Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014810.1 Corchorus olitorius cultivar O-4 contig14843, 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: 21874
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Found at i:595 original size:19 final size:18
Alignment explanation
Indices: 571--606 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
561 TGAAGATTTA
571 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
590 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
607 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:2920 original size:29 final size:29
Alignment explanation
Indices: 2876--2940 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
2866 TTTGTTTTGA
2876 ATTAGA-TTAATTTTTCTATTGTACTTAG
1 ATTAGACTTAATTTTTCTATTGTACTTAG
2904 ATTAGACTTAATTTTTCTATTGTACTTAG
1 ATTAGACTTAATTTTTCTATTGTACTTAG
2933 ATTAGACT
1 ATTAGACT
2941 CATGTTAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (29 bp):
ATTAGACTTAATTTTTCTATTGTACTTAG
Found at i:3829 original size:22 final size:22
Alignment explanation
Indices: 3801--3843 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3791 TTTCCTGCAA
* *
3801 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
3823 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
3844 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:3902 original size:21 final size:21
Alignment explanation
Indices: 3876--3915 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3866 AACAGACCAG
*
3876 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
*
3897 GTCCTGGGTAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
3916 CTGTTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.20, G:0.38, T:0.28
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:9648 original size:25 final size:24
Alignment explanation
Indices: 9611--9657 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
9601 CTAGAAAATT
9611 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
9637 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
9658 AATATAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:10299 original size:21 final size:21
Alignment explanation
Indices: 10273--10312 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
10263 AACAGACCAG
*
10273 GTCCTGGGCAGGAGTTGTCAA
1 GTCCTGGGCAGGACTTGTCAA
10294 GTCCTGGGCAGGACTTGTC
1 GTCCTGGGCAGGACTTGTC
10313 CTGTTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (21 bp):
GTCCTGGGCAGGACTTGTCAA
Found at i:15384 original size:18 final size:19
Alignment explanation
Indices: 15343--15386 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15333 AGCGCGGACA
*
15343 AAAAACCTAGTAACATAAC
1 AAAAACCTAGTAACAAAAC
* *
15362 AAAAACTTAGTACCAAAAC
1 AAAAACCTAGTAACAAAAC
15381 AAAAAC
1 AAAAAC
15387 AAAGATGGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.20, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAACCTAGTAACAAAAC
Found at i:17613 original size:2 final size:2
Alignment explanation
Indices: 17606--17653 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
17596 AACATTGAAT
* *
17606 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TC TA TC TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
17648 TA TA TA
1 TA TA TA
17654 AAAGTATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17630 original size:21 final size:21
Alignment explanation
Indices: 17606--17653 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
17596 AACATTGAAT
17606 TATATATATATATATATAATA
1 TATATATATATATATATAATA
* * *
17627 TATATATATCTATCTATACTA
1 TATATATATATATATATAATA
17648 TATATA
1 TATATA
17654 AAAGTATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATATATATATATATAATA
Found at i:18047 original size:45 final size:45
Alignment explanation
Indices: 17999--18214 Score: 371
Period size: 45 Copynumber: 4.8 Consensus size: 45
17989 AATTCTACTT
* *
17999 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTT
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
18044 CATCTCTAGGTAATTCATCAAAATAAAG-TAAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCT-AATATTCTACTCCTC
*
18089 CATTTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
*
18134 CATCTCTAGGTAATTCATCAAAATAAAGTTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
*
18179 CATCTCTAGGTAATTCATCAAAATAAACCTAATATT
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATT
18215 AATTGTTGCT
Statistics
Matches: 162, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
44 1 0.01
45 160 0.99
46 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
Found at i:19326 original size:127 final size:124
Alignment explanation
Indices: 19167--19451 Score: 453
Period size: 127 Copynumber: 2.3 Consensus size: 124
19157 TATAGTATAT
* ** *
19167 ATATCTTTATAATTACCTTATTTTTACCATTTTACTATTTTTCATTAAAAACTAGGATATATTAA
1 ATATTTTTATAATTATTTTATTTTTACCATTTTACTATTTTTCATCAAAAACTAGGATATATTAA
* * *
19232 AAAATTTTAATATACAGTTTTATTCTACTAAAAACTCTATTTTCATTTTATTAAATTCA
66 AAAATTTTAATATACAGTTTTATTATACTAAAAACTCTATTTTCATTTAATCAAATTCA
*
19291 ATATTTTTATAGTAATTATTTTATTTTTACCATTTTACTATTTTTCATCAAAAACTTGGATATAT
1 ATA-TTTT-TA-TAATTATTTTATTTTTACCATTTTACTATTTTTCATCAAAAACTAGGATATAT
* *
19356 TAAAAATTTTTAATATACAGTTTTATTATACTAAAAACTCTATTTTCATTTAATCAAATTGA
63 TAAAAAATTTTAATATACAGTTTTATTATACTAAAAACTCTATTTTCATTTAATCAAATTCA
19418 ATATTTTTATAATTATTTTATTTTTACCATTTTA
1 ATATTTTTATAATTATTTTATTTTTACCATTTTA
19452 ATTTAAAAGG
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
124 28 0.19
125 5 0.03
126 6 0.04
127 109 0.74
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (124 bp):
ATATTTTTATAATTATTTTATTTTTACCATTTTACTATTTTTCATCAAAAACTAGGATATATTAA
AAAATTTTAATATACAGTTTTATTATACTAAAAACTCTATTTTCATTTAATCAAATTCA
Found at i:20228 original size:2 final size:2
Alignment explanation
Indices: 20221--20251 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20211 TGAAGACTAG
20221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20252 TACATACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20873 original size:163 final size:164
Alignment explanation
Indices: 20603--20929 Score: 611
Period size: 163 Copynumber: 2.0 Consensus size: 164
20593 TCTATAAATG
*
20603 GAAAACTGGATTTGCTTGAAACATATTATATCATTTAAATTGTAAAGCTTGTTTATATAATGTCT
1 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
20668 ACTGTTTAAAAACATACAATACCTAAATGATTAACCTA-TTTTTTATATAGTATCACAAAAATTA
66 ACTGTTTAAAAACATACAATACCTAAATGATTAACCTATTTTTTTATATAGTATCACAAAAATTA
20732 AAGTCTACGCCAATTGGAGAAAATAATTGCATGT
131 AAGTCTACGCCAATTGGAGAAAATAATTGCATGT
20766 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
1 GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
* *
20831 ACTGTTTAAGAACATACAATACCTAAATGATTAACCTATTTTTTTATCTAGTATCACAAAAATTA
66 ACTGTTTAAAAACATACAATACCTAAATGATTAACCTATTTTTTTATATAGTATCACAAAAATTA
*
20896 AAGTCTATGCCAATTGGAGAAAATAATTGCATGT
131 AAGTCTACGCCAATTGGAGAAAATAATTGCATGT
20930 CTTAAGCCAT
Statistics
Matches: 159, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
163 101 0.64
164 58 0.36
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (164 bp):
GAAAACTGGATTTGCTTGAAACATATTATATCATCTAAATTGTAAAGCTTGTTTATATAATGTCT
ACTGTTTAAAAACATACAATACCTAAATGATTAACCTATTTTTTTATATAGTATCACAAAAATTA
AAGTCTACGCCAATTGGAGAAAATAATTGCATGT
Done.