Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006748.1 Corchorus capsularis cultivar CVL-1 contig06769, 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: 12908
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:8006 original size:110 final size:110

Alignment explanation


    Indices: 7813--8033  Score: 442
    Period size: 110  Copynumber: 2.0  Consensus size: 110

       7803 TTATAAAGCA

                                                                             
       7813 AAAATAATTGAGGTAATGTTGATATCCTCCTTGGCTTCCTCTACGTTAACGACATCTCATTTTTA
          1 AAAATAATTGAGGTAATGTTGATATCCTCCTTGGCTTCCTCTACGTTAACGACATCTCATTTTTA

                                                         
       7878 GTTAAAGCAAGTTTAATGCTTGTCTAAGAATATATAATGGAAAGG
         66 GTTAAAGCAAGTTTAATGCTTGTCTAAGAATATATAATGGAAAGG

                                                                             
       7923 AAAATAATTGAGGTAATGTTGATATCCTCCTTGGCTTCCTCTACGTTAACGACATCTCATTTTTA
          1 AAAATAATTGAGGTAATGTTGATATCCTCCTTGGCTTCCTCTACGTTAACGACATCTCATTTTTA

                                                         
       7988 GTTAAAGCAAGTTTAATGCTTGTCTAAGAATATATAATGGAAAGG
         66 GTTAAAGCAAGTTTAATGCTTGTCTAAGAATATATAATGGAAAGG

             
       8033 A
          1 A

       8034 CAGCTACAGG


Statistics
Matches: 111,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 110  111  1.00

ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35


Consensus pattern (110 bp):   
AAAATAATTGAGGTAATGTTGATATCCTCCTTGGCTTCCTCTACGTTAACGACATCTCATTTTTA
GTTAAAGCAAGTTTAATGCTTGTCTAAGAATATATAATGGAAAGG

Found at i:11205 original size:27 final size:28

Alignment explanation


    Indices: 11175--11251  Score: 111
    Period size: 27  Copynumber: 2.8  Consensus size: 28

      11165 AGGGTCACAT

                                       *
      11175 AGGGGCATTTTGGTCATTTTTACATT-C
          1 AGGGGCATTTTGGTCATTTTTACATTAA

                 *               *      
      11202 AGGGGTATTTTGGTCATTTTTGCATTAA
          1 AGGGGCATTTTGGTCATTTTTACATTAA

                 *                
      11230 AGGGGGATTTTGGTCATTTTTA
          1 AGGGGCATTTTGGTCATTTTTA

      11252 GTCCATTTTT


Statistics
Matches: 44,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  27   24  0.55
  28   20  0.45

ACGTcount: A:0.19, C:0.09, G:0.26, T:0.45


Consensus pattern (28 bp):   
AGGGGCATTTTGGTCATTTTTACATTAA

Found at i:11667 original size:24 final size:24

Alignment explanation


    Indices: 11640--11690  Score: 59
    Period size: 25  Copynumber: 2.1  Consensus size: 24

      11630 TTATTCTTAT

                                     
      11640 AAAGATACAAA-AGAAAATACAAAA
          1 AAAG-TACAAACAGAAAATACAAAA

                  *     *            
      11664 AAAGTAGAAACTGGAAAATACAAAA
          1 AAAGTACAAAC-AGAAAATACAAAA

              
      11689 AA
          1 AA

      11691 TGAAAGTTTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  23    5  0.22
  24    4  0.17
  25   14  0.61

ACGTcount: A:0.71, C:0.08, G:0.12, T:0.10


Consensus pattern (24 bp):   
AAAGTACAAACAGAAAATACAAAA
Done.