Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001371.1 Corchorus olitorius cultivar O-4 contig01371, 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: 18884
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:4073 original size:31 final size:31

Alignment explanation


    Indices: 4028--4087  Score: 84
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       4018 AGCGTCTTGG

                                           
       4028 TCTGACATGACATTGCCACGTGGCATTTTGA
          1 TCTGACATGACATTGCCACGTGGCATTTTGA

                  *  *     *     *       
       4059 TCTGACGTGGCATTGTCACGTTGCATTTT
          1 TCTGACATGACATTGCCACGTGGCATTTT

       4088 TGGGAGAAAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   25  1.00

ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37


Consensus pattern (31 bp):   
TCTGACATGACATTGCCACGTGGCATTTTGA

Found at i:4512 original size:31 final size:29

Alignment explanation


    Indices: 4436--4512  Score: 75
    Period size: 31  Copynumber: 2.6  Consensus size: 29

       4426 TTCCAAATTG

                             *  **    *  
       4436 CAAATTTAGGGGCAAAATATCCAAAATTA
          1 CAAATTTAGGGGCAAAACATAAAAAAGTA

                        *                  
       4465 -AAATTTATGGGACAAAACATAAAAAACGTA
          1 CAAATTTA-GGGGCAAAACATAAAAAA-GTA

                              
       4495 CAAATTTAGGGGGCAAAA
          1 CAAATTTA-GGGGCAAAA

       4513 AGAACATTAC


Statistics
Matches: 38,  Mismatches: 7, Indels: 4
        0.78            0.14        0.08

Matches are distributed among these distances:
  28    7  0.18
  29   14  0.37
  30    2  0.05
  31   15  0.39

ACGTcount: A:0.51, C:0.12, G:0.17, T:0.21


Consensus pattern (29 bp):   
CAAATTTAGGGGCAAAACATAAAAAAGTA

Found at i:11624 original size:21 final size:21

Alignment explanation


    Indices: 11591--11630  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      11581 AACTCCGGAT

                *                
      11591 GATGGTGAAGAAGAAGAAGTA
          1 GATGATGAAGAAGAAGAAGTA

                    *    *     
      11612 GATGATGATGAAGGAGAAG
          1 GATGATGAAGAAGAAGAAG

      11631 AGGAGGGGGA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.45, C:0.00, G:0.40, T:0.15


Consensus pattern (21 bp):   
GATGATGAAGAAGAAGAAGTA

Found at i:13414 original size:9 final size:9

Alignment explanation


    Indices: 13400--13424  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

      13390 TTTTCTTCCA

                     
      13400 TTCAAATAG
          1 TTCAAATAG

                     
      13409 TTCAAATAG
          1 TTCAAATAG

                   
      13418 TTCAAAT
          1 TTCAAAT

      13425 GTTATCTTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36


Consensus pattern (9 bp):   
TTCAAATAG
Done.