Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022541.1 Corchorus olitorius cultivar O-4 contig22574, 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: 2917
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Found at i:861 original size:2 final size:2
Alignment explanation
Indices: 854--889 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
844 ACATACATAC
854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
890 GAAAAAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1709 original size:35 final size:35
Alignment explanation
Indices: 1663--2044 Score: 475
Period size: 35 Copynumber: 10.9 Consensus size: 35
1653 ATCAATGTGA
* *
1663 AGATCAACTCTGATCATCGAAAACTTCTTTAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
** *
1698 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAACG
* ** * *
1735 AGATCAACTCTGACCATATAAAAAACTTCTTGGAATG
1 AGATCAACTCTGATC--ATCGAAAACTTCTTGAAACG
* * *
1772 AGATCAACTCTAATCAACAAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTC-TTGAAACG
* *
1807 AGATCAACTCTGATCATTGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
* * *
1842 AGATCAACTCTGACCAT--AAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTG-AAACG
* * *
1876 AGATCAACTCTGATCAT-AAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
*
1910 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
*
1945 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1980 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
2015 AGATCAACTCTGATCATCGAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTG
2045 GAATGACCGC
Statistics
Matches: 309, Mismatches: 29, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
33 10 0.03
34 43 0.14
35 195 0.63
36 2 0.01
37 57 0.18
39 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
Found at i:1978 original size:173 final size:175
Alignment explanation
Indices: 1663--2043 Score: 518
Period size: 173 Copynumber: 2.2 Consensus size: 175
1653 ATCAATGTGA
* * * *
1663 AGATCAACTCTGATCATCGAAAACTTCTTTAAATGAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGACCATC-AAAACATCTTAAAATGAGATCAACTCTGATCAT--AAAAAACTTCC
* * *
1728 TGAAAGGAGATCAACTCTGACCATATAAAAAACTTCTTGGAATGAGATCAACTCTAATCAACAAA
63 TGAAAGGAGATCAACTCTGACCA-ACAAAAAACTTCTTGAAACGAGATCAACTCTAATCAACAAA
* *
1793 AACTCTTTGAAACGAGATCAACTCTGATCATTGAAAACTTCTTGAAATG
127 AACTCTTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAACG
1842 AGATCAACTCTGACCAT-AAAACATCTTGAAAATGAGATCAACTCTGATCAT-AAAAACTTCCTG
1 AGATCAACTCTGACCATCAAAACATCTT-AAAATGAGATCAACTCTGATCATAAAAAACTTCCTG
* ** * * *
1905 AAAGGAGATCAACTCTGATC-ACCGAAAACTTCTTGAAACGAGATCAACTCTGATCACCGAAAAC
65 AAAGGAGATCAACTCTGACCAACAAAAAACTTCTTGAAACGAGATCAACTCTAATCAACAAAAAC
1969 T-TCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAACG
130 TCT-TTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAACG
* *
2015 AGATCAACTCTGATCATCGAAAACTTCTT
1 AGATCAACTCTGACCATC-AAAACATCTT
2044 GGAATGACCG
Statistics
Matches: 181, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
172 1 0.01
173 94 0.52
175 39 0.22
177 9 0.05
178 22 0.12
179 16 0.09
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (175 bp):
AGATCAACTCTGACCATCAAAACATCTTAAAATGAGATCAACTCTGATCATAAAAAACTTCCTGA
AAGGAGATCAACTCTGACCAACAAAAAACTTCTTGAAACGAGATCAACTCTAATCAACAAAAACT
CTTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAACG
Found at i:2097 original size:54 final size:54
Alignment explanation
Indices: 2015--2177 Score: 263
Period size: 54 Copynumber: 3.0 Consensus size: 54
2005 TCTTGAAACG
* *
2015 AGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* *
2069 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACTGCACTGGATCATCTCA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * *
2123 GGATCAACTCTGACCATTGAAAACTTCTTGAAATGACCGCACTAGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
2177 A
1 A
2178 CACCTGTTTC
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (54 bp):
AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
Done.