Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006555.1 Corchorus capsularis cultivar CVL-1 contig06576, 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: 6309
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:77 original size:40 final size:40

Alignment explanation


    Indices: 21--100  Score: 115
    Period size: 40  Copynumber: 2.0  Consensus size: 40

         11 TGGCGCATCA

                 *     *                            
         21 GGAAGGGCAAACTGGGAAACTAAACAACACCTTCCAGTGG
          1 GGAAGCGCAAAATGGGAAACTAAACAACACCTTCCAGTGG

                               *          *    *    
         61 GGAAGCGCAAAATGGGAAAGTAAACAACACGTTCCGGTGG
          1 GGAAGCGCAAAATGGGAAACTAAACAACACCTTCCAGTGG

        101 TGATCGTGTC


Statistics
Matches: 35,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  40   35  1.00

ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12


Consensus pattern (40 bp):   
GGAAGCGCAAAATGGGAAACTAAACAACACCTTCCAGTGG

Found at i:321 original size:6 final size:6

Alignment explanation


    Indices: 310--339  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

        300 GCAAAGCAAT

                           *                  
        310 TCTAAA TCTAAA TTTAAA TCTAAA TCTAAA
          1 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA

        340 GCAGATTAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37


Consensus pattern (6 bp):   
TCTAAA

Found at i:354 original size:13 final size:13

Alignment explanation


    Indices: 336--376  Score: 66
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        326 AATCTAAATC

                   *     
        336 TAAAGCAGATTAA
          1 TAAAGCAAATTAA

                         
        349 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                         
        362 TAAAGCAAA-TAA
          1 TAAAGCAAATTAA

               
        374 TAA
          1 TAA

        377 TTATAAAGCA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  12    6  0.22
  13   21  0.78

ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:2094 original size:46 final size:46

Alignment explanation


    Indices: 1975--2154  Score: 229
    Period size: 47  Copynumber: 3.9  Consensus size: 46

       1965 AAGATGGGAA

                                              *            
       1975 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGAC
          1 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAA-TTGAC

                                *                        * 
       2022 AACTAAACAACACCTTCCGACT-GGGAAGGGCAAACTGGGAATTGGC
          1 AACTAAACAACACCTTCCG-GTGGGGAAGGGCAAACTGGGAATTGAC

                 *           *                              
       2068 AACTAGACAACACCTTCTGGTGGGGAAGGGCAAACTGGGCAGA-TGAC
          1 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-A-ATTGAC

               *       *                 *    *     
       2115 AACAAAACAACCCCTTCCGGTGGGGAAGGACAAATTGGGA
          1 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA

       2155 GTAAGACGAC


Statistics
Matches: 116,  Mismatches: 13, Indels: 9
        0.84            0.09        0.07

Matches are distributed among these distances:
  45    1  0.01
  46   39  0.34
  47   74  0.64
  48    2  0.02

ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16


Consensus pattern (46 bp):   
AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTGAC

Found at i:2141 original size:93 final size:93

Alignment explanation


    Indices: 1975--2154  Score: 245
    Period size: 93  Copynumber: 1.9  Consensus size: 93

       1965 AAGATGGGAA

                                              *      **       *              
       1975 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAATTTGACAACTAAACAACACCTTCC
          1 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAGATGACAACAAAACAACACCTTCC

                       *                
       2040 GACTGGGAAGGGCAAACTGGGAATTGGC
         66 GACTGGGAAGGACAAACTGGGAATTGGC

                 *           *                     *                  *      
       2068 AACTAGACAACACCTTCTGGTGGGGAAGGGCAAACTGGGCAGATGACAACAAAACAACCCCTTCC
          1 AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAGATGACAACAAAACAACACCTTCC

              *              *     
       2133 G-GTGGGGAAGGACAAATTGGGA
         66 GACT-GGGAAGGACAAACTGGGA

       2155 GTAAGACGAC


Statistics
Matches: 75,  Mismatches: 11, Indels: 2
        0.85            0.12        0.02

Matches are distributed among these distances:
  92    1  0.01
  93   74  0.99

ACGTcount: A:0.34, C:0.22, G:0.28, T:0.16


Consensus pattern (93 bp):   
AACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAAGATGACAACAAAACAACACCTTCC
GACTGGGAAGGACAAACTGGGAATTGGC

Found at i:2795 original size:51 final size:48

Alignment explanation


    Indices: 2647--2827  Score: 188
    Period size: 49  Copynumber: 3.7  Consensus size: 48

       2637 TATTTAAAGG

                          **      *     *             *     *
       2647 TTTTATTTCAAATTTGTCAAAAGTCAATATTTTAGCTTAAAGGCTTCAC
          1 TTTTA-TTCAAATTAATCAAAATTCAATCTTTTAGCTTAAAGACTTCAT

                                       *                     
       2696 TTTTATTACAAATTAATCAAAATT-AAACTTTTAGCTTAAAGACTTCAT
          1 TTTTATT-CAAATTAATCAAAATTCAATCTTTTAGCTTAAAGACTTCAT

                     *                                           
       2744 TTTTATTTGTAAATTAATCAAAAGTTCAATCTTTTAG-TTCAAAGA-TCTCAT
          1 TTTTA-TT-CAAATTAATCAAAA-TTCAATCTTTTAGCTT-AAAGACT-TCAT

                                        *    
       2795 TTTTATTCAAATTAATCAAAAATTCAATTTTTT
          1 TTTTATTCAAATTAATC-AAAATTCAATCTTTT

       2828 TTTTAGTTCA


Statistics
Matches: 113,  Mismatches: 12, Indels: 14
        0.81            0.09        0.10

Matches are distributed among these distances:
  48   27  0.24
  49   52  0.46
  50   11  0.10
  51   23  0.20

ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45


Consensus pattern (48 bp):   
TTTTATTCAAATTAATCAAAATTCAATCTTTTAGCTTAAAGACTTCAT
Done.