Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014280.1 Corchorus capsularis cultivar CVL-1 contig14301, 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: 9181
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:1940 original size:6 final size:6
Alignment explanation
Indices: 1929--1971 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
1919 TTTTTCTTCC
1929 TTTTTA TTTTTA TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT
1972 AAAATTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:1950 original size:17 final size:17
Alignment explanation
Indices: 1930--1967 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1920 TTTTCTTCCT
1930 TTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTA
1947 TTTTATTTTTATTTTTA
1 TTTTATTTTTATTTTTA
1964 TTTT
1 TTTT
1968 TATTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTATTTTTATTTTTA
Found at i:2393 original size:11 final size:11
Alignment explanation
Indices: 2369--2403 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2359 TTGACAGCGT
2369 AACAAAAACAA
1 AACAAAAACAA
* *
2380 AACGAAAACGA
1 AACAAAAACAA
2391 AACAAAAACAA
1 AACAAAAACAA
2402 AA
1 AA
2404 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:3242 original size:12 final size:11
Alignment explanation
Indices: 3225--3265 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
3215 TCATAACAAA
3225 TTTATAATTAAT
1 TTTATAATT-AT
3237 TTTATAATTAT
1 TTTATAATTAT
*
3248 TTGATAATTTAT
1 TTTATAA-TTAT
3260 TTTATA
1 TTTATA
3266 TAGAAAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
TTTATAATTAT
Found at i:3243 original size:23 final size:23
Alignment explanation
Indices: 3217--3265 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3207 ATGTATATTC
3217 ATAACAAATTT-ATAATTAATTTT
1 ATAA-AAATTTGATAATTAATTTT
** *
3240 ATAATTATTTGATAATTTATTTT
1 ATAAAAATTTGATAATTAATTTT
3263 ATA
1 ATA
3266 TAGAAAGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATAAAAATTTGATAATTAATTTT
Found at i:6189 original size:20 final size:19
Alignment explanation
Indices: 6160--6203 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
6150 CTAGGTTTAG
6160 TCAG-TTTTTTGAGTTCAGT
1 TCAGTTTTTTTGAG-TCAGT
6179 TCAGTTTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
6198 T-AGTTT
1 TCAGTTT
6204 GAGTCTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 10 0.42
20 9 0.38
ACGTcount: A:0.16, C:0.09, G:0.20, T:0.55
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Done.