Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021734.1 Corchorus olitorius cultivar O-4 contig21767, 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: 13212
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:619 original size:15 final size:15

Alignment explanation


    Indices: 589--630  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        579 TTACTTTGCT

                            
        589 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        605 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
        620 TTGTTTTCTGT
          1 TTGTTTTCTGT

        631 CAACGTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3523 original size:19 final size:18

Alignment explanation


    Indices: 3490--3525  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3480 TTGAGATAAT

                              
       3490 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       3508 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       3526 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:10086 original size:32 final size:33

Alignment explanation


    Indices: 10050--10114  Score: 105
    Period size: 32  Copynumber: 2.0  Consensus size: 33

      10040 GTTTTTCTTT

                                      *      
      10050 TCTGCGTTTTCTCTAAAAAAAAAA-GTTTTTTG
          1 TCTGCGTTTTCTCTAAAAAAAAAATGGTTTTTG

                      *                      
      10082 TCTGCGTTTTTTCTAAAAAAAAAATGGTTTTTG
          1 TCTGCGTTTTCTCTAAAAAAAAAATGGTTTTTG

      10115 CGTTTTTAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  32   23  0.77
  33    7  0.23

ACGTcount: A:0.31, C:0.11, G:0.14, T:0.45


Consensus pattern (33 bp):   
TCTGCGTTTTCTCTAAAAAAAAAATGGTTTTTG

Found at i:12886 original size:16 final size:15

Alignment explanation


    Indices: 12848--12889  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      12838 ACAGAGATTG

                   *       
      12848 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      12863 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      12878 ACTAGAAAACAA
          1 AC-AGAAAACAA

      12890 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.