Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024038.1 Corchorus olitorius cultivar O-4 contig24071, 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: 4540
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37


Found at i:2217 original size:15 final size:16

Alignment explanation


    Indices: 2184--2223  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       2174 TTACTTTGTT

                            
       2184 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
       2200 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
       2215 TTGCTTTCT
          1 TTGTTTTCT

       2224 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:4135 original size:35 final size:35

Alignment explanation


    Indices: 4003--4177  Score: 172
    Period size: 36  Copynumber: 4.8  Consensus size: 35

       3993 CATCAGGTCA

                   *                  *         
       4003 AAGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCATC-AGTTTTT

                                   *            
       4039 AAGTTTTCAAATTGGGAAAGTTCTCATTCAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCA-TCAGTTTTT

                    *                      *  * 
       4075 AAAGTTTTTAAATTGGGAAAGTTCCCATCAGGTTCT
          1 -AAGTTTTCAAATTGGGAAAGTTCCCATCAGTTTTT

                      *                    *        
       4111 -AGTTTTCAATTTAGGGAAAGTTCCCATCATTTTCAGTTT
          1 AAGTTTTCAAATT-GGGAAAGTTCCCATCA-GTT---TTT

            *     *    *                
       4150 TAGTTTCCAAAGTGGGAAAGTTCCCATC
          1 AAGTTTTCAAATTGGGAAAGTTCCCATC

       4178 GAAAATCAGT


Statistics
Matches: 116,  Mismatches: 15, Indels: 13
        0.81            0.10        0.09

Matches are distributed among these distances:
  34   10  0.09
  35   16  0.14
  36   39  0.34
  37   25  0.22
  39   17  0.15
  40    9  0.08

ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39


Consensus pattern (35 bp):   
AAGTTTTCAAATTGGGAAAGTTCCCATCAGTTTTT
Done.