Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006132.1 Corchorus capsularis cultivar CVL-1 contig06150, 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: 20346
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:11013 original size:97 final size:96

Alignment explanation


    Indices: 10879--11056  Score: 250
    Period size: 97  Copynumber: 1.8  Consensus size: 96

      10869 TCACAATTTT

                                                                    *    *   
      10879 AATTTTAAGTTGTCCACCGTGAATACTGGACCTTAAAAAGGGGTTACATTATAAATGTGACTTGA
          1 AATTTTAAGTTGTCCACCGTGAATACTGGACCTTAAAAAGGGGTTACATTATAAATATGACATGA

                                           
      10944 CAGATCATCTTATATTTTTATAAGGTCACAC
         66 CAGATCATCTTATATTTTTATAAGGTCACAC

                         *    **        *           *      *             *   
      10975 AATTTTAAGTTGTTCAGCTTTGAATA-TTGACTCTTAAAAGGGGGTTGCATTATAAATATGTCAT
          1 AATTTTAAGTTGTCCA-CCGTGAATACTGGAC-CTTAAAAAGGGGTTACATTATAAATATGACAT

                              
      11039 GACAGATCATCTTATATT
         64 GACAGATCATCTTATATT

      11057 ATATTATTAT


Statistics
Matches: 71,  Mismatches: 9, Indels: 3
        0.86            0.11        0.04

Matches are distributed among these distances:
  96   19  0.27
  97   52  0.73

ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37


Consensus pattern (96 bp):   
AATTTTAAGTTGTCCACCGTGAATACTGGACCTTAAAAAGGGGTTACATTATAAATATGACATGA
CAGATCATCTTATATTTTTATAAGGTCACAC

Found at i:11167 original size:46 final size:46

Alignment explanation


    Indices: 11037--11169  Score: 189
    Period size: 44  Copynumber: 2.9  Consensus size: 46

      11027 TAAATATGTC

                                                     * *     
      11037 ATGACAGATCATCTTATATTATATTATTATAAGTGCCGTCTAATAGAAA
          1 ATGACAGATCATC-T-TA-TATATTATTATAAGTGCCGTCTGACAGAAA

                  *                 *                     
      11086 ATGACAAATCATC-T-TATATTATAATAAGTGCCGTCTGACAGAAA
          1 ATGACAGATCATCTTATATATTATTATAAGTGCCGTCTGACAGAAA

                                                    
      11130 ATGACAGATCATCTTATATATTATTATAAGTGCCGTCTGA
          1 ATGACAGATCATCTTATATATTATTATAAGTGCCGTCTGA

      11170 AAGAGAGTAG


Statistics
Matches: 76,  Mismatches: 6, Indels: 7
        0.85            0.07        0.08

Matches are distributed among these distances:
  44   39  0.51
  45    1  0.01
  46   24  0.32
  49   12  0.16

ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35


Consensus pattern (46 bp):   
ATGACAGATCATCTTATATATTATTATAAGTGCCGTCTGACAGAAA

Found at i:14246 original size:1 final size:1

Alignment explanation


    Indices: 14240--14277  Score: 76
    Period size: 1  Copynumber: 38.0  Consensus size: 1

      14230 ATGTTTCGGG

                                                  
      14240 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      14278 CTTTCTAACA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   37  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:20232 original size:34 final size:33

Alignment explanation


    Indices: 20175--20334  Score: 207
    Period size: 35  Copynumber: 4.8  Consensus size: 33

      20165 CCGCCTCAAG

                                             
      20175 AGGGCGGCTT-ACCATGGGCAGGCCGCCCCACT
          1 AGGGCGGCTTCACCATGGGCAGGCCGCCCCACT

                                          *    
      20207 AGGGCGGCTTCACCATTGGGCAGGCCGCCCTACTT
          1 AGGGCGGCTTCACCA-TGGGCAGGCCGCCCCAC-T

                                              
      20242 AGGGCGGCTTCACCATTGGGCAGGCCGCCCCACT
          1 AGGGCGGCTTCACCA-TGGGCAGGCCGCCCCACT

                         *   ***             
      20276 AGGGCGGCTTCACTATGAATAGGCCGCCCCACT
          1 AGGGCGGCTTCACCATGGGCAGGCCGCCCCACT

            *          *    *          
      20309 GGGGCGGCTTCGCCA-CGGCAGGCCGC
          1 AGGGCGGCTTCACCATGGGCAGGCCGC

      20335 GCCGATAGGG


Statistics
Matches: 112,  Mismatches: 13, Indels: 6
        0.85            0.10        0.05

Matches are distributed among these distances:
  32   17  0.15
  33   31  0.28
  34   31  0.28
  35   33  0.29

ACGTcount: A:0.15, C:0.36, G:0.34, T:0.15


Consensus pattern (33 bp):   
AGGGCGGCTTCACCATGGGCAGGCCGCCCCACT

Done.