Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001185.1 Corchorus capsularis cultivar CVL-1 contig01185, 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: 2082
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26


Found at i:39 original size:21 final size:22

Alignment explanation


    Indices: 13--67  Score: 67
    Period size: 21  Copynumber: 2.5  Consensus size: 22

          3 GTAAAAGGTA

                               *  
         13 AATCAGTAAAAAGCAAAA-GGC
          1 AATCAGTAAAAAGCAAAACAGC

                       * *       *
         34 AATCAGTAAAAGGTAAAACAGT
          1 AATCAGTAAAAAGCAAAACAGC

                        
         56 AATCAGTAAAAA
          1 AATCAGTAAAAA

         68 AAGAGTAGAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  21   16  0.57
  22   12  0.43

ACGTcount: A:0.58, C:0.11, G:0.16, T:0.15


Consensus pattern (22 bp):   
AATCAGTAAAAAGCAAAACAGC

Found at i:173 original size:21 final size:22

Alignment explanation


    Indices: 105--178  Score: 77
    Period size: 21  Copynumber: 3.5  Consensus size: 22

         95 GAGTAAAAGG

                      *           
        105 GTAATCAGTAAAAAGT-AAGAA
          1 GTAATCAGTACAAAGTAAAGAA

                                     
        126 GGTAATCA--ACAAGAGTAAA-ATA
          1 -GTAATCAGTACAA-AGTAAAGA-A

                                  
        148 GTAATCAGTACAAAGTAAAGAA
          1 GTAATCAGTACAAAGTAAAGAA

                      
        170 -TAATCAGTA
          1 GTAATCAGTA

        179 AAATAGTGAT


Statistics
Matches: 45,  Mismatches: 1, Indels: 13
        0.76            0.02        0.22

Matches are distributed among these distances:
  20    3  0.07
  21   20  0.44
  22   17  0.38
  23    5  0.11

ACGTcount: A:0.54, C:0.08, G:0.18, T:0.20


Consensus pattern (22 bp):   
GTAATCAGTACAAAGTAAAGAA
Done.