Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006781.1 Corchorus capsularis cultivar CVL-1 contig06802, 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: 10639
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:49 original size:29 final size:29

Alignment explanation


    Indices: 1--78  Score: 129
    Period size: 29  Copynumber: 2.7  Consensus size: 29

                       *                  
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
          1 AGGGGGCAAAATGT-CCAAAATTGAAGTTC

                                         
         31 AGGGGGCAAAATGTCCAAAATTGAAGTTC
          1 AGGGGGCAAAATGTCCAAAATTGAAGTTC

                 *             
         60 AGGGGACAAAATGTCCAAA
          1 AGGGGGCAAAATGTCCAAA

         79 CGTTACAAGT


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  29   33  0.72
  30   13  0.28

ACGTcount: A:0.40, C:0.17, G:0.27, T:0.17


Consensus pattern (29 bp):   
AGGGGGCAAAATGTCCAAAATTGAAGTTC

Found at i:102 original size:31 final size:28

Alignment explanation


    Indices: 1--103  Score: 98
    Period size: 29  Copynumber: 3.4  Consensus size: 28

                       *           *      
          1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
          1 AGGGGG-AAAATGT-CCAAAATTCAAGTTC

                                  *      
         31 AGGGGGCAAAATGTCCAAAATTGAAGTTC
          1 AGGGGG-AAAATGTCCAAAATTCAAGTTC

                  *             *          
         60 AGGGGACAAAATGTCCAAACGTTACAAGTTC
          1 AGGGG-GAAAATGTCCAAA-ATT-CAAGTTC

                         
         91 AAGGGGGAAAATG
          1 -AGGGGGAAAATG

        104 GTAGTTTAGT


Statistics
Matches: 64,  Mismatches: 5, Indels: 7
        0.84            0.07        0.09

Matches are distributed among these distances:
  29   32  0.50
  30   15  0.23
  31   12  0.19
  32    5  0.08

ACGTcount: A:0.39, C:0.16, G:0.28, T:0.17


Consensus pattern (28 bp):   
AGGGGGAAAATGTCCAAAATTCAAGTTC

Found at i:1590 original size:30 final size:30

Alignment explanation


    Indices: 1554--1615  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1544 TTTAGTTTAT

                    *                     
       1554 TGTTTTATTTAGCAAATGATTCTCAGATTC
          1 TGTTTTATCTAGCAAATGATTCTCAGATTC

                                          
       1584 TGTTTTATCTAGCAAATGATTCTCAGATTC
          1 TGTTTTATCTAGCAAATGATTCTCAGATTC

              
       1614 TG
          1 TG

       1616 AATAGCAAGC


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.26, C:0.15, G:0.15, T:0.45


Consensus pattern (30 bp):   
TGTTTTATCTAGCAAATGATTCTCAGATTC
Done.