Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013624.1 Corchorus olitorius cultivar O-4 contig13657, 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: 41449
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:27 original size:21 final size:21
Alignment explanation
Indices: 1--103 Score: 170
Period size: 21 Copynumber: 4.9 Consensus size: 21
1 AGGTTCCAAGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
*
22 AGGTTCCATGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
43 AGGTTCCAAGTTCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
*
64 AGGTTCCAAGATCATTGGAGA
1 AGGTTCCAAGTTCATTGGAGA
* *
85 AGGTTTCAAGCTCATTGGA
1 AGGTTCCAAGTTCATTGGA
104 ATTGCCTAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (21 bp):
AGGTTCCAAGTTCATTGGAGA
Found at i:1044 original size:15 final size:15
Alignment explanation
Indices: 1024--1055 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1014 AAACTAAGTG
1024 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
1039 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
1054 GA
1 GA
1056 ACCCCCAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:3462 original size:31 final size:31
Alignment explanation
Indices: 3427--3489 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3417 TCACCTTTAG
* *
3427 TGAATCAAACTCAACTTTGAAATCATGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
3458 TGAATCAAACTCAACTTTGAAACCAAGATCA
1 TGAATCAAACTCAACTTTGAAACCAAGATCA
3489 T
1 T
3490 CTAGTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.27
Consensus pattern (31 bp):
TGAATCAAACTCAACTTTGAAACCAAGATCA
Found at i:8829 original size:29 final size:30
Alignment explanation
Indices: 8786--8854 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
8776 GCCTACGGTC
* * *
8786 AAATAAACCCTTGAACT-TCAATTTTGGCA
1 AAATAAGCCCATGAACTACCAATTTTGGCA
*
8815 AAATAAGCCCATGAACTACCAATTTTGGCT
1 AAATAAGCCCATGAACTACCAATTTTGGCA
*
8845 AGATAAGCCC
1 AAATAAGCCC
8855 TTCTGCTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (30 bp):
AAATAAGCCCATGAACTACCAATTTTGGCA
Found at i:20468 original size:4 final size:4
Alignment explanation
Indices: 20459--20485 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20449 GATGTTGCGT
20459 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
20486 TGTTAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:28794 original size:15 final size:15
Alignment explanation
Indices: 28776--28804 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28766 ATATTAAAAA
28776 AAATTTAATATATCC
1 AAATTTAATATATCC
28791 AAATTTAATATATC
1 AAATTTAATATATC
28805 TGATTGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTAATATATCC
Found at i:37653 original size:19 final size:21
Alignment explanation
Indices: 37618--37656 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
37608 GCAAAAATAA
37618 GATTTTTTTATTGCAAAAACC
1 GATTTTTTTATTGCAAAAACC
37639 GATTTTTTT-TT-CAAAAAC
1 GATTTTTTTATTGCAAAAAC
37657 ACAAACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
GATTTTTTTATTGCAAAAACC
Found at i:41178 original size:49 final size:47
Alignment explanation
Indices: 41120--41252 Score: 207
Period size: 49 Copynumber: 2.8 Consensus size: 47
41110 CAAAATTCTA
*
41120 CTCTATCTCTAGGTAATTCATCAAAATAAAGTTGATATTCTACTCCT
1 CTCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
41167 CCATCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
1 -C-TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
* *
41216 C-C-ATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 CTCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATT
41253 AATTGTTGCT
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
45 33 0.41
46 1 0.01
48 2 0.02
49 45 0.56
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (47 bp):
CTCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
Done.