Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006358.1 Corchorus capsularis cultivar CVL-1 contig06379, 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: 36564
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:2333 original size:11 final size:11
Alignment explanation
Indices: 2317--2345 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2307 CATCAAAGCT
2317 CTTCAATTGAG
1 CTTCAATTGAG
2328 CTTCAATTGAG
1 CTTCAATTGAG
2339 CTTCAAT
1 CTTCAAT
2346 AGTCTTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (11 bp):
CTTCAATTGAG
Found at i:3116 original size:33 final size:33
Alignment explanation
Indices: 3079--3183 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
3069 ATTAGCATCC
* *
3079 AAAACATATTTTGTTTCATCACAAACAACACCT
1 AAAACATATTTAGTATCATCACAAACAACACCT
* * *
3112 AAAACATATTTAGTGTCATCATAAACAACACAT
1 AAAACATATTTAGTATCATCACAAACAACACCT
** ** * *
3145 AAATTAGGTTTAGTATCATCGCAAACAACATCT
1 AAAACATATTTAGTATCATCACAAACAACACCT
3178 AAAACA
1 AAAACA
3184 ATCTTTGCAA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.28
Consensus pattern (33 bp):
AAAACATATTTAGTATCATCACAAACAACACCT
Found at i:4914 original size:16 final size:15
Alignment explanation
Indices: 4893--4925 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
4883 TCTGATCAGA
4893 ATTTTTATTTTATTTT
1 ATTTTTATTTT-TTTT
4909 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
4924 AT
1 AT
4926 ATATTTTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:14391 original size:6 final size:6
Alignment explanation
Indices: 14380--14410 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
14370 CAAGCTGCAC
14380 CACAAT CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT CACAAT C
14411 TAGCCAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:14467 original size:38 final size:38
Alignment explanation
Indices: 14421--14598 Score: 284
Period size: 38 Copynumber: 4.7 Consensus size: 38
14411 TAGCCAACAG
* * *
14421 TTAACCCCCTGAGACACGGGTCCACTCTTACCAACAGT
1 TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
***
14459 TTAACCCCCTGAGGTATGGGTCCACTCTTACCATCAGT
1 TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
*
14497 TTAACCCCCTGAGGCGCGAGTCCACTCTTACCATCAGT
1 TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
*
14535 TTAACCCCCTGAGGCGCGGGCCCACTCTTACCATCAGT
1 TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
14573 TTAACCCCCTGAGGCGCGGGTCCACT
1 TTAACCCCCTGAGGCGCGGGTCCACT
14599 ATGCATAGCC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 129 1.00
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.23
Consensus pattern (38 bp):
TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
Found at i:14794 original size:15 final size:16
Alignment explanation
Indices: 14765--14798 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
14755 ATAGGAAAAC
*
14765 AATTCATAATTCATAT
1 AATTCATAATACATAT
14781 AATT-ATAATACATAT
1 AATTCATAATACATAT
14796 AAT
1 AAT
14799 CTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTCATAATACATAT
Found at i:17951 original size:6 final size:6
Alignment explanation
Indices: 17940--17964 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17930 CAAGCTGCAC
17940 CACAAT CACAAT CACAAT CACAAT C
1 CACAAT CACAAT CACAAT CACAAT C
17965 TAGCCAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (6 bp):
CACAAT
Found at i:18024 original size:38 final size:38
Alignment explanation
Indices: 17975--18152 Score: 284
Period size: 38 Copynumber: 4.7 Consensus size: 38
17965 TAGCCAACAG
* *
17975 TTAACCCCCTGAGGTACGGGTCCACTCTTACCAACAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGT
* *
18013 TTAACCTCCTGAGGCACGGGTACACTCTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGT
**
18051 TTAACCCCCTGAGGCGTGGGTCCACTCTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGT
*
18089 TTAACCCCCTGAGGCGCGGGTCCACTCTTACCATCAGT
1 TTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGT
*
18127 TTAACCCCCTGAGGCACGAGTCCACT
1 TTAACCCCCTGAGGCACGGGTCCACT
18153 ATGCATAGCC
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 129 1.00
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (38 bp):
TTAACCCCCTGAGGCACGGGTCCACTCTTACCATCAGT
Found at i:18348 original size:15 final size:16
Alignment explanation
Indices: 18319--18352 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18309 ATAGGAAAAC
*
18319 AATTCATAATTCATAT
1 AATTCATAATACATAT
18335 AATT-ATAATACATAT
1 AATTCATAATACATAT
18350 AAT
1 AAT
18353 CTTTGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTCATAATACATAT
Done.