Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018413.1 Corchorus olitorius cultivar O-4 contig18446, 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: 17475
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1904 original size:20 final size:21

Alignment explanation


    Indices: 1881--1919  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1871 ATAGCATCAT

                     *           
       1881 AACCT-TTTTAATAACCTTTA
          1 AACCTCTTTGAATAACCTTTA

                       *       
       1901 AACCTCTTTGACTAACCTT
          1 AACCTCTTTGAATAACCTT

       1920 ATATAAGTTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    5  0.31
  21   11  0.69

ACGTcount: A:0.31, C:0.26, G:0.03, T:0.41


Consensus pattern (21 bp):   
AACCTCTTTGAATAACCTTTA

Found at i:2192 original size:24 final size:24

Alignment explanation


    Indices: 2165--2224  Score: 93
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       2155 ATGGATACTA

                                  * 
       2165 TTATATTCATCTTATATAGATTTC
          1 TTATATTCATCTTATATAGATTAC

                             *      
       2189 TTATATTCATCTTATATCGATTAC
          1 TTATATTCATCTTATATAGATTAC

                   *    
       2213 TTATATTAATCT
          1 TTATATTCATCT

       2225 AAAATTATTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   33  1.00

ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53


Consensus pattern (24 bp):   
TTATATTCATCTTATATAGATTAC

Found at i:4232 original size:24 final size:24

Alignment explanation


    Indices: 4205--4258  Score: 65
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       4195 TGAATTTTCT

                                 *   
       4205 ATTA-TATATGATTTATAAAACTTA
          1 ATTATTAT-TGATTTATAAAAATTA

                     **             
       4229 ATTATTATTTTTTTATAAAAATTA
          1 ATTATTATTGATTTATAAAAATTA

                  
       4253 ATTATT
          1 ATTATT

       4259 CATCTTATAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  24   23  0.88
  25    3  0.12

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54


Consensus pattern (24 bp):   
ATTATTATTGATTTATAAAAATTA

Found at i:4269 original size:24 final size:24

Alignment explanation


    Indices: 4218--4269  Score: 61
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       4208 ATATATGATT

                   *            *  *
       4218 TATAAAACTTAATTATTATTTTTT
          1 TATAAAAATTAATTATTATTCTTA

                                     
       4242 TATAAAAATTAATTATTCA-TCTTA
          1 TATAAAAATTAATTATT-ATTCTTA

                
       4266 TATA
          1 TATA

       4270 TATTACAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   23  0.96
  25    1  0.04

ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52


Consensus pattern (24 bp):   
TATAAAAATTAATTATTATTCTTA

Found at i:5085 original size:30 final size:30

Alignment explanation


    Indices: 5049--5110  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       5039 GTTAATAAGC

                                          
       5049 CATTAAAATTTGAGGGTATAAGAGAAAAGT
          1 CATTAAAATTTGAGGGTATAAGAGAAAAGT

                                    *     
       5079 CATTAAAATTTGAGGGTATAAGAGGAAAGT
          1 CATTAAAATTTGAGGGTATAAGAGAAAAGT

              
       5109 CA
          1 CA

       5111 AGATAAAAAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26


Consensus pattern (30 bp):   
CATTAAAATTTGAGGGTATAAGAGAAAAGT

Found at i:8241 original size:18 final size:18

Alignment explanation


    Indices: 8218--8253  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       8208 GCAAAATGTC

                              
       8218 CTTTTTGTGATACTTTAG
          1 CTTTTTGTGATACTTTAG

                              
       8236 CTTTTTGTGATACTTTAG
          1 CTTTTTGTGATACTTTAG

       8254 GGGGATGTTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56


Consensus pattern (18 bp):   
CTTTTTGTGATACTTTAG
Done.