Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006956.1 Corchorus olitorius cultivar O-4 contig06981, 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, 629

Length: 1049
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.32


Found at i:133 original size:26 final size:26

Alignment explanation


    Indices: 86--153  Score: 84
    Period size: 27  Copynumber: 2.6  Consensus size: 26

         76 CACACGCGAT

                 *           *         
         86 GTCACATGTGGAGGTGTCCG-TTGGAG
          1 GTCACGTGT-GAGGTGTACGTTTGGAG

                                       
        112 GTCACGTGTGAGGTCGTACGTTTGGAG
          1 GTCACGTGTGAGGT-GTACGTTTGGAG

                      *    
        139 GTCACGTGTGGGGTG
          1 GTCACGTGTGAGGTG

        154 CCAGCTGGTT


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    5  0.14
  26   13  0.35
  27   19  0.51

ACGTcount: A:0.13, C:0.15, G:0.44, T:0.28


Consensus pattern (26 bp):   
GTCACGTGTGAGGTGTACGTTTGGAG

Found at i:286 original size:23 final size:23

Alignment explanation


    Indices: 256--404  Score: 170
    Period size: 23  Copynumber: 6.8  Consensus size: 23

        246 CGTCGCGATA

                                   
        256 TGGAAGTGGTCGGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTT

                                * *
        279 TGGAAGTGGTCGG--G-C-GCTA
          1 TGGAAGTGGTCGGTCGCCAGGTT

                                   
        298 TGGAAGTGGTCGGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTT

                        *          
        321 TGGAAGTGGTCGATCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTT

                 *              * *
        344 TGGAAATGGTCGG--G-C-GCTA
          1 TGGAAGTGGTCGGTCGCCAGGTT

                       *           
        363 TGGAAGTGGTCAGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTT

                         *     
        386 TGGAAGTGGTCGGGCGCCA
          1 TGGAAGTGGTCGGTCGCCA

        405 AGCAATTGTG


Statistics
Matches: 103,  Mismatches: 15, Indels: 16
        0.77            0.11        0.12

Matches are distributed among these distances:
  19   28  0.27
  20    2  0.02
  21    4  0.04
  22    2  0.02
  23   67  0.65

ACGTcount: A:0.16, C:0.17, G:0.43, T:0.23


Consensus pattern (23 bp):   
TGGAAGTGGTCGGTCGCCAGGTT

Found at i:398 original size:42 final size:42

Alignment explanation


    Indices: 321--402  Score: 139
    Period size: 42  Copynumber: 2.0  Consensus size: 42

        311 TCGCCAGGTT

                                                      
        321 TGGAAGTGGTCGATCGCCAGGTTTGGAAATGGTCGGGCGCTA
          1 TGGAAGTGGTCGATCGCCAGGTTTGGAAATGGTCGGGCGCTA

                                         *           
        363 TGGAAGTGGTC-AGTCGCCAGGTTTGGAAGTGGTCGGGCGC
          1 TGGAAGTGGTCGA-TCGCCAGGTTTGGAAATGGTCGGGCGC

        403 CAAGCAATTG


Statistics
Matches: 38,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  41    1  0.03
  42   37  0.97

ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23


Consensus pattern (42 bp):   
TGGAAGTGGTCGATCGCCAGGTTTGGAAATGGTCGGGCGCTA

Found at i:404 original size:65 final size:65

Alignment explanation


    Indices: 256--404  Score: 262
    Period size: 65  Copynumber: 2.3  Consensus size: 65

        246 CGTCGCGATA

                                        *                        *           
        256 TGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGCTATGGAAGTGGTCGGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTTTGGAAATGGTCGGGCGCTATGGAAGTGGTCAGTCGCCAGGTT

                        *                                                    
        321 TGGAAGTGGTCGATCGCCAGGTTTGGAAATGGTCGGGCGCTATGGAAGTGGTCAGTCGCCAGGTT
          1 TGGAAGTGGTCGGTCGCCAGGTTTGGAAATGGTCGGGCGCTATGGAAGTGGTCAGTCGCCAGGTT

                         *     
        386 TGGAAGTGGTCGGGCGCCA
          1 TGGAAGTGGTCGGTCGCCA

        405 AGCAATTGTG


Statistics
Matches: 79,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  65   79  1.00

ACGTcount: A:0.16, C:0.17, G:0.43, T:0.23


Consensus pattern (65 bp):   
TGGAAGTGGTCGGTCGCCAGGTTTGGAAATGGTCGGGCGCTATGGAAGTGGTCAGTCGCCAGGTT
Done.