Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000692.1 Corchorus olitorius cultivar O-4 contig00692, 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: 13053
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--44  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

                                                                          
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
         43 AT
          1 AT

         45 TATGGACTTT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1968 original size:22 final size:21

Alignment explanation


    Indices: 1924--1969  Score: 56
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       1914 ACAATTCTAT

                        *   * *  
       1924 AATTATAAAAATTTAATAGAA
          1 AATTATAAAAATATAAGAAAA

                                  
       1945 AATTACTAAAAATATAAGAAAA
          1 AATTA-TAAAAATATAAGAAAA

               
       1967 AAT
          1 AAT

       1970 AATATTGATT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  21    5  0.24
  22   16  0.76

ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28


Consensus pattern (21 bp):   
AATTATAAAAATATAAGAAAA

Found at i:11367 original size:75 final size:75

Alignment explanation


    Indices: 11237--11477  Score: 220
    Period size: 75  Copynumber: 3.2  Consensus size: 75

      11227 AGGTTGCTAA

                           *              *           *         *            
      11237 TTCGAATTCAAATA-AAGAGTTTTCTGATGGTG-TTAGGCAAAATCTTGAAGATGATTCACCTTA
          1 TTCGAATTCAAATACTA-AGTTTTCTGATGATGATT-GGCAACATCTTGAAGTTGATTCACCTTA

                        
      11300 TCAGTTTCCTGT
         64 TCAGTTTCCTGT

              *                                *                       *     
      11312 TTTGAATTCAAATACTAAGTTTTCTGATGATGATTTGCAACATCTTGAAGTTGATTCACTTTATC
          1 TTCGAATTCAAATACTAAGTTTTCTGATGATGATTGGCAACATCTTGAAGTTGATTCACCTTATC

                  *   *
      11377 AGGTTTTC-GA
         66 A-GTTTCCTGT

                         ** *   **    *        *                      *   *  
      11387 TTCGAATTCAAATTTTGAG-CATCATAATGATGATAGGCAACATCTTGAAGTTGATTCTCCTAAT
          1 TTCGAATTCAAATACTAAGTTTTC-TGATGATGATTGGCAACATCTTGAAGTTGATTCACCTTAT

               ** *    
      11451 CAGGATGCTGT
         65 CAGTTTCCTGT

                     *      
      11462 TTCGAATTCTAATACT
          1 TTCGAATTCAAATACT

      11478 GAGCTTCCCA


Statistics
Matches: 133,  Mismatches: 28, Indels: 10
        0.78            0.16        0.06

Matches are distributed among these distances:
  74    5  0.04
  75  120  0.90
  76    8  0.06

ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39


Consensus pattern (75 bp):   
TTCGAATTCAAATACTAAGTTTTCTGATGATGATTGGCAACATCTTGAAGTTGATTCACCTTATC
AGTTTCCTGT

Found at i:11481 original size:75 final size:73

Alignment explanation


    Indices: 11270--11510  Score: 216
    Period size: 75  Copynumber: 3.2  Consensus size: 73

      11260 CTGATGGTGT

                   *         *                 *        *             *   *  
      11270 TAGGCAAAATCTTGAAGATGATTCACCTTATCAGTTTCCTGTTTTGAATTCAAATACTAAGTTTT
          1 TAGGCAACATCTTGAAGTTGATTCACCTTATCAG-GTCCTGTTTCGAATTCAAATACTGAG-CTT

                       
      11335 C-TGATGATGA
         64 CAT-ATGATGA

             **                       *         **   *             **     *  
      11345 TTTGCAACATCTTGAAGTTGATTCACTTTATCAGGTTTTCGATTCGAATTCAAATTTTGAGCATC
          1 TAGGCAACATCTTGAAGTTGATTCACCTTATCAGGTCCT-GTTTCGAATTCAAATACTGAGCTTC

                      
      11410 ATAATGATGA
         65 AT-ATGATGA

                                    *   *        *             *             
      11420 TAGGCAACATCTTGAAGTTGATTCTCCTAATCAGGATGCTGTTTCGAATTCTAATACTGAGCTTC
          1 TAGGCAACATCTTGAAGTTGATTCACCTTATCAGG-TCCTGTTTCGAATTCAAATACTGAGCTT-

                       
      11485 CCATA-GATGA
         64 -CATATGATGA

                      *     
      11495 TAGGCAACATTTTGAA
          1 TAGGCAACATCTTGAA

      11511 AATGTTATTG


Statistics
Matches: 132,  Mismatches: 29, Indels: 10
        0.77            0.17        0.06

Matches are distributed among these distances:
  74    4  0.03
  75  122  0.92
  76    3  0.02
  77    3  0.02

ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37


Consensus pattern (73 bp):   
TAGGCAACATCTTGAAGTTGATTCACCTTATCAGGTCCTGTTTCGAATTCAAATACTGAGCTTCA
TATGATGA

Found at i:12502 original size:20 final size:20

Alignment explanation


    Indices: 12477--12516  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      12467 AGCATTTAAG

                        *       
      12477 CCCATTTTTTAATTGGTGTT
          1 CCCATTTTTTAAGTGGTGTT

                                
      12497 CCCATTTTTTAAGTGGTGTT
          1 CCCATTTTTTAAGTGGTGTT

      12517 TACTAAATGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53


Consensus pattern (20 bp):   
CCCATTTTTTAAGTGGTGTT
Done.