Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002690.1 Corchorus olitorius cultivar O-4 contig02692, 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, 669

Length: 1116
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38


Found at i:182 original size:24 final size:24

Alignment explanation


    Indices: 144--436  Score: 353
    Period size: 24  Copynumber: 12.2  Consensus size: 24

        134 GACTCCTTGC

                                 *   
        144 ATCATTATCAGAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                    * *          *   
        168 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        192 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        216 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        240 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        264 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        288 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        312 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        336 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        360 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *          *   
        384 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        408 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                 
        432 ATCAT
          1 ATCAT

        437 AACCACTTGT


Statistics
Matches: 235,  Mismatches: 27, Indels: 14
        0.85            0.10        0.05

Matches are distributed among these distances:
  23    3  0.01
  24  228  0.97
  25    4  0.02

ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40


Consensus pattern (24 bp):   
ATCATTATCAGAACTTTCATCTAA

Found at i:262 original size:72 final size:72

Alignment explanation


    Indices: 165--436  Score: 490
    Period size: 72  Copynumber: 3.8  Consensus size: 72

        155 AACTTTCTGA

                         *                                                   
        165 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        230 TTTCATC
         66 TTTCATC

                       *        *                                            
        237 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        302 TTTCATC
         66 TTTCATC

                       *        *                                            
        309 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        374 TTTCATC
         66 TTTCATC

                         *                                          
        381 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT

        437 AACCACTTGT


Statistics
Matches: 194,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  72  194  1.00

ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40


Consensus pattern (72 bp):   
TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
TTTCATC

Found at i:773 original size:15 final size:15

Alignment explanation


    Indices: 753--783  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        743 AATTACAATG

                           
        753 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

                           
        768 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

             
        783 A
          1 A

        784 ATGTTAACTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45


Consensus pattern (15 bp):   
ATCATAGTTAATGTT
Done.