Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017153.1 Corchorus olitorius cultivar O-4 contig17186, 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: 2583
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34


Found at i:553 original size:16 final size:15

Alignment explanation


    Indices: 528--588  Score: 61
    Period size: 16  Copynumber: 3.9  Consensus size: 15

        518 ATTTCCAAAA

                 *         *
        528 TTCTTATTTTCTTTAT
          1 TTCTTTTTTTCTTT-C

                            
        544 TTCTTTTTTT-TCTTC
          1 TTCTTTTTTTCT-TTC

                            
        559 TTCTTTTTTTTCTTTC
          1 TTC-TTTTTTTCTTTC

                   *      
        575 TTCTTTTCTTCTTT
          1 TTCTTTTTTTCTTT

        589 TGGGCGAGCC


Statistics
Matches: 39,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  15   14  0.36
  16   24  0.62
  17    1  0.03

ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79


Consensus pattern (15 bp):   
TTCTTTTTTTCTTTC

Found at i:565 original size:12 final size:11

Alignment explanation


    Indices: 536--589  Score: 54
    Period size: 12  Copynumber: 4.6  Consensus size: 11

        526 AATTCTTATT

                  *    
        536 TTCTTTATTTC
          1 TTCTTTTTTTC

              *         
        547 TTTTTTTTCTTC
          1 TTCTTTTT-TTC

                        
        559 TTCTTTTTTTTC
          1 TTC-TTTTTTTC

                  *     
        571 TTTCTTCTTTTC
          1 -TTCTTTTTTTC

                   
        583 TTCTTTT
          1 TTCTTTT

        590 GGGCGAGCCC


Statistics
Matches: 35,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
  11   12  0.34
  12   15  0.43
  13    8  0.23

ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80


Consensus pattern (11 bp):   
TTCTTTTTTTC

Found at i:572 original size:24 final size:24

Alignment explanation


    Indices: 543--589  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        533 ATTTTCTTTA

                      *              
        543 TTTCTTT-TTTTTCTTCTTCTTTTT
          1 TTTCTTTCTTCTT-TTCTTCTTTTT

                                   
        567 TTTCTTTCTTCTTTTCTTCTTTT
          1 TTTCTTTCTTCTTTTCTTCTTTT

        590 GGGCGAGCCC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   17  0.81
  25    4  0.19

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (24 bp):   
TTTCTTTCTTCTTTTCTTCTTTTT

Found at i:584 original size:8 final size:8

Alignment explanation


    Indices: 528--589  Score: 55
    Period size: 8  Copynumber: 8.2  Consensus size: 8

        518 ATTTCCAAAA

                 *  
        528 TTCTTATT
          1 TTCTTCTT

                     
        536 TTCTT-TAT
          1 TTCTTCT-T

                    
        544 TTCTT-TT
          1 TTCTTCTT

                    
        551 TT-TTCTT
          1 TTCTTCTT

                     
        558 CTTCTT-TT
          1 -TTCTTCTT

                    
        566 TT-TTC-T
          1 TTCTTCTT

                    
        572 TTCTTCTT
          1 TTCTTCTT

                    
        580 TTCTTCTT
          1 TTCTTCTT

              
        588 TT
          1 TT

        590 GGGCGAGCCC


Statistics
Matches: 47,  Mismatches: 0, Indels: 14
        0.77            0.00        0.23

Matches are distributed among these distances:
   6    7  0.15
   7   11  0.23
   8   27  0.57
   9    2  0.04

ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79


Consensus pattern (8 bp):   
TTCTTCTT
Done.