Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011819.1 Corchorus olitorius cultivar O-4 contig11852, 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: 27422
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6313 original size:21 final size:21
Alignment explanation
Indices: 6289--6335 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6279 GAAGAGTCTA
6289 ATTTTAACATGGAAGAGGATG
1 ATTTTAACATGGAAGAGGATG
** * *
6310 ATTTCGACATGGAAGATGCTG
1 ATTTTAACATGGAAGAGGATG
6331 ATTTT
1 ATTTT
6336 GACGCTGAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.34
Consensus pattern (21 bp):
ATTTTAACATGGAAGAGGATG
Found at i:6410 original size:21 final size:21
Alignment explanation
Indices: 6385--6470 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
6375 AACTTTGTCA
* *
6385 AGGCTGGCTTTGAAATGGAAG
1 AGGCTGGTTTTGACATGGAAG
* **
6406 GGGCTTATTTTGACATGGAAG
1 AGGCTGGTTTTGACATGGAAG
6427 AGGCTGGTTTTGACATGGAAG
1 AGGCTGGTTTTGACATGGAAG
** * *
6448 AGGCTAATTATGACATTGAAG
1 AGGCTGGTTTTGACATGGAAG
6469 AG
1 AG
6471 ACTAATTTCA
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.28
Consensus pattern (21 bp):
AGGCTGGTTTTGACATGGAAG
Found at i:6431 original size:42 final size:42
Alignment explanation
Indices: 6385--6470 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
6375 AACTTTGTCA
* * *
6385 AGGCTGGCTTTGAAATGGAAGGGGCTTATTTTGACATGGAAG
1 AGGCTGGCTTTGAAATGGAAGAGGCTAATTATGACATGGAAG
* * *
6427 AGGCTGGTTTTGACATGGAAGAGGCTAATTATGACATTGAAG
1 AGGCTGGCTTTGAAATGGAAGAGGCTAATTATGACATGGAAG
6469 AG
1 AG
6471 ACTAATTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.28
Consensus pattern (42 bp):
AGGCTGGCTTTGAAATGGAAGAGGCTAATTATGACATGGAAG
Found at i:6475 original size:21 final size:21
Alignment explanation
Indices: 6416--6477 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
6406 GGGCTTATTT
* ** *
6416 TGACATGGAAGAGGCTGGTTT
1 TGACATGGAAGAGACTAATTA
*
6437 TGACATGGAAGAGGCTAATTA
1 TGACATGGAAGAGACTAATTA
*
6458 TGACATTGAAGAGACTAATT
1 TGACATGGAAGAGACTAATT
6478 TCAACATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (21 bp):
TGACATGGAAGAGACTAATTA
Found at i:7945 original size:32 final size:33
Alignment explanation
Indices: 7891--7953 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
7881 TTCTTACTCC
*
7891 TGAAGAAGGCATGGACCAGATTGTTGGTCCTCT
1 TGAAGAAGGCATGGACCAGATTGTTGATCCTCT
*
7924 TGAAGAAGGCGT-GACCAGATTGTTGATCCT
1 TGAAGAAGGCATGGACCAGATTGTTGATCCT
7954 ACTGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (33 bp):
TGAAGAAGGCATGGACCAGATTGTTGATCCTCT
Found at i:15593 original size:25 final size:25
Alignment explanation
Indices: 15550--15600 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 25
15540 TGATAAATTT
15550 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATATAGTTATGA-TT-TTAAAAA
*
15577 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATATAGTTATGATTTTAAAAA
15600 T
1 T
15601 AATGTGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 1 0.04
26 4 0.17
27 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATATATAGTTATGATTTTAAAAA
Found at i:21590 original size:17 final size:17
Alignment explanation
Indices: 21553--21598 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
21543 ATAATCTTTA
*
21553 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTGC
21570 ATCACTGGTGATCTTAG-
1 ATCACTGGTGATCTT-GC
*
21587 ATCACTAGTGAT
1 ATCACTGGTGAT
21599 TTGGGGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (17 bp):
ATCACTGGTGATCTTGC
Found at i:22984 original size:56 final size:56
Alignment explanation
Indices: 22917--23027 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
22907 CCATTTTATC
22917 TCACACAATAAATGTTATAATAAATCCTATCCCCCCTAAT-TCTACTT-ATTATTCTT
1 TCACACAATAAATGTTATAATAAATCCTAT-CCCCCT-ATCTCTACTTAATTATTCTT
22973 TCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
1 TCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCT
23028 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
54 2 0.04
55 13 0.25
56 38 0.72
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (56 bp):
TCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTCTT
Found at i:23154 original size:42 final size:42
Alignment explanation
Indices: 23092--23172 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
23082 TAAGGATCAG
* * *
23092 GATTTGAGTTGAGTATTTCTTAATTTATAAAGAATTTTCTAT
1 GATTTGAATTGAGTAATTCTTAATTTACAAAGAATTTTCTAT
* *
23134 GATTTGAATTGAGTAATTCTTAGTTTACAGAGAATTTTC
1 GATTTGAATTGAGTAATTCTTAATTTACAAAGAATTTTC
23173 AAGACTTAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAATTGAGTAATTCTTAATTTACAAAGAATTTTCTAT
Found at i:24495 original size:14 final size:14
Alignment explanation
Indices: 24476--24523 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
24466 TTTCACCTCC
24476 TATGCACTTGCACA
1 TATGCACTTGCACA
* *
24490 TATGCA-TT-AACC
1 TATGCACTTGCACA
*
24502 TATTCACTTGCACA
1 TATGCACTTGCACA
24516 TATGCACT
1 TATGCACT
24524 AAATATACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.33
Consensus pattern (14 bp):
TATGCACTTGCACA
Done.