Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008518.1 Corchorus olitorius cultivar O-4 contig08545, 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: 2054
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:479 original size:9 final size:9

Alignment explanation


    Indices: 465--540  Score: 62
    Period size: 9  Copynumber: 7.8  Consensus size: 9

        455 CGACCGACAA

                     
        465 ATTATATAT
          1 ATTATATAT

                    * 
        474 ATTATATTTT
          1 ATTATA-TAT

            *         
        484 TTATATATAT
          1 AT-TATATAT

                      
        494 CATTATATAT
          1 -ATTATATAT

                        
        504 ATTAATATTAGT
          1 ATT-ATA-TA-T

                     
        516 ATTATATAT
          1 ATTATATAT

             *       
        525 AATATATAT
          1 ATTATATAT

            *      
        534 TTTATAT
          1 ATTATAT

        541 TAAAACCCTA


Statistics
Matches: 54,  Mismatches: 7, Indels: 12
        0.74            0.10        0.16

Matches are distributed among these distances:
   9   23  0.43
  10   17  0.31
  11   10  0.19
  12    4  0.07

ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57


Consensus pattern (9 bp):   
ATTATATAT

Found at i:606 original size:10 final size:10

Alignment explanation


    Indices: 591--616  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

        581 TTCCCTCTAG

                      
        591 CCTCTCGATT
          1 CCTCTCGATT

                      
        601 CCTCTCGATT
          1 CCTCTCGATT

                  
        611 CCTCTC
          1 CCTCTC

        617 TGTTTTTCTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.08, C:0.46, G:0.08, T:0.38


Consensus pattern (10 bp):   
CCTCTCGATT

Found at i:986 original size:24 final size:24

Alignment explanation


    Indices: 959--1037  Score: 113
    Period size: 24  Copynumber: 3.1  Consensus size: 24

        949 CCATAAATGA

                                    
        959 TTGGGATTTTGTTGTATCTCTGTT
          1 TTGGGATTTTGTTGTATCTCTGTT

                                        
        983 TTGGGATTTTGTTGTATGTATCTCTGTT
          1 TTGGGA--TT-TTGT-TGTATCTCTGTT

                       *            
       1011 TTGGGATTTTGCTGTATCTCTGTT
          1 TTGGGATTTTGTTGTATCTCTGTT

               
       1035 TTG
          1 TTG

       1038 CATTGAAGAG


Statistics
Matches: 50,  Mismatches: 1, Indels: 8
        0.85            0.02        0.14

Matches are distributed among these distances:
  24   21  0.42
  25    3  0.06
  26    4  0.08
  27    4  0.08
  28   18  0.36

ACGTcount: A:0.09, C:0.09, G:0.25, T:0.57


Consensus pattern (24 bp):   
TTGGGATTTTGTTGTATCTCTGTT

Found at i:1006 original size:28 final size:28

Alignment explanation


    Indices: 967--1027  Score: 106
    Period size: 28  Copynumber: 2.2  Consensus size: 28

        957 GATTGGGATT

                                        
        967 TTGT-TGTATCTCTGTTTTGGGATTTTG
          1 TTGTATGTATCTCTGTTTTGGGATTTTG

                                        
        994 TTGTATGTATCTCTGTTTTGGGATTTTG
          1 TTGTATGTATCTCTGTTTTGGGATTTTG

            *     
       1022 CTGTAT
          1 TTGTAT

       1028 CTCTGTTTTG


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  27    4  0.12
  28   28  0.88

ACGTcount: A:0.10, C:0.08, G:0.25, T:0.57


Consensus pattern (28 bp):   
TTGTATGTATCTCTGTTTTGGGATTTTG
Done.