Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006507.1 Corchorus olitorius cultivar O-4 contig06532, 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, 723

Length: 1206
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--25  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

                                             
          1 AAG AAG AAG AAG AAG AAG AAG AAG A
          1 AAG AAG AAG AAG AAG AAG AAG AAG A

         26 GAAAAAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:90 original size:24 final size:23

Alignment explanation


    Indices: 63--109  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 23

         53 GCCGCTTGGG

                   *                
         63 CCAGGCCTGGCGCGGCCCAAGCGC
          1 CCAGGCCAGGCGCGGCCC-AGCGC

                           *       
         87 CCAGGCCAGGCGCGGGCCAGCGC
          1 CCAGGCCAGGCGCGGCCCAGCGC

        110 ATGGCCCAGC


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

Matches are distributed among these distances:
  23    5  0.24
  24   16  0.76

ACGTcount: A:0.13, C:0.45, G:0.40, T:0.02


Consensus pattern (23 bp):   
CCAGGCCAGGCGCGGCCCAGCGC

Found at i:123 original size:35 final size:36

Alignment explanation


    Indices: 76--157  Score: 123
    Period size: 36  Copynumber: 2.3  Consensus size: 36

         66 GGCCTGGCGC

                                                  
         76 GGCCCAAGCGCCCAGGCC-AG-GCGCGGGCCAGCGCAT
          1 GGCCC-AGCGCCCAGGCCTAGTGCGCGGGCCAGC-CAT

                              *                 
        112 GGCCCAGCGCCCAGGCCTGGTGCGCGGGCCAGCCAT
          1 GGCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCAT

                      
        148 GGCCCAGCGC
          1 GGCCCAGCGC

        158 TCAAGCTTGG


Statistics
Matches: 43,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  35   12  0.28
  36   19  0.44
  37   12  0.28

ACGTcount: A:0.13, C:0.43, G:0.39, T:0.05


Consensus pattern (36 bp):   
GGCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCAT

Found at i:1121 original size:28 final size:29

Alignment explanation


    Indices: 1063--1126  Score: 71
    Period size: 28  Copynumber: 2.3  Consensus size: 29

       1053 CTTAGGATGT

                            *   *      * 
       1063 TAAAATTA-CATATTTGCCCTTGGTCGGC
          1 TAAAATTACCATATTTACCCCTGGTCGAC

                                     *   
       1091 TAAAATTACCAT-TTTACCCCTGGTTGAC
          1 TAAAATTACCATATTTACCCCTGGTCGAC

                     
       1119 T-AAATTAC
          1 TAAAATTAC

       1127 AGTTTTGCCC


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  27    7  0.23
  28   21  0.68
  29    3  0.10

ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36


Consensus pattern (29 bp):   
TAAAATTACCATATTTACCCCTGGTCGAC
Done.