Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022919.1 Corchorus olitorius cultivar O-4 contig22952, 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, 992

Length: 1654
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29


Found at i:749 original size:23 final size:23

Alignment explanation


    Indices: 696--750  Score: 67
    Period size: 23  Copynumber: 2.4  Consensus size: 23

        686 AAAAACGCAA

                              *    
        696 AATTTTTTTTATGACGCAGAAAC
          1 AATTTTTTTTATGACGCAAAAAC

              **                   
        719 AAAATTTTTTATGACGCAAAAA-
          1 AATTTTTTTTATGACGCAAAAAC

            *         
        741 TATTTTTTTT
          1 AATTTTTTTT

        751 CTCGATGCAA


Statistics
Matches: 26,  Mismatches: 6, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  22    7  0.27
  23   19  0.73

ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45


Consensus pattern (23 bp):   
AATTTTTTTTATGACGCAAAAAC

Found at i:936 original size:30 final size:28

Alignment explanation


    Indices: 898--972  Score: 87
    Period size: 29  Copynumber: 2.5  Consensus size: 28

        888 TGAGTCTATT

                                         
        898 TTCCTTCCCCTAGCAAAAACCAGAAAAAG
          1 TTCCTTCCCC-AGCAAAAACCAGAAAAAG

                       *     *           
        927 TTCCATTCCCCGGCAAATACCAGAAAAAG
          1 TTCC-TTCCCCAGCAAAAACCAGAAAAAG

                        *    
        956 TTACCCTTCCCCGGCAA
          1 TT--CCTTCCCCAGCAA

        973 CGGCGCCAAA


Statistics
Matches: 41,  Mismatches: 2, Indels: 5
        0.85            0.04        0.10

Matches are distributed among these distances:
  29   22  0.54
  30   17  0.41
  31    2  0.05

ACGTcount: A:0.35, C:0.35, G:0.12, T:0.19


Consensus pattern (28 bp):   
TTCCTTCCCCAGCAAAAACCAGAAAAAG

Found at i:942 original size:29 final size:30

Alignment explanation


    Indices: 910--972  Score: 101
    Period size: 29  Copynumber: 2.1  Consensus size: 30

        900 CCTTCCCCTA

                                          
        910 GCAAAAACCAGAAAAAGTT-CCATTCCCCG
          1 GCAAAAACCAGAAAAAGTTACCATTCCCCG

                 *                *       
        939 GCAAATACCAGAAAAAGTTACCCTTCCCCG
          1 GCAAAAACCAGAAAAAGTTACCATTCCCCG

                
        969 GCAA
          1 GCAA

        973 CGGCGCCAAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  29   18  0.58
  30   13  0.42

ACGTcount: A:0.40, C:0.32, G:0.14, T:0.14


Consensus pattern (30 bp):   
GCAAAAACCAGAAAAAGTTACCATTCCCCG

Found at i:1184 original size:16 final size:15

Alignment explanation


    Indices: 1146--1187  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1136 ACAGAGATTG

                   *       
       1146 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1161 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1176 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1188 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.