Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019151.1 Corchorus olitorius cultivar O-4 contig19184, 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: 9749
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1132 original size:24 final size:23

Alignment explanation


    Indices: 1097--1156  Score: 65
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       1087 TTCCTAACTG

                                    
       1097 TTTATATCAATATATC-CTTTTTT
          1 TTTATATCAATA-ATCACTTTTTT

                                    
       1120 TTTATATCAAATAATCAC--TTTT
          1 TTTATATC-AATAATCACTTTTTT

            *               
       1142 ATTA-ATCAATAATCA
          1 TTTATATCAATAATCA

       1157 GAGATTACAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 7
        0.81            0.02        0.17

Matches are distributed among these distances:
  20    8  0.24
  21    3  0.09
  22    7  0.21
  23   11  0.32
  24    5  0.15

ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50


Consensus pattern (23 bp):   
TTTATATCAATAATCACTTTTTT

Found at i:8503 original size:22 final size:22

Alignment explanation


    Indices: 8461--8516  Score: 67
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       8451 TATTTTTATT

                                 *
       8461 AAATTTTGATAACCACACTATG
          1 AAATTTTGATAACCACACTATA

                        **  *     
       8483 AAATTTTGATAATTACCCTATA
          1 AAATTTTGATAACCACACTATA

                 *      
       8505 AAATTCTGATAA
          1 AAATTTTGATAA

       8517 ACTCCCAAAT


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   29  1.00

ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36


Consensus pattern (22 bp):   
AAATTTTGATAACCACACTATA

Found at i:8833 original size:22 final size:22

Alignment explanation


    Indices: 8728--8914  Score: 114
    Period size: 22  Copynumber: 8.5  Consensus size: 22

       8718 ACATAGTTTT

                              * * 
       8728 ACTATGAAATTTTGATAATCTC
          1 ACTATGAAATTTTGATAACCAC

            *       *     *      * 
       8750 GCTAT-ATTATTTTTATAACCTC
          1 ACTATGA-AATTTTGATAACCAC

                 *      *        * 
       8772 -CTTAAGAAATTGTGATAACCTC
          1 AC-TATGAAATTTTGATAACCAC

            *     *  *   *     *  
       8794 CCTATGGAACTTTAATAACTAC
          1 ACTATGAAATTTTGATAACCAC

                       *           
       8816 ACTATGAAATTCTGATAACCATC
          1 ACTATGAAATTTTGATAACCA-C

                          * *     
       8839 -CTATGAAATTTTGGTCACCAC
          1 ACTATGAAATTTTGATAACCAC

               *                  
       8860 ACTCTGAAATTTTGATAACCAC
          1 ACTATGAAATTTTGATAACCAC

             *                   * 
       8882 AGTAT-AAATTTATGATAACCTC
          1 ACTATGAAATTT-TGATAACCAC

                        
       8904 TA-TATGAAATT
          1 -ACTATGAAATT

       8915 AATTTTAATG


Statistics
Matches: 126,  Mismatches: 30, Indels: 17
        0.73            0.17        0.10

Matches are distributed among these distances:
  21    9  0.07
  22  108  0.86
  23    9  0.07

ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36


Consensus pattern (22 bp):   
ACTATGAAATTTTGATAACCAC

Found at i:9143 original size:22 final size:22

Alignment explanation


    Indices: 8983--9171  Score: 112
    Period size: 22  Copynumber: 8.5  Consensus size: 22

       8973 GATTTGGTAG

                        *     *  *
       8983 ACTATGAAATTTGGATAATCAA
          1 ACTATGAAATTTTGATAACCAC

                                * 
       9005 ACTATGAAATTTTGATAACCTC
          1 ACTATGAAATTTTGATAACCAC

            *     *   *        ** 
       9027 CCTATGGAATGTTGATAACTTC
          1 ACTATGAAATTTTGATAACCAC

            *    *          *   * * 
       9049 CCTATAAAATTTACTGTTAATCTC
          1 ACTATGAAATTT--TGATAACCAC

                              *   
       9073 ACTATGAAATTTTGATAAACAC
          1 ACTATGAAATTTTGATAACCAC

             * *  *  *      *    *
       9095 AATTTGGAACTTTGATTACC-T
          1 ACTATGAAATTTTGATAACCAC

            *                      
       9116 TCTATGAAATCTTTG-TAACCAC
          1 ACTATGAAAT-TTTGATAACCAC

             *               **   
       9138 ATTATGAAATTTTGATAGTCAC
          1 ACTATGAAATTTTGATAACCAC

                        
       9160 ACTATGAAATTT
          1 ACTATGAAATTT

       9172 CAATAATCTA


Statistics
Matches: 124,  Mismatches: 38, Indels: 10
        0.72            0.22        0.06

Matches are distributed among these distances:
  21   13  0.10
  22   94  0.76
  24   17  0.14

ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38


Consensus pattern (22 bp):   
ACTATGAAATTTTGATAACCAC

Found at i:9454 original size:12 final size:12

Alignment explanation


    Indices: 9437--9463  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       9427 GGTCAAGACT

                        
       9437 TTAAATTTATAA
          1 TTAAATTTATAA

                        
       9449 TTAAATTTATAA
          1 TTAAATTTATAA

               
       9461 TTA
          1 TTA

       9464 TTTTCTATTT


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:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (12 bp):   
TTAAATTTATAA
Done.