Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014089.1 Corchorus olitorius cultivar O-4 contig14122, 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: 43955
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2293 original size:15 final size:15
Alignment explanation
Indices: 2273--2302 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2263 ACTTCATTTT
2273 CTTCAAACTTTCTAA
1 CTTCAAACTTTCTAA
*
2288 CTTCAAATTTTCTAA
1 CTTCAAACTTTCTAA
2303 AACATTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTCAAACTTTCTAA
Found at i:2596 original size:29 final size:29
Alignment explanation
Indices: 2564--2631 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
2554 TTAATGATTT
2564 AATTATTAATTTAAATTT-CAA-AATTGTGA
1 AATT-TTAA-TTAAATTTACAATAATTGTGA
*
2593 AA-TTTAATTAAGTTTAACAATAATTGTGA
1 AATTTTAATTAAATTT-ACAATAATTGTGA
2622 AA-TTTAATTA
1 AATTTTAATTA
2632 TTGTGAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 7 0.20
27 4 0.11
28 4 0.11
29 20 0.57
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (29 bp):
AATTTTAATTAAATTTACAATAATTGTGA
Found at i:7369 original size:17 final size:17
Alignment explanation
Indices: 7349--7386 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
7339 AATACTAACA
7349 AATACATAATAA-ATAAT
1 AATAC-TAATAATATAAT
*
7366 AATACTAATAATATTAT
1 AATACTAATAATATAAT
7383 AATA
1 AATA
7387 ATACTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (17 bp):
AATACTAATAATATAAT
Found at i:7450 original size:13 final size:14
Alignment explanation
Indices: 7432--7462 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
7422 AATTAACAAA
7432 AAAATTA-TTTTTT
1 AAAATTATTTTTTT
7445 AAAATTATTTTTTT
1 AAAATTATTTTTTT
7459 AAAA
1 AAAA
7463 AATTGACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAAATTATTTTTTT
Found at i:7464 original size:16 final size:15
Alignment explanation
Indices: 7430--7466 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
7420 ATAATTAACA
7430 AAAAAATTATTTTTT
1 AAAAAATTATTTTTT
7445 --AAAATTATTTTTTT
1 AAAAAATTA-TTTTTT
7459 AAAAAATT
1 AAAAAATT
7467 GACCCTGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.37
14 6 0.32
16 6 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAAAATTATTTTTT
Found at i:9244 original size:52 final size:52
Alignment explanation
Indices: 9172--9274 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 52
9162 TTTAAAGATG
* *
9172 TTTAAGAATCCTTTAAGAATAATGTTT-AAGTATTGAAGAAAGTTTAATAATA
1 TTTAAGAATCCTTTAAGAATAAGGTTTAAAG-ATTGAAAAAAGTTTAATAATA
*
9224 TTTAAGAATCCTTTATGAATAAGGTTTAAAGATTGAAAAAAGTTTAATAAT
1 TTTAAGAATCCTTTAAGAATAAGGTTTAAAGATTGAAAAAAGTTTAATAAT
9275 TGCTTATTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 44 0.94
53 3 0.06
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.38
Consensus pattern (52 bp):
TTTAAGAATCCTTTAAGAATAAGGTTTAAAGATTGAAAAAAGTTTAATAATA
Found at i:23522 original size:15 final size:15
Alignment explanation
Indices: 23504--23533 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23494 TTCTTCATGT
23504 TTCCTTTGTTTCATA
1 TTCCTTTGTTTCATA
23519 TTCCTTTGTTTCATA
1 TTCCTTTGTTTCATA
23534 GTAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.60
Consensus pattern (15 bp):
TTCCTTTGTTTCATA
Found at i:23866 original size:21 final size:21
Alignment explanation
Indices: 23826--23872 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23816 TATAAAAATG
*
23826 AAATTACAATGATTATAACAT
1 AAATTACAATGATTAGAACAT
23847 AAATTACAATAGATT-GAACAT
1 AAATTACAAT-GATTAGAACAT
*
23868 GAATT
1 AAATT
23873 TCCCCATCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (21 bp):
AAATTACAATGATTAGAACAT
Done.