Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010707.1 Corchorus olitorius cultivar O-4 contig10739, 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: 1925
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29


Found at i:1136 original size:10 final size:9

Alignment explanation


    Indices: 1110--1159  Score: 52
    Period size: 9  Copynumber: 5.7  Consensus size: 9

       1100 TAAAAGTAAC

                     
       1110 TAAGAAAAA
          1 TAAGAAAAA

                     
       1119 TAA-AAAAA
          1 TAAGAAAAA

                  *   
       1127 TATA-AGAAA
          1 TA-AGAAAAA

                     
       1136 -AAGAAAAA
          1 TAAGAAAAA

                      
       1144 TAACGAAAAA
          1 TAA-GAAAAA

                  
       1154 TAAGAA
          1 TAAGAA

       1160 GATAAGGGTA


Statistics
Matches: 35,  Mismatches: 2, Indels: 8
        0.78            0.04        0.18

Matches are distributed among these distances:
   7    1  0.03
   8   12  0.34
   9   13  0.37
  10    9  0.26

ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12


Consensus pattern (9 bp):   
TAAGAAAAA

Found at i:1142 original size:25 final size:25

Alignment explanation


    Indices: 1111--1159  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1101 AAAAGTAACT

                                      
       1111 AAGAAAAATAA-AAAAATATAAGAAA
          1 AAGAAAAATAACAAAAA-ATAAGAAA

                        *           
       1136 AAGAAAAATAACGAAAAATAAGAA
          1 AAGAAAAATAACAAAAAATAAGAA

       1160 GATAAGGGTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  25   18  0.82
  26    4  0.18

ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10


Consensus pattern (25 bp):   
AAGAAAAATAACAAAAAATAAGAAA
Done.