Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005083.1 Corchorus capsularis cultivar CVL-1 contig05101, 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: 3675
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:2164 original size:30 final size:28

Alignment explanation


    Indices: 2099--2170  Score: 83
    Period size: 29  Copynumber: 2.5  Consensus size: 28

       2089 ACACAAAACG

                        *              * 
       2099 GCCAAATAAGCCTCTGAACTCTAATTGCA
          1 GCCAAATAAGCCCCTGAACTCT-ATTGAA

                                          
       2128 GCCAAATAAGCCCCTGAACTCT-TTGAAAA
          1 GCCAAATAAGCCCCTGAACTCTATTG--AA

                          
       2157 TGCCAAATAAGCCC
          1 -GCCAAATAAGCCC

       2171 TTTTTGGATG


Statistics
Matches: 38,  Mismatches: 2, Indels: 5
        0.84            0.04        0.11

Matches are distributed among these distances:
  27    3  0.08
  29   22  0.58
  30   13  0.34

ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21


Consensus pattern (28 bp):   
GCCAAATAAGCCCCTGAACTCTATTGAA

Found at i:2966 original size:60 final size:60

Alignment explanation


    Indices: 2865--3026  Score: 213
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       2855 GCAGACACCA

                                    *           *     *                 
       2865 AGGCCTTATTTGAGCATTTTCGCAAACGTTAGGACCCTATTTGACCAAACTAAAAGCATG
          1 AGGCCTTATTTGAGCATTTTCGCATACGTTAGGACCATATTTAACCAAACTAAAAGCATG

                                                               *          
       2925 -GGCGCTTATTTGAGCATTTTCGCATACGTTAGG-CTCATATTTAACCAAATTAAAAGCATG
          1 AGGC-CTTATTTGAGCATTTTCGCATACGTTAGGAC-CATATTTAACCAAACTAAAAGCATG

                  * *     *                            
       2985 AGGCCTAAATTGAGTATTTTCGCATACGTTAAGGACC-TATTT
          1 AGGCCTTATTTGAGCATTTTCGCATACGTT-AGGACCATATTT

       3027 GAGCAATGAG


Statistics
Matches: 90,  Mismatches: 7, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  59    4  0.04
  60   78  0.87
  61    7  0.08
  62    1  0.01

ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Consensus pattern (60 bp):   
AGGCCTTATTTGAGCATTTTCGCATACGTTAGGACCATATTTAACCAAACTAAAAGCATG
Done.