Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014429.1 Corchorus olitorius cultivar O-4 contig14462, 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: 17825
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:4990 original size:18 final size:19
Alignment explanation
Indices: 4961--5000 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
4951 TTACTTACTT
4961 CTTTTACTTTTCTTTTTTC
1 CTTTTACTTTTCTTTTTTC
4980 CTTTT-CTTTTCTTTTTTC
1 CTTTTACTTTTCTTTTTTC
4998 CTT
1 CTT
5001 GTTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTTACTTTTCTTTTTTC
Found at i:7035 original size:15 final size:15
Alignment explanation
Indices: 7017--7062 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
7007 TTTTGATGCG
*
7017 GATGCTGATGCTGCT
1 GATGCTGCTGCTGCT
7032 GATGCTGCTGCTGCT
1 GATGCTGCTGCTGCT
7047 GATGCTGCTGCTGCT
1 GATGCTGCTGCTGCT
7062 G
1 G
7063 CTGTAACACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.09, C:0.24, G:0.35, T:0.33
Consensus pattern (15 bp):
GATGCTGCTGCTGCT
Found at i:7040 original size:3 final size:3
Alignment explanation
Indices: 7019--7065 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
7009 TTGATGCGGA
* * *
7019 TGC TGA TGC TGC TGA TGC TGC TGC TGC TGA TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
7066 TAACACCACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.06, C:0.26, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:8711 original size:9 final size:9
Alignment explanation
Indices: 8693--8727 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
8683 TGAGGATGGT
8693 TGTTGCTGC
1 TGTTGCTGC
*
8702 TGTTGTTGC
1 TGTTGCTGC
8711 TGTTGCTGC
1 TGTTGCTGC
*
8720 TGCTGCTG
1 TGTTGCTG
8728 AAGTTGTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.20, G:0.34, T:0.46
Consensus pattern (9 bp):
TGTTGCTGC
Found at i:12457 original size:18 final size:18
Alignment explanation
Indices: 12430--12512 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
12420 TACTCAAGCG
*
12430 ATCTCTTTCTCTTTCCCT
1 ATCTCGTTCTCTTTCCCT
* * *
12448 ATCTCGTTCTCTATCTCG
1 ATCTCGTTCTCTTTCCCT
*
12466 CTCTC-TATCTCTTTCCCGT
1 ATCTCGT-TCTCTTTCCC-T
* *
12485 -TCTCGTTCCCTCTCCCT
1 ATCTCGTTCTCTTTCCCT
* *
12502 TTCTCGATCTC
1 ATCTCGTTCTC
12513 GATCCTTCTT
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
17 2 0.04
18 46 0.94
19 1 0.02
ACGTcount: A:0.06, C:0.41, G:0.06, T:0.47
Consensus pattern (18 bp):
ATCTCGTTCTCTTTCCCT
Found at i:12461 original size:12 final size:12
Alignment explanation
Indices: 12431--12476 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
12421 ACTCAAGCGA
* *
12431 TCTCTTTCTCTT
1 TCTCTATCTCGT
*
12443 TCCCTATCTCGT
1 TCTCTATCTCGT
*
12455 TCTCTATCTCGC
1 TCTCTATCTCGT
12467 TCTCTATCTC
1 TCTCTATCTC
12477 TTTCCCGTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.07, C:0.39, G:0.04, T:0.50
Consensus pattern (12 bp):
TCTCTATCTCGT
Found at i:13804 original size:15 final size:14
Alignment explanation
Indices: 13766--13809 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
13756 TTGTATAAGT
13766 ATATAATAATA-TA
1 ATATAATAATAGTA
*
13779 ATATTATAATAGTA
1 ATATAATAATAGTA
13793 ATAATAATAATAGTA
1 AT-ATAATAATAGTA
13808 AT
1 AT
13810 TCTTTTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 10 0.37
14 4 0.15
15 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (14 bp):
ATATAATAATAGTA
Found at i:16335 original size:13 final size:13
Alignment explanation
Indices: 16319--16380 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
16309 GCTGGTTCTA
16319 ATATATAT-ATAT
1 ATATATATAATAT
16331 A-ATATATAATAT
1 ATATATATAATAT
*
16343 ATA-ACAATAATA-
1 ATATA-TATAATAT
16355 ATATAGTATAATAT
1 ATATA-TATAATAT
16369 A-ATA-ATAATAT
1 ATATATATAATAT
16380 A
1 A
16381 GTATTTCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
11 14 0.33
12 10 0.24
13 17 0.40
14 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:16344 original size:16 final size:16
Alignment explanation
Indices: 16319--16380 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
16309 GCTGGTTCTA
16319 ATAT-ATATATATAAT
1 ATATAATATATATAAT
*
16334 ATATAATATATAACAAT
1 ATATAATATAT-ATAAT
16351 A-ATAATATAGTATAAT
1 ATATAATATA-TATAAT
16367 ATAATAATA-ATATA
1 AT-ATAATATATATA
16381 GTATTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 4 0.10
16 23 0.57
17 7 0.17
18 6 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
ATATAATATATATAAT
Found at i:16344 original size:18 final size:18
Alignment explanation
Indices: 16321--16380 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
16311 TGGTTCTAAT
16321 ATATATATATAATATATA
1 ATATATATATAATATATA
*
16339 ATATATA-ACAATA-ATA
1 ATATATATATAATATATA
*
16355 ATATA-GTATAATATAATA
1 ATATATATATAATAT-ATA
16373 ATA-ATATA
1 ATATATATA
16381 GTATTTCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 13 0.38
17 6 0.18
18 15 0.44
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATATATATAATATATA
Found at i:16364 original size:21 final size:21
Alignment explanation
Indices: 16329--16384 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
16319 ATATATATAT
*
16329 ATAAT-ATATAATAT-ATAACA
1 ATAATAATATAGTATAAT-ACA
*
16349 ATAATAATATAGTATAATATA
1 ATAATAATATAGTATAATACA
16370 ATAATAATATAGTAT
1 ATAATAATATAGTAT
16385 TTCAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 5 0.16
21 25 0.78
22 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
ATAATAATATAGTATAATACA
Found at i:16607 original size:2 final size:2
Alignment explanation
Indices: 16600--16647 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
16590 TTTTACCATG
16600 TA TA TA TA TA TA TA TA T- TA CTA TA TA TA -A TA TA -A TA TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
16639 TA -A TA TA TA
1 TA TA TA TA TA
16648 GTAGTTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
1 5 0.12
2 33 0.82
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:16613 original size:8 final size:8
Alignment explanation
Indices: 16600--16647 Score: 52
Period size: 7 Copynumber: 6.5 Consensus size: 8
16590 TTTTACCATG
16600 TATATATA
1 TATATATA
16608 TATATATA
1 TATATATA
16616 T-TACTATA
1 TATA-TATA
16624 TATA-ATA
1 TATATATA
16631 TA-ATATA
1 TATATATA
16638 -ATA-ATA
1 TATATATA
16644 TATA
1 TATA
16648 GTAGTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.14
7 14 0.40
8 14 0.40
9 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (8 bp):
TATATATA
Found at i:16893 original size:2 final size:2
Alignment explanation
Indices: 16886--16923 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
16876 GGGTTTTCTA
16886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16924 TGTTACTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.