Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004945.1 Corchorus capsularis cultivar CVL-1 contig04963, 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: 7387
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:244 original size:66 final size:66

Alignment explanation


    Indices: 174--298  Score: 148
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        164 ATTCAATTAT

                                                         *                   
        174 AAAAATAATAATAAA-ATAAATAACTAAA-AGATAATTCT-AGATTTTGCCAATTTGTGGGAAGT
          1 AAAAATAATAA-AAACATAAATAACTAAATA-ATAATT-TGAGATCTTGCCAATTTGTGGGAAGT

                
        236 CTAG
         63 CTAG

                  *            *   *              * *                  
        240 AAAAATCATAAAAACATAATTAATTAAATAATAATTTGGGGTCTTGCCAATTTGTGGGA
          1 AAAAATAATAAAAACATAAATAACTAAATAATAATTTGAGATCTTGCCAATTTGTGGGA

        299 GACTAAATAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 6
        0.81            0.10        0.10

Matches are distributed among these distances:
  65    4  0.08
  66   45  0.90
  67    1  0.02

ACGTcount: A:0.46, C:0.08, G:0.14, T:0.31


Consensus pattern (66 bp):   
AAAAATAATAAAAACATAAATAACTAAATAATAATTTGAGATCTTGCCAATTTGTGGGAAGTCTA
G

Found at i:373 original size:26 final size:26

Alignment explanation


    Indices: 309--365  Score: 98
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        299 GACTAAATAA

                                       
        309 TAAAGATATGATTAAAATTCAAAAAAC
          1 TAAA-ATATGATTAAAATTCAAAAAAC

                                      
        336 TAAAATATGATTAAAATTC-AAAAAC
          1 TAAAATATGATTAAAATTCAAAAAAC

                 
        361 TAAAA
          1 TAAAA

        366 GTGAGATTTG


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  25   11  0.37
  26   15  0.50
  27    4  0.13

ACGTcount: A:0.61, C:0.07, G:0.05, T:0.26


Consensus pattern (26 bp):   
TAAAATATGATTAAAATTCAAAAAAC

Found at i:6752 original size:50 final size:51

Alignment explanation


    Indices: 6692--6812  Score: 174
    Period size: 50  Copynumber: 2.4  Consensus size: 51

       6682 GTCTGATTTT

                       *                                        
       6692 ATTTGATTCAATGGTCTTGATGACTTGATCTTGAATTGATAACTTGATGA-A
          1 ATTTGATTCAAGGGTCTTGATGACTTGATCTTGAATTGATAACTTGAT-ACA

                                       *            * *         
       6743 A-TTGATTCAAGGGTCTTGATGACTTGCTCTTGAATTGATGATTTGATACTA
          1 ATTTGATTCAAGGGTCTTGATGACTTGATCTTGAATTGATAACTTGATAC-A

                               
       6794 ATTTGATTCAAGGGTCTTG
          1 ATTTGATTCAAGGGTCTTG

       6813 GCGACTGATC


Statistics
Matches: 63,  Mismatches: 4, Indels: 5
        0.88            0.06        0.07

Matches are distributed among these distances:
  49    1  0.02
  50   42  0.67
  51    3  0.05
  52   17  0.27

ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41


Consensus pattern (51 bp):   
ATTTGATTCAAGGGTCTTGATGACTTGATCTTGAATTGATAACTTGATACA
Done.