Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000236.1 Corchorus olitorius cultivar O-4 contig00236, 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, 718

Length: 1198
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30


Found at i:1109 original size:10 final size:9

Alignment explanation


    Indices: 1066--1123  Score: 50
    Period size: 10  Copynumber: 6.4  Consensus size: 9

       1056 TAAAAGTAAC

                     
       1066 TAAGAAAAA
          1 TAAGAAAAA

                *     
       1075 TAAACAAAAA
          1 T-AAGAAAAA

                      
       1085 TAA-AAGAAA
          1 TAAGAA-AAA

                     
       1094 -AAGAAAAA
          1 TAAGAAAAA

                      
       1102 TAACGAAAAA
          1 TAA-GAAAAA

                   * 
       1112 TAA-AAAGA
          1 TAAGAAAAA

                
       1120 TAAG
          1 TAAG

       1124 GGTAAGAAAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
   8   14  0.34
   9   10  0.24
  10   17  0.41

ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10


Consensus pattern (9 bp):   
TAAGAAAAA

Found at i:1109 original size:16 final size:17

Alignment explanation


    Indices: 1080--1117  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       1070 AAAAATAAAC

                             
       1080 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       1097 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 
       1113 AAAAA
          1 AAAAA

       1118 GATAAGGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG
Done.