Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006461.1 Corchorus capsularis cultivar CVL-1 contig06482, 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: 12887
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Found at i:275 original size:3 final size:3
Alignment explanation
Indices: 267--297 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
257 TTTTAGTCAT
267 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
298 GTTATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6393 original size:29 final size:30
Alignment explanation
Indices: 6335--6414 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
6325 CGGAGCCGTT
*
6335 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* * *
6365 AAGTTCAGGGGACAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
*
6394 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGGGGGCAAAACGTC
6415 TAAACGCTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Found at i:8509 original size:87 final size:87
Alignment explanation
Indices: 8363--8539 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 87
8353 TCATCTGTTC
8363 AGTTCTCACTCTACAGATCTTACAATTGTGCTCTTTAATTTTTGAATTGATTTTAGTTAGTTTTA
1 AGTTCTCACTCTACAGATCTTACAATTGTGCTCTTTAATTTTTGAATTGATTTTAGTTAGTTTTA
8428 ACAGGAAGGGAAACATGTTCCG
66 ACAGGAAGGGAAACATGTTCCG
*
8450 AGTTCTCACTCTACAGATCTTACAATTGTGCTCTTTAATTTTTGAATTGATTTTCGTTAGTTTTA
1 AGTTCTCACTCTACAGATCTTACAATTGTGCTCTTTAATTTTTGAATTGATTTTAGTTAGTTTTA
8515 ACAGGAAGGGAAACATGTTCCG
66 ACAGGAAGGGAAACATGTTCCG
8537 AGT
1 AGT
8540 AAGTCATTAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (87 bp):
AGTTCTCACTCTACAGATCTTACAATTGTGCTCTTTAATTTTTGAATTGATTTTAGTTAGTTTTA
ACAGGAAGGGAAACATGTTCCG
Found at i:9385 original size:2 final size:2
Alignment explanation
Indices: 9357--9435 Score: 99
Period size: 2 Copynumber: 40.5 Consensus size: 2
9347 TTGCTCTTTT
* * *
9357 TC TC TC TT TC TC T- TC T- TC AC GC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
9397 TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC AC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9436 ATCCACATAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
1 2 0.03
2 64 0.97
ACGTcount: A:0.03, C:0.46, G:0.01, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9843 original size:3 final size:3
Alignment explanation
Indices: 9837--9882 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
9827 TAGTTTGGAC
9837 TCT TCT TCCT TCT TCT TCT T-T TC- TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
9881 TC
1 TC
9883 GCCTACTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:10869 original size:33 final size:33
Alignment explanation
Indices: 10832--10897 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
10822 ATTATAAGCA
*
10832 TTGTTACCTGGATCAGGGTACGATCTGGGTCGT
1 TTGTTACCTGGATCAGGGTACGATCTGAGTCGT
10865 TTGTTACCTGGATCAGGGTACGATCTGAGTCGT
1 TTGTTACCTGGATCAGGGTACGATCTGAGTCGT
10898 GGAACGGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.17, C:0.18, G:0.32, T:0.33
Consensus pattern (33 bp):
TTGTTACCTGGATCAGGGTACGATCTGAGTCGT
Found at i:12031 original size:18 final size:18
Alignment explanation
Indices: 12008--12044 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11998 AACTGCTCAT
12008 TCTCTCTTTCTCTACCTA
1 TCTCTCTTTCTCTACCTA
* *
12026 TCTCTCTTTTTCTTCCTA
1 TCTCTCTTTCTCTACCTA
12044 T
1 T
12045 GGACATCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.35, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTCTCTTTCTCTACCTA
Found at i:12157 original size:2 final size:2
Alignment explanation
Indices: 12150--12180 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12140 TGCTTGAATT
12150 TA TA TA 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 TA TA TA T
12181 CTCTTTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.