Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013770.1 Corchorus capsularis cultivar CVL-1 contig13791, 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: 5171
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:688 original size:15 final size:16

Alignment explanation


    Indices: 656--702  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

        646 TAGTATTTCT

                   *        
        656 AAATTATTAATAATAA
          1 AAATTATAAATAATAA

                            
        672 AAATTATAAAT-ATAA
          1 AAATTATAAATAATAA

                 *          
        687 AACGAATATAAATAAT
          1 AA--ATTATAAATAAT

        703 TTATTATATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  15    6  0.23
  16   10  0.38
  17    8  0.31
  18    2  0.08

ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32


Consensus pattern (16 bp):   
AAATTATAAATAATAA

Found at i:4668 original size:31 final size:31

Alignment explanation


    Indices: 4606--4684  Score: 88
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       4596 GGGGAAACTT

                      *   *                 
       4606 TATATTTTCCGATTATACCCTTATTTTTAAAA
          1 TATATTTT-CAATTGTACCCTTATTTTTAAAA

                                            
       4638 TATATTTTCAATTGTACCCTT-TTTTCTAAAA
          1 TATATTTTCAATTGTACCCTTATTTT-TAAAA

            *        *      
       4669 CATATTTCTAAATTGT
          1 TATATTT-TCAATTGT

       4685 CATTACTAAA


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

Matches are distributed among these distances:
  30    4  0.10
  31   22  0.54
  32   15  0.37

ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51


Consensus pattern (31 bp):   
TATATTTTCAATTGTACCCTTATTTTTAAAA

Found at i:4751 original size:15 final size:16

Alignment explanation


    Indices: 4731--4764  Score: 52
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       4721 TTTAATCATA

                    *       
       4731 AATTATTATATTAT-T
          1 AATTATTAGATTATAT

                            
       4746 AATTATTAGATTATAT
          1 AATTATTAGATTATAT

               
       4762 AAT
          1 AAT

       4765 ACATATATTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15   13  0.76
  16    4  0.24

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (16 bp):   
AATTATTAGATTATAT

Found at i:4864 original size:38 final size:37

Alignment explanation


    Indices: 4800--4877  Score: 120
    Period size: 38  Copynumber: 2.1  Consensus size: 37

       4790 AATTTGACTT

                                                 
       4800 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
          1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC

                           **             *       
       4837 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGTC
          1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTGTC

               
       4875 TTT
          1 TTT

       4878 TTCTTCGATT


Statistics
Matches: 37,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  37   11  0.30
  38   26  0.70

ACGTcount: A:0.13, C:0.17, G:0.12, T:0.59


Consensus pattern (37 bp):   
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC

Done.