Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008993.1 Corchorus capsularis cultivar CVL-1 contig09014, 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: 4092
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34


Found at i:1604 original size:21 final size:21

Alignment explanation


    Indices: 1573--1641  Score: 84
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1563 TCTTTACTGA

                        *         
       1573 TTACTCTTTACTAATTACCATT
          1 TTACTC-TTACTGATTACCATT

              **             *   
       1595 TTGGTCTTACTGATTACTATT
          1 TTACTCTTACTGATTACCATT

                              *  
       1616 TTACTCTTACTGATTACCTTT
          1 TTACTCTTACTGATTACCATT

                 
       1637 TTACT
          1 TTACT

       1642 GATTATTATT


Statistics
Matches: 39,  Mismatches: 8, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  21   35  0.90
  22    4  0.10

ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52


Consensus pattern (21 bp):   
TTACTCTTACTGATTACCATT

Found at i:1884 original size:34 final size:33

Alignment explanation


    Indices: 1844--1970  Score: 121
    Period size: 34  Copynumber: 3.7  Consensus size: 33

       1834 TTTGATTTTT

                                              
       1844 TTAATTACTGACTTTACTGATTAATCTTTTTTAC
          1 TTAATTACTGA-TTTACTGATTAATCTTTTTTAC

                          *       * *    *  *    
       1878 TTAATTACTGATTTGCTGATTACTATTACCTTGACTC
          1 TTAATTACTGATTTACTGATTAATCTT--TTTTA--C

                      *                        
       1915 TTAATTA-TCAATTTACTGATTAATCTCTTTTTAC
          1 TTAATTACT-GATTTACTGATTAATCT-TTTTTAC

            *                     
       1949 ATAATTACTGATTTACTGATTA
          1 TTAATTACTGATTTACTGATTA

       1971 CCATTACTTT


Statistics
Matches: 73,  Mismatches: 13, Indels: 14
        0.73            0.13        0.14

Matches are distributed among these distances:
  33   13  0.18
  34   30  0.41
  35    4  0.05
  36    4  0.05
  37   21  0.29
  38    1  0.01

ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50


Consensus pattern (33 bp):   
TTAATTACTGATTTACTGATTAATCTTTTTTAC

Found at i:1934 original size:70 final size:73

Alignment explanation


    Indices: 1856--1993  Score: 219
    Period size: 71  Copynumber: 1.9  Consensus size: 73

       1846 AATTACTGAC

                                   *             *        *                  
       1856 TTTACTGATTAATCT-TTTTTACTTAATTACTGATTTGCTGATTACTATTACCTTGAC-T-CTTA
          1 TTTACTGATTAATCTCTTTTTACATAATTACTGATTTACTGATTACCATTACCTTGACTTCCTTA

                    
       1918 ATTATCAA
         66 ATTATCAA

                                                                *            
       1926 TTTACTGATTAATCTCTTTTTACATAATTACTGATTTACTGATTACCATTACTTTGACTTCCTTA
          1 TTTACTGATTAATCTCTTTTTACATAATTACTGATTTACTGATTACCATTACCTTGACTTCCTTA

               
       1991 ATT
         66 ATT

       1994 CTTTTACTCT


Statistics
Matches: 61,  Mismatches: 4, Indels: 3
        0.90            0.06        0.04

Matches are distributed among these distances:
  70   15  0.25
  71   38  0.62
  72    1  0.02
  73    7  0.11

ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50


Consensus pattern (73 bp):   
TTTACTGATTAATCTCTTTTTACATAATTACTGATTTACTGATTACCATTACCTTGACTTCCTTA
ATTATCAA

Done.