Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015806.1 Corchorus capsularis cultivar CVL-1 contig15827, 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: 28831
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:7103 original size:8 final size:8

Alignment explanation


    Indices: 7090--7122  Score: 59
    Period size: 8  Copynumber: 4.2  Consensus size: 8

       7080 GATTAATTAA

                    
       7090 TATTTTTT
          1 TATTTTTT

                    
       7098 TATTTTTT
          1 TATTTTTT

                    
       7106 TA-TTTTT
          1 TATTTTTT

                    
       7113 TATTTTTT
          1 TATTTTTT

              
       7121 TA
          1 TA

       7123 AGCAAGAAGA


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

Matches are distributed among these distances:
   7    7  0.29
   8   17  0.71

ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85


Consensus pattern (8 bp):   
TATTTTTT

Found at i:7113 original size:15 final size:15

Alignment explanation


    Indices: 7093--7122  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       7083 TAATTAATAT

                           
       7093 TTTTTTATTTTTTTA
          1 TTTTTTATTTTTTTA

                           
       7108 TTTTTTATTTTTTTA
          1 TTTTTTATTTTTTTA

       7123 AGCAAGAAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87


Consensus pattern (15 bp):   
TTTTTTATTTTTTTA

Found at i:9795 original size:19 final size:20

Alignment explanation


    Indices: 9757--9795  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9747 CTTGGTTCCC

                  *      *      
       9757 TTTGCTTCCAAATTTCAATT
          1 TTTGCTACCAAATCTCAATT

                                
       9777 TTTGCTACCAAA-CTCAATT
          1 TTTGCTACCAAATCTCAATT

       9796 CCAATTTCAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    6  0.35
  20   11  0.65

ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44


Consensus pattern (20 bp):   
TTTGCTACCAAATCTCAATT

Found at i:15400 original size:21 final size:21

Alignment explanation


    Indices: 15366--15419  Score: 99
    Period size: 21  Copynumber: 2.5  Consensus size: 21

      15356 GCATGGGCAA

                                  
      15366 GGCCGGGTCATGCGATGGTGAT
          1 GGCCGGG-CATGCGATGGTGAT

                                 
      15388 GGCCGGGCATGCGATGGTGAT
          1 GGCCGGGCATGCGATGGTGAT

                       
      15409 GGCCGGGCATG
          1 GGCCGGGCATG

      15420 TGGCCGGTCA


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  21   25  0.78
  22    7  0.22

ACGTcount: A:0.13, C:0.20, G:0.48, T:0.19


Consensus pattern (21 bp):   
GGCCGGGCATGCGATGGTGAT

Found at i:16276 original size:12 final size:12

Alignment explanation


    Indices: 16256--16295  Score: 62
    Period size: 12  Copynumber: 3.3  Consensus size: 12

      16246 CATGACCGGC

                        
      16256 CAACGCATGGAG
          1 CAACGCATGGAG

              *         
      16268 CATCGCATGGAG
          1 CAACGCATGGAG

                      * 
      16280 CAACGCATGGGG
          1 CAACGCATGGAG

                
      16292 CAAC
          1 CAAC

      16296 CGGCCAATGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  12   25  1.00

ACGTcount: A:0.30, C:0.28, G:0.33, T:0.10


Consensus pattern (12 bp):   
CAACGCATGGAG

Found at i:28274 original size:67 final size:67

Alignment explanation


    Indices: 28149--28278  Score: 174
    Period size: 67  Copynumber: 1.9  Consensus size: 67

      28139 TTCCTTTTTT

                  *     *                     *                 **           
      28149 ATATCTTCTAAATCTCCCACAATTTGGCAAGATTTAGAAAATATTCTCATTATTATTAAATCTAA
          1 ATATCTCCTAAACCTCCCACAATTTGGCAAGATTCAGAAAATATTCTCATTAAAATTAAATCTAA

              
      28214 AA
         66 AA

                           *                                                 
      28216 ATATCTCCTAAACCTTCCACAATTTGGCAAGATTCA-AAAATATTCT-ATTTACAAATTAAATCT
          1 ATATCTCCTAAACCTCCCACAATTTGGCAAGATTCAGAAAATATTCTCA-TTA-AAATTAAATCT

      28279 TTATAATTTT


Statistics
Matches: 55,  Mismatches: 6, Indels: 4
        0.85            0.09        0.06

Matches are distributed among these distances:
  65    1  0.02
  66   13  0.24
  67   41  0.75

ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36


Consensus pattern (67 bp):   
ATATCTCCTAAACCTCCCACAATTTGGCAAGATTCAGAAAATATTCTCATTAAAATTAAATCTAA
AA
Done.