Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000314.1 Corchorus olitorius cultivar O-4 contig00314, 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, 773

Length: 1289
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36


Found at i:299 original size:50 final size:50

Alignment explanation


    Indices: 175--300  Score: 193
    Period size: 50  Copynumber: 2.5  Consensus size: 50

        165 CGATCAATTT

                   *                  *                         
        175 CTTTGAATTGT-TCTCCAA-TCTAATATTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCT-TCCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATC

                         *                                    
        225 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
          1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

                                      
        275 CTTTGAACTGTCTTCCAATTCAATCT
          1 CTTTGAACTGTCTTCCAATTCAATCT

        301 CGAGAAAACC


Statistics
Matches: 70,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  50   67  0.96
  51    3  0.04

ACGTcount: A:0.25, C:0.26, G:0.11, T:0.37


Consensus pattern (50 bp):   
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC

Found at i:649 original size:64 final size:64

Alignment explanation


    Indices: 459--738  Score: 366
    Period size: 64  Copynumber: 4.4  Consensus size: 64

        449 TCTAAATAGC

                      * *                                      *   *  *      
        459 CGTCTTCCGACCCACTTCTG-AAACTTTTCCGAGAAACCATCTTCTGGTGTGCTTTTTAACAAGA
          1 CGTCTTCCGATCAACTTCTGAAAACTTTT--GAGAAACCATCTTCTGGTGTACTTCTTGACAAGA

             
        523 T
         64 T

                      * *    *           *    *           *   *             
        524 CGTCTTCCGACCGACTTTTGAAAA-TTTTAAGAATCCATCTTCTGGCGTAGTTCTTGACAAGAT
          1 CGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT

                                      *                                     
        587 CGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT
          1 CGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT

             *               **     *                                       
        651 CATCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT
          1 CGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT

             *                      
        715 CATCTTCCGATCAACTTCTGAAAA
          1 CGTCTTCCGATCAACTTCTGAAAA

        739 TTCTTTCTAG


Statistics
Matches: 189,  Mismatches: 24, Indels: 5
        0.87            0.11        0.02

Matches are distributed among these distances:
  63   49  0.26
  64  115  0.61
  65   22  0.12
  66    3  0.02

ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34


Consensus pattern (64 bp):   
CGTCTTCCGATCAACTTCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT

Found at i:851 original size:54 final size:55

Alignment explanation


    Indices: 717--871  Score: 242
    Period size: 54  Copynumber: 2.8  Consensus size: 55

        707 GACAAGATCA

                  *                                                 
        717 TCTTCCGATCAAC-TTCTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTG
          1 TCTTCCAATCAACATT-TGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTG

                                               *             *     
        772 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAACCCGTCTTCCGATGTG-TTG
          1 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTG

                             *             *              
        826 TCTTCCAATCAACATTTAAAAATTCTTTCTAACAAACCGTCTTCCG
          1 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCG

        872 GTGTACTTCT


Statistics
Matches: 93,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  54   46  0.49
  55   45  0.48
  56    2  0.02

ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35


Consensus pattern (55 bp):   
TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGATGAGATTG

Found at i:931 original size:67 final size:67

Alignment explanation


    Indices: 823--1015  Score: 341
    Period size: 67  Copynumber: 2.9  Consensus size: 67

        813 TTCCGATGTG

                           **   *                                            
        823 TTGTCTTCCAATCAACATTTAAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTAATGA
          1 TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTAATGA

              
        888 GA
         66 GA

                                                                 *  *        
        890 TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTTCTCCTTAATGA
          1 TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTAATGA

              
        955 GA
         66 GA

                                                                       
        957 TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCT
          1 TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCT

       1016 AAAATCCTCT


Statistics
Matches: 119,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  67  119  1.00

ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40


Consensus pattern (67 bp):   
TTGTCTTCCAATCAATTTTTGAAAATTCTTTCTAACAAACCGTCTTCCGGTGTACTTCTTAATGA
GA
Done.