Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018379.1 Corchorus olitorius cultivar O-4 contig18412, 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: 33834
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:5063 original size:7 final size:7

Alignment explanation


    Indices: 5048--5079  Score: 55
    Period size: 7  Copynumber: 4.6  Consensus size: 7

       5038 ATATCCGATC

                *  
       5048 TCACTCA
          1 TCACCCA

                   
       5055 TCACCCA
          1 TCACCCA

                   
       5062 TCACCCA
          1 TCACCCA

                   
       5069 TCACCCA
          1 TCACCCA

                
       5076 TCAC
          1 TCAC

       5080 TCATGCCTCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   7   24  1.00

ACGTcount: A:0.28, C:0.53, G:0.00, T:0.19


Consensus pattern (7 bp):   
TCACCCA

Found at i:20493 original size:23 final size:23

Alignment explanation


    Indices: 20467--20515  Score: 71
    Period size: 23  Copynumber: 2.1  Consensus size: 23

      20457 AGAAATTTAG

                      *   * *      
      20467 CTTTATAGAGTTGATTGTTTAAA
          1 CTTTATAGAGATGACTATTTAAA

                                   
      20490 CTTTATAGAGATGACTATTTAAA
          1 CTTTATAGAGATGACTATTTAAA

               
      20513 CTT
          1 CTT

      20516 AGAAATTTAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45


Consensus pattern (23 bp):   
CTTTATAGAGATGACTATTTAAA

Found at i:26819 original size:131 final size:132

Alignment explanation


    Indices: 26668--26930  Score: 388
    Period size: 132  Copynumber: 2.0  Consensus size: 132

      26658 CATTGTTTAA

                                               *                             
      26668 ACTTTTATAATTTTACTCAACT-AAAACTCTATTTTTATTTAATTAAATCAAATATCCTTATA-A
          1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTGTATTTAATTAAATCAAATATCCTTATACA

                    *                *                   *         *      *  
      26731 TTATTTAATTTTTACCATTTTACTATTTTAA-ATAAAAAAACTTATATATATTAGTATTTTTTAA
         66 --ATTTAACTTTTACCATTTTACTAATTTAATATAAAAAAACTTAGATATATTAGAATTTTTAAA

                
      26795 ATAT
        129 ATAT

                     *                                        *              
      26799 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTGTATTTAATTAAATCTAATATCCTTATACA
          1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTGTATTTAATTAAATCAAATATCCTTATACA

                *       *                 *                                  
      26864 ATTTTACTTTTATCATTTTACTAATTTAATTTAAAAAAACTTAGATATATTAGAATTTTTAAAAT
         66 ATTTAACTTTTACCATTTTACTAATTTAATATAAAAAAACTTAGATATATTAGAATTTTTAAAAT

              
      26929 AT
        131 AT

      26931 TAACATTGTT


Statistics
Matches: 118,  Mismatches: 11, Indels: 5
        0.88            0.08        0.04

Matches are distributed among these distances:
 131   46  0.39
 132   71  0.60
 133    1  0.01

ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48


Consensus pattern (132 bp):   
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTGTATTTAATTAAATCAAATATCCTTATACA
ATTTAACTTTTACCATTTTACTAATTTAATATAAAAAAACTTAGATATATTAGAATTTTTAAAAT
AT

Found at i:28117 original size:22 final size:22

Alignment explanation


    Indices: 28089--28130  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      28079 TAATATAATA

                                  
      28089 TTCTTGGGTCATCCGGGTTAGC
          1 TTCTTGGGTCATCCGGGTTAGC

                        *       
      28111 TTCTTGGGTCATTCGGGTTA
          1 TTCTTGGGTCATCCGGGTTA

      28131 TGGGTTTGTC


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

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.10, C:0.19, G:0.31, T:0.40


Consensus pattern (22 bp):   
TTCTTGGGTCATCCGGGTTAGC

Found at i:29031 original size:10 final size:11

Alignment explanation


    Indices: 29007--29044  Score: 51
    Period size: 10  Copynumber: 3.5  Consensus size: 11

      28997 AATTTGAAAT

                       
      29007 AAAGAAAAGAA
          1 AAAGAAAAGAA

                       
      29018 AAAGAAAA-AA
          1 AAAGAAAAGAA

                    *   
      29028 AAAGAAAGGGAA
          1 AAAGAAA-AGAA

                 
      29040 AAAGA
          1 AAAGA

      29045 GAATATGAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    9  0.38
  11    8  0.33
  12    7  0.29

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (11 bp):   
AAAGAAAAGAA

Found at i:32009 original size:21 final size:22

Alignment explanation


    Indices: 31985--32036  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      31975 GGCATGGAAT

                           *      
      31985 GGTGATGGCACGG-GTATGGCC
          1 GGTGATGGCACGGTGCATGGCC

                *               * 
      32006 GGTGGTGGCACGGTGCATGGGC
          1 GGTGATGGCACGGTGCATGGCC

               *     
      32028 GGTAATGGC
          1 GGTGATGGC

      32037 TTGGTAGTGG


Statistics
Matches: 25,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  21   12  0.48
  22   13  0.52

ACGTcount: A:0.13, C:0.17, G:0.50, T:0.19


Consensus pattern (22 bp):   
GGTGATGGCACGGTGCATGGCC

Done.