Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017990.1 Corchorus olitorius cultivar O-4 contig18023, 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: 4041
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35


Found at i:731 original size:32 final size:32

Alignment explanation


    Indices: 674--734  Score: 88
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        664 AAATATGTTT

                                *           
        674 GAAAAATAAGGGTATAATGATCGATTCAATTA
          1 GAAAAATAAGGGTATAATGACCGATTCAATTA

                    *                     
        706 GAAAAATACGGGTATAAT-AGCCGATTCAA
          1 GAAAAATAAGGGTATAATGA-CCGATTCAA

        735 AAGTTTTACA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  31    1  0.04
  32   25  0.96

ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25


Consensus pattern (32 bp):   
GAAAAATAAGGGTATAATGACCGATTCAATTA

Found at i:2036 original size:19 final size:20

Alignment explanation


    Indices: 2009--2046  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1999 ATTCAAAACA

                                
       2009 AAATAAAAACTACCCATTTT
          1 AAATAAAAACTACCCATTTT

                               
       2029 AAAT-AAAACTACCCATTT
          1 AAATAAAAACTACCCATTT

       2047 CAGGATAAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   14  0.78
  20    4  0.22

ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29


Consensus pattern (20 bp):   
AAATAAAAACTACCCATTTT

Found at i:2211 original size:24 final size:24

Alignment explanation


    Indices: 2184--2268  Score: 97
    Period size: 24  Copynumber: 3.7  Consensus size: 24

       2174 AAAAATTAAT

                  *     *           
       2184 TATTAAGTTTTATTTTTAATTGAA
          1 TATTAAATTTTAATTTTAATTGAA

                             *      
       2208 TATTAAATTTTAATTTTGA-T-AA
          1 TATTAAATTTTAATTTTAATTGAA

                  *    *            
       2230 -A-TAACTTTTTATTTTAATTGAA
          1 TATTAAATTTTAATTTTAATTGAA

                             
       2252 TATTAAATTTTAATTTT
          1 TATTAAATTTTAATTTT

       2269 GATAAATAAC


Statistics
Matches: 49,  Mismatches: 8, Indels: 8
        0.75            0.12        0.12

Matches are distributed among these distances:
  20   13  0.27
  21    2  0.04
  22    4  0.08
  23    2  0.04
  24   28  0.57

ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58


Consensus pattern (24 bp):   
TATTAAATTTTAATTTTAATTGAA

Found at i:2238 original size:20 final size:20

Alignment explanation


    Indices: 2215--2282  Score: 73
    Period size: 20  Copynumber: 3.2  Consensus size: 20

       2205 GAATATTAAA

                                
       2215 TTTTAATTTTGATAAATAAC
          1 TTTTAATTTTGATAAATAAC

                *     *            *
       2235 TTTTTATTTTAATTGAATATTAAA
          1 TTTTAATTTTGA-T-AA-A-TAAC

                                
       2259 TTTTAATTTTGATAAATAAC
          1 TTTTAATTTTGATAAATAAC

                
       2279 TTTT
          1 TTTT

       2283 TCAACTGCCG


Statistics
Matches: 38,  Mismatches: 6, Indels: 8
        0.73            0.12        0.15

Matches are distributed among these distances:
  20   17  0.45
  21    2  0.05
  22    4  0.11
  23    2  0.05
  24   13  0.34

ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56


Consensus pattern (20 bp):   
TTTTAATTTTGATAAATAAC

Found at i:2250 original size:44 final size:45

Alignment explanation


    Indices: 2191--2283  Score: 179
    Period size: 44  Copynumber: 2.1  Consensus size: 45

       2181 AATTATTAAG

                                                         
       2191 TTTTATTTTTAATTGAATATTAAATTTTAATTTTGATAAATAACT
          1 TTTTATTTTTAATTGAATATTAAATTTTAATTTTGATAAATAACT

                                                         
       2236 TTTTA-TTTTAATTGAATATTAAATTTTAATTTTGATAAATAACT
          1 TTTTATTTTTAATTGAATATTAAATTTTAATTTTGATAAATAACT

                
       2280 TTTT
          1 TTTT

       2284 CAACTGCCGG


Statistics
Matches: 48,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  44   43  0.90
  45    5  0.10

ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57


Consensus pattern (45 bp):   
TTTTATTTTTAATTGAATATTAAATTTTAATTTTGATAAATAACT
Done.