Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003872.1 Corchorus capsularis cultivar CVL-1 contig03880, 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: 7256
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Found at i:520 original size:45 final size:45
Alignment explanation
Indices: 469--554 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
459 TTCTTCAAAT
469 AAGAACGTGGGTGATTACCTCATTCTTGATGAAGTAACTGCTTTG
1 AAGAACGTGGGTGATTACCTCATTCTTGATGAAGTAACTGCTTTG
*
514 AAGAACGTGGGTGGTTACCTCATTCTTGATGAAGTAACTGC
1 AAGAACGTGGGTGATTACCTCATTCTTGATGAAGTAACTGC
555 CTATTGGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (45 bp):
AAGAACGTGGGTGATTACCTCATTCTTGATGAAGTAACTGCTTTG
Found at i:621 original size:31 final size:31
Alignment explanation
Indices: 583--668 Score: 145
Period size: 31 Copynumber: 2.8 Consensus size: 31
573 TTGGTGAGTG
583 TTTACGGTATACCTTTGGTGGGTATGGAGCA
1 TTTACGGTATACCTTTGGTGGGTATGGAGCA
* *
614 TTTACGGTATACCCTTGGTGGGTATGGAGTA
1 TTTACGGTATACCTTTGGTGGGTATGGAGCA
*
645 TTTACGGTATACATTTGGTGGGTA
1 TTTACGGTATACCTTTGGTGGGTA
669 ATCATGGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (31 bp):
TTTACGGTATACCTTTGGTGGGTATGGAGCA
Found at i:5901 original size:17 final size:17
Alignment explanation
Indices: 5876--5924 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
5866 GATCACCACC
5876 TAGATCACCAGTGATCT
1 TAGATCACCAGTGATCT
*
5893 TATATCACCAGTGATCT
1 TAGATCACCAGTGATCT
*
5910 TAGATCACCATTGAT
1 TAGATCACCAGTGAT
5925 GCAAAATCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (17 bp):
TAGATCACCAGTGATCT
Found at i:6349 original size:3 final size:3
Alignment explanation
Indices: 6343--6367 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6333 TTGTATGTTG
6343 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
6368 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6388 original size:39 final size:40
Alignment explanation
Indices: 6344--6503 Score: 121
Period size: 39 Copynumber: 3.9 Consensus size: 40
6334 TGTATGTTGT
*
6344 TATTATTATTATTATTAT-TATTATATATATATATACACG
1 TATTATTATCATTATTATATATTATATATATATATACACG
* *** *
6383 TATTATTATCATTATTATATA-TATCTACTATCCCCT-CCCTG
1 TATTATTATCATTATTATATATTATATA-TAT-ATATACAC-G
* * *
6424 TTATTGTTGTTATTATTATATAATATATATATATATATATCTACG
1 -TATTATTATCATTATTATAT-AT-TATATATATATATA-C-ACG
* *
6469 TATTA-TATCATTATTATCTAATATATATATATATA
1 TATTATTATCATTATTATATATTATATATATATATA
6504 TATATATATA
Statistics
Matches: 91, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
39 22 0.24
40 7 0.08
41 16 0.18
42 18 0.20
43 13 0.14
44 7 0.08
45 7 0.08
46 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (40 bp):
TATTATTATCATTATTATATATTATATATATATATACACG
Found at i:6451 original size:2 final size:2
Alignment explanation
Indices: 6440--6528 Score: 98
Period size: 2 Copynumber: 46.5 Consensus size: 2
6430 TTGTTATTAT
* **
6440 TA TA TA -A TA TA TA TA TA TA TA TA TC TA CG TA T- TA TA TCA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
*
6480 TA T- TA TC TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6520 TA TA TA TA T
1 TA TA TA TA T
6529 CTACTACTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
1 5 0.07
2 66 0.90
3 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Done.