Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006470.1 Corchorus capsularis cultivar CVL-1 contig06491, 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: 12416
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32


Found at i:159 original size:87 final size:85

Alignment explanation


    Indices: 4--301  Score: 425
    Period size: 87  Copynumber: 3.4  Consensus size: 85

          1 CTG

                *                            *          *              *     
          4 TAAAGCATGATTAGGCAAACCCCTACTAGTAATTGGATCAAACCTCAAATTGTAATGGTTAAACC
          1 TAAAACATGATTAGGCAAA-CCCTACTAGTAATGGGATCAAACCCCAAA-TGTAATGGTCAAACC

                                  
         69 CCAAATCATGTATGGTGAAATT
         64 CCAAATCATGTATGGTGAAATT

                *                                               *          * 
         91 TAAAGCATGATTAGGCAAACCCTTACTAGTAATGGGATCAAACCCCAAATCGCAATGGTCAAATC
          1 TAAAACATGATTAGGCAAACCC-TACTAGTAATGGGATCAAACCCCAAAT-GTAATGGTCAAACC

                         *        
        156 CCAAATCATGTATAGTGAAATT
         64 CCAAATCATGTATGGTGAAATT

                                                          *                  
        178 TAAAACATGATTAGGCAAACTCCTACTAGTAATGGGATCAAACTCCAAAATGTAATGGTCAAACC
          1 TAAAACATGATTAGGCAAAC-CCTACTAGTAATGGGATCAAAC-CCCAAATGTAATGGTCAAACC

                          *       *
        243 CCAAATCATGTATGTTGAAACTG
         64 CCAAATCATGTATGGTGAAA-TT

                                                
        266 TAAAACATGATTAGGCAAATCCCTACTAGTAATGGG
          1 TAAAACATGATTAGGCAAA-CCCTACTAGTAATGGG

        302 TCTAAATAAT


Statistics
Matches: 192,  Mismatches: 13, Indels: 11
        0.89            0.06        0.05

Matches are distributed among these distances:
  86    4  0.02
  87  144  0.75
  88   43  0.22
  89    1  0.01

ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26


Consensus pattern (85 bp):   
TAAAACATGATTAGGCAAACCCTACTAGTAATGGGATCAAACCCCAAATGTAATGGTCAAACCCC
AAATCATGTATGGTGAAATT

Found at i:254 original size:23 final size:23

Alignment explanation


    Indices: 206--247  Score: 61
    Period size: 21  Copynumber: 1.9  Consensus size: 23

        196 ACTCCTACTA

                           *       
        206 GTAATGGGATCAAACTCCAAAAT
          1 GTAATGGGATCAAACCCCAAAAT

                                 
        229 GTAAT-GG-TCAAACCCCAAA
          1 GTAATGGGATCAAACCCCAAA

        248 TCATGTATGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21   11  0.61
  22    2  0.11
  23    5  0.28

ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19


Consensus pattern (23 bp):   
GTAATGGGATCAAACCCCAAAAT

Found at i:2492 original size:21 final size:24

Alignment explanation


    Indices: 2448--2498  Score: 63
    Period size: 22  Copynumber: 2.2  Consensus size: 24

       2438 TATCTTAAAT

                                    
       2448 ATAATATATATTACTAAATGAATA
          1 ATAATATATATTACTAAATGAATA

                         *          
       2472 ATAA-ATATATT-TTAAAT-AATA
          1 ATAATATATATTACTAAATGAATA

                  
       2493 AGTAAT
          1 A-TAAT

       2499 GAGTTAAAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  21    5  0.21
  22    8  0.33
  23    7  0.29
  24    4  0.17

ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39


Consensus pattern (24 bp):   
ATAATATATATTACTAAATGAATA

Found at i:4319 original size:12 final size:13

Alignment explanation


    Indices: 4302--4330  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       4292 ATTACCTACC

                         
       4302 AAACAAATAAA-T
          1 AAACAAATAAACT

                         
       4314 AAACAAATAAACT
          1 AAACAAATAAACT

                
       4327 AAAC
          1 AAAC

       4331 TCACATTCCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14


Consensus pattern (13 bp):   
AAACAAATAAACT

Found at i:4644 original size:21 final size:20

Alignment explanation


    Indices: 4589--4644  Score: 60
    Period size: 21  Copynumber: 2.7  Consensus size: 20

       4579 TAATTTTTAC

                                
       4589 TATTTTAAATATAATATATA
          1 TATTTTAAATATAATATATA

               **                 
       4609 T-TAATAAATAAATAATATATA
          1 TATTTTAAAT--ATAATATATA

                           
       4630 TATTTTAAATGATAA
          1 TATTTTAAAT-ATAA

       4645 GTAATGACTT


Statistics
Matches: 28,  Mismatches: 5, Indels: 5
        0.74            0.13        0.13

Matches are distributed among these distances:
  19    6  0.21
  20    1  0.04
  21   15  0.54
  22    6  0.21

ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45


Consensus pattern (20 bp):   
TATTTTAAATATAATATATA

Found at i:6423 original size:12 final size:13

Alignment explanation


    Indices: 6406--6434  Score: 51
    Period size: 12  Copynumber: 2.3  Consensus size: 13

       6396 ATTACCTACC

                         
       6406 AAACAAATAAA-T
          1 AAACAAATAAACT

                         
       6418 AAACAAATAAACT
          1 AAACAAATAAACT

                
       6431 AAAC
          1 AAAC

       6435 TCACATTCCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.69
  13    5  0.31

ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14


Consensus pattern (13 bp):   
AAACAAATAAACT
Done.