Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011864.1 Corchorus capsularis cultivar CVL-1 contig11885, 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: 5746
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:957 original size:33 final size:32

Alignment explanation


    Indices: 870--1010  Score: 131
    Period size: 33  Copynumber: 4.3  Consensus size: 32

        860 AAAGGATTGT

                                 **         **
        870 GTGGCCGGTTGTGGCCGGGCAAGGCCGA-GTCAA
          1 GTGGCCGG-TGTGGCCGGGCATCGCC-ATGTCGC

                         *        *          
        903 GTGGCCGGGTGTGACCGGGCATGGCCATGTCGC
          1 GTGGCC-GGTGTGGCCGGGCATCGCCATGTCGC

                                   *         
        936 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
          1 GTGGCCGGTG-TGGCCGGGCATCGCCATGTCGC

            *          *           *   *     
        969 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
          1 GTGGCCGGTGTGGC-CGGGCATCGCCATGTCGC

                     
       1002 GTGGCCGGT
          1 GTGGCCGGT

       1011 TACTCGCGCC


Statistics
Matches: 93,  Mismatches: 11, Indels: 8
        0.83            0.10        0.07

Matches are distributed among these distances:
  32    8  0.09
  33   83  0.89
  34    2  0.02

ACGTcount: A:0.11, C:0.28, G:0.43, T:0.19


Consensus pattern (32 bp):   
GTGGCCGGTGTGGCCGGGCATCGCCATGTCGC

Found at i:4459 original size:29 final size:29

Alignment explanation


    Indices: 4401--4474  Score: 105
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       4391 GTAGATTAAG

                         *               
       4401 AATGACCAAAAT-ACCCCCTAAATGCCAA
          1 AATGACCAAAATGCCCCCCTAAATGCCAA

                                 *   **  
       4429 AATGACCAAAATGCCCCCCTAGATGTGAA
          1 AATGACCAAAATGCCCCCCTAAATGCCAA

                             
       4458 AATGACCAAAATGCCCC
          1 AATGACCAAAATGCCCC

       4475 TGGATGCTAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  28   12  0.29
  29   29  0.71

ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15


Consensus pattern (29 bp):   
AATGACCAAAATGCCCCCCTAAATGCCAA

Found at i:4758 original size:45 final size:45

Alignment explanation


    Indices: 4702--4901  Score: 278
    Period size: 45  Copynumber: 4.4  Consensus size: 45

       4692 AAGAGAGTAA

                *                              *          
       4702 TCTGTGGTCAACTTTGATAACTGCTG-AAACCGAAAAAAGACCTGT
          1 TCTGAGGTCAACTTTGATAACTGCTGAAAACCG-AGAAAGACCTGT

             *                             *             
       4747 TTTGAGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
          1 TCTGAGGTCAACTTTGATAACTGCTGAAAACCGAGAAAGACCTGT

                                           **            
       4792 TCTGAGGTCAACTTTGATAACTGCTGAAAACTAAGAAAGACCTGT
          1 TCTGAGGTCAACTTTGATAACTGCTGAAAACCGAGAAAGACCTGT

                                            *             
       4837 TCT-ACGGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGT
          1 TCTGA-GGTCAACTTTGATAACTGCTGAAAACCGAGAAAGACCTGT

             *  *    *          
       4882 TTTGGGGTCGACTTTGATAA
          1 TCTGAGGTCAACTTTGATAA

       4902 TCTTATTGAA


Statistics
Matches: 142,  Mismatches: 10, Indels: 6
        0.90            0.06        0.04

Matches are distributed among these distances:
  44    1  0.01
  45  136  0.96
  46    5  0.04

ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28


Consensus pattern (45 bp):   
TCTGAGGTCAACTTTGATAACTGCTGAAAACCGAGAAAGACCTGT

Found at i:4807 original size:90 final size:90

Alignment explanation


    Indices: 4702--4901  Score: 312
    Period size: 90  Copynumber: 2.2  Consensus size: 90

       4692 AAGAGAGTAA

                *                        *                *                  
       4702 TCTGTGGTCAACTTTGATAACTGCTGAAACCGAAAAAAGACCTGTTTTGA-GGTCAACTTTGATA
          1 TCTGAGGTCAACTTTGATAACTGCTGAAAACGAAAAAAGACCTGTTCT-ACGGTCAACTTTGATA

                                      
       4766 ACTGCTGAAAACTGAGAAAGACCTGT
         65 ACTGCTGAAAACTGAGAAAGACCTGT

                                           *  *                              
       4792 TCTGAGGTCAACTTTGATAACTGCTGAAAACTAAGAAAGACCTGTTCTACGGTCAACTTTGATAA
          1 TCTGAGGTCAACTTTGATAACTGCTGAAAACGAAAAAAGACCTGTTCTACGGTCAACTTTGATAA

                                     
       4857 CTGCTGAAAACTGAGAAAGACCTGT
         66 CTGCTGAAAACTGAGAAAGACCTGT

             *  *    *          
       4882 TTTGGGGTCGACTTTGATAA
          1 TCTGAGGTCAACTTTGATAA

       4902 TCTTATTGAA


Statistics
Matches: 101,  Mismatches: 8, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  89    1  0.01
  90  100  0.99

ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28


Consensus pattern (90 bp):   
TCTGAGGTCAACTTTGATAACTGCTGAAAACGAAAAAAGACCTGTTCTACGGTCAACTTTGATAA
CTGCTGAAAACTGAGAAAGACCTGT
Done.