Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014171.1 Corchorus capsularis cultivar CVL-1 contig14192, 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: 34412
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:623 original size:29 final size:29
Alignment explanation
Indices: 581--637 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
571 TCAAATAGTT
*
581 AAGCAAATTGTATCTTGTAGTCATTTATA
1 AAGCAAATTGTATCTTGTAGCCATTTATA
610 AAGCAAATTGTATCTTGTAGCCATTTAT
1 AAGCAAATTGTATCTTGTAGCCATTTAT
638 TTTCTCGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (29 bp):
AAGCAAATTGTATCTTGTAGCCATTTATA
Found at i:1264 original size:35 final size:33
Alignment explanation
Indices: 1225--1291 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1215 TTTATTTATT
1225 TATATATAATAAAAACATATATAATATATTTTAAC
1 TATAT-TAATAAAAA-ATATATAATATATTTTAAC
* *
1260 TATATTTATATAAAATATATAATATATTTTAA
1 TATATTAATAAAAAATATATAATATATTTTAA
1292 ATTTTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.60
34 7 0.23
35 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (33 bp):
TATATTAATAAAAAATATATAATATATTTTAAC
Found at i:1324 original size:79 final size:79
Alignment explanation
Indices: 1203--1358 Score: 278
Period size: 79 Copynumber: 2.0 Consensus size: 79
1193 ATATTTAAAC
* *
1203 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATATATTTTAACTATAT-TT
1 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATATATTTTAAATACATATT
1267 ATATAAAATATATAA
66 ATATAAAA-ATATAA
1282 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATATATTTTAAATACATATT
1 TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATATATTTTAAATACATATT
1347 ATATAAAAATAT
66 ATATAAAAATAT
1359 CTATTCGGTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 64 0.86
80 10 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (79 bp):
TATATTTTAAATTTTATTTATTTATATATAATAAAAACATATATAATATATTTTAAATACATATT
ATATAAAAATATAA
Found at i:1338 original size:22 final size:22
Alignment explanation
Indices: 1260--1345 Score: 57
Period size: 22 Copynumber: 3.8 Consensus size: 22
1250 ATATTTTAAC
*
1260 TATATTTATATAAA-ATATATAA
1 TATATTT-TAAAAACATATATAA
*** * *
1282 TATATTTTAAATTTTATTTATTTA
1 TATATTTTAAA-AACATATA-TAA
**
1306 TATATAATAAAAACATATATAA
1 TATATTTTAAAAACATATATAA
*
1328 TATATTTTAAATACATAT
1 TATATTTTAAAAACATAT
1346 TATATAAAAA
Statistics
Matches: 46, Mismatches: 15, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
21 3 0.07
22 24 0.52
23 8 0.17
24 11 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATTTTAAAAACATATATAA
Found at i:2851 original size:2 final size:2
Alignment explanation
Indices: 2846--2876 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2836 AAAAAAAATC
*
2846 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2877 CACAATAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14159 original size:13 final size:14
Alignment explanation
Indices: 14136--14164 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
14126 TTAGTAAAAT
14136 AAAGAAAAGAGAAA
1 AAAGAAAAGAGAAA
14150 AAAG-AAAGAGAAA
1 AAAGAAAAGAGAAA
14163 AA
1 AA
14165 CACTAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAGAAA
Found at i:28743 original size:14 final size:15
Alignment explanation
Indices: 28714--28745 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28704 GTATGTAACT
28714 ATTAATAAAAACAAA
1 ATTAATAAAAACAAA
28729 ATTAATAAAAA-AAA
1 ATTAATAAAAACAAA
28743 ATT
1 ATT
28746 GAGAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
ATTAATAAAAACAAA
Found at i:33685 original size:33 final size:32
Alignment explanation
Indices: 33642--33718 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
33632 AAGCCGCGCA
* * *
33642 ACACCGGCCACGCAACTTGGAGATGCCCGGCC
1 ACACCGGCCACGCAACATGGACATGCCCGGAC
* *
33674 ATCACCGGCCACGCGACATGGACATGCCTGGAC
1 A-CACCGGCCACGCAACATGGACATGCCCGGAC
33707 ACAACCGGCCAC
1 AC-ACCGGCCAC
33719 ATGATTCGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.25, C:0.40, G:0.26, T:0.09
Consensus pattern (32 bp):
ACACCGGCCACGCAACATGGACATGCCCGGAC
Done.