Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001282.1 Corchorus capsularis cultivar CVL-1 contig01282, 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: 10022
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:510 original size:30 final size:31

Alignment explanation


    Indices: 474--538  Score: 96
    Period size: 30  Copynumber: 2.1  Consensus size: 31

        464 AACCTATTAA

                          *  *             
        474 TTAATGGAGAGTGAGATGGAAG-TAGACAAG
          1 TTAATGGAGAGTGAAATAGAAGATAGACAAG

                                            
        504 TTAATGGAGAGTGAAATAGAAGTATAGACAAG
          1 TTAATGGAGAGTGAAATAGAAG-ATAGACAAG

               
        536 TTA
          1 TTA

        539 TATTATCATC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  30   20  0.65
  32   11  0.35

ACGTcount: A:0.43, C:0.03, G:0.31, T:0.23


Consensus pattern (31 bp):   
TTAATGGAGAGTGAAATAGAAGATAGACAAG

Found at i:906 original size:27 final size:28

Alignment explanation


    Indices: 857--909  Score: 81
    Period size: 27  Copynumber: 1.9  Consensus size: 28

        847 GATTTCTTTT

                     *        *         
        857 CTTTTCTTTTTTCTTTTTGTTACTATAC
          1 CTTTTCTTTCTTCTTTTTATTACTATAC

                                      
        885 CTTTT-TTTCTTCTTTTTATTACTAT
          1 CTTTTCTTTCTTCTTTTTATTACTAT

        910 TTGAAACATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  27   18  0.78
  28    5  0.22

ACGTcount: A:0.11, C:0.17, G:0.02, T:0.70


Consensus pattern (28 bp):   
CTTTTCTTTCTTCTTTTTATTACTATAC

Found at i:2837 original size:3 final size:3

Alignment explanation


    Indices: 2829--2858  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       2819 AATTTCCAAT

                                                   
       2829 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

       2859 TGTCTTTAAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

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


Consensus pattern (3 bp):   
GAA

Found at i:8600 original size:3 final size:3

Alignment explanation


    Indices: 8592--8620  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       8582 GCAATTTCCA

                                                  
       8592 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       8621 TAATGTCTTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Done.