Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001907.1 Corchorus olitorius cultivar O-4 contig01907, 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: 7761
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:576 original size:36 final size:36

Alignment explanation


    Indices: 525--635  Score: 159
    Period size: 36  Copynumber: 3.1  Consensus size: 36

        515 TCTACACTTG

                  *   *                       * 
        525 GTCGCCTAATACTTGGCTATAACGTCGCTGGCCTCA
          1 GTCGCCCAATGCTTGGCTATAACGTCGCTGGCCTAA

                                              * 
        561 GTCGCCCAATGCTTGGCTATAACGTCGCTGGCCTTA
          1 GTCGCCCAATGCTTGGCTATAACGTCGCTGGCCTAA

                       *       *    *           
        597 GTCGCCCAATGTTTGGCTACAACGCCGCTGGCCTAA
          1 GTCGCCCAATGCTTGGCTATAACGTCGCTGGCCTAA

               
        633 GTC
          1 GTC

        636 ACCTAATACA


Statistics
Matches: 68,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   68  1.00

ACGTcount: A:0.18, C:0.32, G:0.24, T:0.26


Consensus pattern (36 bp):   
GTCGCCCAATGCTTGGCTATAACGTCGCTGGCCTAA

Found at i:1557 original size:24 final size:26

Alignment explanation


    Indices: 1528--1583  Score: 80
    Period size: 24  Copynumber: 2.2  Consensus size: 26

       1518 ATGAGTACCA

                         *            
       1528 ACCAAAGGCATACTGT-AA-ACACCC
          1 ACCAAAGGCATACCGTAAACACACCC

                    *                 
       1552 ACCAAAGGTATACCGTAAACACACCC
          1 ACCAAAGGCATACCGTAAACACACCC

                  
       1578 ACCAAA
          1 ACCAAA

       1584 TGTTATACAC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   14  0.50
  25    2  0.07
  26   12  0.43

ACGTcount: A:0.45, C:0.34, G:0.11, T:0.11


Consensus pattern (26 bp):   
ACCAAAGGCATACCGTAAACACACCC

Found at i:4634 original size:16 final size:16

Alignment explanation


    Indices: 4613--4645  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       4603 GGATGGGAAA

                            
       4613 GGAAGGACTCTTGAAG
          1 GGAAGGACTCTTGAAG

                            
       4629 GGAAGGACTCTTGAAG
          1 GGAAGGACTCTTGAAG

             
       4645 G
          1 G

       4646 AAATGATGGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.30, C:0.12, G:0.39, T:0.18


Consensus pattern (16 bp):   
GGAAGGACTCTTGAAG

Found at i:5656 original size:34 final size:34

Alignment explanation


    Indices: 5618--5688  Score: 99
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       5608 GCGGATCACA

                           *                   
       5618 ACCTGGCCATGGCTCGGGTCGCGA-CCTGCGCGCG
          1 ACCTGGCCATGGCTCAGGTCGCGATCC-GCGCGCG

                          *               *   
       5652 ACCTGGCCATGGCTTAGGTCGCGATCCGCGTGCG
          1 ACCTGGCCATGGCTCAGGTCGCGATCCGCGCGCG

               
       5686 ACC
          1 ACC

       5689 CGCGATTGCA


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  34   31  0.94
  35    2  0.06

ACGTcount: A:0.11, C:0.37, G:0.35, T:0.17


Consensus pattern (34 bp):   
ACCTGGCCATGGCTCAGGTCGCGATCCGCGCGCG
Done.