Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016656.1 Corchorus olitorius cultivar O-4 contig16689, 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: 4310
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31


Found at i:189 original size:22 final size:22

Alignment explanation


    Indices: 159--207  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        149 CCCTTCTTTT

                *          *      
        159 CTCCCCCCACTAACTCTTTCTC
          1 CTCCTCCCACTAACTATTTCTC

                       *          
        181 CTCCTCCCACTCACTATTTCTC
          1 CTCCTCCCACTAACTATTTCTC

            *    
        203 TTCCT
          1 CTCCT

        208 AAATGCTGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.12, C:0.51, G:0.00, T:0.37


Consensus pattern (22 bp):   
CTCCTCCCACTAACTATTTCTC

Found at i:786 original size:11 final size:11

Alignment explanation


    Indices: 770--794  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

        760 ACAACAAAAC

                       
        770 AATCAAACATG
          1 AATCAAACATG

                       
        781 AATCAAACATG
          1 AATCAAACATG

               
        792 AAT
          1 AAT

        795 GTCTGCAAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20


Consensus pattern (11 bp):   
AATCAAACATG

Found at i:2127 original size:23 final size:22

Alignment explanation


    Indices: 2092--2137  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2082 CCAAATTCGG

                  *                
       2092 GTCCAGTCGTCAAACCCGCGCGC
          1 GTCCAGGCGTC-AACCCGCGCGC

                    *      *      
       2115 GTCCAGGCTTCAACCTGCGCGC
          1 GTCCAGGCGTCAACCCGCGCGC

             
       2137 G
          1 G

       2138 GCTAGTGCCA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  22   11  0.55
  23    9  0.45

ACGTcount: A:0.15, C:0.41, G:0.28, T:0.15


Consensus pattern (22 bp):   
GTCCAGGCGTCAACCCGCGCGC

Found at i:4291 original size:2 final size:2

Alignment explanation


    Indices: 4284--4310  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4274 TTCACTTAAA

                                                    
       4284 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.