Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015790.1 Corchorus olitorius cultivar O-4 contig15823, 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, 1000

Length: 3697
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32


Found at i:234 original size:22 final size:22

Alignment explanation


    Indices: 185--314  Score: 93
    Period size: 22  Copynumber: 5.9  Consensus size: 22

        175 TGATAATCAA

                     *     **  *  
        185 ACCAAAATTACATAGAAAGATT
          1 ACCAAAATTTCATAGTGAGGTT

             *         *     *    
        207 ATCAAAATTTCGTAGTGTGGTT
          1 ACCAAAATTTCATAGTGAGGTT

                       *           
        229 ACCAAAATTTCCTA-TAGAGGTT
          1 ACCAAAATTTCATAGT-GAGGTT

             *     *               
        251 ATCAAAACTTCATAGTGTA-GTT
          1 ACCAAAATTTCATAGTG-AGGTT

             *    *       **      
        273 ATCAAAGTTTCATACAGAGGTT
          1 ACCAAAATTTCATAGTGAGGTT

                           *    
        295 ACCAAAATTTCATAGGGAGG
          1 ACCAAAATTTCATAGTGAGG

        315 GAGGTTACCA


Statistics
Matches: 83,  Mismatches: 21, Indels: 8
        0.74            0.19        0.07

Matches are distributed among these distances:
  21    2  0.02
  22   79  0.95
  23    2  0.02

ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31


Consensus pattern (22 bp):   
ACCAAAATTTCATAGTGAGGTT

Found at i:253 original size:44 final size:44

Alignment explanation


    Indices: 185--309  Score: 142
    Period size: 44  Copynumber: 2.8  Consensus size: 44

        175 TGATAATCAA

                     *    * *  *             *      *   
        185 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
          1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT

                       *  *              *              
        229 ACCAAAATTTCCTATAGAGGTTATCAAAACTTCATAGTGTAGTT
          1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT

             *    *                *             
        273 ATCAAAGTTTCATACAGAGGTTACCAAAATTTCATAG
          1 ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAG

        310 GGAGGGAGGT


Statistics
Matches: 67,  Mismatches: 14, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  44   67  1.00

ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32


Consensus pattern (44 bp):   
ACCAAAATTTCATACAGAGGTTATCAAAATTTCATAGTGTAGTT

Found at i:404 original size:22 final size:23

Alignment explanation


    Indices: 335--405  Score: 85
    Period size: 22  Copynumber: 3.2  Consensus size: 23

        325 AAATTTGTGC

                        **         
        335 TTATCAAAATTTCCTA-GAGAGG
          1 TTATCAAAATTTTATAGGAGAGG

               *                   
        357 TTAACAAAATTTTATAGG-GAGG
          1 TTATCAAAATTTTATAGGAGAGG

                *                  
        379 TTATGAAAATTTTAT-GGAGAGG
          1 TTATCAAAATTTTATAGGAGAGG

                 
        401 TTATC
          1 TTATC

        406 GAAGATACAT


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  21    2  0.05
  22   38  0.93
  23    1  0.02

ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35


Consensus pattern (23 bp):   
TTATCAAAATTTTATAGGAGAGG

Found at i:565 original size:22 final size:22

Alignment explanation


    Indices: 540--661  Score: 120
    Period size: 22  Copynumber: 5.5  Consensus size: 22

        530 TATAGGCAGA

                            *  *  
        540 TTATCAAAATTTCACACTGAGG
          1 TTATCAAAATTTCACAGTGTGG

                 *        *       
        562 TTATCGAAATTTCATAGTGTGG
          1 TTATCAAAATTTCACAGTGTGG

               * *                
        584 TTACCCAAATTTCACAGTGTGG
          1 TTATCAAAATTTCACAGTGTGG

                    *        * *  
        606 TTATCAAATTTTCACAGGGAGG
          1 TTATCAAAATTTCACAGTGTGG

                           * *     
        628 TTATC-AAATTTGCAAAATGTGG
          1 TTATCAAAATTT-CACAGTGTGG

                   *    
        650 TTATCAATATTT
          1 TTATCAAAATTT

        662 TTACATTGGA


Statistics
Matches: 80,  Mismatches: 18, Indels: 3
        0.79            0.18        0.03

Matches are distributed among these distances:
  21    5  0.06
  22   70  0.88
  23    5  0.06

ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37


Consensus pattern (22 bp):   
TTATCAAAATTTCACAGTGTGG

Found at i:619 original size:44 final size:43

Alignment explanation


    Indices: 470--662  Score: 133
    Period size: 44  Copynumber: 4.3  Consensus size: 43

        460 TTCCATGGTA

                                   *             *   *    
        470 TGGTTATCAAAATTTTCATAGTGTGGTTACC-AATTTTATTTAGTG
          1 TGGTTATC-AAATTTTCATAGTGAGGTTACCAAATTTCA--CAGTG

              *     *                 *     *          *  
        515 TGATTATTAAAATTTT-ATAG-GCAGATTATCAAAATTTCACACTG
          1 TGGTTA-TCAAATTTTCATAGTG-AGGTTA-CCAAATTTCACAGTG

            *                      *                     
        559 AGGTTATCGAAA-TTTCATAGTGTGGTTACCCAAATTTCACAGTG
          1 TGGTTATC-AAATTTTCATAGTGAGGTTA-CCAAATTTCACAGTG

                             *  *       *          * *  
        603 TGGTTATCAAATTTTCACAGGGAGGTTATCAAATTTGCAAAATG
          1 TGGTTATCAAATTTTCATAGTGAGGTTACCAAATTT-CACAGTG

                            
        647 TGGTTATCAATATTTT
          1 TGGTTATCAA-ATTTT

        663 TACATTGGAG


Statistics
Matches: 115,  Mismatches: 23, Indels: 20
        0.73            0.15        0.13

Matches are distributed among these distances:
  43   15  0.13
  44   74  0.64
  45   19  0.17
  46    7  0.06

ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40


Consensus pattern (43 bp):   
TGGTTATCAAATTTTCATAGTGAGGTTACCAAATTTCACAGTG
Done.