Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024882.1 Corchorus olitorius cultivar O-4 contig24915, 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: 6500
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30


Found at i:3011 original size:30 final size:31

Alignment explanation


    Indices: 2975--3045  Score: 112
    Period size: 30  Copynumber: 2.4  Consensus size: 31

       2965 ATTGAATTGT

                                   *       
       2975 TCAAATCCT-TTGGTTTGAACCTCAGCCTTA
          1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA

                                           
       3005 TCAAAT-CTGTTGGTTTGAACCTAAGCCTTA
          1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA

                        
       3035 TCAAAT-CTGTT
          1 TCAAATCCTGTT

       3046 ACTAGTTCAA


Statistics
Matches: 39,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  29    2  0.05
  30   37  0.95

ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38


Consensus pattern (31 bp):   
TCAAATCCTGTTGGTTTGAACCTAAGCCTTA

Found at i:5103 original size:15 final size:15

Alignment explanation


    Indices: 5083--5121  Score: 69
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       5073 ACAGAGATTG

                   *       
       5083 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       5098 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                     
       5113 ACAGAAAAC
          1 ACAGAAAAC

       5122 CTTAAAGATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.64, C:0.15, G:0.10, T:0.10


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:6283 original size:20 final size:18

Alignment explanation


    Indices: 6250--6286  Score: 56
    Period size: 20  Copynumber: 1.9  Consensus size: 18

       6240 TTGAAATAAA

                              
       6250 TCTTCAATAGTCTTCAAG
          1 TCTTCAATAGTCTTCAAG

                               
       6268 TCTTCAATTAAGTCTTCAA
          1 TCTTCAA-T-AGTCTTCAA

       6287 ATGGTCTTCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18    7  0.41
  19    1  0.06
  20    9  0.53

ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAG
Done.