Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016252.1 Corchorus olitorius cultivar O-4 contig16285, 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: 20397
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Found at i:13261 original size:36 final size:36
Alignment explanation
Indices: 13221--13289 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
13211 ACCATCTTAT
13221 GCTATGAACATTCCAGCTATGGGTCGTAGTATTCCA
1 GCTATGAACATTCCAGCTATGGGTCGTAGTATTCCA
*
13257 GCTATGAACATTCCAGTTATGGGTCGTAGTATT
1 GCTATGAACATTCCAGCTATGGGTCGTAGTATT
13290 AAAAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (36 bp):
GCTATGAACATTCCAGCTATGGGTCGTAGTATTCCA
Found at i:15945 original size:70 final size:69
Alignment explanation
Indices: 15855--16090 Score: 231
Period size: 70 Copynumber: 3.5 Consensus size: 69
15845 ACACAAACCG
* *
15855 GCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATTCTTACCAACCTTTAT
1 GCACCACTATACCTTGATGTATAATAGGAATGCCACC-CCACATAGAATTCTTACCAACCTTTAT
15920 TCGAT
65 TCGAT
* * **** * *
15925 GCACCATTATACCTTGATGTATAATAGGAATGCC-GCTGTTAT-GTATATATTACACAA-----A
1 GCACCACTATACCTTGATGTATAATAGGAATGCCACCCCACATAGAAT-TCTTAC-CAACCTTTA
*
15983 -CCGA-
64 TTCGAT
* * *
15987 -CACCACTATACCTTTATGTATAGTAGGAATGCCACCGCCACATAGAATTCTTATCAACCTTTAT
1 GCACCACTATACCTTGATGTATAATAGGAATGCCACC-CCACATAGAATTCTTACCAACCTTTAT
16051 TCGAT
65 TCGAT
*
16056 GCACCATTATACCTTGATGTATAATAGGAATGCCA
1 GCACCACTATACCTTGATGTATAATAGGAATGCCA
16091 TCATTGCGAC
Statistics
Matches: 127, Mismatches: 26, Indels: 26
0.71 0.15 0.15
Matches are distributed among these distances:
61 30 0.24
62 4 0.03
63 9 0.07
64 4 0.03
67 4 0.03
68 10 0.08
69 4 0.03
70 62 0.49
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (69 bp):
GCACCACTATACCTTGATGTATAATAGGAATGCCACCCCACATAGAATTCTTACCAACCTTTATT
CGAT
Found at i:16028 original size:131 final size:133
Alignment explanation
Indices: 15773--16090 Score: 550
Period size: 131 Copynumber: 2.4 Consensus size: 133
15763 AATTCCCATC
*
15773 ACCAACTTTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTATTATGTATA
1 ACCAACCTTTATTC-GATGCACCATTATACCTTGATGTATAATAGGAATGCCACTATTATGTATA
*
15838 CTATGTTACACAAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAA
65 CTA-GTTACACAAACCGACACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAA
15903 TTCTT
129 TTCTT
* *
15908 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCGCTGTTATGTATA-
1 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTATTATGTATAC
*
15972 TA-TTACACAAACCGACACCACTATACCTTTATGTATAGTAGGAATGCCACCGCCACATAGAATT
66 TAGTTACACAAACCGACACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATT
16036 CTT
131 CTT
*
16039 ATCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCA
1 ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCA
16091 TCATTGCGAC
Statistics
Matches: 176, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
131 113 0.64
133 2 0.01
134 48 0.27
135 13 0.07
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (133 bp):
ACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTATTATGTATAC
TAGTTACACAAACCGACACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATT
CTT
Found at i:17499 original size:216 final size:214
Alignment explanation
Indices: 17186--17647 Score: 739
Period size: 216 Copynumber: 2.2 Consensus size: 214
17176 CTTACAAACC
* *
17186 TTTATTC-GATGCACCATTATACCTAGATGTATAATAGGAATGCCAGTGTTATAGTATATTACAC
1 TTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATAGTATATTACAC
* *
17250 AAACTGGCACCACTATACCTTTATGTATAGTAGGAGTGCCACCACCACATAGAATTCTTACCAAC
