Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016551.1 Corchorus olitorius cultivar O-4 contig16584, 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: 35437
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7406 original size:35 final size:35
Alignment explanation
Indices: 7367--7442 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
7357 AATTAATGAG
7367 AGTAGGGTTCTTCCATATAATAATAATTCAACTAA
1 AGTAGGGTTCTTCCATATAATAATAATTCAACTAA
*
7402 AGTAGAGTTCTTCCATATAATAATAATTCAACTAA
1 AGTAGGGTTCTTCCATATAATAATAATTCAACTAA
7437 AGTAGG
1 AGTAGG
7443 CTCTAGGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (35 bp):
AGTAGGGTTCTTCCATATAATAATAATTCAACTAA
Found at i:12423 original size:11 final size:11
Alignment explanation
Indices: 12407--12431 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12397 GTCGTACTCC
12407 CATATATCAAA
1 CATATATCAAA
12418 CATATATCAAA
1 CATATATCAAA
12429 CAT
1 CAT
12432 TCTACTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (11 bp):
CATATATCAAA
Found at i:14984 original size:17 final size:18
Alignment explanation
Indices: 14962--14995 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
14952 AAAATAAAAA
14962 TTTTCAATGC-TTTAATT
1 TTTTCAATGCGTTTAATT
14979 TTTTCAATGCGTTTAAT
1 TTTTCAATGCGTTTAAT
14996 AATTAAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (18 bp):
TTTTCAATGCGTTTAATT
Found at i:22531 original size:73 final size:73
Alignment explanation
Indices: 22412--22558 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
22402 GTCCAATCTT
22412 GTCACTTTCCGGTATTCAATAACTATATTGGATTCTGATTAATTTAGAGGTAAATTATATCGTAT
1 GTCACTTTCCGGTATTCAATAACTATATTGGATTCTGATTAATTTAGAGGTAAATTATATCGTAT
22477 CTAAATTG
66 CTAAATTG
* *
22485 GTCACTTTTCGGTATTCAATAACTATATTGGATTCTGATTAATTTAGAGTTAAATTATATCGTAT
1 GTCACTTTCCGGTATTCAATAACTATATTGGATTCTGATTAATTTAGAGGTAAATTATATCGTAT
22550 CTAAATTG
66 CTAAATTG
22558 G
1 G
22559 AGAGAAATTC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (73 bp):
GTCACTTTCCGGTATTCAATAACTATATTGGATTCTGATTAATTTAGAGGTAAATTATATCGTAT
CTAAATTG
Found at i:22691 original size:101 final size:101
Alignment explanation
Indices: 22516--22717 Score: 341
Period size: 101 Copynumber: 2.0 Consensus size: 101
22506 ACTATATTGG
* * * *
22516 ATTCTGATTAATTTAGAGTTAAATTATATCGTATCTAAATTGGAGAGAAATTCTCTTGGTGTCTT
1 ATTCTGATTAATCTAGAATTAAATTATATCGTATCTAAATTGGAGAGAAATTCTCTCGGCGTCTT
*
22581 TTCTTTATTCATTTATAAGACTCGAATTTGAGATAT
66 TTCTTTATTCATTTATAAGACTCGAATTCGAGATAT
22617 ATTCTGATTAATCTAGAATTAAATTATATCGTATCTAAATTGGAGAGAAATTCTCTCGGCGTCTT
1 ATTCTGATTAATCTAGAATTAAATTATATCGTATCTAAATTGGAGAGAAATTCTCTCGGCGTCTT
* *
22682 TTCTTTATTCATTTATAAGATTTGAATTCGAGATAT
66 TTCTTTATTCATTTATAAGACTCGAATTCGAGATAT
22718 TACTTATACA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (101 bp):
ATTCTGATTAATCTAGAATTAAATTATATCGTATCTAAATTGGAGAGAAATTCTCTCGGCGTCTT
TTCTTTATTCATTTATAAGACTCGAATTCGAGATAT
Found at i:29330 original size:21 final size:21
Alignment explanation
Indices: 29306--29345 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29296 CACTGGAAAG
* *
29306 TGGAGACTTTACTTCAGTAAT
1 TGGAAACTTTACCTCAGTAAT
*
29327 TGGAAACTTTGCCTCAGTA
1 TGGAAACTTTACCTCAGTA
29346 TTTCATCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
TGGAAACTTTACCTCAGTAAT
Found at i:33614 original size:27 final size:27
Alignment explanation
Indices: 33576--33657 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
33566 GCTTTGGTTT
33576 CCAAAATTGGATCCTGATGGTCATGAG
1 CCAAAATTGGATCCTGATGGTCATGAG
*
33603 CCAAAATTGGATCCCGATGGTCATGAG
1 CCAAAATTGGATCCTGATGGTCATGAG
***
33630 ATGAAATTGGATCCTGATGGTCATGAG
1 CCAAAATTGGATCCTGATGGTCATGAG
33657 C
1 C
33658 AATTTGGATC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (27 bp):
CCAAAATTGGATCCTGATGGTCATGAG
Done.