Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006524.1 Corchorus olitorius cultivar O-4 contig06549, 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, 714

Length: 1191
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                                                                       
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         41 CTAGTTTAAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:249 original size:21 final size:22

Alignment explanation


    Indices: 99--284  Score: 127
    Period size: 22  Copynumber: 8.5  Consensus size: 22

         89 TGAATATTTT

                                *  
         99 TATGAAATTTTGATAA-CTACCC
          1 TATGAAATTTTGATAACCT-TCC

               *            *  *   
        121 TATTAAATTTTGATAATC-ACGC
          1 TATGAAATTTTGATAACCTTC-C

                *    *            *
        143 TATGGAATTCTGATAA--TTACT
          1 TATGAAATTTTGATAACCTT-CC

                     *      *     
        164 TATGAAATTGTGATAAAC-TCC
          1 TATGAAATTTTGATAACCTTCC

                *               ** 
        185 ATATAAAATTTTGATAACCTAAC
          1 -TATGAAATTTTGATAACCTTCC

                       *           
        208 TATGAAATTTTAATAAACCTTCC
          1 TATGAAATTTTGAT-AACCTTCC

                                  
        231 TATGAAATTTTG-TAACCTTCC
          1 TATGAAATTTTGATAACCTTCC

                  *                
        252 TATG-ATTTTTGATAACC-TCTC
          1 TATGAAATTTTGATAACCTTC-C

                 *      
        273 TATGAGATTTTG
          1 TATGAAATTTTG

        285 TTAATTTCCT


Statistics
Matches: 129,  Mismatches: 23, Indels: 24
        0.73            0.13        0.14

Matches are distributed among these distances:
  20    8  0.06
  21   38  0.29
  22   64  0.50
  23   19  0.15

ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40


Consensus pattern (22 bp):   
TATGAAATTTTGATAACCTTCC

Found at i:610 original size:45 final size:45

Alignment explanation


    Indices: 546--636  Score: 146
    Period size: 45  Copynumber: 2.0  Consensus size: 45

        536 CAATCTAATT

                                *                        
        546 CGGTTGAGCTCTTATAGTATGATTATACGTTTAAAAATTCAACTC
          1 CGGTTGAGCTCTTATAGTATAATTATACGTTTAAAAATTCAACTC

                 *  *                        *           
        591 CGGTTTAGTTCTTATAGTATAATTATACGTTTACAAATTCAACTC
          1 CGGTTGAGCTCTTATAGTATAATTATACGTTTAAAAATTCAACTC

             
        636 C
          1 C

        637 TTTGAAAAAT


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   42  1.00

ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40


Consensus pattern (45 bp):   
CGGTTGAGCTCTTATAGTATAATTATACGTTTAAAAATTCAACTC

Found at i:1086 original size:2 final size:2

Alignment explanation


    Indices: 1079--1111  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1069 TTGGCCAATA

                                                             
       1079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1112 ACATAAAAGT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.