Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014502.1 Corchorus capsularis cultivar CVL-1 contig14523, 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: 31308
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:8752 original size:21 final size:21

Alignment explanation


    Indices: 8726--8776  Score: 84
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       8716 TCCCGCCGCC

                               * 
       8726 GTCCGACGATCAAGATGAGGT
          1 GTCCGACGATCAAGATGAGCT

                  *              
       8747 GTCCGATGATCAAGATGAGCT
          1 GTCCGACGATCAAGATGAGCT

                     
       8768 GTCCGACGA
          1 GTCCGACGA

       8777 GGCATTGATA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20


Consensus pattern (21 bp):   
GTCCGACGATCAAGATGAGCT

Found at i:18132 original size:35 final size:33

Alignment explanation


    Indices: 18074--18167  Score: 136
    Period size: 35  Copynumber: 2.8  Consensus size: 33

      18064 AAGAAGAAGA

                                             
      18074 AAACATGTGAA-TTATATTAAATTAAGATTAAG
          1 AAACATGTGAATTTATATTAAATTAAGATTAAG

                                               
      18106 AAACATGTGAATTGCTATATTAAATTAAGATTAAG
          1 AAACATGTGAATT--TATATTAAATTAAGATTAAG

              *                 *      
      18141 AATCATGTGAATTATATATTGAATTAA
          1 AAACATGTGAATT-TATATTAAATTAA

      18168 TTTCATTTCA


Statistics
Matches: 56,  Mismatches: 3, Indels: 4
        0.89            0.05        0.06

Matches are distributed among these distances:
  32   11  0.20
  33    1  0.02
  34   12  0.21
  35   32  0.57

ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36


Consensus pattern (33 bp):   
AAACATGTGAATTTATATTAAATTAAGATTAAG

Found at i:28570 original size:78 final size:78

Alignment explanation


    Indices: 28418--28572  Score: 186
    Period size: 78  Copynumber: 2.0  Consensus size: 78

      28408 AGGAGGCAAC

                                     *  *                         *    *     
      28418 TCGACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACTTGTATCTGTT
          1 TCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTT

            *   *        
      28483 TGCAGAAATCCTG
         66 CGCACAAATCCTG

                          *  *               *     *           *             
      28496 TCGACAATAGAAAGTCAGGGGTGGAAATAGCTCGTGGTGGCCCTATTGAAAGACCTG-AACATGT
          1 TCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TGT

               *         
      28560 TCGTACAAATCCT
         65 TCGCACAAATCCT

      28573 ATCTATGATA


Statistics
Matches: 64,  Mismatches: 12, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  77    2  0.03
  78   62  0.97

ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25


Consensus pattern (78 bp):   
TCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGTT
CGCACAAATCCTG
Done.