Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005914.1 Corchorus olitorius cultivar O-4 contig05939, 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: 2862
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41


Found at i:578 original size:19 final size:19

Alignment explanation


    Indices: 551--640  Score: 76
    Period size: 19  Copynumber: 4.4  Consensus size: 19

        541 AGATTTTTTT

                *               
        551 TATTAATTTAACTA-TTATC
          1 TATTTATTT-ACTATTTATC

                               
        570 TATTTATTTACTATTTATC
          1 TATTTATTTACTATTTATC

                                      
        589 TTTTTATTTATTTTTAACTA-TTATC
          1 ----TATTTA--TTT-ACTATTTATC

                               
        614 TATTTATTTACTATTTATC
          1 TATTTATTTACTATTTATC

             *      
        633 TTTTTATT
          1 TATTTATT

        641 AATTTAGCTG


Statistics
Matches: 60,  Mismatches: 2, Indels: 18
        0.75            0.03        0.22

Matches are distributed among these distances:
  18    8  0.13
  19   28  0.47
  21    6  0.10
  23    6  0.10
  25    8  0.13
  26    4  0.07

ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64


Consensus pattern (19 bp):   
TATTTATTTACTATTTATC

Found at i:608 original size:44 final size:44

Alignment explanation


    Indices: 544--670  Score: 170
    Period size: 44  Copynumber: 2.9  Consensus size: 44

        534 ACCAAAAAGA

                                                          
        544 TTTTT-TTTATTAATTTAACTATTATCTATTTATTTACTATTTATC
          1 TTTTTATTTATT--TTTAACTATTATCTATTTATTTACTATTTATC

                                                        
        589 TTTTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATC
          1 TTTTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATC

                       *    *  *  *            *    
        633 TTTTTA-TTA-ATTTAGCTGTTGTCTATTTATTTATTATT
          1 TTTTTATTTATTTTTAACTATTATCTATTTATTTACTATT

        671 ATCCCTTTTT


Statistics
Matches: 76,  Mismatches: 5, Indels: 5
        0.88            0.06        0.06

Matches are distributed among these distances:
  42   24  0.32
  43    3  0.04
  44   38  0.50
  45    5  0.07
  46    6  0.08

ACGTcount: A:0.24, C:0.08, G:0.02, T:0.65


Consensus pattern (44 bp):   
TTTTTATTTATTTTTAACTATTATCTATTTATTTACTATTTATC

Found at i:612 original size:25 final size:27

Alignment explanation


    Indices: 556--623  Score: 79
    Period size: 25  Copynumber: 2.6  Consensus size: 27

        546 TTTTTTATTA

                 *        *        *   
        556 ATTTAACTA-TTATCTATTTATTTACT
          1 ATTTATCTATTTATTTATTTATTAACT

                    *                  
        582 ATTTATCTTTTTATTTATTT-TTAACT
          1 ATTTATCTATTTATTTATTTATTAACT

                             
        608 A-TTATCTATTTATTTA
          1 ATTTATCTATTTATTTA

        624 CTATTTATCT


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  25   14  0.39
  26   13  0.36
  27    9  0.25

ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63


Consensus pattern (27 bp):   
ATTTATCTATTTATTTATTTATTAACT

Found at i:736 original size:24 final size:23

Alignment explanation


    Indices: 708--762  Score: 65
    Period size: 23  Copynumber: 2.3  Consensus size: 23

        698 ATTATTCTCT

                    *      *   *  * 
        708 TATTTATCTATTATTTTCTGTATC
          1 TATTTATCAATTA-TCTCTATACC

                                   
        732 TATTTATCAATTATCTCTATACC
          1 TATTTATCAATTATCTCTATACC

                    
        755 TATTTATC
          1 TATTTATC

        763 CTTTTTTTTT


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  23   15  0.56
  24   12  0.44

ACGTcount: A:0.25, C:0.16, G:0.02, T:0.56


Consensus pattern (23 bp):   
TATTTATCAATTATCTCTATACC
Done.