Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011518.1 Corchorus capsularis cultivar CVL-1 contig11539, 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: 2183
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34


Found at i:55 original size:25 final size:25

Alignment explanation


    Indices: 24--106  Score: 78
    Period size: 25  Copynumber: 3.1  Consensus size: 25

         14 TTACTATTAC

                                     
         24 CTTGACTCTGATTAATCTCTTCTTA
          1 CTTGACTCTGATTAATCTCTTCTTA

                          *     *         
         49 CTTGACTACTGATTTA-CTGATTACTATTA
          1 CTTGACT-CTGATTAATCT-CTT-C--TTA

                                    * 
         78 CCTTGACTCTGATTAATCTCTTCTCA
          1 -CTTGACTCTGATTAATCTCTTCTTA

               
        104 CTT
          1 CTT

        107 AATTACTGAT


Statistics
Matches: 46,  Mismatches: 5, Indels: 14
        0.71            0.08        0.22

Matches are distributed among these distances:
  25   12  0.26
  26   11  0.24
  27    1  0.02
  28    1  0.02
  29   12  0.26
  30    9  0.20

ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46


Consensus pattern (25 bp):   
CTTGACTCTGATTAATCTCTTCTTA

Found at i:85 original size:55 final size:55

Alignment explanation


    Indices: 1--128  Score: 229
    Period size: 55  Copynumber: 2.3  Consensus size: 55

                                                          *    *   
          1 ACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTCTTACTTGACT
          1 ACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTCTCACTTAACT

                                                                 * 
         56 ACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTCTCACTTAATT
          1 ACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTCTCACTTAACT

                              
        111 ACTGATTTACTGATTACT
          1 ACTGATTTACTGATTACT

        129 GTTCGGATTG


Statistics
Matches: 70,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  55   70  1.00

ACGTcount: A:0.25, C:0.21, G:0.09, T:0.45


Consensus pattern (55 bp):   
ACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTCTCACTTAACT

Found at i:89 original size:29 final size:29

Alignment explanation


    Indices: 2--91  Score: 109
    Period size: 29  Copynumber: 3.2  Consensus size: 29

          1 A

                                         
          2 CTGATTTACTGATTACTATTACCTTGACT
          1 CTGATTTACTGATTACTATTACCTTGACT

                  *     *                 
         31 CTGATTAATCT-CTT-C--TTA-CTTGACT
          1 CTGATTTA-CTGATTACTATTACCTTGACT

                                          
         56 ACTGATTTACTGATTACTATTACCTTGACT
          1 -CTGATTTACTGATTACTATTACCTTGACT

                  
         86 CTGATT
          1 CTGATT

         92 AATCTCTTCT


Statistics
Matches: 50,  Mismatches: 4, Indels: 14
        0.74            0.06        0.21

Matches are distributed among these distances:
  25    9  0.18
  26   12  0.24
  27    1  0.02
  28    1  0.02
  29   18  0.36
  30    9  0.18

ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46


Consensus pattern (29 bp):   
CTGATTTACTGATTACTATTACCTTGACT

Found at i:1108 original size:49 final size:49

Alignment explanation


    Indices: 986--1121  Score: 152
    Period size: 49  Copynumber: 2.8  Consensus size: 49

        976 ACTAATTACT

                             **   *   *      *               
        986 CTAAAAA-TCAATCTTTTGCTCTAAGGTGACATCTTTACTTACTAATCA
          1 CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA

                 **                                        * 
       1034 CTAAAGTTTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATTA
          1 CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA

                                           *         
       1083 CTAAAAATTCAATC-TTCTA-TCCAAAGATGGCATTTTTAC
          1 CTAAAAATTCAATCTTTC-ACT-CAAAGATGACATTTTTAC

       1122 AAAAAGCTTC


Statistics
Matches: 74,  Mismatches: 11, Indels: 5
        0.82            0.12        0.06

Matches are distributed among these distances:
  48    9  0.12
  49   65  0.88

ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38


Consensus pattern (49 bp):   
CTAAAAATTCAATCTTTCACTCAAAGATGACATTTTTACTTACTAATCA
Done.