66 AAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATTCTTACCAAC
* * * * *
17315 CTTTATTTGATGCACCATCATACCTTGATGTATAATAGGAATGGCAGCCCTTTTACTGCAAAGTA
131 ATTTATTCGACGCACCATCATACCTTGATATATAATAGGAATGCCAGCCCTTTTACTGCAAAGTA
*
17380 GAAATTCTCATCACCAACT
196 GAAATTCCCATCACCAACT
17399 TTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTAT-GTATAGTATCA
1 TTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATAGTATA-T-T-A
*
17463 CACAAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCGCCACCACATAGAATTCTTACC
63 CACAAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATTCTTACC
* * * *
17528 AACATTTATTCGACGCACTATTATACCTTGATATATAATAGGAATGCCGGCCTTTTTACTGCAAA
128 AACATTTATTCGACGCACCATCATACCTTGATATATAATAGGAATGCCAGCCCTTTTACTGCAAA
*
17593 GTAGAAATTCCCATCATCAACT
193 GTAGAAATTCCCATCACCAACT
17615 TTTATTCAGATGCACCATTATACCTTGATGTAT
1 TTTATTCAGATGCACCATTATACCTTGATGTAT
17648 CAGAAGAAAT
Statistics
Matches: 229, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
213 12 0.05
214 44 0.19
215 1 0.00
216 172 0.75
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (214 bp):
TTTATTCAGATGCACCATTATACCTTGATGTATAATAGGAATGCCACTGTTATAGTATATTACAC
AAACCGGCACCACTATACCTTTATGTATAGTAGGAATGCCACCACCACATAGAATTCTTACCAAC
ATTTATTCGACGCACCATCATACCTTGATATATAATAGGAATGCCAGCCCTTTTACTGCAAAGTA
GAAATTCCCATCACCAACT
Found at i:19030 original size:90 final size:88
Alignment explanation
Indices: 18890--19053 Score: 240
Period size: 90 Copynumber: 1.8 Consensus size: 88
18880 TGTGCCTTTC
* * *
18890 ACTGCATAATCAGATTCCCATCACCAACCTTTATCGACTGCACCATTATACCTTGATGTATAATA
1 ACTGCAAAATAAGATTCCCATCACCAACCTTTATCGACTGCACCATTATACCTTAATGTATAATA
18955 GGAATGCCATCATTGCGACTTAT
66 GGAATGCCATCATTGCGACTTAT
* * *
18978 ACTGCAAAATAAGATTTCCCGTCACCAACTTTTCTTCAGA-TGCACCATTATACCTTAATGTATA
1 ACTGCAAAATAAGA-TTCCCATCACCAACCTTT-ATC-GACTGCACCATTATACCTTAATGTATA
19042 ATAGGAATGCCA
63 ATAGGAATGCCA
19054 CTTGCCTTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 12 0.18
89 16 0.24
90 37 0.55
91 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (88 bp):
ACTGCAAAATAAGATTCCCATCACCAACCTTTATCGACTGCACCATTATACCTTAATGTATAATA
GGAATGCCATCATTGCGACTTAT
Found at i:20344 original size:132 final size:135
Alignment explanation
Indices: 20037--20367 Score: 497
Period size: 132 Copynumber: 2.5 Consensus size: 135
20027 AGATTTCTTA
* * * *
20037 ATAGGATTCTTACAAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCAGT
1 ATAGAATTCTTACCAACATTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACT
* **
20102 GTTATGTATAGTATATTACACAAAATTGGCACCACCTATACCTTTATGTATAGTAGGAATGCCAC
66 GTTATGTATAG-ATATCACACAAAACCGGCACCACCTATACCTTTATGTATAGTAGGAATGCCAC
20167 CACCAC
130 CACCAC
*
20173 ATAGAATTCTTACCAACCTTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACT
1 ATAGAATTCTTACCAACATTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACT
*
20238 GTTATGTATAG-TATCACAC-AAACCGGCACCA-CTATACCTTTATGTATAGTAGGAATGCCGCC
66 GTTATGTATAGATATCACACAAAACCGGCACCACCTATACCTTTATGTATAGTAGGAATGCCACC
20300 ACCAC
131 ACCAC
* * * * * *
20305 ATATAATTCTTACCTACATTTATTCGACGCACTATTATACCTTGATATATGATAGGAATGCCA
1 ATAGAATTCTTACCAACATTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCA
20368 GCCCTTTTAC
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
132 91 0.50
133 10 0.06
134 7 0.04
136 73 0.40
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.32
Consensus pattern (135 bp):
ATAGAATTCTTACCAACATTTATTCGATGCACCATTATACCTTGATGTATAATAGGAATGCCACT
GTTATGTATAGATATCACACAAAACCGGCACCACCTATACCTTTATGTATAGTAGGAATGCCACC
ACCAC
Done.