Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024774.1 Corchorus olitorius cultivar O-4 contig24807, 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: 14286
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:2267 original size:1 final size:1

Alignment explanation


    Indices: 2261--2286  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

       2251 ATTAATCTTC

                                      
       2261 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

       2287 ACATTTCTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:9079 original size:60 final size:60

Alignment explanation


    Indices: 8986--9148  Score: 256
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       8976 GCTAATTGCT

                      *      *  *                                        
       8986 CAAATAAGGGTCTAACATTTGTC-AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAAC-GTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC

                                                     *                  
       9046 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC

                    **                                 
       9106 CAAATAAGAACCTAACGTTATCGAAAATGCTCAAATAAGGGCC
          1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC

       9149 TGCCATCAGT


Statistics
Matches: 95,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  59    4  0.04
  60   91  0.96

ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC

Found at i:9084 original size:31 final size:31

Alignment explanation


    Indices: 9046--9149  Score: 99
    Period size: 31  Copynumber: 3.4  Consensus size: 31

       9036 TTAATTTGGC

                                           
       9046 CAAATAAGGGCCTAACGTTATCGAAAATGCT
          1 CAAATAAGGGCCTAACGTTATCGAAAATGCT

                         * *       *  **     
       9077 CAAATAAGGGTCCGATC-TT-T-TAATTTGGC-
          1 CAAATAAGGG-CCTAACGTTATCGAAAAT-GCT

                    **                     
       9106 CAAATAAGAACCTAACGTTATCGAAAATGCT
          1 CAAATAAGGGCCTAACGTTATCGAAAATGCT

                         
       9137 CAAATAAGGGCCT
          1 CAAATAAGGGCCT

       9150 GCCATCAGTT


Statistics
Matches: 53,  Mismatches: 14, Indels: 12
        0.67            0.18        0.15

Matches are distributed among these distances:
  28    4  0.08
  29   13  0.25
  30    6  0.11
  31   26  0.49
  32    4  0.08

ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25


Consensus pattern (31 bp):   
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Done.