Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015116.1 Corchorus olitorius cultivar O-4 contig15149, 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: 14282
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Found at i:45 original size:34 final size:34
Alignment explanation
Indices: 1--114 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 34
*
1 ATTTAGGTTTTTCAAATTGGGAAAGTTCCCATCA
1 ATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
35 ATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAAACATTCA
1 ATTTAAGTTTTTCAAATTGGGAAAGTT--C--C---CA-TCA
* *
77 ATTTAAGTTTTTCAAATCGGGAAAGTTCTCATCA
1 ATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
111 ATTT
1 ATTT
115 TCAAAGTATT
Statistics
Matches: 69, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
34 33 0.48
35 2 0.03
36 1 0.01
38 1 0.01
40 1 0.01
41 2 0.03
42 29 0.42
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (34 bp):
ATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCA
Found at i:140 original size:50 final size:49
Alignment explanation
Indices: 32--303 Score: 274
Period size: 42 Copynumber: 5.8 Consensus size: 49
22 AAAGTTCCCA
*
32 TCAATTTAAGTTTTTCAAATTGGGAAAGTT-CC--C-A--TCAAA-CAT
1 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTCAAAGTAT
* *
74 TCAATTTAAGTTTTTCAAATCGGGAAAGTTCTCATCAATTTTCAAAGTAT
1 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAA-TTTCAAAGTAT
* *
124 TCAATTTATGTTTTTCAAATTGGGAAAGTT-CC--C---TTCAAAGCAT
1 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTCAAAGTAT
*
167 TCAATTTAAG-TTTTCAAATTGGGAAAGTTCTCATCAAGTTTTCAAAGTAT
1 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAA--TTTCAAAGTAT
* *
217 TCAATTT-AGCTCTTTTAAAATTGGGAAAGTTCCCATCAGGATTT---AGTTT
1 TCAATTTAAG-T-TTTTCAAATTGGGAAAGTTCCCATCA--ATTTCAAAGTAT
*
266 TCAATTTAAGTTTTTCAAAGTGGGAAAGTTCCCATCAA
1 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAA
304 AAGCATTTTT
Statistics
Matches: 193, Mismatches: 15, Indels: 40
0.78 0.06 0.16
Matches are distributed among these distances:
42 48 0.25
43 20 0.10
45 2 0.01
46 2 0.01
47 1 0.01
48 24 0.12
49 20 0.10
50 48 0.25
52 27 0.14
54 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (49 bp):
TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAATTTCAAAGTAT
Found at i:191 original size:92 final size:93
Alignment explanation
Indices: 32--303 Score: 379
Period size: 92 Copynumber: 2.9 Consensus size: 93
22 AAAGTTCCCA
*
32 TCAATTTAAGTTTTTCAAATTGGGAAAGTTCCCATCAAA-CATTCAATTTAAGTTTTTCAAATCG
1 TCAATTT-AGTTTTTCAAATTGGGAAAGTTCCCATCAAAGCATTCAATTTAAGTTTTTCAAATTG
96 GGAAAGTTCTCATCAA-TTTTCAAAGTAT
65 GGAAAGTTCTCATCAAGTTTTCAAAGTAT
*
124 TCAATTTATGTTTTTCAAATTGGGAAAGTTCCCTTCAAAGCATTCAATTTAAG-TTTTCAAATTG
1 TCAATTTA-GTTTTTCAAATTGGGAAAGTTCCCATCAAAGCATTCAATTTAAGTTTTTCAAATTG
188 GGAAAGTTCTCATCAAGTTTTCAAAGTAT
65 GGAAAGTTCTCATCAAGTTTTCAAAGTAT
* **
217 TCAATTTAGCTCTTTTAAAATTGGGAAAGTTCCCATCAGGATTTAGTTTTCAATTTAAGTTTTTC
1 TCAATTTAG-T-TTTTCAAATTGGGAAAGTTCCCATCA--A---AGCATTCAATTTAAGTTTTTC
* *
282 AAAGTGGGAAAGTTCCCATCAA
59 AAATTGGGAAAGTTCTCATCAA
304 AAGCATTTTT
Statistics
Matches: 161, Mismatches: 8, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
91 1 0.01
92 63 0.39
93 34 0.21
94 24 0.15
96 1 0.01
99 13 0.08
100 25 0.16
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (93 bp):
TCAATTTAGTTTTTCAAATTGGGAAAGTTCCCATCAAAGCATTCAATTTAAGTTTTTCAAATTGG
GAAAGTTCTCATCAAGTTTTCAAAGTAT
Found at i:8046 original size:23 final size:23
Alignment explanation
Indices: 8020--8064 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
8010 AATGCACTAG
8020 ACAAGAGTAA-AATTAATAAAAAC
1 ACAAGAGTAATAA-TAATAAAAAC
*
8043 ACAAGATTAATAATAATAAAAA
1 ACAAGAGTAATAATAATAAAAA
8065 AGTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (23 bp):
ACAAGAGTAATAATAATAAAAAC
Found at i:12182 original size:49 final size:49
Alignment explanation
Indices: 12122--12231 Score: 211
Period size: 49 Copynumber: 2.2 Consensus size: 49
12112 GGCTTGCTGG
12122 GTGTGGCAAGGTCAGTATTGTCGTTCTCTATGCTTCTGGGGCTCCCTGC
1 GTGTGGCAAGGTCAGTATTGTCGTTCTCTATGCTTCTGGGGCTCCCTGC
*
12171 GTGTGGCAAGGTCAGTATTGTCGTTCTCTATGCTTCTGGGGCTCCCTGT
1 GTGTGGCAAGGTCAGTATTGTCGTTCTCTATGCTTCTGGGGCTCCCTGC
12220 GTGTGGCAAGGT
1 GTGTGGCAAGGT
12232 AACCTTCCCG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.35
Consensus pattern (49 bp):
GTGTGGCAAGGTCAGTATTGTCGTTCTCTATGCTTCTGGGGCTCCCTGC
Found at i:13672 original size:24 final size:24
Alignment explanation
Indices: 13640--13697 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
13630 AATGGGAATC
*
13640 GGTGGAGGAATATTCCGATTCTGA
1 GGTGGAGGAACATTCCGATTCTGA
* *
13664 GGTGGAGGAGCGTTCCGATTCTGA
1 GGTGGAGGAACATTCCGATTCTGA
13688 GGTGGAGGAA
1 GGTGGAGGAA
13698 GTGCAGGTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.12, G:0.41, T:0.24
Consensus pattern (24 bp):
GGTGGAGGAACATTCCGATTCTGA
Done.