Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021788.1 Corchorus olitorius cultivar O-4 contig21821, 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: 7464
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33


Found at i:510 original size:36 final size:36

Alignment explanation


    Indices: 463--532  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        453 GAGATTTTGG

                         *      *               
        463 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
        499 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

        533 GGTTATTGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA

Found at i:1883 original size:58 final size:57

Alignment explanation


    Indices: 1787--1900  Score: 165
    Period size: 58  Copynumber: 2.0  Consensus size: 57

       1777 ATAGCATCAT

                  *   *                                              
       1787 GCCTCGGTCCTAAAACGTATTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
          1 GCCTCGATCCGAAAACGTATTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA

                               *       *            *           *    
       1844 GCCTCGATCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
          1 GCCTCGATCCGAAAACGT-ATTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA

       1901 TTTGATTAAT


Statistics
Matches: 50,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  57   16  0.32
  58   34  0.68

ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32


Consensus pattern (57 bp):   
GCCTCGATCCGAAAACGTATTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA

Found at i:3305 original size:3 final size:3

Alignment explanation


    Indices: 3290--3350  Score: 113
    Period size: 3  Copynumber: 20.3  Consensus size: 3

       3280 ACTAGTATAT

                    *                                                      
       3290 ATA ATA TTA 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

                             
       3338 ATA ATA ATA ATA A
          1 ATA ATA ATA ATA A

       3351 AATGCTATTG


Statistics
Matches: 56,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   3   56  1.00

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


Consensus pattern (3 bp):   
ATA

Found at i:6949 original size:51 final size:52

Alignment explanation


    Indices: 6886--6987  Score: 161
    Period size: 51  Copynumber: 2.0  Consensus size: 52

       6876 TTTTCCTTTC

                   *                *                           
       6886 AATTCCTCCACCTTCCATTTAATTTAAATCCCTTTTC-CTTGGTCATTACCT
          1 AATTCCTACACCTTCCATTTAATTCAAATCCCTTTTCACTTGGTCATTACCT

                                                   *           
       6937 AATTCCTACACCTTCCATTTAATTCAAATCCCTTTTCATTTTGGTCATTAC
          1 AATTCCTACACCTTCCATTTAATTCAAATCCCTTTTCA-CTTGGTCATTAC

       6988 TAAGTACATA


Statistics
Matches: 46,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  51   35  0.76
  53   11  0.24

ACGTcount: A:0.24, C:0.29, G:0.04, T:0.43


Consensus pattern (52 bp):   
AATTCCTACACCTTCCATTTAATTCAAATCCCTTTTCACTTGGTCATTACCT
Done.