Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022361.1 Corchorus olitorius cultivar O-4 contig22394, 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: 15678
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:43 original size:24 final size:25

Alignment explanation


    Indices: 15--73  Score: 75
    Period size: 25  Copynumber: 2.4  Consensus size: 25

          5 TTTTTTAGAA

                        **           
         15 AACGCAAAAAC-CCTTTTTTTTTAT
          1 AACGCAAAAACAAATTTTTTTTTAT

            *     *                  
         39 GACGCAGAAACAAATTTTTTTTTAT
          1 AACGCAAAAACAAATTTTTTTTTAT

                      
         64 AACGCAAAAA
          1 AACGCAAAAA

         74 TATTTTTTTC


Statistics
Matches: 28,  Mismatches: 6, Indels: 1
        0.80            0.17        0.03

Matches are distributed among these distances:
  24    9  0.32
  25   19  0.68

ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34


Consensus pattern (25 bp):   
AACGCAAAAACAAATTTTTTTTTAT

Found at i:56 original size:25 final size:23

Alignment explanation


    Indices: 28--82  Score: 74
    Period size: 25  Copynumber: 2.3  Consensus size: 23

         18 GCAAAAACCC

                       *             
         28 TTTTTTTTTATGACGCAGAAACAAA
          1 TTTTTTTTTATAACGCA-AAA-AAA

                                 * 
         53 TTTTTTTTTATAACGCAAAAATA
          1 TTTTTTTTTATAACGCAAAAAAA

                   
         76 TTTTTTT
          1 TTTTTTT

         83 CGACGCAAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    9  0.32
  24    3  0.11
  25   16  0.57

ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51


Consensus pattern (23 bp):   
TTTTTTTTTATAACGCAAAAAAA

Found at i:466 original size:16 final size:15

Alignment explanation


    Indices: 428--469  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        418 AAAACAGTTG

                   *       
        428 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
        443 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        458 ACTAGAAAACAA
          1 AC-AGAAAACAA

        470 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

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


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:8090 original size:19 final size:18

Alignment explanation


    Indices: 8057--8092  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       8047 TTGAAATAAT

                              
       8057 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       8075 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       8093 TGAGTCTTCA


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:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:8100 original size:11 final size:10

Alignment explanation


    Indices: 8057--8103  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       8047 TTGAAATAAT

                      
       8057 TCTTCAATGA
          1 TCTTCAATGA

                      
       8067 TCTTCAA--A
          1 TCTTCAATGA

                     * 
       8075 TCTTCAAATTA
          1 TCTTC-AATGA

                      
       8086 TCTTCAATGA
          1 TCTTCAATGA

                    
       8096 GTCTTCAA
          1 -TCTTCAA

       8104 ACACGAGATT


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    6  0.19
   9    2  0.06
  10   11  0.34
  11   13  0.41

ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40


Consensus pattern (10 bp):   
TCTTCAATGA
Done.