Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016459.1 Corchorus olitorius cultivar O-4 contig16492, 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: 64593
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:7138 original size:67 final size:67

Alignment explanation


    Indices: 7059--7193  Score: 182
    Period size: 67  Copynumber: 2.0  Consensus size: 67

       7049 AAATCCCTTA

                  *                 *                                   *    
       7059 ATTTTATGTTAGTATTGAATA-AGGTTTTAAAAAATATAGCAAGTTTTATAATAACATGTTAGGA
          1 ATTTTAGGTTAGTATTGAATAGA-ATTTTAAAAAATATAGCAAGTTTTATAATAACATGTCAGGA

               
       7123 GAG
         65 GAG

                             *           *         *       *    *            
       7126 ATTTTAGGTTAGTATTGGATAGAATTTTAGAAAATATAGTAAGTTTTCTAATGACATGTCAGGAG
          1 ATTTTAGGTTAGTATTGAATAGAATTTTAAAAAATATAGCAAGTTTTATAATAACATGTCAGGAG

              
       7191 AG
         66 AG

             
       7193 A
          1 A

       7194 CAAGTTGGAT


Statistics
Matches: 59,  Mismatches: 8, Indels: 2
        0.86            0.12        0.03

Matches are distributed among these distances:
  67   58  0.98
  68    1  0.02

ACGTcount: A:0.39, C:0.04, G:0.20, T:0.38


Consensus pattern (67 bp):   
ATTTTAGGTTAGTATTGAATAGAATTTTAAAAAATATAGCAAGTTTTATAATAACATGTCAGGAG
AG

Found at i:18599 original size:17 final size:17

Alignment explanation


    Indices: 18574--18621  Score: 53
    Period size: 17  Copynumber: 2.8  Consensus size: 17

      18564 AAGATTTAGA

                *             
      18574 AAATTATATTTTTTATGG
          1 AAATAATATTTTTTAT-G

                         *  *
      18592 AAA-AATATTTTTGATT
          1 AAATAATATTTTTTATG

                          
      18608 AAATAATATTTTTT
          1 AAATAATATTTTTT

      18622 TTCTTTTGTA


Statistics
Matches: 25,  Mismatches: 4, Indels: 3
        0.78            0.12        0.09

Matches are distributed among these distances:
  16    3  0.12
  17   19  0.76
  18    3  0.12

ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54


Consensus pattern (17 bp):   
AAATAATATTTTTTATG

Found at i:44206 original size:31 final size:30

Alignment explanation


    Indices: 44133--44210  Score: 97
    Period size: 29  Copynumber: 2.6  Consensus size: 30

      44123 TTACAAATTG

                    *                   * 
      44133 CAAGTTTAAGGGGCAAAACGTCCAAAATTA
          1 CAAGTTTAGGGGGCAAAACGTCCAAAATAA

                                            
      44163 -AAGTTTAGGGGGCAAAACGT-CAAAATCGAA
          1 CAAGTTTAGGGGGCAAAACGTCCAAAAT--AA

                 *            
      44193 CAAGTGTAGGGGGCAAAA
          1 CAAGTTTAGGGGGCAAAA

      44211 AGGGCATTAA


Statistics
Matches: 42,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  28    6  0.14
  29   19  0.45
  30    1  0.02
  31   16  0.38

ACGTcount: A:0.42, C:0.14, G:0.27, T:0.17


Consensus pattern (30 bp):   
CAAGTTTAGGGGGCAAAACGTCCAAAATAA

Found at i:49156 original size:31 final size:31

Alignment explanation


    Indices: 49121--49190  Score: 79
    Period size: 31  Copynumber: 2.3  Consensus size: 31

      49111 AGCCATTAGG

                              *   *         
      49121 AAATGCCACAATAGCATGGCACGTGGA-TAGA
          1 AAATGCCACAATAGCATGCCACATGGACT-GA

                    * * *                  
      49152 AAATGCCATATTGGCATGCCACATGGACTGA
          1 AAATGCCACAATAGCATGCCACATGGACTGA

                    
      49183 AAATGCCA
          1 AAATGCCA

      49191 TGTCAGTAAA


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  31   32  0.97
  32    1  0.03

ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19


Consensus pattern (31 bp):   
AAATGCCACAATAGCATGCCACATGGACTGA

Found at i:61262 original size:2 final size:2

Alignment explanation


    Indices: 61255--61279  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      61245 CTTCTTGGAT

                                                 
      61255 TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC T

      61280 ACTTTCCCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Done.