Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000025.1 Corchorus olitorius cultivar O-4 contig00025, 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, 957

Length: 1595
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37


Found at i:55 original size:23 final size:23

Alignment explanation


    Indices: 10--107  Score: 60
    Period size: 22  Copynumber: 4.2  Consensus size: 23

          1 CATAGTGTA

                *             **   
         10 GTTATCAAAA-TTTCATACAGAG
          1 GTTACCAAAATTTTCATAGGGAG

                                       
         32 GTTACCAAAATTTTCATAGGGAGGGAG
          1 GTTACCAAAATTTTCAT----AGGGAG

                           *         
         59 GTTACCAAAATTCGTGC-TA--GAG
          1 GTTACCAAAATT--TTCATAGGGAG

                *         *        
         81 GTTAACAAAATTTTTATAGGGAG
          1 GTTACCAAAATTTTCATAGGGAG

                
        104 GTTA
          1 GTTA

        108 TGAACATTTT


Statistics
Matches: 59,  Mismatches: 7, Indels: 19
        0.69            0.08        0.22

Matches are distributed among these distances:
  20    1  0.02
  21    2  0.03
  22   23  0.39
  23   13  0.22
  24    1  0.02
  27   16  0.27
  28    1  0.02
  29    2  0.03

ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31


Consensus pattern (23 bp):   
GTTACCAAAATTTTCATAGGGAG

Found at i:232 original size:44 final size:45

Alignment explanation


    Indices: 183--384  Score: 139
    Period size: 44  Copynumber: 4.5  Consensus size: 45

        173 GAGGTTATCG

                     *                                    
        183 AAATTTCATGGTGTGGTTATCAAAATTTTCATAGTGCAG-TTA-CC
          1 AAATTTCATAGTGTGGTTATCAAAATTTTCATAG-GCAGATTACCC

                   *          *    *                       *
        227 AAATTTTTATTTAGTGTGATTATTAAAATTTT-ATAGGCAGATTACCA
          1 AAA-TTTCA--TAGTGTGGTTATCAAAATTTTCATAGGCAGATTACCC

                    * *  * *     *               * *      
        274 AAATTTCACACTGAGCTTATCGAAA-TTTCATAGTG-TGGTTACCC
          1 AAATTTCATAGTGTGGTTATCAAAATTTTCATAG-GCAGATTACCC

                    *   *                      *  *   * *
        318 AAATTTCACAGTATGGTTATC-AAATTTTCATAGGAAGTTTATCG
          1 AAATTTCATAGTGTGGTTATCAAAATTTTCATAGGCAGATTACCC

                         *          
        362 AAATTTCATA-TGAGGTTATCAAA
          1 AAATTTCATAGTGTGGTTATCAAA

        385 TTTGCAAAAT


Statistics
Matches: 122,  Mismatches: 26, Indels: 20
        0.73            0.15        0.12

Matches are distributed among these distances:
  43   15  0.12
  44   65  0.53
  45    9  0.07
  46   11  0.09
  47   22  0.18

ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39


Consensus pattern (45 bp):   
AAATTTCATAGTGTGGTTATCAAAATTTTCATAGGCAGATTACCC

Found at i:276 original size:22 final size:23

Alignment explanation


    Indices: 203--279  Score: 70
    Period size: 22  Copynumber: 3.3  Consensus size: 23

        193 GTGTGGTTAT

                                    
        203 CAAAATTTTCATAGTGCAG-TTAC
          1 CAAAATTTT-ATAGTGCAGATTAC

                *             *     *
        226 CAAATTTTTATTTAGTG-TGATTAT
          1 CAAAATTTTA--TAGTGCAGATTAC

            *                      
        250 TAAAATTTTATAG-GCAGATTAC
          1 CAAAATTTTATAGTGCAGATTAC

                    
        272 CAAAATTT
          1 CAAAATTT

        280 CACACTGAGC


Statistics
Matches: 42,  Mismatches: 8, Indels: 9
        0.71            0.14        0.15

Matches are distributed among these distances:
  21    1  0.02
  22   16  0.38
  23    9  0.21
  24   16  0.38

ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42


Consensus pattern (23 bp):   
CAAAATTTTATAGTGCAGATTAC

Found at i:359 original size:22 final size:21

Alignment explanation


    Indices: 166--387  Score: 69
    Period size: 22  Copynumber: 10.0  Consensus size: 21

        156 AGTTTCATTC

                                   
        166 TCATAGAGAGGTTATCGAAA-TT
          1 TCATAG-GAGGTTATC-AAATTT

                *   *              
        188 TCATGGTGTGGTTATCAAAATTT
          1 TCATAG-GAGGTTATC-AAATTT

                           *       
        211 TCATAGTGCA-GTTACCAAATTT
          1 TCATAG-G-AGGTTATCAAATTT

             *        * *     *      
        233 TTATTTAGTGTGATTATTAAAATTT
          1 TCA--TAG-GAGGTTA-TCAAATTT

                      *   *    *  
        258 T-ATAGGCAGATTACCAAAATT
          1 TCATAGG-AGGTTATCAAATTT

               *  *   *            
        279 TCACACTGAGCTTATCGAAA-TT
          1 TCATA-GGAGGTTATC-AAATTT

                    *      *       
        301 TCATAGTGTGGTTACCCAAA-TT
          1 TCATAG-GAGGTTA-TCAAATTT

               *  *               
        323 TCACAGTATGGTTATCAAATTT
          1 TCATAGGA-GGTTATCAAATTT

                      *            
        345 TCATAGGAAGTTTATCGAAA-TT
          1 TCATAGG-AGGTTATC-AAATTT

                 *               
        367 TCATATGAGGTTATCAAATTT
          1 TCATAGGAGGTTATCAAATTT

        388 GCAAAATGTG


Statistics
Matches: 149,  Mismatches: 34, Indels: 35
        0.68            0.16        0.16

Matches are distributed among these distances:
  20    3  0.02
  21   20  0.13
  22   87  0.58
  23   23  0.15
  24    9  0.06
  25    7  0.05

ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39


Consensus pattern (21 bp):   
TCATAGGAGGTTATCAAATTT
Done.