Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022344.1 Corchorus olitorius cultivar O-4 contig22377, 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: 3293
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:3047 original size:14 final size:15

Alignment explanation


    Indices: 3040--3072  Score: 52
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       3030 AAAAAGAAAT

                           
       3040 TCAAAAAAATCAAAA
          1 TCAAAAAAATCAAAA

                           
       3055 TC-AAAAAATC-AAA
          1 TCAAAAAAATCAAAA

                 
       3068 TCAAA
          1 TCAAA

       3073 GTCAATAAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  13    5  0.29
  14   10  0.59
  15    2  0.12

ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15


Consensus pattern (15 bp):   
TCAAAAAAATCAAAA

Found at i:3077 original size:25 final size:24

Alignment explanation


    Indices: 3046--3109  Score: 85
    Period size: 25  Copynumber: 2.6  Consensus size: 24

       3036 AAATTCAAAA

                                    
       3046 AAATCAAAATCAAAAAATCAAATC
          1 AAATCAAAATCAAAAAATCAAATC

                        *        *    
       3070 AAAGTCAATAA-AAAAAAATCGAATC
          1 AAA-TCAA-AATCAAAAAATCAAATC

                           
       3095 AAATCAAAATCAAAA
          1 AAATCAAAATCAAAA

       3110 GAGAATGGAT


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  23    2  0.06
  24   11  0.32
  25   19  0.56
  26    2  0.06

ACGTcount: A:0.67, C:0.14, G:0.03, T:0.16


Consensus pattern (24 bp):   
AAATCAAAATCAAAAAATCAAATC

Found at i:3096 original size:19 final size:18

Alignment explanation


    Indices: 3042--3097  Score: 58
    Period size: 19  Copynumber: 2.9  Consensus size: 18

       3032 AAAGAAATTC

                               
       3042 AAAAAAATCAAAATCAAAA
          1 AAAAAAATC-AAATCAAAA

              **                
       3061 AATCAAATCAAAGTCAATAA
          1 AAAAAAATCAAA-TCAA-AA

                     *       
       3081 AAAAAAATCGAATCAAA
          1 AAAAAAATCAAATCAAA

       3098 TCAAAATCAA


Statistics
Matches: 30,  Mismatches: 5, Indels: 5
        0.75            0.12        0.12

Matches are distributed among these distances:
  18    4  0.13
  19   15  0.50
  20   11  0.37

ACGTcount: A:0.70, C:0.12, G:0.04, T:0.14


Consensus pattern (18 bp):   
AAAAAAATCAAATCAAAA
Done.