Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000203.1 Corchorus olitorius cultivar O-4 contig00203, 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, 759

Length: 1265
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38


Found at i:269 original size:22 final size:22

Alignment explanation


    Indices: 225--437  Score: 121
    Period size: 22  Copynumber: 9.7  Consensus size: 22

        215 CACATTTTGC

                           *      
        225 AAATTT-GATAACCTGA-TATG
          1 AAATTTCGATAACCTCACTATG

                            *     
        245 AAATTTCGATAACCTCCCTATG
          1 AAATTTCGATAACCTCACTATG

               *   *      *       
        267 AAAATTCAATAACCACACTATG
          1 AAATTTCGATAACCTCACTATG

                  * *    **       
        289 AAATTTGGGTAACGACACTATG
          1 AAATTTCGATAACCTCACTATG

                        *    * *  
        311 AAATTTCGATAATCTCAGTGTG
          1 AAATTTCGATAACCTCACTATG

                  *     *         *
        333 AAATTTTGATAATCTGC-CTATA
          1 AAATTTCGATAACCT-CACTATG

                  **    * *         
        355 AAATTTTAATAATCACACTAAAT-
          1 AAATTTCGATAACCTCACT--ATG

               *    *     *       
        378 AAAATT-GGTAACCGCACTATG
          1 AAATTTCGATAACCTCACTATG

                   *       *   *   
        399 AAAATTTTGATAACCACACCATG
          1 -AAATTTCGATAACCTCACTATG

                 *          
        422 AAATTCCGATAACCTC
          1 AAATTTCGATAACCTC

        438 CATATGAGAA


Statistics
Matches: 148,  Mismatches: 36, Indels: 16
        0.74            0.18        0.08

Matches are distributed among these distances:
  20    8  0.05
  21    9  0.06
  22  111  0.75
  23   18  0.12
  24    2  0.01

ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31


Consensus pattern (22 bp):   
AAATTTCGATAACCTCACTATG

Found at i:516 original size:22 final size:22

Alignment explanation


    Indices: 473--533  Score: 61
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        463 CTCTCTATGT

                        *          
        473 ATTTTCGATAACATCTCCATAAA
          1 ATTTTC-ATAACCTCTCCATAAA

            *                      
        496 CTTTTCATAACCTC-CCTATAAA
          1 ATTTTCATAACCTCTCC-ATAAA

                 **         
        518 ATTTTGTTAACCTCTC
          1 ATTTTCATAACCTCTC

        534 TAGGAAATTT


Statistics
Matches: 31,  Mismatches: 5, Indels: 4
        0.77            0.12        0.10

Matches are distributed among these distances:
  21    2  0.06
  22   23  0.74
  23    6  0.19

ACGTcount: A:0.31, C:0.26, G:0.03, T:0.39


Consensus pattern (22 bp):   
ATTTTCATAACCTCTCCATAAA

Found at i:604 original size:22 final size:22

Alignment explanation


    Indices: 579--679  Score: 84
    Period size: 22  Copynumber: 4.6  Consensus size: 22

        569 CCCTCCCTAT

                     *             
        579 GAAATTTTGGTAACCT-CTGTAC
          1 GAAATTTTGATAACCTACT-TAC

                                  *
        601 GAAATTTTGATAA-CTACATTAT
          1 GAAATTTTGATAACCTAC-TTAC

               *         *        *
        623 GAAGTTTTGATAATCT-CTATAT
          1 GAAATTTTGATAACCTACT-TAC

                     *             
        645 GAAATTTTGGTAACCATAC-TAC
          1 GAAATTTTGATAACC-TACTTAC

                         
        667 GAAATTTTGATAA
          1 GAAATTTTGATAA

        680 TCTTTCTATG


Statistics
Matches: 65,  Mismatches: 8, Indels: 12
        0.76            0.09        0.14

Matches are distributed among these distances:
  21    3  0.05
  22   57  0.88
  23    4  0.06
  24    1  0.02

ACGTcount: A:0.36, C:0.12, G:0.14, T:0.39


Consensus pattern (22 bp):   
GAAATTTTGATAACCTACTTAC

Found at i:675 original size:44 final size:44

Alignment explanation


    Indices: 579--696  Score: 119
    Period size: 44  Copynumber: 2.7  Consensus size: 44

        569 CCCTCCCTAT

                     *   *    *  *              *   *  *
        579 GAAATTTTGGTAACCTCTGTACGAAATTTTGATAACTACATTAT
          1 GAAATTTTGATAATCTCTATATGAAATTTTGATAACCACACTAC

               *                           *      *     
        623 GAAGTTTTGATAATCTCTATATGAAATTTTGGTAACCATACTAC
          1 GAAATTTTGATAATCTCTATATGAAATTTTGATAACCACACTAC

                            * *    *      
        667 GAAATTTTGATAATCTTTCTATGTAATTTT
          1 GAAATTTTGATAATCTCTATATGAAATTTT

        697 AGTTTGATTG


Statistics
Matches: 60,  Mismatches: 14, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  44   60  1.00

ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42


Consensus pattern (44 bp):   
GAAATTTTGATAATCTCTATATGAAATTTTGATAACCACACTAC

Found at i:694 original size:22 final size:22

Alignment explanation


    Indices: 575--696  Score: 77
    Period size: 22  Copynumber: 5.5  Consensus size: 22

        565 ACCTCCCTCC

                         *   *  * 
        575 CTATGAAATTTTGGTAACCTCT
          1 CTATGAAATTTTGATAATCTTT

            *  *                 *
        597 GTACGAAATTTTGATAA-C-TA
          1 CTATGAAATTTTGATAATCTTT

                     *            * 
        617 CATTATGAAGTTTTGATAATCTCT
          1 C--TATGAAATTTTGATAATCTTT

            *            *   * * *
        641 ATATGAAATTTTGGTAACCATA
          1 CTATGAAATTTTGATAATCTTT

               *                  
        663 CTACGAAATTTTGATAATCTTT
          1 CTATGAAATTTTGATAATCTTT

                 *      
        685 CTATGTAATTTT
          1 CTATGAAATTTT

        697 AGTTTGATTG


Statistics
Matches: 71,  Mismatches: 25, Indels: 8
        0.68            0.24        0.08

Matches are distributed among these distances:
  21    1  0.01
  22   69  0.97
  23    1  0.01

ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43


Consensus pattern (22 bp):   
CTATGAAATTTTGATAATCTTT
Done.