Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000836.1 Corchorus capsularis cultivar CVL-1 contig00836, 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, 703

Length: 1173
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31


Found at i:307 original size:22 final size:22

Alignment explanation


    Indices: 257--334  Score: 88
    Period size: 22  Copynumber: 3.6  Consensus size: 22

        247 TCACATTCTG

                                * 
        257 AAAA-TTTGATAACCTCTTTCT
          1 AAAATTTTGATAACCTCTTTAT

            *                     
        278 GAAATTTTGATAACCTCTTTAT
          1 AAAATTTTGATAACCTCTTTAT

                     *   *         
        300 AAAATTTTGTTGATCC-CTTTAT
          1 AAAATTTTGAT-AACCTCTTTAT

                  *      
        322 AAAATTCTGATAA
          1 AAAATTTTGATAA

        335 TCAGATTATG


Statistics
Matches: 47,  Mismatches: 8, Indels: 4
        0.80            0.14        0.07

Matches are distributed among these distances:
  21    4  0.09
  22   40  0.85
  23    3  0.06

ACGTcount: A:0.35, C:0.14, G:0.08, T:0.44


Consensus pattern (22 bp):   
AAAATTTTGATAACCTCTTTAT

Found at i:393 original size:22 final size:23

Alignment explanation


    Indices: 338--400  Score: 76
    Period size: 22  Copynumber: 2.8  Consensus size: 23

        328 CTGATAATCA

                   *             * 
        338 GATTATGTAATTTTGATAACATC
          1 GATTATGAAATTTTGATAACAAC

             *     *               
        361 GCTT-TGGAATTTTGATAACAAC
          1 GATTATGAAATTTTGATAACAAC

                               
        383 -ATTATGAAATTTTGATAA
          1 GATTATGAAATTTTGATAA

        401 TCTTCCTATA


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  21    2  0.06
  22   29  0.85
  23    3  0.09

ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41


Consensus pattern (23 bp):   
GATTATGAAATTTTGATAACAAC

Found at i:439 original size:25 final size:22

Alignment explanation


    Indices: 385--484  Score: 82
    Period size: 21  Copynumber: 4.5  Consensus size: 22

        375 ATAACAACAT

                                  
        385 TATGAAATTTTGATAATCTTCC
          1 TATGAAATTTTGATAATCTTCC

                                     
        407 TAT-AAATTTTGATAATCTGATCTC
          1 TATGAAATTTTGATAATCT--TC-C

                *     *        *   
        431 TATGGAATTTCGATAATC-ACTC
          1 TATGAAATTTTGATAATCTTC-C

                 *          *     
        453 TATGAGA-TTTGATAACCTT-C
          1 TATGAAATTTTGATAATCTTCC

               *        
        473 TATTAAATTTTG
          1 TATGAAATTTTG

        485 GTACTCCTTA


Statistics
Matches: 62,  Mismatches: 10, Indels: 13
        0.73            0.12        0.15

Matches are distributed among these distances:
  20    6  0.10
  21   27  0.44
  22   11  0.18
  23    2  0.03
  24    4  0.06
  25   12  0.19

ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44


Consensus pattern (22 bp):   
TATGAAATTTTGATAATCTTCC

Found at i:536 original size:22 final size:22

Alignment explanation


    Indices: 368--646  Score: 71
    Period size: 22  Copynumber: 12.5  Consensus size: 22

        358 ATCGCTTTGG

                         **        
        368 AATTTTGATAA-CAACATTATGA
          1 AATTTTGATAACCTTCA-TATGA

                       *    *     
        390 AATTTTGATAATCTTCCTAT-A
          1 AATTTTGATAACCTTCATATGA

                       *       *    *
        411 AATTTTGATAATCTGATCTCTATGG
          1 AATTTTGATAACCT--TC-ATATGA

                 *                  
        436 AATTTCGATAATCAC-TC-TATGA
          1 AATTTTGATAA-C-CTTCATATGA

            *                   * 
        458 GA-TTTGATAACCTTC-TATTA
          1 AATTTTGATAACCTTCATATGA

                   *   *               
        478 AATTTTGGTACTCCTT-ATGAAATTGA
          1 AATTTTGATA-ACCTTCAT---A-TGA

              *                    
        504 GACTTTT-ATAACCTTCATATGA
          1 -AATTTTGATAACCTTCATATGA

                          *  *   * 
        526 AATTTTGATAACC-ACGCTATAA
          1 AATTTTGATAACCTTC-ATATGA

                          * **    
        548 AATTTTGATAACCTCCCCATGA
          1 AATTTTGATAACCTTCATATGA

               *           *  *    
        570 AATATT-AGTAACCTCCAAATGA
          1 AATTTTGA-TAACCTTCATATGA

                   *   *  *        
        592 AATTTTGTTAATC-ACACTATGA
          1 AATTTTGATAACCTTCA-TATGA

                              *     
        614 AATTCTT-ATAACC-TCGCTATGA
          1 AATT-TTGATAACCTTC-ATATGA

            *          
        636 CATTTTGATAA
          1 AATTTTGATAA

        647 TCTCTTTGAT


Statistics
Matches: 194,  Mismatches: 37, Indels: 52
        0.69            0.13        0.18

Matches are distributed among these distances:
  19    1  0.01
  20    8  0.04
  21   39  0.20
  22  105  0.54
  23    8  0.04
  24    6  0.03
  25   15  0.08
  26    6  0.03
  27    6  0.03

ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39


Consensus pattern (22 bp):   
AATTTTGATAACCTTCATATGA

Found at i:743 original size:24 final size:22

Alignment explanation


    Indices: 682--747  Score: 78
    Period size: 22  Copynumber: 2.9  Consensus size: 22

        672 TTGTGAAAAT

                  *            *  
        682 TAACCACCCTATGAAATTTCAA
          1 TAACCAACCTATGAAATTTTAA

                       *          
        704 TAACCAACCTAAGAAATTTTAA
          1 TAACCAACCTATGAAATTTTAA

                    *             
        726 TAACCTGATCCTATGAAATTTT
          1 TAACC--AACCTATGAAATTTT

        748 GGTAACCACA


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  22   24  0.65
  24   13  0.35

ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32


Consensus pattern (22 bp):   
TAACCAACCTATGAAATTTTAA
Done.