Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015334.1 Corchorus olitorius cultivar O-4 contig15367, 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: 80937
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7527 original size:17 final size:17
Alignment explanation
Indices: 7507--7540 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
7497 TCTTTATATT
7507 ATTTT-TTTTCTTATTTA
1 ATTTTATTTT-TTATTTA
7524 ATTTTATTTTTTATTTA
1 ATTTTATTTTTTATTTA
7541 TGAATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTTTATTTA
Found at i:13128 original size:2 final size:2
Alignment explanation
Indices: 13121--13153 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13111 TCACAATCAC
13121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13154 TACTCCACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20030 original size:4 final size:4
Alignment explanation
Indices: 20021--20049 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
20011 ATATTATGTA
20021 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
20050 GGATCCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:20763 original size:31 final size:31
Alignment explanation
Indices: 20725--20800 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
20715 CATGCGACCG
*
20725 GTACCAAAAAGTGACACATGGCACGTCACGT
1 GTACCAAAAAGTGACACATGGCACGCCACGT
* * * * *
20756 GTGCCAAAGAGTGACACGTGTCGCGCCACGT
1 GTACCAAAAAGTGACACATGGCACGCCACGT
20787 GTACCAAAAAGTGA
1 GTACCAAAAAGTGA
20801 TGCCACGTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.16
Consensus pattern (31 bp):
GTACCAAAAAGTGACACATGGCACGCCACGT
Found at i:25021 original size:13 final size:13
Alignment explanation
Indices: 25003--25028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24993 TAAAAATCCA
25003 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
25016 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
25029 CTGCCTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:31369 original size:77 final size:77
Alignment explanation
Indices: 31266--31422 Score: 287
Period size: 77 Copynumber: 2.0 Consensus size: 77
31256 GGTTGGTTCA
* *
31266 ACAGATTGGTCTCACCACTATCTAAGTGGAGTTTTGTTACAAAACATGGGATGACTAGCAATGAC
1 ACAGATTGATCCCACCACTATCTAAGTGGAGTTTTGTTACAAAACATGGGATGACTAGCAATGAC
31331 ACGTCATGTGGG
66 ACGTCATGTGGG
*
31343 ACAGATTGATCCCACCACTATTTAAGTGGAGTTTTGTTACAAAACATGGGATGACTAGCAATGAC
1 ACAGATTGATCCCACCACTATCTAAGTGGAGTTTTGTTACAAAACATGGGATGACTAGCAATGAC
31408 ACGTCATGTGGG
66 ACGTCATGTGGG
31420 ACA
1 ACA
31423 AAATTCTGGT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (77 bp):
ACAGATTGATCCCACCACTATCTAAGTGGAGTTTTGTTACAAAACATGGGATGACTAGCAATGAC
ACGTCATGTGGG
Found at i:31953 original size:55 final size:55
Alignment explanation
Indices: 31869--32030 Score: 252
Period size: 55 Copynumber: 2.9 Consensus size: 55
31859 TAACAATTGT
* *
31869 TTTTTTTCATTCATAAAACTCGAATTCGAGACTTTATTTAGTGGTTTCGAAATAA
1 TTTTTTTCATTCATAAAACTCGAATTCGAGACGTTATTTAGTGGTCTCGAAATAA
* *
31924 TTTTTTTCATTCATAAAACTCGAATTCGAGAAGTTATTTAGTGATCTCGAAATAA
1 TTTTTTTCATTCATAAAACTCGAATTCGAGACGTTATTTAGTGGTCTCGAAATAA
* * *
31979 TTTTATTAATTCATAAGACTCAGAATTCGAGACGTTATTTAGTGGTCTCGAA
1 TTTTTTTCATTCATAAAACTC-GAATTCGAGACGTTATTTAGTGGTCTCGAA
32031 TTTGAATCAA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 69 0.71
56 28 0.29
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (55 bp):
