Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010438.1 Corchorus olitorius cultivar O-4 contig10470, 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: 24088
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:197 original size:3 final size:3
Alignment explanation
Indices: 191--219 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
181 ATTATATTTT
191 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
220 TAATTAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6889 original size:27 final size:27
Alignment explanation
Indices: 6851--6960 Score: 202
Period size: 27 Copynumber: 4.1 Consensus size: 27
6841 TGAAGTTGAT
* *
6851 CAAGGCTATGTTGAACAGGGGGATGAA
1 CAAGGCTATGTTGAACAGGCGGAGGAA
6878 CAAGGCTATGTTGAACAGGCGGAGGAA
1 CAAGGCTATGTTGAACAGGCGGAGGAA
6905 CAAGGCTATGTTGAACAGGCGGAGGAA
1 CAAGGCTATGTTGAACAGGCGGAGGAA
6932 CAAGGCTATGTTGAACAGGCGGAGGAA
1 CAAGGCTATGTTGAACAGGCGGAGGAA
6959 CA
1 CA
6961 GTTACAAGAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 81 1.00
ACGTcount: A:0.34, C:0.15, G:0.36, T:0.15
Consensus pattern (27 bp):
CAAGGCTATGTTGAACAGGCGGAGGAA
Found at i:6894 original size:15 final size:15
Alignment explanation
Indices: 6845--6948 Score: 59
Period size: 15 Copynumber: 7.5 Consensus size: 15
6835 CATGGCTGAA
*
6845 GTTGATCAAGGCTAT
1 GTTGAACAAGGCTAT
**
6860 GTTGAAC-AGG--GG
1 GTTGAACAAGGCTAT
*
6872 GATGAACAAGGCTAT
1 GTTGAACAAGGCTAT
*
6887 GTTGAAC-AGGCGGA-
1 GTTGAACAAGGC-TAT
6901 G--GAACAAGGCTAT
1 GTTGAACAAGGCTAT
*
6914 GTTGAAC-AGGCGGA-
1 GTTGAACAAGGC-TAT
6928 G--GAACAAGGCTAT
1 GTTGAACAAGGCTAT
6941 GTTGAACA
1 GTTGAACA
6949 GGCGGAGGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 26
0.64 0.11 0.25
Matches are distributed among these distances:
12 16 0.25
13 13 0.20
14 13 0.20
15 23 0.35
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (15 bp):
GTTGAACAAGGCTAT
Found at i:7001 original size:18 final size:18
Alignment explanation
Indices: 6976--7111 Score: 114
Period size: 18 Copynumber: 7.6 Consensus size: 18
6966 AAGAAACTGA
*
6976 AAACTTGGAGCACAACTT
1 AAACTTGGAGCAGAACTT
* *
6994 AGACTTGGAGCAGAA-TCC
1 AAACTTGGAGCAGAACT-T
* *
7012 AAACTTGGAACATG-GCTT
1 AAACTTGGAGCA-GAACTT
* *
7030 GAACTTGGAACAGAACTT
1 AAACTTGGAGCAGAACTT
* * *
7048 AAACTTAGAGCACAACAT
1 AAACTTGGAGCAGAACTT
*
7066 AAACTTGGAGCAGAACAT
1 AAACTTGGAGCAGAACTT
* * *
7084 AGATTTGGAGCAGAACAT
1 AAACTTGGAGCAGAACTT
7102 AAACTTGGAG
1 AAACTTGGAG
7112 GAAAATCAGG
Statistics
Matches: 94, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
17 2 0.02
18 90 0.96
19 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.21
Consensus pattern (18 bp):
AAACTTGGAGCAGAACTT
Found at i:12537 original size:27 final size:27
Alignment explanation
Indices: 12507--12591 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
12497 TACTCTTATT
12507 TTATTGCCACATAAATATTCTTTCCAA
1 TTATTGCCACATAAATATTCTTTCCAA
** * *
12534 TTATTGGTAGATAAATAATTACTCTT--ATT
1 TTATTGCCACATAAAT-ATT-CT-TTCCA-A
*
12563 TTATTTCCACATAAATATTCTTTCCAA
1 TTATTGCCACATAAATATTCTTTCCAA
12590 TT
1 TT
12592 GTTCATAGAT
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
26 2 0.05
27 17 0.40
28 8 0.19
29 14 0.33
30 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46
Consensus pattern (27 bp):
TTATTGCCACATAAATATTCTTTCCAA
Found at i:12576 original size:29 final size:29
Alignment explanation
Indices: 12493--12579 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
12483 ACTTCTCATC
12493 TAATTACTCTTATTTTATTGCCACATAAA
1 TAATTACTCTTATTTTATTGCCACATAAA
* ** *
12522 T-ATT-CT-TTCCA-ATTATTGGTAGATAAA
1 TAATTACTCTT--ATTTTATTGCCACATAAA
*
12549 TAATTACTCTTATTTTATTTCCACATAAA
1 TAATTACTCTTATTTTATTGCCACATAAA
12578 TA
1 TA
12580 TTCTTTCCAA
Statistics
Matches: 43, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
26 2 0.05
27 15 0.35
28 8 0.19
29 16 0.37
30 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (29 bp):
TAATTACTCTTATTTTATTGCCACATAAA
Found at i:12601 original size:56 final size:56
Alignment explanation
Indices: 12493--12601 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
12483 ACTTCTCATC
**
12493 TAATTACTCTTATTTTATTGCCACATAAATATTCTTTCCAATTATTGGTAGATAAA
1 TAATTACTCTTATTTTATTGCCACATAAATATTCTTTCCAATTATTCATAGATAAA
* *
12549 TAATTACTCTTATTTTATTTCCACATAAATATTCTTTCCAATTGTTCATAGAT
1 TAATTACTCTTATTTTATTGCCACATAAATATTCTTTCCAATTATTCATAGAT
12602 GTTAAGGCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.47
Consensus pattern (56 bp):
TAATTACTCTTATTTTATTGCCACATAAATATTCTTTCCAATTATTCATAGATAAA
Found at i:13402 original size:15 final size:15
Alignment explanation
Indices: 13391--13419 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13381 CAACAAACTC
13391 AACTGACTCAAACAA
1 AACTGACTCAAACAA
13406 AACTGACTCAAACA
1 AACTGACTCAAACA
13420 TCCAAGATCT
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:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AACTGACTCAAACAA
Done.