Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009292.1 Corchorus capsularis cultivar CVL-1 contig09313, 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: 3409
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41


Found at i:205 original size:19 final size:20

Alignment explanation


    Indices: 174--212  Score: 55
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        164 TATTGACATT

                                
        174 TAAAAATTGAAATT-AAAAA
          1 TAAAAATTGAAATTCAAAAA

                                 
        193 TAAAATATT-AAATTCAAAAA
          1 TAAAA-ATTGAAATTCAAAAA

        213 ATAATAGTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19   10  0.56
  20    8  0.44

ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28


Consensus pattern (20 bp):   
TAAAAATTGAAATTCAAAAA

Found at i:607 original size:2 final size:2

Alignment explanation


    Indices: 600--651  Score: 68
    Period size: 2  Copynumber: 25.0  Consensus size: 2

        590 TTCGTATTTT

                               *                                 *          
        600 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TC TA TA CTA
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA

                       
        644 TA TA TA TA
          1 TA TA TA TA

        652 CATGAAATCG


Statistics
Matches: 44,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
   2   40  0.91
   3    4  0.09

ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:1777 original size:28 final size:27

Alignment explanation


    Indices: 1732--1808  Score: 86
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       1722 TTTATTATCT

                       *                
       1732 CAAAAAAA-TCAATATTTTATTTTACT-
          1 CAAAAAAACTCTAT-TTTTATTTTACTG

                                     *   
       1758 CAACTAAAAACTCTATTTTTATTTTTCTG
          1 CAA--AAAAACTCTATTTTTATTTTACTG

            *                     
       1787 TAAAAAAACTCTATTTTTATTT
          1 CAAAAAAACTCTATTTTTATTT

       1809 AATTAAATCT


Statistics
Matches: 44,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  26    3  0.07
  27   19  0.43
  28   16  0.36
  29    6  0.14

ACGTcount: A:0.39, C:0.13, G:0.01, T:0.47


Consensus pattern (27 bp):   
CAAAAAAACTCTATTTTTATTTTACTG

Found at i:1815 original size:25 final size:27

Alignment explanation


    Indices: 1763--1815  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1753 TTACTCAACT

                                **     
       1763 AAAAACTCTATTTTTATTTTTCTGTAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

                                       
       1790 AAAAACTCTATTTTTA-TTTAAT-TAA
          1 AAAAACTCTATTTTTATTTTAATGTAA

             
       1815 A
          1 A

       1816 TCTAATATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  25    4  0.17
  26    4  0.17
  27   16  0.67

ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49


Consensus pattern (27 bp):   
AAAAACTCTATTTTTATTTTAATGTAA

Found at i:1964 original size:29 final size:30

Alignment explanation


    Indices: 1928--1991  Score: 114
    Period size: 29  Copynumber: 2.2  Consensus size: 30

       1918 TAAAAACAAA

                                          
       1928 CTTTTACAATTATTCTACT-AAAACTCTAT
          1 CTTTTACAATTATTCTACTAAAAACTCTAT

                                          
       1957 CTTTTACAATTATTCTACTAAAAACTCTAT
          1 CTTTTACAATTATTCTACTAAAAACTCTAT

                  
       1987 -TTTTA
          1 CTTTTA

       1992 TTCAATTAAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  29   24  0.71
  30   10  0.29

ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47


Consensus pattern (30 bp):   
CTTTTACAATTATTCTACTAAAAACTCTAT

Found at i:3085 original size:109 final size:109

Alignment explanation


    Indices: 2873--3165  Score: 432
    Period size: 109  Copynumber: 2.7  Consensus size: 109

       2863 ACTATTATAG

                         *                     *                             
       2873 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTAC-T
          1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT

                                                             
       2937 TATTTTT-CCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
         61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                   *                                                         
       2985 TTTTATTATACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT

                                 *                      
       3050 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
         66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                                                                       **    
       3094 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATATGATTTTTTTA
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA--ATTACTTTA

                     
       3157 TTTTTACCA
         63 TTTTTACCA

       3166 TTTTTAATTT


Statistics
Matches: 169,  Mismatches: 7, Indels: 12
        0.90            0.04        0.06

Matches are distributed among these distances:
 107   30  0.18
 108   18  0.11
 109   85  0.50
 110   16  0.09
 112   20  0.12

ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50


Consensus pattern (109 bp):   
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.