Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015633.1 Corchorus olitorius cultivar O-4 contig15666, 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: 12123
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:7360 original size:19 final size:18

Alignment explanation


    Indices: 7327--7362  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7317 TTGAAATTAT

                    *         
       7327 TCTTCAATGGTCTTCAAA
          1 TCTTCAATAGTCTTCAAA

                              
       7345 TCTTCAAATAGTCTTCAA
          1 TCTTC-AATAGTCTTCAA

       7363 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAA

Found at i:7803 original size:15 final size:15

Alignment explanation


    Indices: 7783--7824  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       7773 ACAGAGATTG

                           
       7783 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                   *       
       7798 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                        
       7813 ACTAGAAAACAA
          1 AC-AGAAAACAA

       7825 AGCAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:11108 original size:21 final size:21

Alignment explanation


    Indices: 11084--11156  Score: 65
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      11074 GGCAGTGAAT

                                 
      11084 GGTGATGGCACGGGCATAGCC
          1 GGTGATGGCACGGGCATAGCC

                *          *  *  
      11105 GGTGGTGGCACGGGCTTAACC
          1 GGTGATGGCACGGGCATAGCC

                *  *       *  *   
      11126 GGTGGTGTCACGGTGAATGGCC
          1 GGTGATGGCACGG-GCATAGCC

               *     
      11148 GGTAATGGC
          1 GGTGATGGC

      11157 TTGGTAGTGG


Statistics
Matches: 40,  Mismatches: 11, Indels: 1
        0.77            0.21        0.02

Matches are distributed among these distances:
  21   30  0.75
  22   10  0.25

ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19


Consensus pattern (21 bp):   
GGTGATGGCACGGGCATAGCC

Done.