Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024468.1 Corchorus olitorius cultivar O-4 contig24501, 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: 27774
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:702 original size:22 final size:22

Alignment explanation


    Indices: 676--717  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        666 TAAATTGACT

                  *               
        676 AAGAAAGCAATCAAGAAAATTC
          1 AAGAAAACAATCAAGAAAATTC

                       *  *     
        698 AAGAAAACAATTAATAAAAT
          1 AAGAAAACAATCAAGAAAAT

        718 CCTCCAACAT


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.64, C:0.10, G:0.10, T:0.17


Consensus pattern (22 bp):   
AAGAAAACAATCAAGAAAATTC

Found at i:5201 original size:19 final size:18

Alignment explanation


    Indices: 5177--5212  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5167 TGAAGACTTA

                               
       5177 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       5196 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       5213 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:5219 original size:30 final size:30

Alignment explanation


    Indices: 5165--5224  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       5155 GAAGTTTGTG

                      *              *    
       5165 TTTGAAGACTTATTGAAGACAATTTGAAGA
          1 TTTGAAGACTCATTGAAGACAATTTCAAGA

                                *          
       5195 TTTGAAGAC-CATTGAAGAATAATTTCAAGA
          1 TTTGAAGACTCATTGAAG-ACAATTTCAAGA

       5225 GCAAGAATTG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  29    7  0.27
  30   19  0.73

ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32


Consensus pattern (30 bp):   
TTTGAAGACTCATTGAAGACAATTTCAAGA

Found at i:17565 original size:25 final size:25

Alignment explanation


    Indices: 17531--17581  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      17521 GGTTGTGCAG

                                     
      17531 CATCGGGATGTGCAGTTTATTCATA
          1 CATCGGGATGTGCAGTTTATTCATA

                                     
      17556 CATCGGGATGTGCAGTTTATTCATA
          1 CATCGGGATGTGCAGTTTATTCATA

             
      17581 C
          1 C

      17582 GGAGATTGTT


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

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35


Consensus pattern (25 bp):   
CATCGGGATGTGCAGTTTATTCATA

Found at i:21045 original size:2 final size:2

Alignment explanation


    Indices: 21033--21097  Score: 78
    Period size: 2  Copynumber: 33.0  Consensus size: 2

      21023 ACAAGAATAC

                  *            *        *                *        *       
      21033 AT AT TT AT AT AT AG AT AT AG AT AT AT AT AT CT AT AT CT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                               
      21075 AT AT AT AT AT AT AT AT -T AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT

      21098 CTGTGTGTGT


Statistics
Matches: 52,  Mismatches: 10, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
   1    1  0.02
   2   51  0.98

ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:21104 original size:2 final size:2

Alignment explanation


    Indices: 21099--21123  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      21089 ATTATATATC

                                                 
      21099 TG TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG TG T

      21124 TTATACCTCA


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

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52


Consensus pattern (2 bp):   
TG

Done.