Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001797.1 Corchorus olitorius cultivar O-4 contig01797, 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, 616

Length: 1028
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34


Found at i:336 original size:26 final size:25

Alignment explanation


    Indices: 306--354  Score: 71
    Period size: 26  Copynumber: 1.9  Consensus size: 25

        296 ATTTCCTTAT

                               *      
        306 TTCCTTCTTCTTCTTCTTTTTTTTTC
          1 TTCCTTCTTCTT-TTCTTTCTTTTTC

                  *                
        332 TTCCTTTTTCTTTTCTTTCTTTT
          1 TTCCTTCTTCTTTTCTTTCTTTT

        355 CCTTTCTATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   10  0.48
  26   11  0.52

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (25 bp):   
TTCCTTCTTCTTTTCTTTCTTTTTC

Found at i:345 original size:15 final size:14

Alignment explanation


    Indices: 310--373  Score: 62
    Period size: 14  Copynumber: 4.6  Consensus size: 14

        300 CCTTATTTCC

                           
        310 TTCTTCTTCTTCTTT
          1 TTCTT-TTCTTCTTT

                           
        325 TT-TTTTCTTCCTTT
          1 TTCTTTTCTT-CTTT

                           
        339 TTCTTTTCTT-TCTT
          1 TTCTTTTCTTCT-TT

               *      *   
        353 TTCCTTTC-TATTT
          1 TTCTTTTCTTCTTT

                    
        366 TTCTTTTC
          1 TTCTTTTC

        374 CCTTTTTGGG


Statistics
Matches: 43,  Mismatches: 2, Indels: 10
        0.78            0.04        0.18

Matches are distributed among these distances:
  13   16  0.37
  14   18  0.42
  15    9  0.21

ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75


Consensus pattern (14 bp):   
TTCTTTTCTTCTTT

Found at i:350 original size:19 final size:19

Alignment explanation


    Indices: 305--352  Score: 53
    Period size: 19  Copynumber: 2.5  Consensus size: 19

        295 AATTTCCTTA

                *              
        305 TTTCCTTCTTCTTCTTCTT
          1 TTTCTTTCTTCTTCTTCTT

               *          *     
        324 TTTTTTTCTTCCTTTTTC-T
          1 TTTCTTTCTT-CTTCTTCTT

                      
        343 TTTCTTTCTT
          1 TTTCTTTCTT

        353 TTCCTTTCTA


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  19   18  0.75
  20    6  0.25

ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75


Consensus pattern (19 bp):   
TTTCTTTCTTCTTCTTCTT

Found at i:574 original size:32 final size:28

Alignment explanation


    Indices: 505--560  Score: 94
    Period size: 29  Copynumber: 2.0  Consensus size: 28

        495 CTGGGCCGCG

                                        
        505 CGCTGGCCTGCTGTGCGCAGGCCCAGCA
          1 CGCTGGCCTGCTGTGCGCAGGCCCAGCA

             *                          
        533 CACTGGCCTGCCTGTGCGCAGGCCCAGC
          1 CGCTGGCCTG-CTGTGCGCAGGCCCAGC

        561 GGCCTGCTGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  28    9  0.35
  29   17  0.65

ACGTcount: A:0.11, C:0.41, G:0.34, T:0.14


Consensus pattern (28 bp):   
CGCTGGCCTGCTGTGCGCAGGCCCAGCA
Done.