Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023046.1 Corchorus olitorius cultivar O-4 contig23079, 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: 13054
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34


Found at i:3136 original size:39 final size:38

Alignment explanation


    Indices: 3066--3164  Score: 112
    Period size: 39  Copynumber: 2.6  Consensus size: 38

       3056 AATCAATTAA

                                  *   *            
       3066 TTTCCAAAATCTTCTTTTGGGACATCTTAAACTTTTATT
          1 TTTCCAAAATCTTCTTTT-GGAAATCCTAAACTTTTATT

                                                    
       3105 TTTCCAAAATCTTCTTTT-GAAATTACCTAAACTTTTA-T
          1 TTTCCAAAATCTTCTTTTGGAAA-T-CCTAAACTTTTATT

                 *  *   *         
       3143 TTTCCGAATTCTCCTTTTGGAA
          1 TTTCCAAAATCTTCTTTTGGAA

       3165 GTACTTAATT


Statistics
Matches: 52,  Mismatches: 5, Indels: 6
        0.83            0.08        0.10

Matches are distributed among these distances:
  37    3  0.06
  38   17  0.33
  39   32  0.62

ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47


Consensus pattern (38 bp):   
TTTCCAAAATCTTCTTTTGGAAATCCTAAACTTTTATT

Found at i:3971 original size:40 final size:42

Alignment explanation


    Indices: 3882--3973  Score: 109
    Period size: 41  Copynumber: 2.3  Consensus size: 42

       3872 ATAGTTTCTA

                                            *         
       3882 AAATCAGGGA-TCAAACTGAATCAAATAGTAACTAAAATCCT
          1 AAATCAGGGACTCAAACTGAATCAAATAGTAAATAAAATCCT

                            *  *    *               * 
       3923 AAATCAGGGACT-AAATTGCATCATATAGTAAAT-AAATCTT
          1 AAATCAGGGACTCAAACTGAATCAAATAGTAAATAAAATCCT

            *          
       3963 GAATCAGGGAC
          1 AAATCAGGGAC

       3974 CATGTTGAAC


Statistics
Matches: 44,  Mismatches: 6, Indels: 3
        0.83            0.11        0.06

Matches are distributed among these distances:
  40   16  0.36
  41   27  0.61
  42    1  0.02

ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24


Consensus pattern (42 bp):   
AAATCAGGGACTCAAACTGAATCAAATAGTAAATAAAATCCT

Found at i:4173 original size:17 final size:16

Alignment explanation


    Indices: 4132--4179  Score: 51
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       4122 CCAGATCCCT

                        **  
       4132 TTTTTTCTTCTTTTTC
          1 TTTTTTCTTCTTCCTC

                             
       4148 TTTTCTTCTTCTTCCTC
          1 TTTT-TTCTTCTTCCTC

                     *     
       4165 TTTATTTCTCCTTCC
          1 TTT-TTTCTTCTTCC

       4180 CCTAAACCCT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  16    4  0.15
  17   22  0.81
  18    1  0.04

ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69


Consensus pattern (16 bp):   
TTTTTTCTTCTTCCTC
Done.