Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022329.1 Corchorus olitorius cultivar O-4 contig22362, 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: 3219
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29


Found at i:2620 original size:34 final size:32

Alignment explanation


    Indices: 2551--2693  Score: 101
    Period size: 33  Copynumber: 4.3  Consensus size: 32

       2541 ATGATCAACC

                                    ** *   * 
       2551 AAAACAGATTTGTTTTCATCACAATTAGCA-TT
          1 AAAACAGATTTG-TTTCATCACAAACAACACCT

                                              
       2583 AAAAACAGAATTTGTTTCATCACAAACAACACCT
          1 -AAAACAG-ATTTGTTTCATCACAAACAACACCT

                          *     *            
       2617 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
          1 AAAACAGATTT-GTTTCATCACAAACAACACCT

                **  *      *       *  *    *  
       2649 CAAATTAGGTTTAGTATCATCACTAATAACATCT
          1 -AAAACAGATTT-GTTTCATCACAAACAACACCT

                       
       2683 AAAACAGATTT
          1 AAAACAGATTT

       2694 CATGTCATTG


Statistics
Matches: 89,  Mismatches: 16, Indels: 10
        0.77            0.14        0.09

Matches are distributed among these distances:
  32    6  0.07
  33   75  0.84
  34    8  0.09

ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29


Consensus pattern (32 bp):   
AAAACAGATTTGTTTCATCACAAACAACACCT

Found at i:2621 original size:33 final size:33

Alignment explanation


    Indices: 2584--2713  Score: 113
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       2574 ATTAGCATTA

                           *                  
       2584 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT

                                *            
       2617 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

                **  *      *       *  *    *  
       2649 CAAATTAGGTTTAGTATCATCACTAATAACATCT
          1 -AAAACAGATTTAGTGTCATCACAAACAACACCT

                                **          
       2683 AAAACAGATTTCA-TGTCATTGCAAACAACAC
          1 AAAACAGATTT-AGTGTCATCACAAACAACAC

       2714 TCAAATTAGG


Statistics
Matches: 75,  Mismatches: 18, Indels: 8
        0.74            0.18        0.08

Matches are distributed among these distances:
  32    6  0.08
  33   66  0.88
  34    3  0.04

ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26


Consensus pattern (33 bp):   
AAAACAGATTTAGTGTCATCACAAACAACACCT

Found at i:2670 original size:66 final size:66

Alignment explanation


    Indices: 2599--2725  Score: 202
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       2589 AGAATTTGTT

                                                                             
       2599 TCATCACAAACAACACCTAAAACAGATTT-AGTGTCATCGCAAACAACACTCAAATTAGGTTTAG
          1 TCATCACAAACAACACCTAAAACAGATTTCA-TGTCATCGCAAACAACACTCAAATTAGGTTTAG

              
       2663 TA
         65 TA

                   *  *    *                     *                       
       2665 TCATCACTAATAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATTAGGTT
          1 TCATCACAAACAACACCTAAAACAGATTTCATGTCATCGCAAACAACACTCAAATTAGGTT

       2726 CAGAATTACT


Statistics
Matches: 56,  Mismatches: 4, Indels: 2
        0.90            0.06        0.03

Matches are distributed among these distances:
  66   55  0.98
  67    1  0.02

ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAGATTTCATGTCATCGCAAACAACACTCAAATTAGGTTTAGT
A
Done.