Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010507.1 Corchorus capsularis cultivar CVL-1 contig10528, 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: 28658
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:3880 original size:1 final size:1

Alignment explanation


    Indices: 3874--3898  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

       3864 AAAGGGTACG

                                     
       3874 TTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTT

       3899 GGAGAAGATG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

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


Consensus pattern (1 bp):   
T

Found at i:4447 original size:13 final size:13

Alignment explanation


    Indices: 4429--4453  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4419 TTCAATATTC

                         
       4429 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       4442 TAAATATTATTT
          1 TAAATATTATTT

       4454 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:5439 original size:29 final size:29

Alignment explanation


    Indices: 5402--5459  Score: 98
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       5392 TCTCGTTTTT

                *                        
       5402 AAAAGTTAAGGGCCCAATTTATCCCAAAA
          1 AAAAATTAAGGGCCCAATTTATCCCAAAA

                        *                
       5431 AAAAATTAAGGGGCCAATTTATCCCAAAA
          1 AAAAATTAAGGGCCCAATTTATCCCAAAA

       5460 TGGATAGTTA


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   27  1.00

ACGTcount: A:0.47, C:0.19, G:0.14, T:0.21


Consensus pattern (29 bp):   
AAAAATTAAGGGCCCAATTTATCCCAAAA

Found at i:26048 original size:45 final size:45

Alignment explanation


    Indices: 25980--26070  Score: 137
    Period size: 45  Copynumber: 2.0  Consensus size: 45

      25970 ACTGCTTAGA

                         *                   *      *    
      25980 CCCTATTGATAAATATCCCTTAAAGCAAGGAATTAACAATGCTGT
          1 CCCTATTGATAAAAATCCCTTAAAGCAAGGAATAAACAATCCTGT

                            * *                          
      26025 CCCTATTGATAAAAATGCTTTAAAGCAAGGAATAAACAATCCTGT
          1 CCCTATTGATAAAAATCCCTTAAAGCAAGGAATAAACAATCCTGT

             
      26070 C
          1 C

      26071 TGCCAAACAC


Statistics
Matches: 41,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  45   41  1.00

ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27


Consensus pattern (45 bp):   
CCCTATTGATAAAAATCCCTTAAAGCAAGGAATAAACAATCCTGT
Done.