Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009215.1 Corchorus capsularis cultivar CVL-1 contig09236, 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: 1777
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37


Found at i:1451 original size:31 final size:31

Alignment explanation


    Indices: 1391--1469  Score: 88
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       1381 GGGGAAATTT

                      *                     
       1391 TATATTTTCCGATTGTACCCTTATTTTTAAAA
          1 TATATTTT-CAATTGTACCCTTATTTTTAAAA

                            *               
       1423 TATATTTTCAATTGTATCCTT-TTCTTTAAAA
          1 TATATTTTCAATTGTACCCTTATT-TTTAAAA

            *        *      
       1454 CATATTTCTAAATTGT
          1 TATATTT-TCAATTGT

       1470 CATTACTAAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  30    2  0.05
  31   24  0.59
  32   15  0.37

ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52


Consensus pattern (31 bp):   
TATATTTTCAATTGTACCCTTATTTTTAAAA

Found at i:1627 original size:38 final size:35

Alignment explanation


    Indices: 1563--1639  Score: 109
    Period size: 38  Copynumber: 2.1  Consensus size: 35

       1553 AATTTGACTT

                                                 
       1563 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
          1 TTTGTTTCCAACGTCCTATTTAATTTTG-C-TTTGTC

                           **                   
       1600 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTGTC
          1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCTTTGTC

                
       1636 TTTG
          1 TTTG

       1640 GTCTTAAATT


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  36   10  0.27
  37   12  0.32
  38   15  0.41

ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57


Consensus pattern (35 bp):   
TTTGTTTCCAACGTCCTATTTAATTTTGCTTTGTC
Done.