TTTTTTTCATTCATAAAACTCGAATTCGAGACGTTATTTAGTGGTCTCGAAATAA
Found at i:49264 original size:3 final size:3
Alignment explanation
Indices: 49256--49299 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
49246 CAAAAAAGAT
* * * *
49256 AAG AAG AAG AAA AAC AAG AAG AAA AAG GAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
49300 CAAACAGAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:49299 original size:12 final size:12
Alignment explanation
Indices: 49256--49309 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
49246 CAAAAAAGAT
49256 AAGAAGAAGAAA
1 AAGAAGAAGAAA
*
49268 AACAAGAAGAAA
1 AAGAAGAAGAAA
* *
49280 AAGGAGAAGAAG
1 AAGAAGAAGAAA
*
49292 AAGAAGAACAAA
1 AAGAAGAAGAAA
*
49304 CAGAAG
1 AAGAAG
49310 GTAGCTTTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.69, C:0.06, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:50045 original size:22 final size:22
Alignment explanation
Indices: 50017--50062 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
50007 AAAAATGAAC
50017 TTTAGTTCTTATTATGCTAATA
1 TTTAGTTCTTATTATGCTAATA
50039 TTTAGTTCTTATTATGCTAATA
1 TTTAGTTCTTATTATGCTAATA
50061 TT
1 TT
50063 ATACTAGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTAGTTCTTATTATGCTAATA
Found at i:53556 original size:80 final size:80
Alignment explanation
Indices: 53443--53602 Score: 293
Period size: 80 Copynumber: 2.0 Consensus size: 80
53433 GCATTCGTTC
*
53443 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTTCAGCCAACCCATCTTCAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
53508 GTCGTCTAAGATCCG
66 GTCGTCTAAGATCCG
* *
53523 TGCAACTCCCCCTCGTTTTTATTTCCCTTCCCAAAATAGGTTTTCCAGCCGACCCATCTTCAAAA
1 TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
53588 GTCGTCTAAGATCCG
66 GTCGTCTAAGATCCG
53603 AAATCTCTTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 77 1.00
ACGTcount: A:0.23, C:0.34, G:0.12, T:0.31
Consensus pattern (80 bp):
TGCAACTCCCCCTCGTTTTCATTTCCCTTCCCAAAATAGGTTTTCCAGCCAACCCATCTTCAAAA
GTCGTCTAAGATCCG
Found at i:69948 original size:27 final size:27
Alignment explanation
Indices: 69917--69974 Score: 100
Period size: 27 Copynumber: 2.1 Consensus size: 27
69907 TTGCTCCACA
69917 CAATGGATCAGGCGTCCC-AAGAGAATC
1 CAATGGATCAGGCG-CCCTAAGAGAATC
69944 CAATGGATCAGGCGCCCTAAGAGAATC
1 CAATGGATCAGGCGCCCTAAGAGAATC
69971 CAAT
1 CAAT
69975 TCCAAACCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (27 bp):
CAATGGATCAGGCGCCCTAAGAGAATC
Found at i:77164 original size:23 final size:23
Alignment explanation
Indices: 77138--77187 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
77128 GTAATATAAC
*
77138 AATAAAT-CATTTTACATAAATTT
1 AATAAATACATTTTAC-TAAAATT
* *
77161 AATACATACATTTTTCTAAAATT
1 AATAAATACATTTTACTAAAATT
77184 AATA
1 AATA
77188 TAACAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAATACATTTTACTAAAATT
Found at i:79105 original size:30 final size:32
Alignment explanation
Indices: 79071--79148 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 32
79061 TAGGATAAGT
*
79071 AATAATTCGTAA-AT-AATTTTTTTTAGGGAA
1 AATAATTCGTAACATAAATTTTTTTGAGGGAA
79101 AATAATTCGTAACATAAATTTTTTTGAGGG--
1 AATAATTCGTAACATAAATTTTTTTGAGGGAA
79131 AA-AATTCGTAACATAAAT
1 AATAATTCGTAACATAAAT
79149 GATTATACCA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 16 0.36
30 14 0.31
31 2 0.04
32 13 0.29
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (32 bp):
AATAATTCGTAACATAAATTTTTTTGAGGGAA
Done.