Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006956.1 Corchorus capsularis cultivar CVL-1 contig06977, 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: 14909
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:13497 original size:25 final size:25

Alignment explanation


    Indices: 13460--13510  Score: 84
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      13450 TTTCCTAAGT

                 *                   
      13460 TTCTATGTCTGTAATGTACTTTCTC
          1 TTCTACGTCTGTAATGTACTTTCTC

                    *                
      13485 TTCTACGTTTGTAATGTACTTTCTC
          1 TTCTACGTCTGTAATGTACTTTCTC

             
      13510 T
          1 T

      13511 GTAAGTTTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.16, C:0.20, G:0.12, T:0.53


Consensus pattern (25 bp):   
TTCTACGTCTGTAATGTACTTTCTC

Found at i:13804 original size:105 final size:104

Alignment explanation


    Indices: 13558--13844  Score: 322
    Period size: 103  Copynumber: 2.8  Consensus size: 104

      13548 AAAAAACTTT

                                      *  **  *        *                      
      13558 ATAATAATAAATCTTAAATTATAA-TGCTTTCCTTATAAATTTTTATTTTTTA--AATTT-G-GC
          1 ATAATAATAAATCTTAAATT-TAAGTACTAACCCTATAAA-TATTATTTTTTATTAATTTGGAGC

                                 **          *        
      13618 TAAACATTATGAAATTATGGTTGAATATTCAACCTAAAACCC
         64 TAAAC-TTATGAAATTATGGTCAAATATTCAACATAAAACCC

                                  *                                          
      13660 TATAATAATAAATCTTAAATTTTAGTACTAACCCTATAAACTATTATTTTTTGATTAATTTGGAG
          1 -ATAATAATAAATCTTAAATTTAAGTACTAACCCTATAAA-TATTATTTTTT-ATTAATTTGGAG

                                                       
      13725 CTAAACTCTATGAAATTATGGTCAAATATTCAA-ATAAAACCC
         63 CTAAACT-TATGAAATTATGGTCAAATATTCAACATAAAACCC

                                                                   *         
      13767 -TAATAATAAATCTTAAATTTAAGTACTAACCCTATAAATCA--ATTCTTTTATTGATTTGGAGC
          1 ATAATAATAAATCTTAAATTTAAGTACTAACCCTATAAAT-ATTATT-TTTTATTAATTTGGAGC

                 *          
      13829 TAAATTTTATGAAATT
         64 TAAA-CTTATGAAATT

      13845 TAAATAAATT


Statistics
Matches: 161,  Mismatches: 13, Indels: 20
        0.83            0.07        0.10

Matches are distributed among these distances:
 102    2  0.01
 103   69  0.43
 104    7  0.04
 105   38  0.24
 106    5  0.03
 107   10  0.06
 108   30  0.19

ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41


Consensus pattern (104 bp):   
ATAATAATAAATCTTAAATTTAAGTACTAACCCTATAAATATTATTTTTTATTAATTTGGAGCTA
AACTTATGAAATTATGGTCAAATATTCAACATAAAACCC

Found at i:14883 original size:2 final size:2

Alignment explanation


    Indices: 14876--14909  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      14866 GAAGTTACTA

                                                              
      14876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.