Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012988.1 Corchorus capsularis cultivar CVL-1 contig13009, 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: 6639
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:874 original size:19 final size:18

Alignment explanation


    Indices: 850--890  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 18

        840 TTTGAAGATT

                     *         
        850 AATTGAAGATAATTTGAAG
          1 AATTGAAGACAA-TTGAAG

                              
        869 AATTGAAGACAATTGAAG
          1 AATTGAAGACAATTGAAG

                
        887 AATT
          1 AATT

        891 ATTTCAAGAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  18   10  0.48
  19   11  0.52

ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29


Consensus pattern (18 bp):   
AATTGAAGACAATTGAAG

Found at i:900 original size:30 final size:30

Alignment explanation


    Indices: 841--900  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        831 AAGTTCGTGT

                    *               *     
        841 TTGAAGATTAATTGAAGATAATTTGAAGAA
          1 TTGAAGATCAATTGAAGATAATTTCAAGAA

                                *          
        871 TTGAAGA-CAATTGAAGAATTATTTCAAGAA
          1 TTGAAGATCAATTGAAG-ATAATTTCAAGAA

        901 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    8  0.31
  30   18  0.69

ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTGAAGATCAATTGAAGATAATTTCAAGAA

Found at i:2515 original size:26 final size:26

Alignment explanation


    Indices: 2486--2565  Score: 160
    Period size: 26  Copynumber: 3.1  Consensus size: 26

       2476 AAGTGAAAAT

                                      
       2486 CAAATTATTAAGAACAAGAATCTCCC
          1 CAAATTATTAAGAACAAGAATCTCCC

                                      
       2512 CAAATTATTAAGAACAAGAATCTCCC
          1 CAAATTATTAAGAACAAGAATCTCCC

                                      
       2538 CAAATTATTAAGAACAAGAATCTCCC
          1 CAAATTATTAAGAACAAGAATCTCCC

              
       2564 CA
          1 CA

       2566 TAAATCAAAT


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   54  1.00

ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23


Consensus pattern (26 bp):   
CAAATTATTAAGAACAAGAATCTCCC

Found at i:5939 original size:21 final size:21

Alignment explanation


    Indices: 5910--5958  Score: 53
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5900 CAGAATAGGT

                *    *     *     
       5910 TGGGGGCTGTGGCATGCGGCA
          1 TGGGCGCTGAGGCATACGGCA

                         *      *
       5931 TGGGCGCTGAGGCCTACGGCC
          1 TGGGCGCTGAGGCATACGGCA

                   
       5952 TGGGCGC
          1 TGGGCGC

       5959 CCAGCTGCCA


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.08, C:0.27, G:0.49, T:0.16


Consensus pattern (21 bp):   
TGGGCGCTGAGGCATACGGCA
Done.