Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013248.1 Corchorus olitorius cultivar O-4 contig13281, 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: 13153
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1477 original size:11 final size:11
Alignment explanation
Indices: 1461--1485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1451 AGAAAATTGT
1461 TTGTTTTTGGA
1 TTGTTTTTGGA
1472 TTGTTTTTGGA
1 TTGTTTTTGGA
1483 TTG
1 TTG
1486 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Found at i:8191 original size:28 final size:28
Alignment explanation
Indices: 8160--8226 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
8150 ATTTCCTTCA
8160 AAGTTTTCAAAATGGGAAAGTTCCCATC
1 AAGTTTTCAAAATGGGAAAGTTCCCATC
8188 AAGTTTTCAAAATGGGAAAGTTCCCATC
1 AAGTTTTCAAAATGGGAAAGTTCCCATC
8216 AAGTTTTCAAA
1 AAGTTTTCAAA
8227 GTTTTCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (28 bp):
AAGTTTTCAAAATGGGAAAGTTCCCATC
Found at i:8229 original size:37 final size:37
Alignment explanation
Indices: 8188--8259 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
8178 AGTTCCCATC
8188 AAGTTTTCAAAATGGGAAAGTTCCCATCAAGTTTTCA
1 AAGTTTTCAAAATGGGAAAGTTCCCATCAAGTTTTCA
* *
8225 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTTT
1 AAGTTTTCAAAATGGGAAAGTTCCCATCAAGTTTT
8260 TTAAGCATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (37 bp):
AAGTTTTCAAAATGGGAAAGTTCCCATCAAGTTTTCA
Found at i:8271 original size:37 final size:37
Alignment explanation
Indices: 8193--8287 Score: 118
Period size: 37 Copynumber: 2.5 Consensus size: 37
8183 CCATCAAGTT
* **
8193 TTCAAAATGGGAAAGTTCCCATCAAGTTTTCAAAGTT
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGCA
* **
8230 TTCAAATTGGGAAAGTTCCCATCAGGTTTTTTAAGCA
1 TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGCA
*
8267 TTCAATTTAGGGAAAGTTCCC
1 TTCAAATT-GGGAAAGTTCCC
8288 GCCGGTTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 38 0.76
38 12 0.24
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (37 bp):
TTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGCA
Found at i:9298 original size:21 final size:21
Alignment explanation
Indices: 9272--9313 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9262 GCATCTTAGG
*
9272 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
9293 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
9314 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:10329 original size:32 final size:32
Alignment explanation
Indices: 10278--10423 Score: 213
Period size: 32 Copynumber: 4.5 Consensus size: 32
10268 TTAAAGCAAT
*
10278 TAAATATAGCGGCGTTTTGTAT-TGTAGACGCCGC
1 TAAATA-AG-GGCGTTTTGT-TCTATAGACGCCGC
*
10312 TAAATAAGGGCATTTTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
* *
10344 TAAATAAGGGCATTTTGTTCTGTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
*
10376 TAAATAAGGGCGTATTGTTCTATAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
10408 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
10424 CTTTTCGCGC
Statistics
Matches: 104, Mismatches: 7, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
31 1 0.01
32 95 0.91
33 2 0.02
34 6 0.06
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.32
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
Found at i:10849 original size:6 final size:6
Alignment explanation
Indices: 10792--10848 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
10782 AAAGGTTCCA
*
10792 CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATCT
1 CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG CCATCG
*
10840 CCACCG CCA
1 CCATCG CCA
10849 CTAATATTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.18, C:0.53, G:0.14, T:0.16
Consensus pattern (6 bp):
CCATCG
Found at i:12838 original size:27 final size:27
Alignment explanation
Indices: 12800--12899 Score: 164
Period size: 27 Copynumber: 3.7 Consensus size: 27
12790 ACCCGAGGCA
*
12800 AAGTGGGAGGATCCACTGTTGGGGTCG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
* *
12827 AAGTGTGAGGATCCATTGCTGGGGTCG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
*
12854 AAGTGGGAGGATCCACTGCTGGGGTAG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
12881 AAGTGGGAGGATCCACTGC
1 AAGTGGGAGGATCCACTGC
12900 GGCATCAGTC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (27 bp):
AAGTGGGAGGATCCACTGCTGGGGTCG
Done.