Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021030.1 Corchorus olitorius cultivar O-4 contig21063, 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: 17976
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:7724 original size:34 final size:34

Alignment explanation


    Indices: 7681--7749  Score: 120
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       7671 TCCCAAACAA

                       *      *               
       7681 AAGATAAGATTTATCAAACGAAGAGGGATGCTCT
          1 AAGATAAGATTCATCAAAAGAAGAGGGATGCTCT

                                              
       7715 AAGATAAGATTCATCAAAAGAAGAGGGATGCTCT
          1 AAGATAAGATTCATCAAAAGAAGAGGGATGCTCT

             
       7749 A
          1 A

       7750 TGGATGCTCT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22


Consensus pattern (34 bp):   
AAGATAAGATTCATCAAAAGAAGAGGGATGCTCT

Found at i:10109 original size:3 final size:3

Alignment explanation


    Indices: 10101--10162  Score: 124
    Period size: 3  Copynumber: 20.7  Consensus size: 3

      10091 ACCCATTGGC

                                                                           
      10101 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                              
      10149 ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA AT

      10163 TTTAGTATTG


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   59  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:10383 original size:14 final size:14

Alignment explanation


    Indices: 10364--10391  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      10354 GCACTAAACT

                          
      10364 AAATATAAGAGATA
          1 AAATATAAGAGATA

                          
      10378 AAATATAAGAGATA
          1 AAATATAAGAGATA

      10392 TTATTTCTTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21


Consensus pattern (14 bp):   
AAATATAAGAGATA

Found at i:12254 original size:3 final size:3

Alignment explanation


    Indices: 12246--12271  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

      12236 CAAATAAATA

                                              
      12246 AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AA

      12272 AAAAAGCATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (3 bp):   
AAT

Found at i:16211 original size:31 final size:31

Alignment explanation


    Indices: 16187--16263  Score: 127
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      16177 TTTTTCTGTT

                 *                         
      16187 TTTAGGCTCAAATTGAGCAACTTTTGAAATG
          1 TTTAGCCTCAAATTGAGCAACTTTTGAAATG

                                         * 
      16218 TTTAGCCTCAAATTGAGCAACTTTTGAAAGG
          1 TTTAGCCTCAAATTGAGCAACTTTTGAAATG

                 *         
      16249 TTTAGACTCAAATTG
          1 TTTAGCCTCAAATTG

      16264 GTAATTTGAC


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   43  1.00

ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35


Consensus pattern (31 bp):   
TTTAGCCTCAAATTGAGCAACTTTTGAAATG

Found at i:16702 original size:12 final size:12

Alignment explanation


    Indices: 16685--16714  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      16675 ATCGATATCT

                        
      16685 CGATATATCCGC
          1 CGATATATCCGC

                       *
      16697 CGATATATCCGT
          1 CGATATATCCGC

                  
      16709 CGATAT
          1 CGATAT

      16715 CTGGATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30


Consensus pattern (12 bp):   
CGATATATCCGC
Done.