Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001084.1 Corchorus capsularis cultivar CVL-1 contig01084, 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: 14981
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:2657 original size:20 final size:19

Alignment explanation


    Indices: 2612--2669  Score: 59
    Period size: 20  Copynumber: 3.1  Consensus size: 19

       2602 AATATTACGG

                               
       2612 GATATCCGTCGATATATCC
          1 GATATCCGTCGATATATCC

              *                   
       2631 GTGTATCCGTCGATATTTAT-C
          1 G-ATATCCGTCGATA--TATCC

                               
       2652 GATAT-C-TCGATATATCC
          1 GATATCCGTCGATATATCC

             
       2669 G
          1 G

       2670 TAAATATCCG


Statistics
Matches: 33,  Mismatches: 2, Indels: 10
        0.73            0.04        0.22

Matches are distributed among these distances:
  16    3  0.09
  17    2  0.06
  18    6  0.18
  19    2  0.06
  20   15  0.45
  21    2  0.06
  22    3  0.09

ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36


Consensus pattern (19 bp):   
GATATCCGTCGATATATCC

Found at i:2676 original size:10 final size:10

Alignment explanation


    Indices: 2663--2698  Score: 63
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       2653 ATATCTCGAT

                      
       2663 ATATCCGTAA
          1 ATATCCGTAA

                      
       2673 ATATCCGTAA
          1 ATATCCGTAA

                  *   
       2683 ATATCCATAA
          1 ATATCCGTAA

                  
       2693 ATATCC
          1 ATATCC

       2699 ATGTTAAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  10   25  1.00

ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31


Consensus pattern (10 bp):   
ATATCCGTAA

Found at i:4349 original size:36 final size:36

Alignment explanation


    Indices: 4309--4377  Score: 86
    Period size: 35  Copynumber: 1.9  Consensus size: 36

       4299 TTTTATGAAA

                                        *        
       4309 TATTTTGTGAAAATGGGAAAAATA-TGGTATTTTCAG
          1 TATTTT-TGAAAATGGGAAAAATATTGGGATTTTCAG

                     **    *                 
       4345 TATTTTTGACTATGGTAAAAATATTGGGATTTT
          1 TATTTTTGAAAATGGGAAAAATATTGGGATTTT

       4378 TGTGTTTAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  35   14  0.50
  36   14  0.50

ACGTcount: A:0.33, C:0.03, G:0.20, T:0.43


Consensus pattern (36 bp):   
TATTTTTGAAAATGGGAAAAATATTGGGATTTTCAG

Found at i:5801 original size:13 final size:12

Alignment explanation


    Indices: 5771--5813  Score: 77
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       5761 CATCGATACC

                        
       5771 TCGATATATCCG
          1 TCGATATATCCG

                        
       5783 TCGATATATCCG
          1 TCGATATATCCG

                         
       5795 TTCGATATATCCG
          1 -TCGATATATCCG

                  
       5808 TCGATA
          1 TCGATA

       5814 CCTGTATTAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   18  0.60
  13   12  0.40

ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35


Consensus pattern (12 bp):   
TCGATATATCCG

Found at i:10843 original size:21 final size:20

Alignment explanation


    Indices: 10797--10843  Score: 51
    Period size: 21  Copynumber: 2.2  Consensus size: 20

      10787 GTGAACGTTC

                *               
      10797 TTATATTAAATTAATTATTA
          1 TTATTTTAAATTAATTATTA

                                   
      10817 TATATTTTAAA-TAATTAATTTA
          1 T-TATTTTAAATTAATT-A-TTA

                 
      10839 TTATT
          1 TTATT

      10844 CATAAAAACG


Statistics
Matches: 23,  Mismatches: 1, Indels: 5
        0.79            0.03        0.17

Matches are distributed among these distances:
  20    6  0.26
  21   13  0.57
  22    4  0.17

ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57


Consensus pattern (20 bp):   
TTATTTTAAATTAATTATTA

Found at i:12229 original size:40 final size:40

Alignment explanation


    Indices: 12182--12262  Score: 135
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      12172 ATTATAACTA

                         *         *                
      12182 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATTAG
          1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG

                                      *             
      12222 GGGGCTAAACCTGAATTTAATTTATTTCCTTAATTATTAG
          1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG

             
      12262 G
          1 G

      12263 AGAGTCAAAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  40   38  1.00

ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41


Consensus pattern (40 bp):   
GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAG

Found at i:12279 original size:13 final size:13

Alignment explanation


    Indices: 12261--12290  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      12251 TTAATTATTA

                  *      
      12261 GGAGAGTCAAATT
          1 GGAGAGACAAATT

                         
      12274 GGAGAGACAAATT
          1 GGAGAGACAAATT

                
      12287 GGAG
          1 GGAG

      12291 GGTAAAAAAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.40, C:0.07, G:0.37, T:0.17


Consensus pattern (13 bp):   
GGAGAGACAAATT
Done.