Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022139.1 Corchorus olitorius cultivar O-4 contig22172, 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: 9179
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:1293 original size:135 final size:135

Alignment explanation


    Indices: 1053--1402  Score: 584
    Period size: 135  Copynumber: 2.6  Consensus size: 135

       1043 TTTCTAACAA

                                  *        *                                 
       1053 AAAACGCCGCTAAAT-GTCTTACTTTA-CTTCTAACTTTTCCTTTAATTATTTTT-GGGGGAATT
          1 AAAACGCCGCTAAATGGT-TTAGTTTATCTTTTAACTTTTCCTTTAATTATTTTTGGGGGGAATT

                                                  *                          
       1115 TTTCCCACCAATTTTTCTAAATAGCGGCATCTTTATATGAAACGCCACTAAATAGTGGCGTTTCA
         65 TTTCCCACCAATTTTTCTAAATAGCGGCATCTTTATATAAAACGCCACTAAATAGTGGCGTTTCA

                  
       1180 AATACC
        130 AATACC

                         *                                                   
       1186 AAAACGCCGCTAAGTGGTTTAGTTTATCTTTTAACTTTTCCTTTAATTATTTTTGGGGGGAATTT
          1 AAAACGCCGCTAAATGGTTTAGTTTATCTTTTAACTTTTCCTTTAATTATTTTTGGGGGGAATTT

                                       *                                     
       1251 TTCCCACCAATTTTTCTAAATAGCGGCGTCTTTATATAAAACGCCACTAAATAGTGGCGTTTCAA
         66 TTCCCACCAATTTTTCTAAATAGCGGCATCTTTATATAAAACGCCACTAAATAGTGGCGTTTCAA

                 
       1316 ATACC
        131 ATACC

                                                   *   *                     
       1321 AAAACGCCGCTAAATGGTTTAGTTTATCTTTTAACTTTTTCTTGAATTA-TTTTGGGGGGAA-TT
          1 AAAACGCCGCTAAATGGTTTAGTTTATCTTTTAACTTTTCCTTTAATTATTTTTGGGGGGAATTT

                        *      
       1384 TTCCCACCAATTATTCTAA
         66 TTCCCACCAATTTTTCTAA

       1403 TTTAGCGGTG


Statistics
Matches: 205,  Mismatches: 9, Indels: 6
        0.93            0.04        0.03

Matches are distributed among these distances:
 133   41  0.20
 134   40  0.20
 135  124  0.60

ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39


Consensus pattern (135 bp):   
AAAACGCCGCTAAATGGTTTAGTTTATCTTTTAACTTTTCCTTTAATTATTTTTGGGGGGAATTT
TTCCCACCAATTTTTCTAAATAGCGGCATCTTTATATAAAACGCCACTAAATAGTGGCGTTTCAA
ATACC

Found at i:5980 original size:12 final size:13

Alignment explanation


    Indices: 5948--5981  Score: 52
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       5938 TCATGCACCC

                         
       5948 AAAACATTTTATT
          1 AAAACATTTTATT

                         
       5961 AAAACATTTTA-T
          1 AAAACATTTTATT

               *     
       5973 AAAGCATTT
          1 AAAACATTT

       5982 AAATAAAAGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41


Consensus pattern (13 bp):   
AAAACATTTTATT

Found at i:7587 original size:10 final size:10

Alignment explanation


    Indices: 7546--7595  Score: 55
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       7536 ACCCAAAAAA

                      
       7546 AAAAAGAAAG
          1 AAAAAGAAAG

                        
       7556 AAAGAAAGAAAG
          1 -AA-AAAGAAAG

                **    
       7568 AAAACCAAAG
          1 AAAAAGAAAG

                      
       7578 AAAAAGAAAG
          1 AAAAAGAAAG

             *      
       7588 ATAAAGAA
          1 AAAAAGAA

       7596 CGTTAACCAA


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  10   21  0.64
  11    4  0.12
  12    8  0.24

ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02


Consensus pattern (10 bp):   
AAAAAGAAAG
Done.