Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011933.1 Corchorus capsularis cultivar CVL-1 contig11954, 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: 2912
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30


Found at i:857 original size:16 final size:16

Alignment explanation


    Indices: 836--891  Score: 51
    Period size: 16  Copynumber: 3.4  Consensus size: 16

        826 TGTGACTGAA

                            
        836 ATGCAAGAATATTGAG
          1 ATGCAAGAATATTGAG

                     * *      *
        852 ATGCAA-AAAAATGCCAAA
          1 ATGCAAGAATATTG---AG

                            
        870 ATGCAAGAATATTGAG
          1 ATGCAAGAATATTGAG

                  
        886 ATGCAA
          1 ATGCAA

        892 AAAATGCCAA


Statistics
Matches: 30,  Mismatches: 6, Indels: 8
        0.68            0.14        0.18

Matches are distributed among these distances:
  15    5  0.17
  16   13  0.43
  18    7  0.23
  19    5  0.17

ACGTcount: A:0.50, C:0.11, G:0.20, T:0.20


Consensus pattern (16 bp):   
ATGCAAGAATATTGAG

Found at i:899 original size:33 final size:34

Alignment explanation


    Indices: 834--903  Score: 133
    Period size: 34  Copynumber: 2.1  Consensus size: 34

        824 TATGTGACTG

                                              
        834 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
          1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA

                                              
        868 AAATGCAAGAATATTGAGATGC-AAAAAATGCCA
          1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA

               
        901 AAA
          1 AAA

        904 GTACACATCA


Statistics
Matches: 36,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  33   14  0.39
  34   22  0.61

ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17


Consensus pattern (34 bp):   
AAATGCAAGAATATTGAGATGCAAAAAAATGCCA

Found at i:1078 original size:28 final size:27

Alignment explanation


    Indices: 986--1086  Score: 100
    Period size: 28  Copynumber: 3.7  Consensus size: 27

        976 AGGTGTACTA

                 *         *     *  *  
        986 AAAATTACCAAAATGTCCCTAAATATG
          1 AAAATGACCAAAATGCCCCTATATGTG

            *              *           
       1013 CAAATGACCAAAAT-ACCCT-TA-GTG
          1 AAAATGACCAAAATGCCCCTATATGTG

                                          
       1037 CAAGAATGACCAAAATGCCCCTATGATGTG
          1 -AA-AATGACCAAAATGCCCCTAT-ATGTG

                                
       1067 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

       1087 GGATGACCCT


Statistics
Matches: 61,  Mismatches: 7, Indels: 11
        0.77            0.09        0.14

Matches are distributed among these distances:
  24    2  0.03
  25    2  0.03
  26   16  0.26
  27   16  0.26
  28   19  0.31
  29    3  0.05
  30    3  0.05

ACGTcount: A:0.43, C:0.24, G:0.13, T:0.21


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTATATGTG

Found at i:1401 original size:45 final size:45

Alignment explanation


    Indices: 1335--1568  Score: 362
    Period size: 45  Copynumber: 5.2  Consensus size: 45

       1325 TCCGTTGTTG

                                    *                  * 
       1335 ACTTTGATAACTGCTG-AAACTGAAAAAGACCTGTTCTGAGGTTA
          1 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

                        *                             *  
       1379 ACTTTGATAACTACTGAAAACTGAGAAAGACCTGTTCTGAGGCCA
          1 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

                      *    *                             
       1424 ACTTTGATAATTGCTAAAAACTGAGAAAGACCTGTTCTGAGGTCA
          1 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

                                                   *     
       1469 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGCGGTCA
          1 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

                                           *    *  *    *
       1514 ACTTTGATAACTGCTGAAAACTGAGAAAGACTTGTTTTGGGGTCG
          1 ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

                      
       1559 ACTTTGATAA
          1 ACTTTGATAA

       1569 TCTTATTGAA


Statistics
Matches: 174,  Mismatches: 15, Indels: 1
        0.92            0.08        0.01

Matches are distributed among these distances:
  44   15  0.09
  45  159  0.91

ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


Consensus pattern (45 bp):   
ACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGAGGTCA

Done.