Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007390.1 Corchorus capsularis cultivar CVL-1 contig07411, 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: 8304
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34


Found at i:3200 original size:33 final size:33

Alignment explanation


    Indices: 3163--3336  Score: 303
    Period size: 33  Copynumber: 5.3  Consensus size: 33

       3153 CAAAATAGTC

                                             
       3163 TTATTTTCAATGCTATGATCAACCAAAACAGAA
          1 TTATTTTCAATGCTATGATCAACCAAAACAGAA

                                          *  
       3196 TTATTTTCAATGCTATGATCAACCAAAACAAAA
          1 TTATTTTCAATGCTATGATCAACCAAAACAGAA

                       *                     
       3229 TTATTTTCAATTCTATGATCAACCAAAACAGAA
          1 TTATTTTCAATGCTATGATCAACCAAAACAGAA

                                          *  
       3262 TTATTTTCAATGCTATGATCAACCAAAACAAAA
          1 TTATTTTCAATGCTATGATCAACCAAAACAGAA

                                            *
       3295 TTATTTTCAATGCTATGATCAACCAAAACAGAT
          1 TTATTTTCAATGCTATGATCAACCAAAACAGAA

              *      
       3328 TTGTTTTCA
          1 TTATTTTCA

       3337 TCACAATTAG


Statistics
Matches: 133,  Mismatches: 8, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33  133  1.00

ACGTcount: A:0.41, C:0.18, G:0.07, T:0.33


Consensus pattern (33 bp):   
TTATTTTCAATGCTATGATCAACCAAAACAGAA

Found at i:3357 original size:99 final size:99

Alignment explanation


    Indices: 3163--3359  Score: 288
    Period size: 99  Copynumber: 2.0  Consensus size: 99

       3153 CAAAATAGTC

                                          *                                  
       3163 TTATTTTCAATGCTATGATCAACCAAAACAGAATTATTTTCAATGCTATGATCAACCAAAACAAA
          1 TTATTTTCAATGCTATGATCAACCAAAACAAAATTATTTTCAATGCTATGATCAACCAAAACAAA

                        * *    *              
       3228 ATTATTTTCAATTCTATGATCAACCAAAACAGAA
         66 ATTATTTTCAATACAATGAGCAACCAAAACAGAA

                                                                           * 
       3262 TTATTTTCAATGCTATGATCAACCAAAACAAAATTATTTTCAATGCTATGATCAACCAAAACAGA
          1 TTATTTTCAATGCTATGATCAACCAAAACAAAATTATTTTCAATGCTATGATCAACCAAAACAAA

            *  *              *    *  *       
       3327 TTTGTTTTC-ATCACAATTAGCATCCCAAACAGA
         66 ATTATTTTCAAT-ACAATGAGCAACCAAAACAGA

       3360 TTTAGTATCA


Statistics
Matches: 87,  Mismatches: 10, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  98    2  0.02
  99   85  0.98

ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31


Consensus pattern (99 bp):   
TTATTTTCAATGCTATGATCAACCAAAACAAAATTATTTTCAATGCTATGATCAACCAAAACAAA
ATTATTTTCAATACAATGAGCAACCAAAACAGAA

Found at i:3390 original size:33 final size:33

Alignment explanation


    Indices: 3353--3447  Score: 127
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       3343 TTAGCATCCC

                               *           * 
       3353 AAACAGATTTAGTATCATCACAAACAACACTTA
          1 AAACAGATTTAGTATCATCGCAAACAACACTCA

                 *       *    *              
       3386 AAACAAATTTAGTGTCATTGCAAACAACACTCA
          1 AAACAGATTTAGTATCATCGCAAACAACACTCA

              **                         
       3419 AATTAGATTTAGTATCATCGCAAACAACA
          1 AAACAGATTTAGTATCATCGCAAACAACA

       3448 TCTAATACAC


Statistics
Matches: 52,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   52  1.00

ACGTcount: A:0.46, C:0.20, G:0.08, T:0.25


Consensus pattern (33 bp):   
AAACAGATTTAGTATCATCGCAAACAACACTCA
Done.