Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013178.1 Corchorus capsularis cultivar CVL-1 contig13199, 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, 973

Length: 1622
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36


Found at i:149 original size:2 final size:2

Alignment explanation


    Indices: 142--174  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        132 AAGAAAAAGA

                                                             
        142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        175 CTAGTTTTAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:301 original size:21 final size:21

Alignment explanation


    Indices: 233--306  Score: 94
    Period size: 22  Copynumber: 3.4  Consensus size: 21

        223 TGAATATTTT

                   *   *         
        233 TATGAAACTTTAATAATTACC
          1 TATGAAATTTTGATAATTACC

                *            *     
        254 TTATTAAATTTTGATAACTATCC
          1 -TATGAAATTTTGATAATTA-CC

                                 
        277 TATGAAATTTTGATAATTACC
          1 TATGAAATTTTGATAATTACC

                     
        298 TATGAAATT
          1 TATGAAATT

        307 ATAAAATTGT


Statistics
Matches: 45,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  21   11  0.24
  22   32  0.71
  23    2  0.04

ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43


Consensus pattern (21 bp):   
TATGAAATTTTGATAATTACC

Found at i:351 original size:18 final size:18

Alignment explanation


    Indices: 328--363  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        318 ATAAACTCCA

                       *      
        328 TATGAAACTTTGATAAAC
          1 TATGAAACTTTAATAAAC

                   *          
        346 TATGAAATTTTAATAAAC
          1 TATGAAACTTTAATAAAC

        364 CATCCAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36


Consensus pattern (18 bp):   
TATGAAACTTTAATAAAC

Found at i:414 original size:21 final size:22

Alignment explanation


    Indices: 389--447  Score: 75
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        379 TGTAACCTTT

                                  
        389 CTATGA-TTTTTGATAATCTCC
          1 CTATGAGTTTTTGATAATCTCC

                   *     *        
        410 CTATGAGATTTTGTTAATCTCC
          1 CTATGAGTTTTTGATAATCTCC

                * *         
        432 CTATAATTTTTTGATA
          1 CTATGAGTTTTTGATA

        448 CTATAGTATG


Statistics
Matches: 31,  Mismatches: 6, Indels: 1
        0.82            0.16        0.03

Matches are distributed among these distances:
  21    6  0.19
  22   25  0.81

ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49


Consensus pattern (22 bp):   
CTATGAGTTTTTGATAATCTCC

Done.