Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007326.1 Corchorus olitorius cultivar O-4 contig07351, 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, 772

Length: 1288
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38


Found at i:82 original size:34 final size:36

Alignment explanation


    Indices: 5--109  Score: 144
    Period size: 34  Copynumber: 3.0  Consensus size: 36

          1 TACT

                               *  *              
          5 AAACTCTTTCATCTATG-TTTGGTGCCAAAAAAAAAA
          1 AAACTCTTTCATCTATGCTATGCTGCC-AAAAAAAAA

                                             *  
         41 AAACTCTTTCATCTATGCTAT-C-GCCAAAAAATAA
          1 AAACTCTTTCATCTATGCTATGCTGCCAAAAAAAAA

              *                                
         75 AATCTCTTTCATCTATGCTATGCTGCCAAAAAAAA
          1 AAACTCTTTCATCTATGCTATGCTGCCAAAAAAAA

        110 CTTTCATCTA


Statistics
Matches: 61,  Mismatches: 5, Indels: 6
        0.85            0.07        0.08

Matches are distributed among these distances:
  34   28  0.46
  35    4  0.07
  36   27  0.44
  37    2  0.03

ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30


Consensus pattern (36 bp):   
AAACTCTTTCATCTATGCTATGCTGCCAAAAAAAAA

Found at i:116 original size:30 final size:30

Alignment explanation


    Indices: 35--120  Score: 95
    Period size: 34  Copynumber: 2.7  Consensus size: 30

         25 GGTGCCAAAA

                                           
         35 AAAAAAAAACTCTTTCATCTATGCTATCGCC
          1 AAAAAAAAA-TCTTTCATCTATGCTATCGCC

                                                
         66 AAAAAATAAAATCTCTTTCATCTATGCTATGCTGCC
          1 -AAAAA-AAAA--TCTTTCATCTATGCTAT-C-GCC

                                 
        102 -AAAAAAAA-CTTTCATCTAT
          1 AAAAAAAAATCTTTCATCTAT

        121 TACTAATTGA


Statistics
Matches: 50,  Mismatches: 0, Indels: 10
        0.83            0.00        0.17

Matches are distributed among these distances:
  30   11  0.22
  32    5  0.10
  33    8  0.16
  34   22  0.44
  35    1  0.02
  36    3  0.06

ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31


Consensus pattern (30 bp):   
AAAAAAAAATCTTTCATCTATGCTATCGCC

Found at i:609 original size:139 final size:142

Alignment explanation


    Indices: 344--624  Score: 311
    Period size: 139  Copynumber: 2.0  Consensus size: 142

        334 TTGTACGTAT

                         *           *    *             *                    
        344 CCCACCAAAATTATTAAAAGCTCTAGTCTACTTTCTTTTAGGGTTGAAATAACTATACCATCTTT
          1 CCCACCAAAATTACTAAAAGCTCTAATCTAATTTCTTTTAGGGTAGAAATAACTATACCATCTTT

                  * *  *            *      *   **   *       *  **   *     ** 
        409 GTCTTTTCTCCTATGTATTTAAGAGTTATAATAGCGTTTATTAATAAGTCCGGATTGAACGGGTT
         66 GTCTTTCCCCCCATGTATTTAAGAATTATAACAGCACTTACTAATAAGCCCAAATTCAACGGACT

                        
        474 TATTCATGTGTA
        131 TATTCATGTGTA

                *                              *                             
        486 CCCATCAAAATTACTAAAAGCT-TCAATC-AATTTTTTTTAGGGTAGAAATAACTAT-CCTAT-T
          1 CCCACCAAAATTACTAAAAGCTCT-AATCTAATTTCTTTTAGGGTAGAAATAACTATACC-ATCT

                          *                     *                            
        547 TTGT-TTTCCCCCCGTGTATTTAAGAATTATAACAGTACTTACTAATAAGCCCAAATTCAACGGA
         64 TTGTCTTTCCCCCCATGTATTTAAGAATTATAACAGCACTTACTAATAAGCCCAAATTCAACGGA

                          
        611 CTTATTCATGTGTA
        129 CTTATTCATGTGTA

        625 AACTCATGGC


Statistics
Matches: 115,  Mismatches: 22, Indels: 7
        0.80            0.15        0.05

Matches are distributed among these distances:
 139   58  0.50
 140    7  0.06
 141   27  0.23
 142   23  0.20

ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38


Consensus pattern (142 bp):   
CCCACCAAAATTACTAAAAGCTCTAATCTAATTTCTTTTAGGGTAGAAATAACTATACCATCTTT
GTCTTTCCCCCCATGTATTTAAGAATTATAACAGCACTTACTAATAAGCCCAAATTCAACGGACT
TATTCATGTGTA

Found at i:1152 original size:13 final size:13

Alignment explanation


    Indices: 1134--1158  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1124 TTAGAATTCC

                         
       1134 AAATAATATTTAT
          1 AAATAATATTTAT

                        
       1147 AAATAATATTTA
          1 AAATAATATTTA

       1159 GAACATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT
Done.