Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006923.1 Corchorus capsularis cultivar CVL-1 contig06944, 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: 22257
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:9329 original size:28 final size:26

Alignment explanation


    Indices: 9275--9329  Score: 65
    Period size: 28  Copynumber: 2.0  Consensus size: 26

       9265 TCATGGGATC

                         *        *   
       9275 TACTAATAATTTGTAAGTTGAAGATT
          1 TACTAATAATTTGAAAGTTGAACATT

                                  *     
       9301 TACTAATAGATTTGAAAGGTTGCACATT
          1 TACTAATA-ATTTGAAA-GTTGAACATT

             
       9329 T
          1 T

       9330 TTCTTCTTTC


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26    8  0.33
  27    7  0.29
  28    9  0.38

ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40


Consensus pattern (26 bp):   
TACTAATAATTTGAAAGTTGAACATT

Found at i:10091 original size:78 final size:78

Alignment explanation


    Indices: 9943--10095  Score: 202
    Period size: 78  Copynumber: 2.0  Consensus size: 78

       9933 GAGGCAAGTC

                                   *  *                              *     * 
       9943 GACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGTTTG
          1 GACAATAGAAAGCCAAGGGTGGACATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTTCG

                         
      10008 CAGAAATCCTGTT
         66 CAGAAATCCTGTT

                           *               *                  *              
      10021 GACAATAGAAAGCCAGGGGTGGACATAGCTCGTGGTTG-CCCTATTGAAAGACCTG-AACATGTT
          1 GACAATAGAAAGCCAAGGGTGGACATAGCTCATGG-TGACCCTATTGAAAAACCTGTAAC-TGTT

              *         
      10084 CGTAGAAATCCT
         64 CGCAGAAATCCT

      10096 ATCTATGATA


Statistics
Matches: 65,  Mismatches: 8, Indels: 4
        0.84            0.10        0.05

Matches are distributed among these distances:
  77    2  0.03
  78   61  0.94
  79    2  0.03

ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24


Consensus pattern (78 bp):   
GACAATAGAAAGCCAAGGGTGGACATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTTCG
CAGAAATCCTGTT

Found at i:21035 original size:12 final size:12

Alignment explanation


    Indices: 21018--21044  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      21008 CTGCAAATCT

                        
      21018 TATTTTCTGGTC
          1 TATTTTCTGGTC

                        
      21030 TATTTTCTGGTC
          1 TATTTTCTGGTC

               
      21042 TAT
          1 TAT

      21045 GTGGACGATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59


Consensus pattern (12 bp):   
TATTTTCTGGTC
Done.