Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008915.1 Corchorus capsularis cultivar CVL-1 contig08936, 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: 19116
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:297 original size:29 final size:30

Alignment explanation


    Indices: 242--308  Score: 82
    Period size: 30  Copynumber: 2.3  Consensus size: 30

        232 CTTGGCAACA

                          ****            
        242 GGGTTTATTTGGCCTTTTTAAAGAGTTCAG
          1 GGGTTTATTTGGCCAAAATAAAGAGTTCAG

                                          
        272 GGGTTTATTTGGCCAAAATAAA-AGTTCAG
          1 GGGTTTATTTGGCCAAAATAAAGAGTTCAG

               *    
        301 GGGCTTAT
          1 GGGTTTAT

        309 AATTTGACGG


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  29   14  0.44
  30   18  0.56

ACGTcount: A:0.25, C:0.10, G:0.27, T:0.37


Consensus pattern (30 bp):   
GGGTTTATTTGGCCAAAATAAAGAGTTCAG

Found at i:10702 original size:1 final size:1

Alignment explanation


    Indices: 10696--10721  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      10686 TGATATAGGG

                                      
      10696 TTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTT

      10722 GAGCATATGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:10964 original size:24 final size:24

Alignment explanation


    Indices: 10931--10976  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      10921 CCCTTAACTG

                 *                  
      10931 TATAGTGGCGTTTAAACGCCGCAA
          1 TATAGGGGCGTTTAAACGCCGCAA

                            *     
      10955 TATAGGGGCGTTTAAATGCCGC
          1 TATAGGGGCGTTTAAACGCCGC

      10977 TATAATGCAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26


Consensus pattern (24 bp):   
TATAGGGGCGTTTAAACGCCGCAA

Found at i:11147 original size:30 final size:30

Alignment explanation


    Indices: 11111--11167  Score: 96
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      11101 CATTTCTTCT

                                          
      11111 ATAGACGCCTCAAAATAGGGGCATTTTCAA
          1 ATAGACGCCTCAAAATAGGGGCATTTTCAA

                          *       *    
      11141 ATAGACGCCTCAAAGTAGGGGCCTTTT
          1 ATAGACGCCTCAAAATAGGGGCATTTT

      11168 TTTCAGTAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25


Consensus pattern (30 bp):   
ATAGACGCCTCAAAATAGGGGCATTTTCAA

Found at i:15009 original size:2 final size:2

Alignment explanation


    Indices: 15002--15053  Score: 77
    Period size: 2  Copynumber: 26.0  Consensus size: 2

      14992 CCCCTTCCTT

                                       *  *  *                            
      15002 TA TA TA TA TA TA TA TA TA CA CA CA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                          
      15044 TA TA TA TA TA
          1 TA TA TA TA TA

      15054 AATGGCATTG


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   48  1.00

ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44


Consensus pattern (2 bp):   
TA

Found at i:15949 original size:8 final size:7

Alignment explanation


    Indices: 15922--15964  Score: 52
    Period size: 8  Copynumber: 6.0  Consensus size: 7

      15912 AGAGTAGTTG

                   
      15922 TATTATA
          1 TATTATA

                  *
      15929 T-TTATT
          1 TATTATA

                   
      15935 TATTATA
          1 TATTATA

                    
      15942 TATATATA
          1 TAT-TATA

                    
      15950 TATTATTA
          1 TATTA-TA

                   
      15958 TATTATA
          1 TATTATA

      15965 GTAAGACCAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
   6    5  0.16
   7   12  0.39
   8   14  0.45

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (7 bp):   
TATTATA
Done.