Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005208.1 Corchorus capsularis cultivar CVL-1 contig05226, 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: 5391
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:1576 original size:31 final size:31

Alignment explanation


    Indices: 1534--1641  Score: 96
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       1524 GCTAAATAAC

                 *                   **     
       1534 CAATTCAGGATATAACGTTTGCT-GCCACGAT
          1 CAATTTAGGATATAACGTTT-CTGGAAACGAT

                  *                    *   
       1565 CAATTTGGGATATAACGTTTCTGGAAATGAT
          1 CAATTTAGGATATAACGTTTCTGGAAACGAT

              *                   **        
       1596 CATTTTAGGATATAACGTTTC-AAAAAGCGAT
          1 CAATTTAGGATATAACGTTTCTGGAAA-CGAT

                            
       1627 C-ATTTCAGGATATAA
          1 CAATTT-AGGATATAA

       1642 AGAATGATTG


Statistics
Matches: 63,  Mismatches: 11, Indels: 6
        0.79            0.14        0.08

Matches are distributed among these distances:
  30    8  0.13
  31   55  0.87

ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32


Consensus pattern (31 bp):   
CAATTTAGGATATAACGTTTCTGGAAACGAT

Found at i:2581 original size:20 final size:20

Alignment explanation


    Indices: 2534--2582  Score: 55
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       2524 TATATAATTT

                                
       2534 ATTAACCCGACATTAACCCA
          1 ATTAACCCGACATTAACCCA

               *        *        
       2554 ATTGACCCGACGGTTAA-CCA
          1 ATTAACCCGAC-ATTAACCCA

            *        
       2574 CTTAACCCG
          1 ATTAACCCG

       2583 TGATCCGGAG


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  20   20  0.83
  21    4  0.17

ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20


Consensus pattern (20 bp):   
ATTAACCCGACATTAACCCA
Done.