Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022519.1 Corchorus olitorius cultivar O-4 contig22552, 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: 47241
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:401 original size:10 final size:11
Alignment explanation
Indices: 376--404 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
366 TAAGGCTAGG
376 CCCGGCCCGAA
1 CCCGGCCCGAA
387 CCCGGCCCG-A
1 CCCGGCCCGAA
397 CCCGGCCC
1 CCCGGCCC
405 ATGAACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.62, G:0.28, T:0.00
Consensus pattern (11 bp):
CCCGGCCCGAA
Found at i:1141 original size:82 final size:82
Alignment explanation
Indices: 1004--1167 Score: 301
Period size: 82 Copynumber: 2.0 Consensus size: 82
994 AAATGCAATT
* *
1004 ACTTGAATATTCTAGTTGAAACAGGTCTTATGTTCAAAACCAGGTGCGAATCCAAATTAGTAAAA
1 ACTTGAATATTCTAGTTGAAACAGGTCTCAGGTTCAAAACCAGGTGCGAATCCAAATTAGTAAAA
1069 TCCAAATTACAAATTAG
66 TCCAAATTACAAATTAG
1086 ACTTGAATATTCTAGTTGAAACAGGTCTCAGGTTCAAAACCAGGTGCGAATCCAAATTAGTAAAA
1 ACTTGAATATTCTAGTTGAAACAGGTCTCAGGTTCAAAACCAGGTGCGAATCCAAATTAGTAAAA
*
1151 TTCAAATTACAAATTAG
66 TCCAAATTACAAATTAG
1168 TAAGAGGTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (82 bp):
ACTTGAATATTCTAGTTGAAACAGGTCTCAGGTTCAAAACCAGGTGCGAATCCAAATTAGTAAAA
TCCAAATTACAAATTAG
Found at i:15874 original size:45 final size:45
Alignment explanation
Indices: 15807--15903 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
15797 AGCAACAATT
* * * * *
15807 AATATTTGCTTTATTTTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGATTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
* *
15852 AATATTAGATTTATTTTAATGAATTACCTAGAGATTGAGTACTAG
1 AATATTAGATTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
15897 AAT-TTAG
1 AATATTAG
15904 GTAATACACT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (45 bp):
AATATTAGATTTATTTTAATGAATTACCTAGAGATGGAGGACTAG
Found at i:16144 original size:14 final size:14
Alignment explanation
Indices: 16125--16152 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16115 ACATTCATTT
16125 CAATCAAATGTTGC
1 CAATCAAATGTTGC
16139 CAATCAAATGTTGC
1 CAATCAAATGTTGC
16153 TACTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
CAATCAAATGTTGC
Found at i:18496 original size:135 final size:132
Alignment explanation
Indices: 18278--18544 Score: 358
Period size: 136 Copynumber: 2.0 Consensus size: 132
18268 CATTGTTTAA
*
18278 ACTTTTATAATTTCACTCAGCTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAC
1 ACTTTTATAATTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAC
* * * * *
18343 TATTTAATTTTTAACATTTTACTATTTTAAAT-AAAAAACTTATATATATTAGTATTTTTTAAAA
66 AATTTAATTTTTAACATTTTACTAGTTTAAATAAAAAAAATTAGATATATTAG-AATTTTTAAAA
18407 TAT
130 TAT
* * *
18410 ACTTTTATAGTTTTACTCAACTAAAAACTCATCATTTTTTTATTTAATTAAATCTAATATCCTT-
1 ACTTTTATAATTTCACTCAACTAAAAACTC-T-A--TTTTTATTTAATTAAATCTAATATACTTA
* * * *
18474 TTACAATTTTATTTTTATCATTTTACTAGTTTAATTAAAAAAAATTAGATATATTAGAATTTTTA
62 TAACAATTTAATTTTTAACATTTTACTAGTTTAAATAAAAAAAATTAGATATATTAGAATTTTTA
18539 AAATAT
127 AAATAT
18545 TAACATTGTT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
132 27 0.23
133 1 0.01
134 1 0.01
135 43 0.37
136 45 0.38
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (132 bp):
ACTTTTATAATTTCACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATACTTATAAC
AATTTAATTTTTAACATTTTACTAGTTTAAATAAAAAAAATTAGATATATTAGAATTTTTAAAAT
AT
Found at i:24896 original size:42 final size:42
Alignment explanation
Indices: 24837--24921 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
24827 AGACCTGAAG
24837 AGAGGTTACAATTCTAGATAATTAAAAGAAATAGGATTTATT
1 AGAGGTTACAATTCTAGATAATTAAAAGAAATAGGATTTATT
24879 AGAGGTTACAATTCTAGATAATTAAAAGAAATAGGATTTATT
1 AGAGGTTACAATTCTAGATAATTAAAAGAAATAGGATTTATT
24921 A
1 A
24922 TAACATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (42 bp):
AGAGGTTACAATTCTAGATAATTAAAAGAAATAGGATTTATT
Found at i:24961 original size:44 final size:44
Alignment explanation
Indices: 24895--24984 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
24885 TACAATTCTA
24895 GATAATTAAAAGAAATAGGATTTATTATAACATTTATGTGAAAG
1 GATAATTAAAAGAAATAGGATTTATTATAACATTTATGTGAAAG
*
24939 GATAATTAAAAGAAATATGATTTATTATAACATTTATGTGAAAG
1 GATAATTAAAAGAAATAGGATTTATTATAACATTTATGTGAAAG
24983 GA
1 GA
24985 AAGGATAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (44 bp):
GATAATTAAAAGAAATAGGATTTATTATAACATTTATGTGAAAG
Found at i:29272 original size:13 final size:13
Alignment explanation
Indices: 29245--29284 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
29235 GTTGTAAGTG
*
29245 TCTTCTATTTCTTT
1 TCTT-TATTTTTTT
29259 TCTTTATTTTTTTT
1 TCTTTA-TTTTTTT
29273 TCTTTATTTTTT
1 TCTTTATTTTTT
29285 CTTATGGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTATTTTTTT
Found at i:29273 original size:14 final size:14
Alignment explanation
Indices: 29256--29284 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29246 CTTCTATTTC
29256 TTTTCTTTATTTTT
1 TTTTCTTTATTTTT
29270 TTTTCTTTATTTTT
1 TTTTCTTTATTTTT
29284 T
1 T
29285 CTTATGGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTATTTTT
Done.