Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005079.1 Corchorus capsularis cultivar CVL-1 contig05097, 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: 6302
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:1104 original size:16 final size:16

Alignment explanation


    Indices: 1083--1117  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1073 ACAATTCAGA

                            
       1083 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

                            
       1099 AAGCAGAAAAGCTCTG
          1 AAGCAGAAAAGCTCTG

               
       1115 AAG
          1 AAG

       1118 TATCTCAGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11


Consensus pattern (16 bp):   
AAGCAGAAAAGCTCTG

Found at i:1526 original size:50 final size:50

Alignment explanation


    Indices: 1432--1527  Score: 140
    Period size: 51  Copynumber: 1.9  Consensus size: 50

       1422 ATTCAAATTA

                      *   *                                    
       1432 TTATCAATTCGAGATCAAGTCATCAAGACCCTCGAATCAAATCAAACTCCC
          1 TTATCAATTCAAGACCAAGTCATC-AGACCCTCGAATCAAATCAAACTCCC

                                            *             
       1483 TTATCAATTCAAGACCAAGTCATTC-GACCCTTGAATCAAATCAAA
          1 TTATCAATTCAAGACCAAGTCA-TCAGACCCTCGAATCAAATCAAA

       1528 TCAAATCAAG


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  50   19  0.46
  51   20  0.49
  52    2  0.05

ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25


Consensus pattern (50 bp):   
TTATCAATTCAAGACCAAGTCATCAGACCCTCGAATCAAATCAAACTCCC

Found at i:3692 original size:3 final size:3

Alignment explanation


    Indices: 3684--3719  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

       3674 AACTAGTAGC

                                                           
       3684 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

       3720 TACATAGACA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Done.