Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006804.1 Corchorus olitorius cultivar O-4 contig06829, 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: 2362
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32


Found at i:1184 original size:27 final size:27

Alignment explanation


    Indices: 1154--1226  Score: 69
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       1144 AGTCTTCTTT

                                   *   
       1154 GAATTGTCTTCCAATTCAATCTTCTGG
          1 GAATTGTCTTCCAATTCAATCTTATGG

                *                     **
       1181 GAATCGTCTTCCGAA-TCAA-CTTATTT
          1 GAATTGTCTTCC-AATTCAATCTTATGG

               *           *    
       1207 GAAGTGTCTTCCAATCCAAT
          1 GAATTGTCTTCCAATTCAAT

       1227 ATTAAAAGGA


Statistics
Matches: 36,  Mismatches: 7, Indels: 6
        0.73            0.14        0.12

Matches are distributed among these distances:
  25    2  0.06
  26   17  0.47
  27   15  0.42
  28    2  0.06

ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37


Consensus pattern (27 bp):   
GAATTGTCTTCCAATTCAATCTTATGG

Found at i:1282 original size:50 final size:50

Alignment explanation


    Indices: 1204--1943  Score: 1133
    Period size: 51  Copynumber: 14.6  Consensus size: 50

       1194 AATCAACTTA

                  *     *     *    *                          
       1204 TTTGAAGTGTCTTCCAATCCAATATTAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC

               *        *                    *                
       1254 TTTAAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC

                        *                          *  *       
       1304 TTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTCCCACTTATCC
          1 TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC

                                                               
       1354 TTTGAACTGTCTACCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATC-TTAAAAGGACCGTCTTCCGCTTATCC

                  * *                 *    *                   
       1405 TTTGAAATTTCTACCAATTCAATTCTAAAAATGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAA-TCTTAAAAGGACCGTCTTCCGCTTATCC

                                      *         *              
       1456 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCATCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAA-TCTTAAAAGGACCGTCTTCCGCTTATCC

                                                               
       1507 TTTGAACTGTCTACCAATTCAATCTTTAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATC-TTAAAAGGACCGTCTTCCGCTTATCC

                                      *                        
       1558 TTTGAACTGTCTACCAATTCAAATCTAAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTC-AATCTTAAAAGGACCGTCTTCCGCTTATCC

                                                    *          
       1609 TTTGAACTGTCTACCAATTCAATCTTTAAAAGGACCGTCTCCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATC-TTAAAAGGACCGTCTTCCGCTTATCC

                                                               
       1660 TTTGAACTGTCTACCAATTCAAT-TCTAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATCT-TAAAAGGACCGTCTTCCGCTTATCC

                                      *                        
       1710 TTTGAACTGTCTACCAATTCAATTCTAAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAA-TCTTAAAAGGACCGTCTTCCGCTTATCC

                    *                      *                   
       1761 TTTGAACTTTCTACCAATTCAAT-TCTAAAAAGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATCT-TAAAAGGACCGTCTTCCGCTTATCC

                                                              
       1811 TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC

                  *                              *              
       1861 TTTGAATTGTCTACCAATTCAATTCTATAAAAGGACCATCTTCCGCTTATCC
          1 TTTGAACTGTCTACCAATTCAA-TCT-TAAAAGGACCGTCTTCCGCTTATCC

                 *       *                 
       1913 TTTGAGCTGTCTATCAATTCAATCTTGAAAA
          1 TTTGAACTGTCTACCAATTCAATCTT-AAAA

       1944 AAAAGGTAAT


Statistics
Matches: 640,  Mismatches: 37, Indels: 25
        0.91            0.05        0.04

Matches are distributed among these distances:
  49    2  0.00
  50  258  0.40
  51  330  0.52
  52   50  0.08

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


Consensus pattern (50 bp):   
TTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATCC

Found at i:2066 original size:50 final size:50

Alignment explanation


    Indices: 1995--2188  Score: 311
    Period size: 50  Copynumber: 3.9  Consensus size: 50

       1985 AAACCAAGGT

                                       * *                    
       1995 TTGA-AAT-GACTCGTATGGAAACGAGCTCGGCTTGTGGAAAAGCCTATG
          1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG

                    *                                         
       2043 TTGATAATTGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG
          1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG

                                                           *  
       2093 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTGTG
          1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG

              *                            *   *          
       2143 TTAATAATCGACTCGTATGGAAACGAGTTTGACTTATGGAAAAGCC
          1 TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCC

       2189 AAAACATTCG


Statistics
Matches: 137,  Mismatches: 7, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  48    4  0.03
  49    3  0.02
  50  130  0.95

ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29


Consensus pattern (50 bp):   
TTGATAATCGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATG

Done.