Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022078.1 Corchorus olitorius cultivar O-4 contig22111, 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: 9372
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:3217 original size:16 final size:15

Alignment explanation


    Indices: 3175--3222  Score: 53
    Period size: 16  Copynumber: 3.1  Consensus size: 15

       3165 CTCCATTTAC

                *           
       3175 TTTTTCTTTGCATTG-
          1 TTTTGCTTTG-ATTGA

                   *       
       3190 TTTTGCTCTGATTGA
          1 TTTTGCTTTGATTGA

                            
       3205 TTATTGCTTTGATTGA
          1 TT-TTGCTTTGATTGA

              
       3221 TT
          1 TT

       3223 GCCTATTCCT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  14    4  0.14
  15   10  0.36
  16   14  0.50

ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60


Consensus pattern (15 bp):   
TTTTGCTTTGATTGA

Found at i:6171 original size:15 final size:15

Alignment explanation


    Indices: 6145--6182  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6135 TTTGCTTTGT

                            
       6145 TTTCTAGTTTAATTGC
          1 TTTCT-GTTTAATTGC

                           
       6161 TTTCTGTTTAATTGC
          1 TTTCTGTTTAATTGC

                   
       6176 TTTCTGT
          1 TTTCTGT

       6183 CAACCTCTGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.13, C:0.13, G:0.13, T:0.61


Consensus pattern (15 bp):   
TTTCTGTTTAATTGC

Found at i:9340 original size:2 final size:2

Alignment explanation


    Indices: 9328--9372  Score: 81
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       9318 GTCTATGATT

                                                                           
       9328 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

              
       9371 TA
          1 TA


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   40  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.