Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005894.1 Corchorus olitorius cultivar O-4 contig05919, 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, 751

Length: 1252
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41


Found at i:48 original size:18 final size:17

Alignment explanation


    Indices: 2--49  Score: 51
    Period size: 18  Copynumber: 2.7  Consensus size: 17

          1 C

                        *     
          2 ATTTATAAATTAAATTAA
          1 ATTTAT-AATTATATTAA

              *   *           
         20 ATATATTATTATATTAAA
          1 ATTTATAATTATATT-AA

                        
         38 ATTTATAATTAT
          1 ATTTATAATTAT

         50 TTTACCGCAC


Statistics
Matches: 24,  Mismatches: 5, Indels: 2
        0.77            0.16        0.06

Matches are distributed among these distances:
  17    7  0.29
  18   17  0.71

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


Consensus pattern (17 bp):   
ATTTATAATTATATTAA

Found at i:186 original size:24 final size:25

Alignment explanation


    Indices: 159--205  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        149 AATACTTATA

                                     
        159 TTAATT-AAATTCTTAGGTATTTTT
          1 TTAATTCAAATTCTTAGGTATTTTT

                                   
        183 TTAATTCAAATTCTTAGGTATTT
          1 TTAATTCAAATTCTTAGGTATTT

        206 GTGCAAACGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (25 bp):   
TTAATTCAAATTCTTAGGTATTTTT

Found at i:541 original size:200 final size:205

Alignment explanation


    Indices: 287--682  Score: 685
    Period size: 200  Copynumber: 2.0  Consensus size: 205

        277 AAATAAATCG

                                                   *      *                  
        287 GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGATATTGATCTAATTTAATTTAATAAAT
          1 GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTAATTTAATAAAT

                        *                          *               *         
        352 CAACCACTAATGTTCAACTAA-TTTTTTTGGTATAG-TTCTATAT-AT-ATAACAGTAATGTGTT
         66 CAACCACTAATGCTCAACTAATTTTTTTTGGTATAGTTTATATATAATAATAACAATAATGTGTT

                                                                             
        413 GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTT-AAAAAATTAATAACATTCACCATT
        131 GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATTCACCATT

                      
        477 AAAAAAAACC
        196 AAAAAAAACC

                                                                             
        487 GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTAATTTAATAAAT
          1 GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTAATTTAATAAAT

                                         *                        *          
        552 CAACCACTAATGCTCAACTAATTTTTTTTTGTATAGTTTTATATATAATAATAATAATAATGTGT
         66 CAACCACTAATGCTCAACTAATTTTTTTTGGTATAG-TTTATATATAATAATAACAATAATGTGT

                                                                             
        617 TGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATTCACCAT
        130 TGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATTCACCAT

             
        682 T
        195 T

        683 GATAAAGTTA


Statistics
Matches: 183,  Mismatches: 7, Indels: 6
        0.93            0.04        0.03

Matches are distributed among these distances:
 200   83  0.45
 201   13  0.07
 203    7  0.04
 204    2  0.01
 205   54  0.30
 206   24  0.13

ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44


Consensus pattern (205 bp):   
GATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTTAATTTAATAAAT
CAACCACTAATGCTCAACTAATTTTTTTTGGTATAGTTTATATATAATAATAACAATAATGTGTT
GTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAAATTAATAACATTCACCATT
AAAAAAAACC
Done.