTTCGAGTTTTATGAA
Found at i:11212 original size:11 final size:11
Alignment explanation
Indices: 11188--11222 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11178 TTGACAGCGT
11188 AACAAAAACAA
1 AACAAAAACAA
* *
11199 AACGAAAACGA
1 AACAAAAACAA
11210 AACAAAAACAA
1 AACAAAAACAA
11221 AA
1 AA
11223 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:12155 original size:15 final size:17
Alignment explanation
Indices: 12127--12166 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
12117 TCATCTATTA
*
12127 TTTTTATTAGT-TCTAG
1 TTTTTAGTAGTCTCTAG
*
12143 TTTTTAGTATTCTCTAG
1 TTTTTAGTAGTCTCTAG
12160 TTTTTAG
1 TTTTTAG
12167 AGGGAGTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTTTAGTAGTCTCTAG
Found at i:19724 original size:86 final size:86
Alignment explanation
Indices: 19579--19818 Score: 426
Period size: 86 Copynumber: 2.8 Consensus size: 86
19569 CATTGCAAAT
**
19579 TTATTGGTTATAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
1 TTATTGGTTCCAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
19644 AAGAAAATATCGGATGAAAGG
66 AAGAAAATATCGGATGAAAGG
19665 TTATTGGTTCCAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
1 TTATTGGTTCCAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
19730 AAGAAAATATCGGATGAAAGG
66 AAGAAAATATCGGATGAAAGG
* * * *
19751 TTATTGGTTCCAATGCCCACAAAGTCATAGTCTTTGGTCTGCTTGACGAAATTTCCAATCAAATT
1 TTATTGGTTCCAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
19816 AAG
66 AAG
19819 CTATTAACAA
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 148 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (86 bp):
TTATTGGTTCCAATGCCCACAAAGTCATGGTCTTTGGTCTACTTGACGAAACTTCCAAACAAATT
AAGAAAATATCGGATGAAAGG
Found at i:20002 original size:17 final size:17
Alignment explanation
Indices: 19982--20014 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19972 AAGGTACAGA
19982 TTTTTCAAAAAATAATT
1 TTTTTCAAAAAATAATT
*
19999 TTTTTCCAAAAATAAT
1 TTTTTCAAAAAATAAT
20015 CGACGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTTCAAAAAATAATT
Found at i:20572 original size:167 final size:167
Alignment explanation
Indices: 20285--20591 Score: 449
Period size: 167 Copynumber: 1.8 Consensus size: 167
20275 AAAGATTAGT
* * *
20285 TCTTTTATTAAGTCCACTACTCTATTCAAGTCCATTGAGAAATGACCAAAAAGATTACTTATTTA
1 TCTTTTAGTAAGTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGATTACTTATTTA
* * *
20350 ATCCCCTCAAGAATCAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA
66 ATCACCTCAAAAAACAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA
20415 TAAGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGA
131 TAAGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGA
* * * *
20452 TCTTTTAGTAATTCCACTATTCTATTAAATTCAATTGAGAAATGACCAAAAAG-TCTAGTTATTT
1 TCTTTTAGTAAGTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGAT-TACTTATTT
* *
20516 AATCACCTCAAAAAACAAAAGTTAGGGCATTTAAGTAATC-GATCAAGT-GTGAAAAGACGAAAA
65 AATCACCTCAAAAAACAAAAGTTAGGACATTTAAGTAATCTG-CCAAGTAG-GAAAAGACGAAAA
*
20579 AAATTAGTTCTCT
128 AAATAAGTTCTCT
20592 CGCTCCTCAT
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
166 3 0.02
167 121 0.98
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (167 bp):
TCTTTTAGTAAGTCCACTACTCTATTAAAGTCAATTGAGAAATGACCAAAAAGATTACTTATTTA
ATCACCTCAAAAAACAAAAGTTAGGACATTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAA
TAAGTTCTCTAACTCCAAAAGCAAGCCTTGGTAGGGA
Done.