Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011951.1 Corchorus capsularis cultivar CVL-1 contig11972, 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: 6130
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29


Found at i:785 original size:55 final size:55

Alignment explanation


    Indices: 682--913  Score: 330
    Period size: 55  Copynumber: 4.3  Consensus size: 55

        672 GTAAAAAGAA

                       *                                  * *      
        682 AATCAGTAAATAAGTAA--AA--AAAAA-AGATTAATCAGAGTTAAAGTAATAGT
          1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT

                               *                                   
        732 AATCAGTAAATCAGTAATTGAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT
          1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT

                                                                   
        787 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT
          1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT

                                   *                 * *    *   *  
        842 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAATCAAGGTAATGGT
          1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT

               *        *    
        897 AATAAGTAAATCGGTAA
          1 AATCAGTAAATCAGTAA

        914 AAAGAGATTG


Statistics
Matches: 165,  Mismatches: 12, Indels: 5
        0.91            0.07        0.03

Matches are distributed among these distances:
  50   16  0.10
  52    1  0.01
  54    5  0.03
  55  143  0.87

ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25


Consensus pattern (55 bp):   
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAGGAAATAGT

Found at i:986 original size:72 final size:71

Alignment explanation


    Indices: 901--1112  Score: 205
    Period size: 72  Copynumber: 2.9  Consensus size: 71

        891 AATGGTAATA

                  *               **        *     * *                        
        901 AGTAAATCGGTAAAAAGAGATTGGTCAGTAAAGTGATAGTCAAGAATCAAGGTAATATTAATCAG
          1 AGTAAAGC-GTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATATTAATCAG

                  *
        966 TAAAATT
         65 TAAAATC

                              * *    *                    *          *    *  
        973 AGTAAAGCAGTAAAAAGATAGTAATTAGTAAATTGATAATTAAGAACCAAGGTAATAGTAATTAG
          1 AGTAAAGC-GTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATATTAATCAG

              *    
       1038 -ACAATC
         65 TAAAATC

                                                          *           *      
       1044 AGTAATTAG-GT-AAAAGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAAT
          1 AGTAA--AGCGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGT-A-ATATTAAT

                  
       1107 CAGTAA
         62 CAGTAA

       1113 TTAAGGAGTC


Statistics
Matches: 111,  Mismatches: 24, Indels: 9
        0.77            0.17        0.06

Matches are distributed among these distances:
  70   36  0.32
  71   12  0.11
  72   60  0.54
  73    3  0.03

ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26


Consensus pattern (71 bp):   
AGTAAAGCGTAAAAAGAGATTAATCAGTAAATTGATAATTAAGAATCAAGGTAATATTAATCAGT
AAAATC

Found at i:1115 original size:31 final size:32

Alignment explanation


    Indices: 1079--1142  Score: 96
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       1069 AGTAAATTGA

                                             
       1079 TAATTAA-GAGTCAAGGTAAGAAAT-TAATCAG
          1 TAATTAAGGAGTCAAGGTAA-AAATATAATCAG

                                             
       1110 TAATTAAGGAGTCAAGGTAAAAATAGTAATCAG
          1 TAATTAAGGAGTCAAGGTAAAAATA-TAATCAG

       1143 AAAATCGATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  31   11  0.37
  32   12  0.40
  33    7  0.23

ACGTcount: A:0.48, C:0.06, G:0.20, T:0.25


Consensus pattern (32 bp):   
TAATTAAGGAGTCAAGGTAAAAATATAATCAG

Found at i:1592 original size:33 final size:32

Alignment explanation


    Indices: 1536--1602  Score: 84
    Period size: 33  Copynumber: 2.1  Consensus size: 32

       1526 TGGTGATCAA

                          *                 
       1536 AAGAAAAAGAGAGTGAAAATGGT-ATT-AAGT
          1 AAGAAAAAGAGAGTAAAAATGGTAATTAAAGT

                                               
       1566 AAGAAAAGAGAGAGTAAAAAAATGGTAATTAAAGT
          1 AAGAAAA-AGAGAGT--AAAAATGGTAATTAAAGT

              
       1601 AA
          1 AA

       1603 AAGAGTAAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 5
        0.84            0.03        0.14

Matches are distributed among these distances:
  30    7  0.23
  31    7  0.23
  33    8  0.26
  34    3  0.10
  35    6  0.19

ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18


Consensus pattern (32 bp):   
AAGAAAAAGAGAGTAAAAATGGTAATTAAAGT

Found at i:1619 original size:27 final size:27

Alignment explanation


    Indices: 1576--1648  Score: 87
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       1566 AAGAAAAGAG

                                         
       1576 AGAGTAAAAAAATGGTAATTAAAGTA-AA
          1 AGAGT-AAAAAATGGTAATT-AAGTACAA

                     *         *       
       1604 AGAGTAAAATATGGTAA-TCAGTACAA
          1 AGAGTAAAAAATGGTAATTAAGTACAA

             *                 
       1630 ATAGTAAAAAATGGTAATT
          1 AGAGTAAAAAATGGTAATT

       1649 GGCAATCAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 5
        0.81            0.08        0.10

Matches are distributed among these distances:
  25    4  0.10
  26   18  0.46
  27   12  0.31
  28    5  0.13

ACGTcount: A:0.55, C:0.03, G:0.18, T:0.25


Consensus pattern (27 bp):   
AGAGTAAAAAATGGTAATTAAGTACAA
Done.