Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010837.1 Corchorus olitorius cultivar O-4 contig10869, 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: 6533
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40


Found at i:569 original size:2 final size:2

Alignment explanation


    Indices: 556--633  Score: 88
    Period size: 2  Copynumber: 37.5  Consensus size: 2

        546 ACTAAAAATA

                                                *                          
        556 AT AT AT AGT AT AT AT AGT AT A- AGT GT AT AT AT AT AT AT AT AGT
          1 AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT A-T

                                                                 
        599 AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        634 AACAAACAAT


Statistics
Matches: 67,  Mismatches: 2, Indels: 14
        0.81            0.02        0.17

Matches are distributed among these distances:
   1    2  0.03
   2   58  0.87
   3    7  0.10

ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:948 original size:40 final size:41

Alignment explanation


    Indices: 900--990  Score: 107
    Period size: 40  Copynumber: 2.2  Consensus size: 41

        890 GATTATCTTA

                                                       
        900 CTTAGGGTTTAACA-TGATTTTAGGG-AATTCTTCT-ATCTCT
          1 CTTAGGGTTTAACATTG-TTTT-GGGCAATTCTTCTAATCTCT

                       *             **     *        
        940 CTTAGGGTTTAGCATTGTTTTGGGCTCTTCTTTTAATCTCT
          1 CTTAGGGTTTAACATTGTTTTGGGCAATTCTTCTAATCTCT

                      
        981 CTTAGGGTTT
          1 CTTAGGGTTT

        991 GTCTATCATG


Statistics
Matches: 44,  Mismatches: 4, Indels: 5
        0.83            0.08        0.09

Matches are distributed among these distances:
  39    3  0.07
  40   23  0.52
  41   18  0.41

ACGTcount: A:0.16, C:0.15, G:0.20, T:0.48


Consensus pattern (41 bp):   
CTTAGGGTTTAACATTGTTTTGGGCAATTCTTCTAATCTCT

Found at i:3088 original size:23 final size:23

Alignment explanation


    Indices: 3037--3088  Score: 68
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       3027 AGCAGCTAAT

                                  *
       3037 TATTGTTCCTATATTCATGAGTG
          1 TATTGTTCCTATATTCATGAGTA

             *          *       *  
       3060 TTTTGTTCCTATTTTCATGATTA
          1 TATTGTTCCTATATTCATGAGTA

                  
       3083 TATTGT
          1 TATTGT

       3089 CAGTTTGTGT


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.19, C:0.12, G:0.13, T:0.56


Consensus pattern (23 bp):   
TATTGTTCCTATATTCATGAGTA
Done.