Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002789.1 Corchorus capsularis cultivar CVL-1 contig02797, 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, 620

Length: 1034
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38


Found at i:901 original size:23 final size:23

Alignment explanation


    Indices: 873--953  Score: 92
    Period size: 23  Copynumber: 3.5  Consensus size: 23

        863 CTTCACTACG

                                   
        873 AAATTTTGATAAATCTTCCTATA
          1 AAATTTTGATAAATCTTCCTATA

                         *  *      
        896 AAATTTTGATAAACCTCCCTATA
          1 AAATTTTGATAAATCTTCCTATA

                         *     *   *
        919 AAATTTTAGATAACT-TTCTTATG
          1 AAATTTT-GATAAATCTTCCTATA

                *       
        942 AAATCTTGATAA
          1 AAATTTTGATAA

        954 CTACAAATTT


Statistics
Matches: 49,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  22    5  0.10
  23   39  0.80
  24    5  0.10

ACGTcount: A:0.40, C:0.14, G:0.06, T:0.41


Consensus pattern (23 bp):   
AAATTTTGATAAATCTTCCTATA

Found at i:1002 original size:23 final size:22

Alignment explanation


    Indices: 961--1003  Score: 59
    Period size: 23  Copynumber: 1.9  Consensus size: 22

        951 TAACTACAAA

                         *        
        961 TTTTGATAACCTCCCTATGATT
          1 TTTTGATAACCTCACTATGATT

                           *     
        983 TTTTGAATAACCTCATTATGA
          1 TTTTG-ATAACCTCACTATGA

       1004 AATTTTGTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  22    5  0.28
  23   13  0.72

ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44


Consensus pattern (22 bp):   
TTTTGATAACCTCACTATGATT

Found at i:1009 original size:23 final size:22

Alignment explanation


    Indices: 582--1034  Score: 167
    Period size: 22  Copynumber: 20.6  Consensus size: 22

        572 ATGATCCCAT

                               *  
        582 TATGAAATTTTGATAACCTTCC
          1 TATGAAATTTTGATAACCTCCC

                       *      *  * 
        604 TATGAAATTTTAATAACGAT-AC
          1 TATGAAATTTTGATAAC-CTCCC

                *        *     ***
        626 TATGGAATTTTGAGAACCTTTT
          1 TATGAAATTTTGATAACCTCCC

                        **      * *
        648 TAT-AAATTTTTTTTAACCTTCT
          1 TATGAAA-TTTTGATAACCTCCC

               *      * *         
        670 TATAAAATTTGGTTAACCTCCC
          1 TATGAAATTTTGATAACCTCCC

              * *                **
        692 TAAGGAATTTTGA-AGACCTCAA
          1 TATGAAATTTTGATA-ACCTCCC

                             * *  
        714 TATGAAATTTTGATAACTTTCC
          1 TATGAAATTTTGATAACCTCCC

            *                  * * 
        736 AATGAAATTTTGATAACCAACAC
          1 TATGAAATTTTGATAACC-TCCC

                 *  *            **
        759 TATGATATGTTGATAACCAT-GT
          1 TATGAAATTTTGATAACC-TCCC

                   *   * *  *    *
        781 TATGAAAATTTAAAAAGCTCCA
          1 TATGAAATTTTGATAACCTCCC

             *                * * * 
        803 TCTG-AATTGTT-AGTAATCACAC
          1 TATGAAATT-TTGA-TAACCTCCC

             *              * *    
        825 TCTGAAATTTTGATAATCACACC
          1 TATGAAATTTTGATAACCTC-CC

                     *       *  * 
        848 -ATGAAATTGTGATAACTTCAC
          1 TATGAAATTTTGATAACCTCCC

              *              *  *  
        869 TACGAAATTTTGATAAATCTTCC
          1 TATGAAATTTTGAT-AACCTCCC

               *                   
        892 TATAAAATTTTGATAAACCTCCC
          1 TATGAAATTTTGAT-AACCTCCC

               *              * * *
        915 TATAAAATTTTAGATAACTTTCT
          1 TATGAAATTTT-GATAACCTCCC

                    *             
        938 TATGAAATCTTGATAA-----C
          1 TATGAAATTTTGATAACCTCCC

               *                  
        955 TA-CAAATTTTGATAACCTCCC
          1 TATGAAATTTTGATAACCTCCC

                 **              **
        976 TATGATTTTTTGAATAACCTCAT
          1 TATGAAATTTTG-ATAACCTCCC

                        *   *     
        999 TATGAAATTTTGTTAATCTCCC
          1 TATGAAATTTTGATAACCTCCC

                          
       1021 TATGAAATTTTGAT
          1 TATGAAATTTTGAT


Statistics
Matches: 314,  Mismatches: 94, Indels: 46
        0.69            0.21        0.10

Matches are distributed among these distances:
  16   11  0.04
  17    2  0.01
  21   13  0.04
  22  191  0.61
  23   94  0.30
  24    3  0.01

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTCCC
Done.