Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023125.1 Corchorus olitorius cultivar O-4 contig23158, 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: 5465
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:180 original size:16 final size:15

Alignment explanation


    Indices: 142--183  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        132 ACAGAGGTTG

                           
        142 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
        157 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        172 ACTAGAAAACAA
          1 AC-AGAAAACAA

        184 AGCAGAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3060 original size:14 final size:15

Alignment explanation


    Indices: 3041--3070  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3031 CAATTAAAGC

                           
       3041 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       3055 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       3070 A
          1 A

       3071 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:3450 original size:21 final size:20

Alignment explanation


    Indices: 3426--3499  Score: 94
    Period size: 21  Copynumber: 3.5  Consensus size: 20

       3416 GGCACTGAAT

                *                
       3426 GGTGATGGCACGGGCATAGCC
          1 GGTGGTGGCACGGGC-TAGCC

                            *    
       3447 GGTGGTGGCACGGGCTTGACC
          1 GGTGGTGGCACGGGCTAG-CC

                              *  
       3468 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGC-TAGCC

                       
       3489 GGTGGTGGCAC
          1 GGTGGTGGCAC

       3500 TGCTTTGGAC


Statistics
Matches: 47,  Mismatches: 4, Indels: 4
        0.85            0.07        0.07

Matches are distributed among these distances:
  20    2  0.04
  21   44  0.94
  22    1  0.02

ACGTcount: A:0.14, C:0.23, G:0.46, T:0.18


Consensus pattern (20 bp):   
GGTGGTGGCACGGGCTAGCC
Done.