Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019297.1 Corchorus olitorius cultivar O-4 contig19330, 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: 6609
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:712 original size:21 final size:21

Alignment explanation


    Indices: 688--758  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        678 CTTAGGCAAT

                         *       
        688 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
        709 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
        730 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
        751 TCCAATGA
          1 TCCAATGA

        759 TCTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:1871 original size:41 final size:40

Alignment explanation


    Indices: 1814--1918  Score: 111
    Period size: 41  Copynumber: 2.6  Consensus size: 40

       1804 TTTTTCCGTT

                  *                  ** *   *        
       1814 TTCAATATAGTCCCTGATTTAAGTTTGTGTTTGTTAATTGA
          1 TTCAATTTAGTCCCTGATTTAAG-TAATATTTATTAATTGA

                    *                          *     
       1855 TTCAATTTTGTCCCTGATTTAGAGTAATATTTATTTATTGA
          1 TTCAATTTAGTCCCTGATTTA-AGTAATATTTATTAATTGA

                    * *            
       1896 TTCAATTTCGCCCCTGATTTAAG
          1 TTCAATTTAGTCCCTGATTTAAG

       1919 ATTTTATTTT


Statistics
Matches: 54,  Mismatches: 9, Indels: 3
        0.82            0.14        0.05

Matches are distributed among these distances:
  40    2  0.04
  41   50  0.93
  42    2  0.04

ACGTcount: A:0.25, C:0.13, G:0.14, T:0.48


Consensus pattern (40 bp):   
TTCAATTTAGTCCCTGATTTAAGTAATATTTATTAATTGA

Found at i:3004 original size:6 final size:6

Alignment explanation


    Indices: 2993--3024  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       2983 CAGGCTGCAC

                                                 
       2993 CACAAT CACAAT CACAAT CACAAT CACAAT CA
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CA

       3025 TCCGTTAACG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16


Consensus pattern (6 bp):   
CACAAT

Found at i:3218 original size:39 final size:38

Alignment explanation


    Indices: 3054--3239  Score: 302
    Period size: 38  Copynumber: 4.9  Consensus size: 38

       3044 TCGAGTCTAG

                                            *     
       3054 CCAACAG-TTAACCCCCTGAGGCACGGGTCCAATCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
       3091 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
       3129 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                               *  * *              
       3167 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA

               *                  *           
       3206 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT

       3240 ATGCACAGCC


Statistics
Matches: 140,  Mismatches: 7, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  37    7  0.05
  38   99  0.71
  39   34  0.24

ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Done.