Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021150.1 Corchorus olitorius cultivar O-4 contig21183, 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: 17232
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33


Found at i:9332 original size:29 final size:29

Alignment explanation


    Indices: 9300--9541  Score: 287
    Period size: 29  Copynumber: 8.4  Consensus size: 29

       9290 TAGAGCATTC

                         **              
       9300 AAAATGACCAAAACACCCCTGAAAGTGCA
          1 AAAATGACCAAAATGCCCCTGAAAGTGCA

                              *           
       9329 AAAATGACCAAAATGCCCATGAAAGTGCAA
          1 AAAATGACCAAAATGCCCCTGAAAGTGC-A

                 *                        
       9359 AAAATAACCAAAATGCCCCTGAACA-TGCA
          1 AAAATGACCAAAATGCCCCTGAA-AGTGCA

                      * *          *     
       9388 AAAATGACCAGAGTGCCCCTGAATGTGCA
          1 AAAATGACCAAAATGCCCCTGAAAGTGCA

                              *           
       9417 AAAATGACCAAAATGCCCTTGAATA-TGCA
          1 AAAATGACCAAAATGCCCCTGAA-AGTGCA

                 *                        
       9446 AAAATAACCAAAATGCCCCTGAATA-TGCA
          1 AAAATGACCAAAATGCCCCTGAA-AGTGCA

                 *                 *     
       9475 AAAATTACCAAAATGCCCCTG--TGTGCA
          1 AAAATGACCAAAATGCCCCTGAAAGTGCA

                          *      * *     
       9502 AAAATGACCAAAATACCCCTGGATGTGCA
          1 AAAATGACCAAAATGCCCCTGAAAGTGCA

                       
       9531 AAAATGACCAA
          1 AAAATGACCAA

       9542 TTAAGAAATA


Statistics
Matches: 187,  Mismatches: 19, Indels: 14
        0.85            0.09        0.06

Matches are distributed among these distances:
  27   23  0.12
  29  138  0.74
  30   25  0.13
  31    1  0.01

ACGTcount: A:0.45, C:0.24, G:0.15, T:0.16


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAAAGTGCA

Found at i:9474 original size:87 final size:87

Alignment explanation


    Indices: 9300--9541  Score: 328
    Period size: 88  Copynumber: 2.8  Consensus size: 87

       9290 TAGAGCATTC

                         **        *                                         
       9300 AAAATGACCAAAACACCCCTGAAAGTGCAAAAATGACCAAAATGCCCATGAA-AGTGCAAAAAAT
          1 AAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCATGAATA-TGC-AAAAAT

                                    
       9364 AACCAAAATGCCCCTGAACATGCA
         64 AACCAAAATGCCCCTGAACATGCA

                      * *                                  *                 
       9388 AAAATGACCAGAGTGCCCCTGAATGTGCAAAAATGACCAAAATGCCCTTGAATATGCAAAAATAA
          1 AAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCATGAATATGCAAAAATAA

                            *     
       9453 CCAAAATGCCCCTGAATATGCA
         66 CCAAAATGCCCCTGAACATGCA

                 *                                     *   *  *  *         * 
       9475 AAAATTACCAAAATGCCCCTG--TGTGCAAAAATGACCAAAATACCCCTGGATGTGCAAAAATGA
          1 AAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCATGAATATGCAAAAATAA

                
       9538 CCAA
         66 CCAA

       9542 TTAAGAAATA


Statistics
Matches: 138,  Mismatches: 15, Indels: 5
        0.87            0.09        0.03

Matches are distributed among these distances:
  85   41  0.30
  87   47  0.34
  88   49  0.36
  89    1  0.01

ACGTcount: A:0.45, C:0.24, G:0.15, T:0.16


Consensus pattern (87 bp):   
AAAATGACCAAAATGCCCCTGAATGTGCAAAAATGACCAAAATGCCCATGAATATGCAAAAATAA
CCAAAATGCCCCTGAACATGCA

Found at i:17138 original size:2 final size:2

Alignment explanation


    Indices: 17131--17172  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      17121 GTTATTATGG

                                                                          
      17131 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      17173 AAGAAAACTA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.