Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015550.1 Corchorus capsularis cultivar CVL-1 contig15571, 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: 20983
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:12202 original size:13 final size:13
Alignment explanation
Indices: 12180--12219 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12170 CAGAGAATAT
12180 TATCAACAGAAGA
1 TATCAACAGAAGA
*
12193 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
12206 TTTCAACTGAAGA
1 TATCAACAGAAGA
12219 T
1 T
12220 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:12232 original size:11 final size:11
Alignment explanation
Indices: 12212--12242 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12202 AAGATTTCAA
12212 CTGAAGATTAT
1 CTGAAGATTAT
*
12223 CTGGAGATTAT
1 CTGAAGATTAT
12234 CTGAAGATT
1 CTGAAGATT
12243 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:12650 original size:41 final size:41
Alignment explanation
Indices: 12593--12772 Score: 204
Period size: 41 Copynumber: 4.4 Consensus size: 41
12583 AATAATATTG
*
12593 AAAATTACCT-TTGACACCAGAAGTTGTCATTTTGGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * *
12634 AAAATTACTGCTGACACTAGAAGTTGTCACCCTTGGTAAATT
1 AAAATTACTGTTGACACCAGAAGTTGTCA-CTTTGGTAAATT
* * * *
12676 GAAATTACTTTTGACACCATAAGTTGTCATTTTGGTAAATT
1 AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
12717 AAAATTACCT-TTGACACTAGAAG-TGTCACTCTGGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
12757 ATAATTAATGTTGACA
1 AAAATTACTGTTGACA
12773 TTGAATTACC
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 29 0.25
41 51 0.44
42 36 0.31
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (41 bp):
AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:12732 original size:83 final size:82
Alignment explanation
Indices: 12589--12756 Score: 259
Period size: 83 Copynumber: 2.0 Consensus size: 82
12579 AGTAAATAAT
12589 ATTGAAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTACTGCTGACACTAG
1 ATTGAAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTACTGCTGACACTAG
12654 AAGTTGTCACCCTTGGTAA
66 AAG-TGTCACCC-TGGTAA
* * *
12673 ATTG-AAATTACTTTTGACACCATAAGTTGTCATTTTGGTAAATTAAAATTACCT-TTGACACTA
1 ATTGAAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTA-CTGCTGACACTA
*
12736 GAAGTGTCACTCTGGTAA
65 GAAGTGTCACCCTGGTAA
12754 ATT
1 ATT
12757 ATAATTAATG
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
81 9 0.11
82 7 0.09
83 57 0.72
84 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (82 bp):
ATTGAAAATTACCTTTGACACCAGAAGTTGTCATTTTGGTAAATTAAAATTACTGCTGACACTAG
AAGTGTCACCCTGGTAA
Found at i:16506 original size:13 final size:13
Alignment explanation
Indices: 16484--16523 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
16474 TAGAGAATAT
16484 TATCAACAGAAGA
1 TATCAACAGAAGA
*
16497 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
16510 TTTCAACTGAAGA
1 TATCAACAGAAGA
16523 T
1 T
16524 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:16536 original size:11 final size:11
Alignment explanation
Indices: 16516--16546 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16506 AAGATTTCAA
16516 CTGAAGATTAT
1 CTGAAGATTAT
*
16527 CTGGAGATTAT
1 CTGAAGATTAT
16538 CTGAAGATT
1 CTGAAGATT
16547 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:20738 original size:30 final size:30
Alignment explanation
Indices: 20665--20754 Score: 153
Period size: 31 Copynumber: 3.0 Consensus size: 30
20655 CCATATTTGA
20665 TAAGAACCATCATTCTTATCATTGGACTTT
1 TAAGAACCATCATTCTTATCATTGGACTTT
* *
20695 TATATAGCCATCATTCTTATCATTGGACTTT
1 TA-AGAACCATCATTCTTATCATTGGACTTT
20726 TAAGAACCATCATTCTTATCATTGGACTT
1 TAAGAACCATCATTCTTATCATTGGACTT
20755 AAAATCCAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 27 0.49
31 28 0.51
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (30 bp):
TAAGAACCATCATTCTTATCATTGGACTTT
Done.