Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004396.1 Corchorus capsularis cultivar CVL-1 contig04404, 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, 731

Length: 1219
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:290 original size:72 final size:73

Alignment explanation


    Indices: 171--310  Score: 255
    Period size: 72  Copynumber: 1.9  Consensus size: 73

        161 AATCAGATGC

                                                                    *        
        171 CAGGAACCAGATTTGAACTGGTGACACGAGGATTTTCAGTCCTCTGCTCTACCAACTGAGCTATC
          1 CAGGAACCAGATTTGAACTGGT-ACACGAGGATTTTCAGTCCTCTGCTCTACCAACCGAGCTATC

                     
        236 CCGACCGTT
         65 CCGACCGTT

                                                                             
        245 CAGGAACCAGATTTGAACTGGT-CACGAGGATTTTCAGTCCTCTGCTCTACCAACCGAGCTATCC
          1 CAGGAACCAGATTTGAACTGGTACACGAGGATTTTCAGTCCTCTGCTCTACCAACCGAGCTATCC

              
        309 CG
         66 CG

        311 CCCATTACCG


Statistics
Matches: 65,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  72   43  0.66
  74   22  0.34

ACGTcount: A:0.24, C:0.29, G:0.21, T:0.25


Consensus pattern (73 bp):   
CAGGAACCAGATTTGAACTGGTACACGAGGATTTTCAGTCCTCTGCTCTACCAACCGAGCTATCC
CGACCGTT

Found at i:693 original size:20 final size:20

Alignment explanation


    Indices: 668--708  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        658 AAAAGGTCGG

                                
        668 ATAAAATAAATAGATAGCAA
          1 ATAAAATAAATAGATAGCAA

                                
        688 ATAAAATAAATAGATAGCAA
          1 ATAAAATAAATAGATAGCAA

             
        708 A
          1 A

        709 AGGGCTTTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20


Consensus pattern (20 bp):   
ATAAAATAAATAGATAGCAA

Done.