Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006162.1 Corchorus capsularis cultivar CVL-1 contig06180, 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: 35111
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5481 original size:23 final size:23
Alignment explanation
Indices: 5455--5510 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
5445 TTCATAAGAT
* *
5455 GAACAAAAATTGCTAGAATCTCA
1 GAACCAAAATTGCTAAAATCTCA
5478 GAACCAAAATTGCTAAAATCTCA
1 GAACCAAAATTGCTAAAATCTCA
*
5501 TAACCAAAAT
1 GAACCAAAAT
5511 CATCGCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (23 bp):
GAACCAAAATTGCTAAAATCTCA
Found at i:5996 original size:14 final size:15
Alignment explanation
Indices: 5979--6011 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5969 GAAAACAGGG
*
5979 ATTATGAA-ATAACA
1 ATTATGAAGAAAACA
5993 ATTATGAAGAAAACA
1 ATTATGAAGAAAACA
6008 ATTA
1 ATTA
6012 AACTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (15 bp):
ATTATGAAGAAAACA
Found at i:6084 original size:13 final size:13
Alignment explanation
Indices: 6066--6100 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6056 AAAGCAGATT
6066 ATAAAGCAAATCA
1 ATAAAGCAAATCA
* *
6079 ATAAAGCAGATTA
1 ATAAAGCAAATCA
6092 ATAAAGCAA
1 ATAAAGCAA
6101 GCAATAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (13 bp):
ATAAAGCAAATCA
Found at i:6105 original size:25 final size:25
Alignment explanation
Indices: 6055--6107 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
6045 AATCTAAATC
*
6055 TAAAGCAGATTATAAAGCAAATCAA
1 TAAAGCAGATTATAAAGCAAAGCAA
6080 TAAAGCAGATTAATAAAGC-AAGCAA
1 TAAAGCAGATT-ATAAAGCAAAGCAA
6105 TAA
1 TAA
6108 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (25 bp):
TAAAGCAGATTATAAAGCAAAGCAA
Found at i:14326 original size:177 final size:178
Alignment explanation
Indices: 13997--14333 Score: 527
Period size: 177 Copynumber: 1.9 Consensus size: 178
13987 TTCCACCATA
* ** * *
13997 AGCACAAATTATGTAATATTAAGTAGACCATCTATTTTCGTTAACCGAAACAACTAATTCTTTGG
1 AGCACAAATTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCGG
14062 AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCAT
66 AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCAT
*
14127 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTAG
131 GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATTAGACATCTAG
* *
14175 AGCA-AAAGTTATATAATGTTAAGTGGACCATCTATTCCCGTTAACCGAAACAACAAATT-TTCG
1 AGCACAAA-TTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCG
*
14238 GAAGCATTTTTTATA-CTTAAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATC
65 GAAGCATTTTTTATACCTT-AAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATC
* * *
14302 ATGGAACAATCTTTTAATAGACACTTAAATCA
129 ATGGAACAACCTTTCAAGAGACACTTAAATCA
14334 CCCTAATCGG
Statistics
Matches: 145, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
176 3 0.02
177 93 0.64
178 49 0.34
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (178 bp):
AGCACAAATTATATAATATTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCGG
AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCAT
GGAACAACCTTTCAAGAGACACTTAAATCATCTCAATTAGACATCTAG
Found at i:14366 original size:177 final size:177
Alignment explanation
Indices: 13997--14373 Score: 519
Period size: 177 Copynumber: 2.1 Consensus size: 177
13987 TTCCACCATA
* * ** * *
13997 AGCACAAATTATGTAATATTAAGTAGACCATCTATTTTCGTTAACCGAAACAACTAATTCTTTGG
1 AGCA-AAATTATATAATGTTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCGG
14062 AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCAT
65 AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCAT
* * * *
14127 GGAACAACCTTTCAAGAGACACTTGAATCATCTCAATTAGACATCTAG
130 GGAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACTAG
*
14175 AGCAAAAGTTATATAATGTTAAGTGGACCATCTATTCCCGTTAACCGAAACAACAAATT-TTCGG
1 AGCAAAA-TTATATAATGTTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCGG
*
