Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015577.1 Corchorus olitorius cultivar O-4 contig15610, 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: 2760
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.36


Found at i:1381 original size:12 final size:11

Alignment explanation


    Indices: 1336--1392  Score: 51
    Period size: 12  Copynumber: 4.8  Consensus size: 11

       1326 CCCGTTGAGG

                       
       1336 AAATGTTTTAT
          1 AAATGTTTTAT

            * *          
       1347 TACTGTTTTATAT
          1 AAATG-TTT-TAT

                 *     
       1360 AAATGATTTAT
          1 AAATGTTTTAT

                         
       1371 AAAATGTTTTAGT
          1 -AAATGTTTTA-T

                     
       1384 AAATGTTTT
          1 AAATGTTTT

       1393 GGGTGCATGA


Statistics
Matches: 36,  Mismatches: 6, Indels: 7
        0.73            0.12        0.14

Matches are distributed among these distances:
  11    6  0.17
  12   23  0.64
  13    7  0.19

ACGTcount: A:0.35, C:0.02, G:0.11, T:0.53


Consensus pattern (11 bp):   
AAATGTTTTAT

Found at i:2655 original size:25 final size:24

Alignment explanation


    Indices: 2616--2663  Score: 69
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       2606 ACGTTTGCAC

                  *   *              
       2616 AAATACGTAATAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                   
       2641 AAATACCTAAGAATTTAATTAAA
          1 AAATACCTAAGAATTTAATTAAA

       2664 TGTAAGTATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    7  0.33
  25   14  0.67

ACGTcount: A:0.56, C:0.06, G:0.06, T:0.31


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:2710 original size:22 final size:22

Alignment explanation


    Indices: 2653--2712  Score: 58
    Period size: 17  Copynumber: 2.9  Consensus size: 22

       2643 ATACCTAAGA

                                 * 
       2653 ATTTAATTAAATGTAAGTATTTC
          1 ATTTAATT-AATGTAAGTATTGC

             *                    
       2676 AGTT-ATT-A--T-AGTATTGC
          1 ATTTAATTAATGTAAGTATTGC

                                
       2693 ATTTAATTAATGTAAGTATT
          1 ATTTAATTAATGTAAGTATT

       2713 TTAGTTATTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 11
        0.67            0.07        0.26

Matches are distributed among these distances:
  17   10  0.34
  18    4  0.14
  19    1  0.03
  20    1  0.03
  21    1  0.03
  22    9  0.31
  23    3  0.10

ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48


Consensus pattern (22 bp):   
ATTTAATTAATGTAAGTATTGC
Done.