Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013767.1 Corchorus capsularis cultivar CVL-1 contig13788, 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: 2991
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37


Found at i:729 original size:23 final size:23

Alignment explanation


    Indices: 703--770  Score: 56
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        693 TTAATAAATC

                                   
        703 TAATCTTTCATGGTACCAATCAA
          1 TAATCTTTCATGGTACCAATCAA

                **  **       *     
        726 TAATAATTGTTGGTA--GA-C--
          1 TAATCTTTCATGGTACCAATCAA

                                   
        744 TAATCTTTCATGGTACCAATCAA
          1 TAATCTTTCATGGTACCAATCAA

                
        767 TAAT
          1 TAAT

        771 AATTGTTGGT


Statistics
Matches: 30,  Mismatches: 10, Indels: 10
        0.60            0.20        0.20

Matches are distributed among these distances:
  18   11  0.37
  20    2  0.07
  21    2  0.07
  23   15  0.50

ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37


Consensus pattern (23 bp):   
TAATCTTTCATGGTACCAATCAA

Found at i:759 original size:41 final size:41

Alignment explanation


    Indices: 702--785  Score: 168
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        692 CTTAATAAAT

                                                     
        702 CTAATCTTTCATGGTACCAATCAATAATAATTGTTGGTAGA
          1 CTAATCTTTCATGGTACCAATCAATAATAATTGTTGGTAGA

                                                     
        743 CTAATCTTTCATGGTACCAATCAATAATAATTGTTGGTAGA
          1 CTAATCTTTCATGGTACCAATCAATAATAATTGTTGGTAGA

              
        784 CT
          1 CT

        786 GCTCTTATTT


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  41   43  1.00

ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37


Consensus pattern (41 bp):   
CTAATCTTTCATGGTACCAATCAATAATAATTGTTGGTAGA

Found at i:931 original size:46 final size:46

Alignment explanation


    Indices: 881--974  Score: 152
    Period size: 46  Copynumber: 2.0  Consensus size: 46

        871 AACCTTTGAA

                          *             *    *            
        881 TGAAAAGTGAGAGTCATTAATTTAGTATTATCCTAAATTATTATTT
          1 TGAAAAGTGAGAGTAATTAATTTAGTATCATCCCAAATTATTATTT

                 *                                        
        927 TGAAATGTGAGAGTAATTAATTTAGTATCATCCCAAATTATTATTT
          1 TGAAAAGTGAGAGTAATTAATTTAGTATCATCCCAAATTATTATTT

              
        973 TG
          1 TG

        975 GGTGAGTGAA


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  46   44  1.00

ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43


Consensus pattern (46 bp):   
TGAAAAGTGAGAGTAATTAATTTAGTATCATCCCAAATTATTATTT

Found at i:1988 original size:31 final size:31

Alignment explanation


    Indices: 1945--2042  Score: 106
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       1935 AAAAAGTCGT

                *                      *   
       1945 GCCATATGTACCAAAAAGTGACACATGTCAC
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                                    *     *
       1976 GCCACATGTACCAAAAAGTGACACGTGGCAT
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                     **      *  *   *     *
       2007 GCCACATGTTTCAAAAATTGGCACGTGGCAT
          1 GCCACATGTACCAAAAAGTGACACATGGCAC

                 
       2038 GCCAC
          1 GCCAC

       2043 GTGCACAAAA


Statistics
Matches: 59,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   59  1.00

ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19


Consensus pattern (31 bp):   
GCCACATGTACCAAAAAGTGACACATGGCAC
Done.