Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023225.1 Corchorus olitorius cultivar O-4 contig23258, 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: 3213
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31


Found at i:1182 original size:34 final size:34

Alignment explanation


    Indices: 1144--1227  Score: 123
    Period size: 34  Copynumber: 2.5  Consensus size: 34

       1134 AAAAATTGAA

                             **               
       1144 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                         *                 *  
       1178 TGGGAACTTTCCCGATTACAAAACTTAAAACTGG
          1 TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

                      *     
       1212 TGGGAACTTTTCCAAT
          1 TGGGAACTTTCCCAAT

       1228 AAAAAAAACT


Statistics
Matches: 44,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  34   44  1.00

ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Consensus pattern (34 bp):   
TGGGAACTTTCCCAATTACAAAACTTAAAACCGG

Found at i:1236 original size:35 final size:34

Alignment explanation


    Indices: 1144--1240  Score: 113
    Period size: 34  Copynumber: 2.8  Consensus size: 34

       1134 AAAAATTGAA

                            ***               
       1144 TGGGAACTTTCCCAATTTGAAAACTTAAAACCGG
          1 TGGGAACTTTCCCAATAAAAAAACTTAAAACCGG

                         *  * *            *  
       1178 TGGGAACTTTCCCGATTACAAAACTTAAAACTGG
          1 TGGGAACTTTCCCAATAAAAAAACTTAAAACCGG

                      *                  
       1212 TGGGAACTTTTCCAATAAAAAAAACTTAA
          1 TGGGAACTTTCCCAAT-AAAAAAACTTAA

       1241 TGATATTCTC


Statistics
Matches: 54,  Mismatches: 8, Indels: 1
        0.86            0.13        0.02

Matches are distributed among these distances:
  34   44  0.81
  35   10  0.19

ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27


Consensus pattern (34 bp):   
TGGGAACTTTCCCAATAAAAAAACTTAAAACCGG

Found at i:1268 original size:14 final size:14

Alignment explanation


    Indices: 1251--1277  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       1241 TGATATTCTC

                          
       1251 TTTTTGATTTTGAG
          1 TTTTTGATTTTGAG

                         
       1265 TTTTTGATTTTGA
          1 TTTTTGATTTTGA

       1278 CAACCTTTTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.19, T:0.67


Consensus pattern (14 bp):   
TTTTTGATTTTGAG
Done.