Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011122.1 Corchorus capsularis cultivar CVL-1 contig11143, 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: 26556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2209 original size:12 final size:12
Alignment explanation
Indices: 2149--2217 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
2139 TTTGATGGTA
2149 AATATATATAGT
1 AATATATATAGT
*
2161 ACTATATATAGT
1 AATATATATAGT
2173 ATATAGTATAGCTAGT
1 A-ATA-TATA--TAGT
2189 AAT-TA-ATA-T
1 AATATATATAGT
2198 AATAATATATA-T
1 AAT-ATATATAGT
2210 AATATATA
1 AATATATA
2218 ATTAAGTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
9 4 0.08
10 2 0.04
11 7 0.15
12 20 0.42
13 4 0.08
14 4 0.08
15 2 0.04
16 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (12 bp):
AATATATATAGT
Found at i:7464 original size:1 final size:1
Alignment explanation
Indices: 7458--7485 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
7448 GGCCTGCAAT
7458 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
7486 CCCAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9019 original size:15 final size:15
Alignment explanation
Indices: 8965--9019 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
8955 TGAAGATGAA
*
8965 GAAGAGGAGGAGGAG
1 GAAGAGGACGAGGAG
* *
8980 GAAGAGGAAGAGGAA
1 GAAGAGGACGAGGAG
* *
8995 GACGACGACGAGGAG
1 GAAGAGGACGAGGAG
*
9010 GAGGAGGACG
1 GAAGAGGACG
9020 TCGAAGAAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.53, T:0.00
Consensus pattern (15 bp):
GAAGAGGACGAGGAG
Found at i:10390 original size:11 final size:11
Alignment explanation
Indices: 10374--10402 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10364 GTGTGAGTAC
10374 TTAAATATCTA
1 TTAAATATCTA
10385 TTAAATATCTA
1 TTAAATATCTA
10396 -TAAATAT
1 TTAAATAT
10403 ACATATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAATATCTA
Found at i:14428 original size:33 final size:33
Alignment explanation
Indices: 14383--14445 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
14373 CAGAAATTTT
*
14383 TTCTTAAGCCATAGGTTTTCAAATCTCTTTTGA
1 TTCTCAAGCCATAGGTTTTCAAATCTCTTTTGA
*
14416 TTCTCAAGCCATAGGTTTTGAAATCTCTTT
1 TTCTCAAGCCATAGGTTTTCAAATCTCTTT
14446 CGACCAGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (33 bp):
TTCTCAAGCCATAGGTTTTCAAATCTCTTTTGA
Found at i:24625 original size:65 final size:65
Alignment explanation
Indices: 24517--24646 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
24507 GGAAAATTAA
*
24517 AACTAGTTTTATGTCACTAATGTGATTATATGTGAGTAGTATTAATATAGAAAATACATTATATT
1 AACTAGTTTTATGTCACTAATGTGATTATATGTGAGTAATATTAATATAGAAAATACATTATATT
24582 AACTAGTTTTATGTCACTAATGTGATTATATGTGAGTAATATTAATATAGAAAATACATTATATT
1 AACTAGTTTTATGTCACTAATGTGATTATATGTGAGTAATATTAATATAGAAAATACATTATATT
24647 TATATACGTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (65 bp):
AACTAGTTTTATGTCACTAATGTGATTATATGTGAGTAATATTAATATAGAAAATACATTATATT
Done.