Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009571.1 Corchorus olitorius cultivar O-4 contig09603, 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: 12901
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:4857 original size:118 final size:117

Alignment explanation


    Indices: 4647--4882  Score: 445
    Period size: 118  Copynumber: 2.0  Consensus size: 117

       4637 ATTAAAAATG

                                                                             
       4647 CTGGATAAGAATTCTGCCAAACTACAAGTACTAACCTCAAAGGATCAGATTTTGTCGAAAACGGC
          1 CTGGATAAGAATTCTGCCAAACTACAAGTACTAACCTCAAAGGATCAGATTTTGTCGAAAACGGC

                                  *                              
       4712 TTTGAATGTTCTTCTCTATAAAGGAAACAACTTGGTAATTTTTTTTTCTTGTT
         66 TTTGAATGTTCTTCTCTATAAAAGAAACAACTTGGTAA-TTTTTTTTCTTGTT

                                                                     *       
       4765 CTGGATAAGAATTCTGCCAAACTACAAGTACTAACCTCAAAGGATCAGATTTTGTCGGAAACGGC
          1 CTGGATAAGAATTCTGCCAAACTACAAGTACTAACCTCAAAGGATCAGATTTTGTCGAAAACGGC

                                                                
       4830 TTTGAATGTTCTTCTCTATAAAAGAAACAACTTGGTAATTTTTTTTCTTGTT
         66 TTTGAATGTTCTTCTCTATAAAAGAAACAACTTGGTAATTTTTTTTCTTGTT

             
       4882 C
          1 C

       4883 AAATGTTGCT


Statistics
Matches: 116,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 117   15  0.13
 118  101  0.87

ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35


Consensus pattern (117 bp):   
CTGGATAAGAATTCTGCCAAACTACAAGTACTAACCTCAAAGGATCAGATTTTGTCGAAAACGGC
TTTGAATGTTCTTCTCTATAAAAGAAACAACTTGGTAATTTTTTTTCTTGTT

Found at i:10936 original size:2 final size:2

Alignment explanation


    Indices: 10929--10967  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      10919 TAGCATTTGT

                           *     *                                    
      10929 TA TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10968 GTGGTTTGTT


Statistics
Matches: 33,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:11230 original size:112 final size:111

Alignment explanation


    Indices: 11034--11261  Score: 438
    Period size: 112  Copynumber: 2.0  Consensus size: 111

      11024 TCTTAACTAA

                                                                             
      11034 ATGAAGAATTCACATTAGTAACATGCTATGATCAAGTTCTTAATTGAGTTGATTTTGCAAATTTT
          1 ATGAAGAATTCACATTAGTAACATGCTATGATCAAGTTCTTAATTGAGTTGATTTTGCAAATTTT

               *                                          
      11099 GAGTCTCAATTACCTAGTTATAAAGTTGCAAAATCTCAAAAGCTAT
         66 GAGCCTCAATTACCTAGTTATAAAGTTGCAAAATCTCAAAAGCTAT

                                                                             
      11145 ATGAAGAATTCACATTAGTAACATAGCTATGATCAAGTTCTTAATTGAGTTGATTTTGCAAATTT
          1 ATGAAGAATTCACATTAGTAACAT-GCTATGATCAAGTTCTTAATTGAGTTGATTTTGCAAATTT

                                                           
      11210 TGAGCCTCAATTACCTAGTTATAAAGTTGCAAAATCTCAAAAGCTAT
         65 TGAGCCTCAATTACCTAGTTATAAAGTTGCAAAATCTCAAAAGCTAT

                 
      11257 ATGAA
          1 ATGAA

      11262 CTTAGCTGCC


Statistics
Matches: 115,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 111   24  0.21
 112   91  0.79

ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Consensus pattern (111 bp):   
ATGAAGAATTCACATTAGTAACATGCTATGATCAAGTTCTTAATTGAGTTGATTTTGCAAATTTT
GAGCCTCAATTACCTAGTTATAAAGTTGCAAAATCTCAAAAGCTAT

Found at i:12021 original size:13 final size:13

Alignment explanation


    Indices: 11989--12029  Score: 57
    Period size: 13  Copynumber: 3.2  Consensus size: 13

      11979 TTTTGCTGGG

                         
      11989 TTGCTGCTGTTTT
          1 TTGCTGCTGTTTT

              *          
      12002 TTTCTGCT-TTTT
          1 TTGCTGCTGTTTT

                          
      12014 CTTGCTGCTGTTTT
          1 -TTGCTGCTGTTTT

              
      12028 TT
          1 TT

      12030 TTCTTTGAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  12    4  0.17
  13   16  0.67
  14    4  0.17

ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66


Consensus pattern (13 bp):   
TTGCTGCTGTTTT

Found at i:12145 original size:17 final size:16

Alignment explanation


    Indices: 12123--12159  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 16

      12113 GCTGCCTTTC

                            
      12123 AAAAAAAAAAAATTGG
          1 AAAAAAAAAAAATTGG

                        *    
      12139 TAAAAAAAAAAACTTGG
          1 -AAAAAAAAAAAATTGG

                
      12156 AAAA
          1 AAAA

      12160 TCATACCTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    4  0.21
  17   15  0.79

ACGTcount: A:0.73, C:0.03, G:0.11, T:0.14


Consensus pattern (16 bp):   
AAAAAAAAAAAATTGG
Done.