14239 AAGCATTTTTTATA-CTTAAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCA
65 AAGCATTTTTTATACCTT-AAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCA
* * * * *
14303 TGGAACAATCTTTTAATAGACACTTAAATCACC-CTAATCGGATAACTGGAG
129 TGGAACAACCTTTCAAGAGACACTTAAATCACCTC-AATCAGACAACT--AG
14354 AG-AAAATTATATAATGTTAA
1 AGCAAAATTATATAATGTTAA
14374 ATATACCTTT
Statistics
Matches: 177, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
176 4 0.02
177 116 0.66
178 53 0.30
179 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
AGCAAAATTATATAATGTTAAGTAGACCATCTATTCCCGTTAACCGAAACAACAAATTCTTCGGA
AGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCGAGTCCATCATGAAAGTTGTAGATCATG
GAACAACCTTTCAAGAGACACTTAAATCACCTCAATCAGACAACTAG
Found at i:15136 original size:34 final size:34
Alignment explanation
Indices: 15093--15157 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
15083 TATTTTATAG
*
15093 CTCTATTTTTACTTCAAAA-TAGGTTTCGAAAACC
1 CTCTATTTTTAC-TAAAAATTAGGTTTCGAAAACC
* *
15127 CTCTTTTTTTTCTAAAAATTAGGTTTCGAAA
1 CTCTATTTTTACTAAAAATTAGGTTTCGAAA
15158 TCCTCTGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 5 0.19
34 22 0.81
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (34 bp):
CTCTATTTTTACTAAAAATTAGGTTTCGAAAACC
Found at i:15475 original size:21 final size:21
Alignment explanation
Indices: 15432--15477 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15422 GTTGCCGAAA
*
15432 TTGGGTTTGTTTAGTTGCATT
1 TTGGGTTTGTTTAGTTACATT
*
15453 TTGGGTTTGTTT-GTTTACGTT
1 TTGGGTTTGTTTAG-TTACATT
15474 TTGG
1 TTGG
15478 TAATCAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.07, C:0.04, G:0.30, T:0.59
Consensus pattern (21 bp):
TTGGGTTTGTTTAGTTACATT
Found at i:19912 original size:2 final size:2
Alignment explanation
Indices: 19905--19929 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19895 ATTTTATTAA
19905 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19930 GTGGGACGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21585 original size:3 final size:3
Alignment explanation
Indices: 21577--21621 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
21567 CCTTGACCCT
21577 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
21622 AAAAAGAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28897 original size:29 final size:29
Alignment explanation
Indices: 28821--28929 Score: 110
Period size: 29 Copynumber: 3.7 Consensus size: 29
28811 ACTAAACAGC
** *
28821 CATTTTGCCCCCTGAACTTGTATCGTTTAGA
1 CATTTTGCCCCCTGAACTTCAATC--TTGGA
* *
28852 CGTTTTGCCCCCCGAACTTCAATCTTGGA
1 CATTTTGCCCCCTGAACTTCAATCTTGGA
* *
28881 CATTTTGCACCCTGAACTTCAATTTTGGGA
1 CATTTTGCCCCCTGAACTTCAATCTT-GGA
* *
28911 CGTTTTGCCCCCTCAACTT
1 CATTTTGCCCCCTGAACTT
28930 AACGGCTCCG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 26 0.40
30 19 0.29
31 20 0.31
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (29 bp):
CATTTTGCCCCCTGAACTTCAATCTTGGA
Found at i:28993 original size:33 final size:33
Alignment explanation
Indices: 28951--29030 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
28941 TAAGTCGCTG
28951 ACGTGGCATTGCCATGTCAGACAAACCTAACCC
1 ACGTGGCATTGCCATGTCAGACAAACCTAACCC
28984 ACGTGGCATTGCCATGTCAGACAAACCTAACCC
1 ACGTGGCATTGCCATGTCAGACAAACCTAACCC
29017 ACGTGGCATTGCCA
1 ACGTGGCATTGCCA
29031 CGTTGGACCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.29, C:0.33, G:0.20, T:0.19
Consensus pattern (33 bp):
ACGTGGCATTGCCATGTCAGACAAACCTAACCC
Found at i:29156 original size:29 final size:31
Alignment explanation
Indices: 29123--29195 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
29113 CGTTAGGTTG
* **
29123 AGGGGGCAAAATGTC-CAA-GATTGAAGTTC
1 AGGGGGCAAAATGTCTAAACGATACAAGTTC
* *
29152 AGGGGGCAAAACGTCTAAACGCTACAAGTTC
1 AGGGGGCAAAATGTCTAAACGATACAAGTTC
29183 AGGGGGCAAAATG
1 AGGGGGCAAAATG
29196 GTAGATTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 14 0.39
30 2 0.06
31 20 0.56
