Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014965.1 Corchorus capsularis cultivar CVL-1 contig14986, 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: 17487
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Found at i:13829 original size:71 final size:70
Alignment explanation
Indices: 13709--13848 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 70
13699 TCGGTGAATC
* *
13709 AGATGACTCGGCGTAGCATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATCTTCAAAAATT
1 AGATGACTCGGCATAGCATCTTCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTCAAAAA-T
13774 GAAATT
65 GAAATT
* * * *
13780 AGATGACTCGGTATAGCATCTTTAAAGTT-GAAATCAGATGACTCGGTGTAGCATCTTCAAAGAT
1 AGATGACTCGGCATAGCATCTTCAAAGTTAG-AATCAGATGACTCAGTGTAGCATCTTCAAAAAT
13844 GAAAT
65 GAAAT
13849 CAGCATCTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
70 7 0.11
71 55 0.89
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (70 bp):
AGATGACTCGGCATAGCATCTTCAAAGTTAGAATCAGATGACTCAGTGTAGCATCTTCAAAAATG
AAATT
Found at i:13847 original size:35 final size:35
Alignment explanation
Indices: 13705--13851 Score: 188
Period size: 35 Copynumber: 4.2 Consensus size: 35
13695 CGGTTCGGTG
* *
13705 AATCAGATGACTCGGCGTAGCATCTTCAAAG-TTA
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
* * *
13739 GATTCAGATGACTCAGTGTAGCATCTTCAAAAATTGA
1 -AATCAGATGACTCGGTGTAGCATCTTCAAAGA-TGA
* * * *
13776 AATTAGATGACTCGGTATAGCATCTTTAAAGTTGA
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
13811 AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
1 AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
13846 AATCAG
1 AATCAG
13852 CATCTTCAAG
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
35 67 0.71
36 25 0.27
37 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (35 bp):
AATCAGATGACTCGGTGTAGCATCTTCAAAGATGA
Found at i:13890 original size:35 final size:35
Alignment explanation
Indices: 13850--13963 Score: 140
Period size: 35 Copynumber: 3.2 Consensus size: 35
13840 AGATGAAATC
* *
13850 AGCATCTTCAAGGTTGGATTCAGATGACTCGGTGT
1 AGCATCTTCAAAGTTGGATTCAGATGACTCGGTGA
* * * *
13885 AGCATCCTCAAAGTGGTGAATCAGATGACCCGGTGCA
1 AGCATCTTCAAAGTTG-GATTCAGATGACTCGGTG-A
*
13922 A-CATCTTCAAAGTTGGATTAAGATGACTCGGTGA
1 AGCATCTTCAAAGTTGGATTCAGATGACTCGGTGA
13956 AGCATCTT
1 AGCATCTT
13964 TGAAATGGGA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
34 2 0.03
35 34 0.52
36 28 0.43
37 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (35 bp):
AGCATCTTCAAAGTTGGATTCAGATGACTCGGTGA
Found at i:13949 original size:127 final size:127
Alignment explanation
Indices: 13723--13963 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 127
13713 GACTCGGCGT
* * *
13723 AGCATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATCTTCAAAAATTGAAATTAGATGACT
1 AGCATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATCCTCAAAAATTGAAATCAGATGACC
* * * * *
13788 CGGTATAGCATCTTTAAAGTTGAAATCAGATGACTCGGTGTAGCATCTTCAAAGATGAAATC
66 CGGTACAACATCTTCAAAGTTGAAATAAGATGACTCGGTGAAGCATCTTCAAAGATGAAATC
* * * *
13850 AGCATCTTCAAGGTTGGATTCAGATGACTCGGTGTAGCATCCTC-AAAGTGGTG-AATCAGATGA
1 AGCATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATCCTCAAAAAT--TGAAATCAGATGA
* * *
13913 CCCGGTGCAACATCTTCAAAGTTGGATTAAGATGACTCGGTGAAGCATCTT
64 CCCGGTACAACATCTTCAAAGTTGAAATAAGATGACTCGGTGAAGCATCTT
13964 TGAAATGGGA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
