Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010812.1 Corchorus olitorius cultivar O-4 contig10844, 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: 7214
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:3293 original size:22 final size:22

Alignment explanation


    Indices: 3264--3313  Score: 73
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       3254 AAAAGGATGG

                                  
       3264 ATGCAAAAGATACCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

            *        * *          
       3286 TTGCAAAAGGTGCCATGCAAAA
          1 ATGCAAAAGATACCATGCAAAA

                  
       3308 ATGCAA
          1 ATGCAA

       3314 CTATTACTAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16


Consensus pattern (22 bp):   
ATGCAAAAGATACCATGCAAAA

Found at i:3700 original size:29 final size:29

Alignment explanation


    Indices: 3667--3740  Score: 80
    Period size: 28  Copynumber: 2.6  Consensus size: 29

       3657 GCACTTGAAG

                                  *  *    
       3667 TGACCAAAATGCCCCCTAG-ATGTGTAAAA
          1 TGACCAAAATGCCCCCT-GCATATGCAAAA

                        *             *  
       3696 TGACCAAAATG-ACCCTGCATATGCAGAA
          1 TGACCAAAATGCCCCCTGCATATGCAAAA

                  *          
       3724 TGACCATAATGCCCCCT
          1 TGACCAAAATGCCCCCT

       3741 TAAGTGACCC


Statistics
Matches: 37,  Mismatches: 6, Indels: 4
        0.79            0.13        0.09

Matches are distributed among these distances:
  27    1  0.03
  28   21  0.57
  29   15  0.41

ACGTcount: A:0.35, C:0.28, G:0.16, T:0.20


Consensus pattern (29 bp):   
TGACCAAAATGCCCCCTGCATATGCAAAA

Found at i:4044 original size:35 final size:35

Alignment explanation


    Indices: 3995--4301  Score: 442
    Period size: 35  Copynumber: 8.8  Consensus size: 35

       3985 CGAGTTCATA

                                               
       3995 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

              *                            *    
       4030 TTAAAGATGCTACACCGAGTCATCT-AAGTTTATCT
          1 TTGAAGATGCTACACCGAGTCATCTGAA-TTCATCT

                                     *       *  
       4065 TTGAAGATGCTACACCGAGTCATCTAAATAT-AACT
          1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCATCT

                                             * 
       4100 TTGAAGATGCTACACCGAGTCATCTGAATTCATGT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                           *   
       4135 TTGAAGATGCTACACCGAGTCATCTGAATTCGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                       ***   * 
       4170 TTGAAGATGCTACACCGAGTCATCTGAGGCCATTT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

                                      *         
       4205 TTGAAGATGCTACACCGAGTCATCTGGATTCGA-CT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT

                                             *  
       4240 TTGAAGATGCTACACCGAGTCATCTGAATAT-AACT
          1 TTGAAGATGCTACACCGAGTCATCTGAAT-TCATCT

                                       
       4275 TTGAAGATGCTACACCGAGTCATCTGA
          1 TTGAAGATGCTACACCGAGTCATCTGA

       4302 GAAGATGGTA


Statistics
Matches: 245,  Mismatches: 20, Indels: 14
        0.88            0.07        0.05

Matches are distributed among these distances:
  34    4  0.02
  35  236  0.96
  36    5  0.02

ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT

Found at i:4407 original size:50 final size:50

Alignment explanation


    Indices: 4317--4503  Score: 320
    Period size: 50  Copynumber: 3.7  Consensus size: 50

       4307 TGGTAATGTA

                           * *      *          *               
       4317 TCGTATGGAAACGAACTGTGGCTTATGGAAAAGCCCATGTTGATAATTGAC
          1 TCGTATGGAAACG-AGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC

                                          *                   
       4368 TCGTATGGAAACGAGTTTGGCTTGTGGAAATGCCTATGTTGATAATTGAC
          1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC

                                                              
       4418 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC
          1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC

                                                
       4468 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
          1 TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA

       4504 AACATTCGGA


Statistics
Matches: 130,  Mismatches: 6, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  50  117  0.90
  51   13  0.10

ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30


Consensus pattern (50 bp):   
TCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGAC

Found at i:5387 original size:13 final size:13

Alignment explanation


    Indices: 5371--5403  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       5361 CTTTTTTTCG

                         
       5371 TCATTTTTTCATT
          1 TCATTTTTTCATT

                         
       5384 TCA-TTTTTCATT
          1 TCATTTTTTCATT

                     
       5396 TC-TTTTTT
          1 TCATTTTTT

       5404 TTTGGTTAGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  12   16  0.84
  13    3  0.16

ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73


Consensus pattern (13 bp):   
TCATTTTTTCATT

Done.