Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012046.1 Corchorus olitorius cultivar O-4 contig12079, 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: 18778
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:71 original size:18 final size:20

Alignment explanation


    Indices: 48--84  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

         38 GTAATTAGGT

                                
         48 TGTC-AATCCCT-CTAATTC
          1 TGTCAAATCCCTACTAATTC

                               
         66 TGTCAAATCCCTACTAATT
          1 TGTCAAATCCCTACTAATT

         85 AGTCTGTACA


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

Matches are distributed among these distances:
  18    4  0.24
  19    7  0.41
  20    6  0.35

ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38


Consensus pattern (20 bp):   
TGTCAAATCCCTACTAATTC

Found at i:3264 original size:18 final size:20

Alignment explanation


    Indices: 3241--3278  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       3231 AGCAATTAGG

                                
       3241 TTGTC-AATCCCT-CTAATT
          1 TTGTCAAATCCCTACTAATT

                                
       3259 TTGTCAAATCCCTACTAATT
          1 TTGTCAAATCCCTACTAATT

       3279 AGTTTGTACA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  18    5  0.28
  19    7  0.39
  20    6  0.33

ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42


Consensus pattern (20 bp):   
TTGTCAAATCCCTACTAATT

Found at i:7189 original size:17 final size:17

Alignment explanation


    Indices: 7146--7181  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       7136 AAAGAAAGAA

                             
       7146 GCAAAAGCTAGGCTTAT
          1 GCAAAAGCTAGGCTTAT

                             
       7163 GCAAAAGCTAGGCTTAT
          1 GCAAAAGCTAGGCTTAT

              
       7180 GC
          1 GC

       7182 GATAGCTATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22


Consensus pattern (17 bp):   
GCAAAAGCTAGGCTTAT

Found at i:8747 original size:14 final size:14

Alignment explanation


    Indices: 8728--8773  Score: 58
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       8718 TTACTATTTA

                          
       8728 AATTTTTAATTTGT
          1 AATTTTTAATTTGT

                        * 
       8742 AATTTTTAATTTCT
          1 AATTTTTAATTTGT

                 *   *    
       8756 AATTTCTAACTTG-
          1 AATTTTTAATTTGT

                 
       8769 AATTT
          1 AATTT

       8774 ATTTTGTCTT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  13    5  0.18
  14   23  0.82

ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59


Consensus pattern (14 bp):   
AATTTTTAATTTGT
Done.