Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015501.1 Corchorus capsularis cultivar CVL-1 contig15522, 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: 24001
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32


Found at i:2700 original size:9 final size:8

Alignment explanation


    Indices: 2666--2699  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       2656 GAATCGGCTA

                    
       2666 TGAATTTT
          1 TGAATTTT

                    *
       2674 TGAAGTTTC
          1 TGAA-TTTT

                    
       2683 TGAATTTT
          1 TGAATTTT

                    
       2691 TGAATTTT
          1 TGAATTTT

             
       2699 T
          1 T

       2700 TCAAGAAGGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59


Consensus pattern (8 bp):   
TGAATTTT

Found at i:2815 original size:31 final size:31

Alignment explanation


    Indices: 2779--2850  Score: 135
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2769 AGGATAGATT

                                           
       2779 TACCGATTGAAGATGACAACCTATGCTCTGA
          1 TACCGATTGAAGATGACAACCTATGCTCTGA

                                           
       2810 TACCGATTGAAGATGACAACCTATGCTCTGA
          1 TACCGATTGAAGATGACAACCTATGCTCTGA

                *     
       2841 TACCAATTGA
          1 TACCGATTGA

       2851 TACGAATCTA


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  31   40  1.00

ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26


Consensus pattern (31 bp):   
TACCGATTGAAGATGACAACCTATGCTCTGA

Found at i:3706 original size:33 final size:34

Alignment explanation


    Indices: 3669--3739  Score: 101
    Period size: 33  Copynumber: 2.1  Consensus size: 34

       3659 AGTCATTTGA

                           *                  
       3669 CCGGTTG-TAGCTGGCCATGTCCATGTCGCGTGG
          1 CCGGTTGATAGCTGGACATGTCCATGTCGCGTGG

                     * *                      
       3702 CCGG-TGATGGTTGGACATGTCCATGTCGCGTGG
          1 CCGGTTGATAGCTGGACATGTCCATGTCGCGTGG

                 
       3735 CCGGT
          1 CCGGT

       3740 CTTGTGGCCG


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  32    2  0.06
  33   31  0.94

ACGTcount: A:0.10, C:0.25, G:0.38, T:0.27


Consensus pattern (34 bp):   
CCGGTTGATAGCTGGACATGTCCATGTCGCGTGG

Found at i:5527 original size:27 final size:27

Alignment explanation


    Indices: 5497--5601  Score: 156
    Period size: 27  Copynumber: 3.9  Consensus size: 27

       5487 AGGTGGACTT

                     *            *    
       5497 AAAAATGACTAAAATGCCCCTGAGTGC
          1 AAAAATGACCAAAATGCCCCTGGGTGC

                                      *
       5524 AAAAATGACCAAAATGCCCCTGGGTGA
          1 AAAAATGACCAAAATGCCCCTGGGTGC

                               *       
       5551 AAAAATGACCAAAATGCCCATGGGTGC
          1 AAAAATGACCAAAATGCCCCTGGGTGC

                           *   *    
       5578 AAAAATGACCAAAATACCCTTGGG
          1 AAAAATGACCAAAATGCCCCTGGG

       5602 CGACCCTAAT


Statistics
Matches: 71,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   71  1.00

ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16


Consensus pattern (27 bp):   
AAAAATGACCAAAATGCCCCTGGGTGC

Found at i:22062 original size:65 final size:65

Alignment explanation


    Indices: 21991--22129  Score: 251
    Period size: 65  Copynumber: 2.1  Consensus size: 65

      21981 AAAGCCCCAA

                          *               *                                  
      21991 CACCCAGCCGCAAGGGCCTGTGCTGGAGGCTGACTCAGGGTGGGCGCCCAGGTGCTTTGCCTGAG
          1 CACCCAGCCGCAAGCGCCTGTGCTGGAGGCCGACTCAGGGTGGGCGCCCAGGTGCTTTGCCTGAG

                             *                                               
      22056 CACCCAGCCGCAAGCGCTTGTGCTGGAGGCCGACTCAGGGTGGGCGCCCAGGTGCTTTGCCTGAG
          1 CACCCAGCCGCAAGCGCCTGTGCTGGAGGCCGACTCAGGGTGGGCGCCCAGGTGCTTTGCCTGAG

                     
      22121 CACCCAGCC
          1 CACCCAGCC

      22130 CGATGGCTTG


Statistics
Matches: 71,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  65   71  1.00

ACGTcount: A:0.14, C:0.34, G:0.36, T:0.16


Consensus pattern (65 bp):   
CACCCAGCCGCAAGCGCCTGTGCTGGAGGCCGACTCAGGGTGGGCGCCCAGGTGCTTTGCCTGAG
Done.