Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024632.1 Corchorus olitorius cultivar O-4 contig24665, 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: 3252
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29


Found at i:1033 original size:35 final size:35

Alignment explanation


    Indices: 988--1359  Score: 512
    Period size: 35  Copynumber: 10.5  Consensus size: 35

        978 ATCAATGTGA

                                             **
        988 AGATCAACTCTGATCATCGAAAACTTCTTGAAACA
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                                
       1023 AGATCAACTCTGATCATCGAAAACTTTCTTGAAATG
          1 AGATCAACTCTGATCATCGAAAAC-TTCTTGAAATG

                                               
       1059 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                 *           *               * 
       1094 AGATCGACTCTGATCATGGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                             * 
       1129 AGATCAACTCTGATCATCGAAAACTTCTTGAAACG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                                       *  *    
       1164 AGATCAACTCTGATCATCGAAAACTTCATGGAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                           **                  
       1199 AGATCAACTCTGATCGCCGAAAACTTCTTGAAATG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                             *               * 
       1234 AGATCAACTCTGATCATTGAAAACTTCTTGAAAGG
          1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

                              *            *   *
       1269 AGATCAACTCTGATCAT-AAAAATCTTCTTGGAATA
          1 AGATCAACTCTGATCATCGAAAA-CTTCTTGAAATG

             *                  **               * 
       1304 AAATCAACTCTGATCATAAAAAAAAACTTCTTGAAAACG
          1 AGATCAACTCTGATCAT---CGAAAACTTCTTG-AAATG

                             
       1343 AGATCAACTCTGATCAT
          1 AGATCAACTCTGATCAT

       1360 TTCAGCAGCT


Statistics
Matches: 303,  Mismatches: 27, Indels: 10
        0.89            0.08        0.03

Matches are distributed among these distances:
  34    4  0.01
  35  236  0.78
  36   33  0.11
  38    7  0.02
  39   23  0.08

ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27


Consensus pattern (35 bp):   
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG

Found at i:1324 original size:18 final size:18

Alignment explanation


    Indices: 1271--1324  Score: 51
    Period size: 16  Copynumber: 3.1  Consensus size: 18

       1261 TTGAAAGGAG

                               
       1271 ATCAACTCTGATCATAAAA
          1 ATCAACTCTGATCAT-AAA

               **              
       1290 ATCTTCT-TGGA--ATAAA
          1 ATCAACTCT-GATCATAAA

                              
       1306 ATCAACTCTGATCATAAA
          1 ATCAACTCTGATCATAAA

             
       1324 A
          1 A

       1325 AAAAACTTCT


Statistics
Matches: 27,  Mismatches: 4, Indels: 9
        0.68            0.10        0.22

Matches are distributed among these distances:
  16   10  0.37
  17    3  0.11
  18    7  0.26
  19    7  0.26

ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30


Consensus pattern (18 bp):   
ATCAACTCTGATCATAAA

Found at i:2431 original size:23 final size:22

Alignment explanation


    Indices: 2396--2441  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2386 CCAAATTCGG

                  *                
       2396 GTCCAGTCGTCAAACCCGCGCGC
          1 GTCCAGGCGTC-AACCCGCGCGC

                    *             
       2419 GTCCAGGCTTCAACCCGCGCGC
          1 GTCCAGGCGTCAACCCGCGCGC

             
       2441 G
          1 G

       2442 GCTAGTGCCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22   12  0.57
  23    9  0.43

ACGTcount: A:0.15, C:0.43, G:0.28, T:0.13


Consensus pattern (22 bp):   
GTCCAGGCGTCAACCCGCGCGC
Done.