Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008158.1 Corchorus capsularis cultivar CVL-1 contig08179, 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: 13089
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27


Found at i:10677 original size:63 final size:61

Alignment explanation


    Indices: 10367--10708  Score: 272
    Period size: 63  Copynumber: 5.6  Consensus size: 61

      10357 CTCGTTCATC

                      *  *           *                      *                
      10367 TCAAATCCTGTTTTAGGTCTCTAGTTGAGAGTCTT-TTGTATCAA-TCTAAATC-CAGTTTCA-T
          1 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGT-TTCTTGT-TCAATTCAAAATCTC-G-TT-AGT

             
      10428 T
         61 T

                      **  *               *  *   *             *       **   
      10429 TCCAAATCCTAATTAAGGTCTCTAGTCGAGGGTCTCTAGTGTCAATTCAAAGTCTCGTTTCTAT
          1 T-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGT-TCAATTCAAAATCTCGTTAGT-T

                                                                          
      10493 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-T---TTCAAAATCGT-GTTAGTT
          1 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTCAATTCAAAATC-TCGTTAGTT

                      *       *                                        *   
      10550 TCAAATCCTGTTTGAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGTT
          1 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTG-TTCAA-TTCAAAATCTCGTTAGTT

                 *                                    *        *   *       
      10613 TCAAACCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTCTCGATTCCAAAGTCTTGTTAGTT
          1 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGT-TCAATT-CAAAATCTCGTTAGTT

              *   *     **        *           
      10676 TCTAATACTGCTAAAGGTCTCTGGTCGAG-GTTT
          1 TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT

      10709 GTCAATTCCA


Statistics
Matches: 228,  Mismatches: 36, Indels: 32
        0.77            0.12        0.11

Matches are distributed among these distances:
  57   37  0.16
  58   12  0.05
  59    2  0.01
  61    1  0.00
  62   10  0.04
  63  156  0.68
  64    9  0.04
  65    1  0.00

ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Consensus pattern (61 bp):   
TCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTCAATTCAAAATCTCGTTAGTT

Found at i:10714 original size:120 final size:118

Alignment explanation


    Indices: 10443--10720  Score: 278
    Period size: 120  Copynumber: 2.3  Consensus size: 118

      10433 AATCCTAATT

                            *                     *       *         *        
      10443 AAGGTCTCTAGTCGAGGGTCTCTAGTGTCAA-TTCAAAGTCTCGTTTCTATTCAAATCCTGCTTG
          1 AAGGTCTCTAGTCGAGAGT-TCT--TGTCAATTTCAAAATCTCGTTGCTATTCAAACCCTGCTTG

                                                             *   * *
      10507 AGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAATCGTGTTAGTTTCAAATCCTGTTT
         63 AGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAATCGTGTTAGTTTCAAATACTGCTA

            *    *                                         *                 
      10563 GAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATTTCAAAATCTCGTTGGT-TTCAAACCCTGCTTG
          1 AAGGTCTCTAGTCGAGAG-TTCTTG--TCAATTTCAAAATCTCGTTGCTATTCAAACCCTGCTTG

                                                 *  *          *          
      10627 AGGTCTCTAGTCGAGAGTTTCTTGTCTCGATTCCAAAGTCTTGTTAGTTTCTAATACTGCTA
         63 AGGTCTCTAGTCGAGAGTTTCTTG--T---TT-CAAAATCGTGTTAGTTTCAAATACTGCTA

                     *                    *    
      10689 AAGGTCTCTGGTCGAG-G-T-TTGTCAATTCCAAA
          1 AAGGTCTCTAGTCGAGAGTTCTTGTCAATTTCAAA

      10721 TCATGTTTCA


Statistics
Matches: 131,  Mismatches: 17, Indels: 20
        0.78            0.10        0.12

Matches are distributed among these distances:
 118    2  0.02
 120   70  0.53
 121   15  0.11
 122    4  0.03
 123    1  0.01
 125    3  0.02
 126   36  0.27

ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39


Consensus pattern (118 bp):   
AAGGTCTCTAGTCGAGAGTTCTTGTCAATTTCAAAATCTCGTTGCTATTCAAACCCTGCTTGAGG
TCTCTAGTCGAGAGTTTCTTGTTTCAAAATCGTGTTAGTTTCAAATACTGCTA
Done.