Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010258.1 Corchorus olitorius cultivar O-4 contig10290, 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, 984

Length: 1641
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38


Found at i:585 original size:44 final size:45

Alignment explanation


    Indices: 537--643  Score: 110
    Period size: 44  Copynumber: 2.4  Consensus size: 45

        527 TGACCACCTT

                            *   *            *            
        537 ATGAAATTTTGATAA-TTATCCTATGAAATTGTGATAAAC-TCCCA
          1 ATGAAATTTTGATAACCTA-ACTATGAAATTGTAATAAACATCCCA

                   **                     *          ** *
        581 ATGAAATACTGATAACCTAACTATGAAATTTTAATAAACATTTCT
          1 ATGAAATTTTGATAACCTAACTATGAAATTGTAATAAACATCCCA

                              
        626 ATGAAATTTTGATAACCT
          1 ATGAAATTTTGATAACCT

        644 CCATATGATT


Statistics
Matches: 50,  Mismatches: 11, Indels: 3
        0.78            0.17        0.05

Matches are distributed among these distances:
  44   30  0.60
  45   20  0.40

ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36


Consensus pattern (45 bp):   
ATGAAATTTTGATAACCTAACTATGAAATTGTAATAAACATCCCA

Found at i:680 original size:23 final size:23

Alignment explanation


    Indices: 624--702  Score: 83
    Period size: 23  Copynumber: 3.6  Consensus size: 23

        614 ATAAACATTT

                         *         
        624 CTATGAAA-TTTTGATAACCTCC
          1 CTATGAAATTTTTTATAACCTCC

            *     **               
        646 ATATGATTTTTTTTATAACCTCC
          1 CTATGAAATTTTTTATAACCTCC

                        *     *    
        669 CTATGAAATTTTAT-TAATCTCC
          1 CTATGAAATTTTTTATAACCTCC

                         
        691 CTAT-AAATTTTT
          1 CTATGAAATTTTT

        703 GATACCATAG


Statistics
Matches: 46,  Mismatches: 10, Indels: 3
        0.78            0.17        0.05

Matches are distributed among these distances:
  21    7  0.15
  22   16  0.35
  23   23  0.50

ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47


Consensus pattern (23 bp):   
CTATGAAATTTTTTATAACCTCC

Found at i:690 original size:22 final size:22

Alignment explanation


    Indices: 601--701  Score: 80
    Period size: 23  Copynumber: 4.5  Consensus size: 22

        591 GATAACCTAA

                           *   * **
        601 CTATGAAATTTTAATAAACATTT
          1 CTATGAAATTTT-ATTAACCTCC

                                   
        624 CTATGAAATTTTGA-TAACCTCC
          1 CTATGAAATTTT-ATTAACCTCC

            *     **    *          
        646 ATATGATTTTTTTTATAACCTCC
          1 CTATGAAATTTTAT-TAACCTCC

                             *    
        669 CTATGAAATTTTATTAATCTCC
          1 CTATGAAATTTTATTAACCTCC

                        
        691 CTAT-AAATTTT
          1 CTATGAAATTTT

        702 TGATACCATA


Statistics
Matches: 62,  Mismatches: 14, Indels: 6
        0.76            0.17        0.07

Matches are distributed among these distances:
  21    7  0.11
  22   24  0.39
  23   31  0.50

ACGTcount: A:0.34, C:0.16, G:0.05, T:0.46


Consensus pattern (22 bp):   
CTATGAAATTTTATTAACCTCC

Found at i:702 original size:22 final size:22

Alignment explanation


    Indices: 514--702  Score: 96
    Period size: 22  Copynumber: 8.5  Consensus size: 22

        504 TAAATATTTT

                       *  *   *  *
        514 TATGAAATTTTGATGACCACCT
          1 TATGAAATTTTTATAACCTCCC

                       *     *  *  
        536 TATGAAATTTTGATAA-TTATCC
          1 TATGAAATTTTTATAACCT-CCC

                     * *    *     
        558 TATGAAATTGTGATAAACTCCC
          1 TATGAAATTTTTATAACCTCCC

            *       ** *       ** 
        580 AATGAAATACTGATAACCTAAC
          1 TATGAAATTTTTATAACCTCCC

                       *      * ** 
        602 TATGAAATTTTAATAAACATTTC
          1 TATGAAATTTTTAT-AACCTCCC

                       *         *
        625 TATGAAATTTTGATAACCTCCA
          1 TATGAAATTTTTATAACCTCCC

                  **               
        647 TATGATTTTTTTTATAACCTCCC
          1 TATGA-AATTTTTATAACCTCCC

                             *     
        670 TATGAAA-TTTTATTAATCTCCC
          1 TATGAAATTTTTA-TAACCTCCC

                        
        692 TAT-AAATTTTT
          1 TATGAAATTTTT

        703 GATACCATAG


Statistics
Matches: 128,  Mismatches: 33, Indels: 12
        0.74            0.19        0.07

Matches are distributed among these distances:
  21    8  0.06
  22   83  0.65
  23   37  0.29

ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41


Consensus pattern (22 bp):   
TATGAAATTTTTATAACCTCCC

Found at i:1576 original size:43 final size:45

Alignment explanation


    Indices: 1528--1617  Score: 139
    Period size: 46  Copynumber: 2.0  Consensus size: 45

       1518 ATTTTAATAA

                                                         
       1528 TGGCAATTTTATATAT-TT-TAATAATGACAAAATTAAAATATAT
          1 TGGCAATTTTATATATGTTATAATAATGACAAAATTAAAATATAT

                                         *  *             
       1571 TGGCAATTTTATATATGTTAATAATAATGGCATAATTAAAATATAT
          1 TGGCAATTTTATATATGTT-ATAATAATGACAAAATTAAAATATAT

             
       1617 T
          1 T

       1618 TTAATAATAT


Statistics
Matches: 42,  Mismatches: 2, Indels: 3
        0.89            0.04        0.06

Matches are distributed among these distances:
  43   16  0.38
  44    2  0.05
  46   24  0.57

ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42


Consensus pattern (45 bp):   
TGGCAATTTTATATATGTTATAATAATGACAAAATTAAAATATAT

Done.