Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018311.1 Corchorus olitorius cultivar O-4 contig18344, 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: 21972
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:1745 original size:31 final size:32
Alignment explanation
Indices: 1684--1750 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 32
1674 CCGAATCTGC
*
1684 ATGACCCTAAATCCAGCAGACCTGAGACCCGA
1 ATGACCCTAAATCCAGCAGACCTGAAACCCGA
1716 ATGA-CCTAAATCCAG-ATGAGCC-GAAACCCGA
1 ATGACCCTAAATCCAGCA-GA-CCTGAAACCCGA
1747 ATGA
1 ATGA
1751 TCTGAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 1 0.03
31 25 0.78
32 6 0.19
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.13
Consensus pattern (32 bp):
ATGACCCTAAATCCAGCAGACCTGAAACCCGA
Found at i:4720 original size:24 final size:24
Alignment explanation
Indices: 4675--4723 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4665 AGGAATAATA
*
4675 TTATTATATAAGATTATTTTATTT
1 TTATTATATAAGATTATATTATTT
*
4699 TTATTATATAGGATTGA-ATTATTT
1 TTATTATATAAGATT-ATATTATTT
4723 T
1 T
4724 ATTTGTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (24 bp):
TTATTATATAAGATTATATTATTT
Found at i:5065 original size:29 final size:29
Alignment explanation
Indices: 5009--5066 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
4999 GCATGGTAGT
*
5009 AATAATTTTGCTTTTATTTGTATAAAAAA
1 AATAATTTTGCTTTTATTTATATAAAAAA
*
5038 AATAATTTTGCTTTTATTTCATTTAAAAA
1 AATAATTTTGCTTTTATTT-ATATAAAAA
5067 GGAATTAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (29 bp):
AATAATTTTGCTTTTATTTATATAAAAAA
Found at i:6135 original size:33 final size:33
Alignment explanation
Indices: 6097--6159 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6087 CTAAACCTGA
*
6097 ATTTAATTTATTACCTTAATTATTGGGAGGTGG
1 ATTTAATTTATTACCTTAATTATTAGGAGGTGG
* *
6130 ATTTAATTTGTTATCTTAATTATTAGGAGG
1 ATTTAATTTATTACCTTAATTATTAGGAGG
6160 GACAACTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.48
Consensus pattern (33 bp):
ATTTAATTTATTACCTTAATTATTAGGAGGTGG
Found at i:9437 original size:52 final size:52
Alignment explanation
Indices: 9378--9486 Score: 218
Period size: 52 Copynumber: 2.1 Consensus size: 52
9368 GACCTTACAA
9378 AATATTAAATTGTGACTGATAATTGTAAATTTGTAACACAATAATTGTAGGT
1 AATATTAAATTGTGACTGATAATTGTAAATTTGTAACACAATAATTGTAGGT
9430 AATATTAAATTGTGACTGATAATTGTAAATTTGTAACACAATAATTGTAGGT
1 AATATTAAATTGTGACTGATAATTGTAAATTTGTAACACAATAATTGTAGGT
9482 AATAT
1 AATAT
9487 GCTCTAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.39
Consensus pattern (52 bp):
AATATTAAATTGTGACTGATAATTGTAAATTTGTAACACAATAATTGTAGGT
Found at i:13262 original size:15 final size:15
Alignment explanation
Indices: 13242--13272 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13232 TGAAACAGAG
13242 TTCTCTTCTCTTCCT
1 TTCTCTTCTCTTCCT
*
13257 TTCTCTTCTTTTCCT
1 TTCTCTTCTCTTCCT
13272 T
1 T
13273 CTCAAAGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TTCTCTTCTCTTCCT
Found at i:13464 original size:4 final size:4
Alignment explanation
Indices: 13455--13486 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
13445 GCTCTGTTTT
13455 TTTC TTTC TTTC TTTC TTTC TTTC TTTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTT
13487 GGTGCTGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:16738 original size:28 final size:28
Alignment explanation
Indices: 16698--16753 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
16688 TTTTCTTTGT
16698 AATCACATTGGGTACTGACGTATTCGGA
1 AATCACATTGGGTACTGACGTATTCGGA
* *
16726 AATCACATTGGGTTCTGATGTATTCGGA
1 AATCACATTGGGTACTGACGTATTCGGA
16754 GTCTAGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (28 bp):
AATCACATTGGGTACTGACGTATTCGGA
Done.