Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019676.1 Corchorus olitorius cultivar O-4 contig19709, 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: 3062
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33


Found at i:1146 original size:54 final size:54

Alignment explanation


    Indices: 1004--1247  Score: 368
    Period size: 54  Copynumber: 4.6  Consensus size: 54

        994 AGATCTAAGC

                   *           * *                                
       1004 TGATCTTTTGATGGTCCTGGGTGACCTTTCAATCAA-TTTCAG-AAATCTATGT
          1 TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTATGT

                               * *                                 
       1056 TGAT-TTCTGATGGTCCTGGGTGACCTTTCAAGTCAATTTTCAGAAAATCTATGT
          1 TGATCTTCTGATGGTCCTGAGCGACCTTTCAA-TCAATTTTCAGAAAATCTATGT

                                                                  
       1110 TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTATGT
          1 TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTATGT

                                                              *  *
       1164 TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTCTGC
          1 TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTATGT

                      *      * *          
       1218 TGATCTTCTGGTGGTCCCGTGCGACCTTTC
          1 TGATCTTCTGATGGTCCTGAGCGACCTTTC

       1248 CATTAATCTT


Statistics
Matches: 180,  Mismatches: 8, Indels: 6
        0.93            0.04        0.03

Matches are distributed among these distances:
  51   26  0.14
  52    8  0.04
  53    6  0.03
  54  115  0.64
  55   25  0.14

ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38


Consensus pattern (54 bp):   
TGATCTTCTGATGGTCCTGAGCGACCTTTCAATCAATTTTCAGAAAATCTATGT

Found at i:1854 original size:3 final size:3

Alignment explanation


    Indices: 1846--1880  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       1836 TCTTGTTTTC

                                                          
       1846 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

       1881 ATAAAATCGG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:2427 original size:12 final size:12

Alignment explanation


    Indices: 2408--2446  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       2398 ACCCAATAGC

                        
       2408 AAAAAAAAA-AA
          1 AAAAAAAAACAA

              *         
       2419 AAGAAAAAACAA
          1 AAAAAAAAACAA

               *        
       2431 AAACAAAAACAA
          1 AAAAAAAAACAA

                
       2443 AAAA
          1 AAAA

       2447 TTCGGGTAGT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  11    8  0.35
  12   15  0.65

ACGTcount: A:0.90, C:0.08, G:0.03, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAACAA

Found at i:2734 original size:10 final size:10

Alignment explanation


    Indices: 2719--2750  Score: 64
    Period size: 10  Copynumber: 3.2  Consensus size: 10

       2709 ATTTTCCGGC

                      
       2719 GGCCGGCGGT
          1 GGCCGGCGGT

                      
       2729 GGCCGGCGGT
          1 GGCCGGCGGT

                      
       2739 GGCCGGCGGT
          1 GGCCGGCGGT

              
       2749 GG
          1 GG

       2751 TGGTTGGTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   22  1.00

ACGTcount: A:0.00, C:0.28, G:0.62, T:0.09


Consensus pattern (10 bp):   
GGCCGGCGGT

Found at i:2825 original size:10 final size:9

Alignment explanation


    Indices: 2784--2823  Score: 62
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       2774 CCGGTGGTGG

                *    
       2784 TTGGGGTTC
          1 TTGGTGTTC

                     
       2793 TTGGTGTTC
          1 TTGGTGTTC

                     
       2802 TTGGTGTTC
          1 TTGGTGTTC

                      
       2811 TTGAGTGTTC
          1 TTG-GTGTTC

               
       2821 TTG
          1 TTG

       2824 AGAAAAAGGG


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   9   20  0.69
  10    9  0.31

ACGTcount: A:0.03, C:0.10, G:0.35, T:0.53


Consensus pattern (9 bp):   
TTGGTGTTC
Done.