Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008686.1 Corchorus olitorius cultivar O-4 contig08713, 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, 625

Length: 1042
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30


Found at i:170 original size:24 final size:24

Alignment explanation


    Indices: 97--223  Score: 105
    Period size: 24  Copynumber: 5.0  Consensus size: 24

         87 ACAAAAATTT

                                     
         97 TTTTTTCTTTTTATGACGCAAAAAC
          1 TTTTTT-TTTTTATGACGCAAAAAC

                          *               
        122 TCTTTTTTTTTTGAAGAAAATCGCAAAAAC
          1 T-TTTTTTTTTT-ATG---A-CGCAAAAAC

                               *    
        152 TTTTTTTTTTTATGACGCAGAAAC
          1 TTTTTTTTTTTATGACGCAAAAAC

            **                      
        176 AATTTTTTTTTATGACGCAAAAA-
          1 TTTTTTTTTTTATGACGCAAAAAC

                 *        *           
        199 TATATATTTTTTT-CGACGCAAAAAC
          1 T-T-TTTTTTTTTATGACGCAAAAAC

        224 AAACATATTT


Statistics
Matches: 83,  Mismatches: 10, Indels: 18
        0.75            0.09        0.16

Matches are distributed among these distances:
  24   38  0.46
  25   15  0.18
  26    7  0.08
  28    2  0.02
  29   11  0.13
  30   10  0.12

ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44


Consensus pattern (24 bp):   
TTTTTTTTTTTATGACGCAAAAAC

Found at i:249 original size:26 final size:25

Alignment explanation


    Indices: 156--249  Score: 79
    Period size: 24  Copynumber: 3.7  Consensus size: 25

        146 AAAAACTTTT

                                      *
        156 TTTTTTTATGACGCAGAAAC--A-ATT
          1 TTTTTTT-TGACGCA-AAACAAACATA

                                * *   
        180 TTTTTTTATGACGCAAAA-ATATATA
          1 TTTTTTT-TGACGCAAAACAAACATA

                   *                  
        205 TTTTTTTCGACGCAAAAACAAACATA
          1 TTTTTTTTGACGC-AAAACAAACATA

                               
        231 TTTTTTCTTGACGCAAAAC
          1 TTTTTT-TTGACGCAAAAC

        250 GCAAAACCCT


Statistics
Matches: 59,  Mismatches: 5, Indels: 10
        0.80            0.07        0.14

Matches are distributed among these distances:
  23    3  0.05
  24   21  0.36
  25   13  0.22
  26   16  0.27
  27    6  0.10

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39


Consensus pattern (25 bp):   
TTTTTTTTGACGCAAAACAAACATA

Found at i:738 original size:16 final size:15

Alignment explanation


    Indices: 700--741  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        690 ACAGAGATTG

                   *       
        700 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
        715 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        730 ACTAGAAAACAA
          1 AC-AGAAAACAA

        742 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.