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (31 bp):
AGGGGGCAAAATGTCTAAACGATACAAGTTC
Found at i:31535 original size:31 final size:31
Alignment explanation
Indices: 31485--31552 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
31475 CTCAAAAGGA
* * *
31485 GATCAATTTATTCCTTGTACACACAAGATTG
1 GATCAAGTTACTCCCTGTACACACAAGATTG
*
31516 GATCAAGTTACTCCCTGTACTCACAAGATTG
1 GATCAAGTTACTCCCTGTACACACAAGATTG
*
31547 GGTCAA
1 GATCAA
31553 TTGAGTCTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (31 bp):
GATCAAGTTACTCCCTGTACACACAAGATTG
Found at i:32033 original size:31 final size:31
Alignment explanation
Indices: 31988--32164 Score: 194
Period size: 31 Copynumber: 5.7 Consensus size: 31
31978 GATGTCCGAT
* *
31988 GTGGCATGCCACGTGTACCAAAAAGTGACAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
* * * *
32019 ATGTCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
*
32050 GTGGCACGCCACATGTACCAAAAAGTGAAAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
* * * **
32081 ATGTCACGCCACGTGTATTAAAAAGTGACAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
* ** *
32112 GTGGCATGCCACATGTTTCAAAAAGTGGCAC
1 GTGGCACGCCACATGTACCAAAAAGTGACAC
*
32143 GTGGCATGCCACATGTA-CAAAA
1 GTGGCACGCCACATGTACCAAAA
32165 GGATACGTGC
Statistics
Matches: 123, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
30 5 0.04
31 118 0.96
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (31 bp):
GTGGCACGCCACATGTACCAAAAAGTGACAC
Found at i:32083 original size:62 final size:62
Alignment explanation
Indices: 31986--32138 Score: 234
Period size: 62 Copynumber: 2.5 Consensus size: 62
31976 ACGATGTCCG
* *
31986 ATGTGGCATGCCACGTGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ATGTGGCATGCCACATGTACCAAAAAGTGAAACATGTCACGCCACGTGTACCAAAAAGTGAC
* **
32048 ATGTGGCACGCCACATGTACCAAAAAGTGAAACATGTCACGCCACGTGTATTAAAAAGTGAC
1 ATGTGGCATGCCACATGTACCAAAAAGTGAAACATGTCACGCCACGTGTACCAAAAAGTGAC
* **
32110 ACGTGGCATGCCACATGTTTCAAAAAGTG
1 ATGTGGCATGCCACATGTACCAAAAAGTG
32139 GCACGTGGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 82 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (62 bp):
ATGTGGCATGCCACATGTACCAAAAAGTGAAACATGTCACGCCACGTGTACCAAAAAGTGAC
Found at i:32154 original size:62 final size:62
Alignment explanation
Indices: 31988--32164 Score: 230
Period size: 62 Copynumber: 2.9 Consensus size: 62
31978 GATGTCCGAT
* *
31988 GTGGCATGCCACGTGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCATGCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGACAC
* * **
32050 GTGGCACGCCACATGTACCAAAAAGTGAAACATGTCACGCCACGTGTATTAAAAAGTGACAC
1 GTGGCATGCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGACAC
** * * * * *
32112 GTGGCATGCCACATGTTTCAAAAAGTGGCACGTGGCATGCCACATGTA-CAAAA
1 GTGGCATGCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAA
32165 GGATACGTGC
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 4 0.04
62 95 0.96
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (62 bp):
GTGGCATGCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGACAC
Found at i:32154 original size:93 final size:92
Alignment explanation
Indices: 31995--32164 Score: 232
Period size: 93 Copynumber: 1.8 Consensus size: 92
31985 GATGTGGCAT
* * *
31995 GCCACGTGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAGTGACATGTGGCACGCC
1 GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTGACACGTGGCACGCC
32060 ACATGTACCAAAAAGTGAAACATGTCAC
66 ACATGTA-CAAAAAGTGAAACATGTCAC
** * * ** * *
32088 GCCACGTGTATTAAAAAGTGACACGTGGCATGCCACATGTTTCAAAAAGTGGCACGTGGCATGCC
1 GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTGACACGTGGCACGCC
32153 ACATGTACAAAA
66 ACATGTACAAAA
32165 GGATACGTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
92 5 0.08
93 61 0.92
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (92 bp):
GCCACGTGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTGACACGTGGCACGCC
ACATGTACAAAAAGTGAAACATGTCAC
Done.