Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020229.1 Corchorus olitorius cultivar O-4 contig20262, 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: 10638
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:215 original size:25 final size:24

Alignment explanation


    Indices: 181--227  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        171 ACGTTTGCAC

                                     
        181 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
        206 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        228 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:272 original size:39 final size:40

Alignment explanation


    Indices: 218--298  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        208 ATACCTAAGA

                                             *      
        218 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        257 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        297 AT
          1 AT

        299 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:1996 original size:127 final size:126

Alignment explanation


    Indices: 1704--2025  Score: 454
    Period size: 126  Copynumber: 2.5  Consensus size: 126

       1694 CCCCATGCAA

                                                                **   *  *    
       1704 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACGCACTACATATTT
          1 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCAAATTT

                                                                         
       1769 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT
         66 ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT

                 *                                        *                  
       1830 ATGGAGCTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAGACGACATACTGCAAATTT
          1 ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCAAATTT

                                                                            
       1895 ATTCTCACATTCTCTTATATATATGAAACACGTGTTGTCA-A-A-A-CATCTCACTCTGTATAT
         66 A-TCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTC--TATAT

                    *        *                  *              *     *    ** 
       1955 ATGGAACTCGTGTTTGTTGAAACTTTTTCCATAACACATGTCGTTATAAACAACATATTGCATGT
          1 ATGGAACTAGTGTTTGTCGAAAC-TTTTCC-TAACATATGTCGTTATAAACGACATACTGCAAAT

                  
       2020 TTATCT
         64 TTATCT

       2026 TACACCTACT


Statistics
Matches: 176,  Mismatches: 15, Indels: 10
        0.88            0.07        0.05

Matches are distributed among these distances:
 123   10  0.06
 124    1  0.01
 125   26  0.15
 126   70  0.40
 127   69  0.39

ACGTcount: A:0.30, C:0.19, G:0.13, T:0.37


Consensus pattern (126 bp):   
ATGGAACTAGTGTTTGTCGAAACTTTTCCTAACATATGTCGTTATAAACGACATACTGCAAATTT
ATCTCACATTCTCTTATATATATGAAACACGTGTTGTCATACATAGCATCTCACTCTATAT

Found at i:2920 original size:54 final size:55

Alignment explanation


    Indices: 2858--2963  Score: 162
    Period size: 54  Copynumber: 1.9  Consensus size: 55

       2848 TGATAACTTG

                            *                                       
       2858 GATCATCATCAACAACGAGCAGCTGATCC-TGGTCAG-CAAGAGGCAGCAAAGGAC
          1 GATCATCATCAACAACCAGCAGCTGATCCATGGTC-GCCAAGAGGCAGCAAAGGAC

                                                                
       2912 GATCATCATCAACAACCAGCAGCTGATCCAGTTGGTCGCCAAGAGGCAGCAA
          1 GATCATCATCAACAACCAGCAGCTGATCCA--TGGTCGCCAAGAGGCAGCAA

       2964 GTGAACTGCC


Statistics
Matches: 47,  Mismatches: 1, Indels: 5
        0.89            0.02        0.09

Matches are distributed among these distances:
  54   28  0.60
  56    1  0.02
  57   18  0.38

ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14


Consensus pattern (55 bp):   
GATCATCATCAACAACCAGCAGCTGATCCATGGTCGCCAAGAGGCAGCAAAGGAC

Found at i:3220 original size:6 final size:6

Alignment explanation


    Indices: 3190--3242  Score: 61
    Period size: 6  Copynumber: 8.7  Consensus size: 6

       3180 ACCTCAAACA

                      *     *   *                                  *
       3190 AAAAGG AAGCAGG ATAAGA AAAAGG AAAAGG AAAAGG AAAAGG AAAAGT
          1 AAAAGG AA-AAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG

                
       3239 AAAA
          1 AAAA

       3243 TTCTTTTGAT


Statistics
Matches: 39,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
   6   35  0.90
   7    4  0.10

ACGTcount: A:0.66, C:0.02, G:0.28, T:0.04


Consensus pattern (6 bp):   
AAAAGG

Done.