Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020186.1 Corchorus olitorius cultivar O-4 contig20219, 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: 18241
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35


Found at i:390 original size:29 final size:29

Alignment explanation


    Indices: 358--415  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        348 TGATTACTTT

                                         
        358 CAATTTTCACACAAATTCAAATTTAGAAC
          1 CAATTTTCACACAAATTCAAATTTAGAAC

                     *                   
        387 CAATTTTCATACAAATTCAAATTTAGAAC
          1 CAATTTTCACACAAATTCAAATTTAGAAC

        416 ACTAGAAATC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33


Consensus pattern (29 bp):   
CAATTTTCACACAAATTCAAATTTAGAAC

Found at i:7522 original size:2 final size:2

Alignment explanation


    Indices: 7515--7548  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7505 GTAACAATAC

                                                              
       7515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7549 CTAAACAACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:8194 original size:20 final size:20

Alignment explanation


    Indices: 8169--8216  Score: 78
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       8159 GAGAGGCAGG

                          *     
       8169 TGTTGATTCAGAAGGCCAGC
          1 TGTTGATTCAGAAGCCCAGC

                      *         
       8189 TGTTGATTCATAAGCCCAGC
          1 TGTTGATTCAGAAGCCCAGC

                    
       8209 TGTTGATT
          1 TGTTGATT

       8217 TGTGGTTATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33


Consensus pattern (20 bp):   
TGTTGATTCAGAAGCCCAGC

Found at i:8382 original size:44 final size:44

Alignment explanation


    Indices: 8330--8417  Score: 176
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       8320 GCATTTTCTT

                                                        
       8330 CTTTCAATTCCTCTCTTTTATAAATTTCCATTTATTTTCCCATC
          1 CTTTCAATTCCTCTCTTTTATAAATTTCCATTTATTTTCCCATC

                                                        
       8374 CTTTCAATTCCTCTCTTTTATAAATTTCCATTTATTTTCCCATC
          1 CTTTCAATTCCTCTCTTTTATAAATTTCCATTTATTTTCCCATC

       8418 GTTAACTTTT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   44  1.00

ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52


Consensus pattern (44 bp):   
CTTTCAATTCCTCTCTTTTATAAATTTCCATTTATTTTCCCATC

Found at i:8498 original size:14 final size:14

Alignment explanation


    Indices: 8479--8507  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       8469 AAGGAGGCTC

                          
       8479 AACAAAATCCTTTG
          1 AACAAAATCCTTTG

                          
       8493 AACAAAATCCTTTG
          1 AACAAAATCCTTTG

             
       8507 A
          1 A

       8508 GCTATGGGTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28


Consensus pattern (14 bp):   
AACAAAATCCTTTG

Found at i:15235 original size:2 final size:2

Alignment explanation


    Indices: 15228--15254  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      15218 GATCTATAAG

                                                    
      15228 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      15255 GACACACTTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:15822 original size:20 final size:20

Alignment explanation


    Indices: 15797--15835  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      15787 AAAGTAGTAT

                                 
      15797 TAATTAAAAT-AAAAGGAAAG
          1 TAATT-AAATCAAAAGGAAAG

                  *            
      15817 TAATTACATCAAAAGGAAA
          1 TAATTAAATCAAAAGGAAA

      15836 CAATGAAAAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    3  0.18
  20   14  0.82

ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21


Consensus pattern (20 bp):   
TAATTAAATCAAAAGGAAAG
Done.