126 4 0.04
127 91 0.94
128 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (127 bp):
AGCATCTTCAAAGTTAGATTCAGATGACTCAGTGTAGCATCCTCAAAAATTGAAATCAGATGACC
CGGTACAACATCTTCAAAGTTGAAATAAGATGACTCGGTGAAGCATCTTCAAAGATGAAATC
Found at i:13975 original size:35 final size:35
Alignment explanation
Indices: 13850--13976 Score: 123
Period size: 35 Copynumber: 3.6 Consensus size: 35
13840 AGATGAAATC
* * * *
13850 AGCATCTTCAAGGTTGGATTCAGATGACTCGGTGT
1 AGCATCTTCAAAGTGGGATTAAGATGACTCGGTGA
* * * *
13885 AGCATCCTCAAAGTGGTGAATCAGATGACCCGGTGCA
1 AGCATCTTCAAAGTGG-GATTAAGATGACTCGGTG-A
*
13922 A-CATCTTCAAAGTTGGATTAAGATGACTCGGTGA
1 AGCATCTTCAAAGTGGGATTAAGATGACTCGGTGA
*
13956 AGCATCTTTGAAA-TGGGATTA
1 AGCATC-TTCAAAGTGGGATTA
13977 GGTGAATCAG
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
34 2 0.03
35 39 0.52
36 33 0.44
37 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (35 bp):
AGCATCTTCAAAGTGGGATTAAGATGACTCGGTGA
Found at i:14030 original size:42 final size:43
Alignment explanation
Indices: 13942--14036 Score: 122
Period size: 42 Copynumber: 2.2 Consensus size: 43
13932 AGTTGGATTA
* *
13942 AGATGACTCGGTGAAGCATCTTTGAAATGGGATTAGGTGAATC
1 AGATGACTCGGTGAAGCATCTTTCAAATGGGATTAGGTGAACC
* * *
13985 AGATGACTCGGTGCAGTATC-TTCAAGA-GGGATTCGGTGAACC
1 AGATGACTCGGTGAAGCATCTTTCAA-ATGGGATTAGGTGAACC
14027 AGATGACTCG
1 AGATGACTCG
14037 ATTATTTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
42 27 0.59
43 19 0.41
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (43 bp):
AGATGACTCGGTGAAGCATCTTTCAAATGGGATTAGGTGAACC
Found at i:14163 original size:91 final size:91
Alignment explanation
Indices: 14051--14276 Score: 312
Period size: 91 Copynumber: 2.5 Consensus size: 91
14041 TTTGTTCATT
* * * *
14051 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAGACAGTTTAA-GATGATTCGGTGAATCAAG
1 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGGACGACTCGGTGAATCAAG
*
14115 TTG-AGGCGGTGCCTTACTTCTTCAAG
66 -TGAACGCGGTGCCTTACTTCTTCAAG
* *
14141 ATTGGAATTCGGTGAGCTCGGTGCAGCATATTTTCAAACAGTTCAAGGACGACTCGGTGGATCAA
1 ATTGG-ATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGGACGACTCGGTGAATCAA
* *
14206 GTGAACGCGGTGCTTTATTTCTTCAAG
65 GTGAACGCGGTGCCTTACTTCTTCAAG
* * *
14233 ATTGGATTCGGTGAGCTCGGTGCAGCACATTCTCAAAGAGTTCA
1 ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCA
14277 GGATGATTTG
Statistics
Matches: 121, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
90 5 0.04
91 75 0.62
92 41 0.34
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (91 bp):
ATTGGATTCGGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGGACGACTCGGTGAATCAAG
TGAACGCGGTGCCTTACTTCTTCAAG
Found at i:14998 original size:14 final size:14
Alignment explanation
Indices: 14979--15012 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14969 GCATAATAAC
14979 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
14993 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
15007 ATTAGT
1 TTTAGT
15013 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:15189 original size:20 final size:20
Alignment explanation
Indices: 15153--15191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15143 AAATACAAGG
*
15153 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
15173 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
15192 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Done.