Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009362.1 Corchorus olitorius cultivar O-4 contig09392, 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, 702

Length: 1171
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36


Found at i:434 original size:24 final size:24

Alignment explanation


    Indices: 396--688  Score: 353
    Period size: 24  Copynumber: 12.2  Consensus size: 24

        386 GACTCCTTGC

                                 *   
        396 ATCATTATCAGAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                    * *          *   
        420 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        444 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        468 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        492 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        516 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        540 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        564 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        588 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        612 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *          *   
        636 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        660 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                 
        684 ATCAT
          1 ATCAT

        689 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:514 original size:72 final size:72

Alignment explanation


    Indices: 417--688  Score: 490
    Period size: 72  Copynumber: 3.8  Consensus size: 72

        407 AACTTTCTGA

                         *                                                   
        417 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        482 TTTCATC
         66 TTTCATC

                       *        *                                            
        489 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        554 TTTCATC
         66 TTTCATC

                       *        *                                            
        561 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        626 TTTCATC
         66 TTTCATC

                         *                                          
        633 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT

        689 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:1025 original size:15 final size:15

Alignment explanation


    Indices: 1005--1035  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        995 AATTACAATG

                           
       1005 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

                           
       1020 ATCATAGTTAATGTT
          1 ATCATAGTTAATGTT

             
       1035 A
          1 A

       1036 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.