Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000933.1 Corchorus capsularis cultivar CVL-1 contig00933, 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: 3892
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:3577 original size:31 final size:31

Alignment explanation


    Indices: 3542--3831  Score: 237
    Period size: 31  Copynumber: 9.5  Consensus size: 31

       3532 TATGGCCAAT

                                       *    
       3542 TGCTCAAATAAGGGCCTAACGTT-TGCCAAAA
          1 TGCTCAAATAAGGGCCTAACGTTAT-CGAAAA

                             *         *  **
       3573 TGCTCAAATAAGGGCCCGAAC-TT-T-TAATT
          1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA

                                *      *    
       3602 TGGC-CAAATAAGGGCCTAATGTTATCAAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA

                             * *       *  **
       3633 TGCTCAAATAAGGGCCCGATC-TT-T-TAATT
          1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA

                                            
       3662 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA

                       *       *      *    
       3693 TGCTCAAATAATGGCCTAATGTTATCAAAAA
          1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA

                             * *       *  **
       3724 TGCTCAAATAAGGGCCCGATC-TT-T-TAATT
          1 TGCTCAAATAAGGG-CCTAACGTTATCGAAAA

                           *                
       3753 TGGC-CAAATAAGGGTCTAACGTTATCGAAAA
          1 T-GCTCAAATAAGGGCCTAACGTTATCGAAAA

                                           
       3784 TGCTCAAATAAGGGCCTAACGTTATCGAAAA
          1 TGCTCAAATAAGGGCCTAACGTTATCGAAAA

                             
       3815 TGCTCAAATAAGGGCCT
          1 TGCTCAAATAAGGGCCT

       3832 GATGTCAGTT


Statistics
Matches: 204,  Mismatches: 37, Indels: 36
        0.74            0.13        0.13

Matches are distributed among these distances:
  28   11  0.05
  29   45  0.22
  30   17  0.08
  31  120  0.59
  32   11  0.05

ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26


Consensus pattern (31 bp):   
TGCTCAAATAAGGGCCTAACGTTATCGAAAA

Found at i:3617 original size:60 final size:60

Alignment explanation


    Indices: 3546--3708  Score: 265
    Period size: 60  Copynumber: 2.7  Consensus size: 60

       3536 GCCAATTGCT

                                   *                                     
       3546 CAAATAAGGGCCTAACGTT-TGCCAAAATGCTCAAATAAGGGCCCGAACTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTAT-CAAAAATGCTCAAATAAGGGCCCGAACTTTTAATTTGGC

                           *                              *             
       3606 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
          1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGAACTTTTAATTTGGC

                                  *               *    
       3666 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAATGGCC
          1 CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCC

       3709 TAATGTTATC


Statistics
Matches: 96,  Mismatches: 6, Indels: 2
        0.92            0.06        0.02

Matches are distributed among these distances:
  60   95  0.99
  61    1  0.01

ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25


Consensus pattern (60 bp):   
CAAATAAGGGCCTAACGTTATCAAAAATGCTCAAATAAGGGCCCGAACTTTTAATTTGGC

Found at i:3677 original size:29 final size:29

Alignment explanation


    Indices: 3577--3677  Score: 105
    Period size: 29  Copynumber: 3.4  Consensus size: 29

       3567 CCAAAATGCT

                           *             
       3577 CAAATAAGGGCCCGAACTTTTAATTTGGC
          1 CAAATAAGGGCCCGATCTTTTAATTTGGC

                        **  *     *  **    
       3606 CAAATAAGGGCCTAATGTTATCAAAAAT-GC
          1 CAAATAAGGGCCCGATCTT-T-TAATTTGGC

                                          
       3636 TCAAATAAGGGCCCGATCTTTTAATTTGGC
          1 -CAAATAAGGGCCCGATCTTTTAATTTGGC

                        
       3666 CAAATAAGGGCC
          1 CAAATAAGGGCC

       3678 TAACGTTATC


Statistics
Matches: 55,  Mismatches: 13, Indels: 8
        0.72            0.17        0.11

Matches are distributed among these distances:
  29   30  0.55
  30    6  0.11
  31   19  0.35

ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26


Consensus pattern (29 bp):   
CAAATAAGGGCCCGATCTTTTAATTTGGC

Found at i:3702 original size:91 final size:91

Alignment explanation


    Indices: 3606--3830  Score: 414
    Period size: 91  Copynumber: 2.5  Consensus size: 91

       3596 TTAATTTGGC

                                                                             
       3606 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAT
          1 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAT

                                      
       3671 AAGGGCCTAACGTTATCGAAAATGCT
         66 AAGGGCCTAACGTTATCGAAAATGCT

                   *                                                         
       3697 CAAATAATGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAT
          1 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAT

                 *                    
       3762 AAGGGTCTAACGTTATCGAAAATGCT
         66 AAGGGCCTAACGTTATCGAAAATGCT

                           *      *                    
       3788 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCC
          1 CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCC

       3831 TGATGTCAGT


Statistics
Matches: 129,  Mismatches: 5, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  91  129  1.00

ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26


Consensus pattern (91 bp):   
CAAATAAGGGCCTAATGTTATCAAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAAT
AAGGGCCTAACGTTATCGAAAATGCT
Done.