Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014139.1 Corchorus capsularis cultivar CVL-1 contig14160, 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: 19584
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10181 original size:19 final size:18
Alignment explanation
Indices: 10157--10194 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
10147 TTGAAGATTT
10157 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAA-TTGAAGA
*
10176 ATTGAAGATCATTGAAGA
1 ATTGAAGATAATTGAAGA
10194 A
1 A
10195 ATATTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (18 bp):
ATTGAAGATAATTGAAGA
Found at i:10206 original size:30 final size:30
Alignment explanation
Indices: 10146--10206 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
10136 GAAGTTTGTG
* * *
10146 ATTGAAGATTTATTGAAGATAATTTGAAGA
1 ATTGAAGATTCATTGAAGAAAATTTCAAGA
10176 ATTGAAGA-TCATTGAAGAAATATTTCAAGA
1 ATTGAAGATTCATTGAAGAAA-ATTTCAAGA
10206 A
1 A
10207 GTAAGAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.46, C:0.03, G:0.18, T:0.33
Consensus pattern (30 bp):
ATTGAAGATTCATTGAAGAAAATTTCAAGA
Found at i:12829 original size:5 final size:5
Alignment explanation
Indices: 12819--12853 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
12809 TTTGAAAGTC
*
12819 TATTA TATTA TATTA TATTA TATATA TAGTA TATT
1 TATTA TATTA TATTA TATTA TAT-TA TATTA TATT
12854 TAGTATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:12860 original size:16 final size:16
Alignment explanation
Indices: 12819--12853 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12809 TTTGAAAGTC
*
12819 TATTATAT-TATATTA
1 TATTATATATATAGTA
12834 TATTATATATATAGTA
1 TATTATATATATAGTA
12850 TATT
1 TATT
12854 TAGTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTATATATATAGTA
Found at i:13230 original size:15 final size:17
Alignment explanation
Indices: 13200--13232 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
13190 AAAACGACCC
13200 AACCCAGAATTGATCCG
1 AACCCAGAATTGATCCG
13217 AACCCA-AA-TGATCCG
1 AACCCAGAATTGATCCG
13232 A
1 A
13233 CATTTGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.15
Consensus pattern (17 bp):
AACCCAGAATTGATCCG
Found at i:15067 original size:17 final size:19
Alignment explanation
Indices: 15026--15069 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
15016 GATTTCTCTG
15026 TCTTTT-TTCTTTTAACTT
1 TCTTTTCTTCTTTTAACTT
15044 TCTTTTTCTTCTTTT-A-TT
1 TC-TTTTCTTCTTTTAACTT
15062 TCTTTTCT
1 TCTTTTCT
15070 GATGGGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 5 0.21
20 7 0.29
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (19 bp):
TCTTTTCTTCTTTTAACTT
Found at i:15508 original size:22 final size:20
Alignment explanation
Indices: 15469--15509 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
15459 AACGTTTCAC
*
15469 TTTTTTTATTATTCTTATTA
1 TTTTTTTATTATTATTATTA
15489 TTTTATTTATTTATTATTATT
1 TTTT-TTTA-TTATTATTATT
15510 TTGAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 4 0.22
22 10 0.56
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTATTATTATTATTA
Found at i:19296 original size:50 final size:50
Alignment explanation
Indices: 19221--19397 Score: 309
Period size: 50 Copynumber: 3.5 Consensus size: 50
19211 CTCTCTTTGA
*
19221 TTGTAATCAGTGAGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGT
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGT
*
19271 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGG
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGT
* *
19321 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGGAAAGCTTAGGT
1 TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGT
*
19371 TTGTGATCAGTGCGGGGAGCACTTGTT
1 TTGTAATCAGTGCGGGGAGCACTTGTT
19398 TGAACTTGGG
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.31
Consensus pattern (50 bp):
TTGTAATCAGTGCGGGGAGCACTTGTTCTAAGCTTGGGAAAATCTTAGGT
Done.