Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009813.1 Corchorus capsularis cultivar CVL-1 contig09834, 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: 3648
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Found at i:371 original size:14 final size:15
Alignment explanation
Indices: 352--393 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
342 AATGCGTGGT
352 GAAAAAAAGA-AAGA
1 GAAAAAAAGAGAAGA
366 GAAAAAAA-AGAAGA
1 GAAAAAAAGAGAAGA
380 -AAAAAAAGAGAAGA
1 GAAAAAAAGAGAAGA
394 AGGAAATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAAAGAGAAGA
Found at i:375 original size:11 final size:11
Alignment explanation
Indices: 355--391 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
345 GCGTGGTGAA
355 AAAAAGAAAGAG
1 AAAAA-AAAGAG
367 AAAAAAAAGAAG
1 AAAAAAAAG-AG
379 AAAAAAAAGAG
1 AAAAAAAAGAG
390 AA
1 AA
392 GAAGGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:1512 original size:12 final size:12
Alignment explanation
Indices: 1490--1520 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1480 TGTGCGGTCA
1490 TTTCA-AGAAGT
1 TTTCAGAGAAGT
1501 TTTCAGAGAAGT
1 TTTCAGAGAAGT
1513 TTTCAGAG
1 TTTCAGAG
1521 GTCAGAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (12 bp):
TTTCAGAGAAGT
Found at i:1546 original size:35 final size:35
Alignment explanation
Indices: 1501--2170 Score: 967
Period size: 35 Copynumber: 19.1 Consensus size: 35
1491 TTCAAGAAGT
1501 TTTCAGAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCA-AGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1537 TTTCAAGAAGTTTTCAGAGGTCGGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1572 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
1607 TATCAAGAAGTTTTAAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1642 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCG
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
1677 TATCAAGAAGTTTTAAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1712 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1747 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
1782 -TTCAAAGAAGTTTTAAGAGGTCAGAGTCGATCTCA
1 TTTC-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1817 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
*
1852 TTTCAAGAAGTTTTCAGAGGTCAAAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1887 -TTCAGAGGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCA-A-GAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
1923 ATCCAAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA
*
1958 TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
1994 TTGCAAGAAGTTTTCAGAGGTCAGAGTTAATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* *
2029 TTCCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
2064 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
* * *
2099 TTCCAAGAAGTTTCCCACGA--TCAGAGTTGATCGCA
1 TTTCAAGAAGTTT-TCA-GAGGTCAGAGTTGATCTCA
** * * *
2134 TTTTTAGTA-TTTTCA-ACGATCAGAGTTGATCGCA
1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA
2168 TTT
1 TTT
2171 TCAGTATTCT
Statistics
Matches: 577, Mismatches: 44, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
31 1 0.00
33 2 0.00
34 31 0.05
35 469 0.81
36 65 0.11
37 9 0.02
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
Found at i:2194 original size:35 final size:35
Alignment explanation
Indices: 2049--2374 Score: 358
Period size: 35 Copynumber: 9.3 Consensus size: 35
2039 TTTTCAGTGG
* * * *
2049 TCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GG
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCA-ACGA
* * * *
2084 TCAGAGTTGATCTCA-TTCCAAGAAGTTTCCCACGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
* *
2119 TCAGAGTTGATCGCATTTTTAGTA-TTTTCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2153 TCAGAGTTGATCGCATTTTCAGTA-TTCTCTAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTT-TCCAACGA
2188 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
2223 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
** *
2258 TCAGAGTTGATCATATTTTCAGTAGTTTCCAATGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * *
2293 TCAAAGTTGATCACATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * * *
2328 ACAGAGGTGATCTCA-TTTCAAGAAATTTCCAATGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
2363 TCAGAGTTGATC
1 TCAGAGTTGATC
2375 CAGAGGAGTT
Statistics
Matches: 255, Mismatches: 31, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
34 38 0.15
35 213 0.84
36 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Done.