Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019501.1 Corchorus olitorius cultivar O-4 contig19534, 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: 12428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:656 original size:46 final size:46

Alignment explanation


    Indices: 589--687  Score: 162
    Period size: 46  Copynumber: 2.2  Consensus size: 46

        579 ATTTTGTGCA

                                                    *     
        589 TGTAACCTCCAATTACTAAATACCTTGAAGAAACGTTACATGTATT
          1 TGTAACCTCCAATTACTAAATACCTTGAAGAAACGTTACAAGTATT

                       *           *       *              
        635 TGTAACCTCCATTTACTAAATACTTTGAAGAGACGTTACAAGTATT
          1 TGTAACCTCCAATTACTAAATACCTTGAAGAAACGTTACAAGTATT

                   
        681 TGTAACC
          1 TGTAACC

        688 GCCCAAATAT


Statistics
Matches: 49,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  46   49  1.00

ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33


Consensus pattern (46 bp):   
TGTAACCTCCAATTACTAAATACCTTGAAGAAACGTTACAAGTATT

Found at i:4290 original size:4 final size:4

Alignment explanation


    Indices: 4283--4314  Score: 55
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       4273 ACTTTTTAAA

                                                   
       4283 AAAG AAAG AAAG AAAG AAAG AAAG AAAAG AAA
          1 AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAA

       4315 AATTGATGTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4   23  0.85
   5    4  0.15

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:8057 original size:24 final size:24

Alignment explanation


    Indices: 8029--8076  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       8019 TAGTTTCTAC

                                    
       8029 CAATAATGGATCTACTAGCACTAA
          1 CAATAATGGATCTACTAGCACTAA

                                    
       8053 CAATAATGGATCTACTAGCACTAA
          1 CAATAATGGATCTACTAGCACTAA

       8077 GGGGCCGTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25


Consensus pattern (24 bp):   
CAATAATGGATCTACTAGCACTAA

Found at i:9486 original size:21 final size:21

Alignment explanation


    Indices: 9460--9530  Score: 97
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       9450 AATCAACATA

                                 
       9460 AAAAATCCACAAACATTCAAC
          1 AAAAATCCACAAACATTCAAC

                   *             
       9481 AAAAATCTACAAACATTCAAC
          1 AAAAATCCACAAACATTCAAC

             *             *  *  
       9502 ATAAATCCACAAACAATCCAC
          1 AAAAATCCACAAACATTCAAC

                    
       9523 AAACAATC
          1 AAA-AATC

       9531 AACATTAAAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  21   39  0.91
  22    4  0.09

ACGTcount: A:0.56, C:0.28, G:0.00, T:0.15


Consensus pattern (21 bp):   
AAAAATCCACAAACATTCAAC

Found at i:9521 original size:11 final size:11

Alignment explanation


    Indices: 9463--9530  Score: 68
    Period size: 11  Copynumber: 6.4  Consensus size: 11

       9453 CAACATAAAA

                       
       9463 AATCCACAAAC
          1 AATCCACAAAC

             *  *      
       9474 ATTCAACAAA-
          1 AATCCACAAAC

                *      
       9484 AATCTACAAAC
          1 AATCCACAAAC

             *  *   *  
       9495 ATTCAACATA-
          1 AATCCACAAAC

                       
       9505 AATCCACAAAC
          1 AATCCACAAAC

                       
       9516 AATCCACAAAC
          1 AATCCACAAAC

                
       9527 AATC
          1 AATC

       9531 AACATTAAAA


Statistics
Matches: 45,  Mismatches: 10, Indels: 4
        0.76            0.17        0.07

Matches are distributed among these distances:
  10   15  0.33
  11   30  0.67

ACGTcount: A:0.54, C:0.29, G:0.00, T:0.16


Consensus pattern (11 bp):   
AATCCACAAAC
Done.