Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023513.1 Corchorus olitorius cultivar O-4 contig23546, 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: 26784
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1954 original size:14 final size:14
Alignment explanation
Indices: 1935--1970 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1925 ATTAAGTATA
1935 ATTACTTGGCCTTC
1 ATTACTTGGCCTTC
1949 ATTACTTGGCCTTC
1 ATTACTTGGCCTTC
1963 ATTACTTG
1 ATTACTTG
1971 TTATTATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.14, T:0.44
Consensus pattern (14 bp):
ATTACTTGGCCTTC
Found at i:10429 original size:16 final size:16
Alignment explanation
Indices: 10404--10436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10394 TTTCTCTCTC
*
10404 TATATGTATCTATATA
1 TATATATATCTATATA
10420 TATATATATCTATATA
1 TATATATATCTATATA
10436 T
1 T
10437 GTGTGTGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
TATATATATCTATATA
Found at i:10830 original size:12 final size:12
Alignment explanation
Indices: 10814--10847 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10804 AAAATTTGGG
10814 ATTGTTTTTGTT
1 ATTGTTTTTGTT
*
10826 TTTGTTTTTGTT
1 ATTGTTTTTGTT
*
10838 ATGGTTTTTG
1 ATTGTTTTTG
10848 GTTACTTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.21, T:0.74
Consensus pattern (12 bp):
ATTGTTTTTGTT
Found at i:16363 original size:23 final size:23
Alignment explanation
Indices: 16337--16387 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
16327 ACTTGTTCGT
*
16337 GAACAATAAATGAACGTGTTCAC
1 GAACAATAAATGAACATGTTCAC
* * **
16360 GAACACTAATTGAGTATGTTCAC
1 GAACAATAAATGAACATGTTCAC
16383 GAACA
1 GAACA
16388 CATATTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
GAACAATAAATGAACATGTTCAC
Found at i:16432 original size:21 final size:20
Alignment explanation
Indices: 16408--16450 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
16398 GAAATATTTT
* *
16408 ATTAGAAATTAATTTTTAATA
1 ATTACAAATTAA-TTCTAATA
*
16429 ATTACATATTAATTCTAATA
1 ATTACAAATTAATTCTAATA
16449 AT
1 AT
16451 ATTTATTGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTACAAATTAATTCTAATA
Found at i:17739 original size:24 final size:24
Alignment explanation
Indices: 17689--17742 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
17679 AAATCTTCTG
*
17689 TTTTAGTTTATTTTTTTTTCATCAT
1 TTTTAGTTTATTTTTTTTT-ATAAT
17714 TTTTAGTTTGATTTTTTTTT-TAAT
1 TTTTAGTTT-ATTTTTTTTTATAAT
17738 TTTTA
1 TTTTA
17743 TGTAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 9 0.33
26 10 0.37
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTAGTTTATTTTTTTTTATAAT
Found at i:18548 original size:19 final size:19
Alignment explanation
Indices: 18508--18544 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18498 AATTTTTAAG
18508 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
18527 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
18545 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Done.