Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010975.1 Corchorus capsularis cultivar CVL-1 contig10996, 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: 13142
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Found at i:6076 original size:21 final size:22

Alignment explanation


    Indices: 6047--6097  Score: 79
    Period size: 21  Copynumber: 2.4  Consensus size: 22

       6037 TGATAGCTTG

                                  
       6047 TCTTCAATCCTCCGCAATTAAA
          1 TCTTCAATCCTCCGCAATTAAA

                                  
       6069 TCTT-AATCCTCCGCAATTAAA
          1 TCTTCAATCCTCCGCAATTAAA

            *        
       6090 GC-TCAATC
          1 TCTTCAATC

       6098 TTCAATTCTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20    1  0.04
  21   22  0.81
  22    4  0.15

ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31


Consensus pattern (22 bp):   
TCTTCAATCCTCCGCAATTAAA

Found at i:8601 original size:8 final size:8

Alignment explanation


    Indices: 8588--8621  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       8578 CACCTTCTTG

                    
       8588 AAAAATTC
          1 AAAAATTC

                    
       8596 AAAAATTC
          1 AAAAATTC

                 *   
       8604 AGAAACTTC
          1 A-AAAATTC

                    
       8613 AAAAATTC
          1 AAAAATTC

             
       8621 A
          1 A

       8622 TAGCCAATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:8710 original size:11 final size:11

Alignment explanation


    Indices: 8694--8731  Score: 53
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       8684 AGTTATATCG

                       
       8694 AAAAATATAAA
          1 AAAAATATAAA

                       
       8705 AAAAAT-TAAA
          1 AAAAATATAAA

                        
       8715 ATAAAATA-AAA
          1 A-AAAATATAAA

                  
       8726 AAAAAT
          1 AAAAAT

       8732 TTCGACCAGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  10   10  0.40
  11   15  0.60

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (11 bp):   
AAAAATATAAA
Done.