Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022176.1 Corchorus olitorius cultivar O-4 contig22209, 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: 4405
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:119 original size:22 final size:24

Alignment explanation


    Indices: 62--120  Score: 68
    Period size: 24  Copynumber: 2.5  Consensus size: 24

         52 GCCATGCCAT

                *      *            
         62 ATATCAAAGAAGAAAGGAAACACG
          1 ATATAAAAGAAAAAAGGAAACACG

                *              *    
         86 ATATCAAAGAAAAAAGGAAGCAC-
          1 ATATAAAAGAAAAAAGGAAACACG

                         
        109 A-ATAAAAGAAAA
          1 ATATAAAAGAAAA

        121 TGGTAACATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  22   10  0.31
  23    1  0.03
  24   21  0.66

ACGTcount: A:0.64, C:0.10, G:0.17, T:0.08


Consensus pattern (24 bp):   
ATATAAAAGAAAAAAGGAAACACG

Found at i:997 original size:40 final size:40

Alignment explanation


    Indices: 862--1166  Score: 373
    Period size: 40  Copynumber: 7.7  Consensus size: 40

        852 TGAAATTGAC

                       *        *      *   *    *  *
        862 TGATAAAGCAAGGATCCTGAATAGGATACTGTAATTGA-C
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                       *        *               *  *
        901 TGATAAAGCAAGGATCCTGAATAGGATTCTGAAATTGA-C
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

             *                  **         *    * * 
        940 TAATAAAG-AATGATCCTGAACAGGATTCTGCAATTCACT
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                                                    
        979 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                                 * *    *           
       1019 TGATAAAGCAATGATCCTGAGCATGATTTTGAAATTAATT
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                   *                                
       1059 TGATAAAACAATGATCCTGAGTAGGATTCTGAAATTAATT
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                   *             *               *  
       1099 TGATAAAACAATGATCCTGAGCAGGATTCTGAAATTAGTT
          1 TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

                            *           
       1139 TGATAAAGCAATGATCATGAGTAGGATT
          1 TGATAAAGCAATGATCCTGAGTAGGATT

       1167 GACTGGTAAA


Statistics
Matches: 238,  Mismatches: 26, Indels: 3
        0.89            0.10        0.01

Matches are distributed among these distances:
  38   25  0.11
  39   51  0.21
  40  162  0.68

ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30


Consensus pattern (40 bp):   
TGATAAAGCAATGATCCTGAGTAGGATTCTGAAATTAATT

Found at i:2709 original size:7 final size:7

Alignment explanation


    Indices: 2697--2742  Score: 51
    Period size: 7  Copynumber: 6.9  Consensus size: 7

       2687 ATCTTATACT

                   
       2697 TTTTCAA
          1 TTTTCAA

                   
       2704 TTTTCAA
          1 TTTTCAA

                   
       2711 TTTTCAA
          1 TTTTCAA

            **     
       2718 GCTTC-A
          1 TTTTCAA

            *      
       2724 CTTTC-A
          1 TTTTCAA

                   
       2730 TTTTCAA
          1 TTTTCAA

                  
       2737 TTTTCA
          1 TTTTCA

       2743 CTTCTTTTTT


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
   6    9  0.27
   7   24  0.73

ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54


Consensus pattern (7 bp):   
TTTTCAA

Found at i:2759 original size:26 final size:26

Alignment explanation


    Indices: 2695--2758  Score: 78
    Period size: 26  Copynumber: 2.5  Consensus size: 26

       2685 CCATCTTATA

                                       
       2695 CTTTTTCAATTTTCAATTTTCAAGCTT
          1 CTTTTTC-ATTTTCAATTTTCAAGCTT

             **                       
       2722 CACTTTCATTTTCAATTTTC-A-CTT
          1 CTTTTTCATTTTCAATTTTCAAGCTT

                         
       2746 CTTTTTTCATTTT
          1 C-TTTTTCATTTT

       2759 TTTGTTTTTG


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  24    4  0.12
  25   10  0.31
  26   13  0.41
  27    5  0.16

ACGTcount: A:0.19, C:0.20, G:0.02, T:0.59


Consensus pattern (26 bp):   
CTTTTTCATTTTCAATTTTCAAGCTT

Found at i:2766 original size:6 final size:6

Alignment explanation


    Indices: 2757--2783  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       2747 TTTTTTCATT

                                           
       2757 TTTTTG TTTTTG TTTTTG TTTTTG TTT
          1 TTTTTG TTTTTG TTTTTG TTTTTG TTT

       2784 GTTTTTTTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85


Consensus pattern (6 bp):   
TTTTTG

Done.