Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006927.1 Corchorus capsularis cultivar CVL-1 contig06948, 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: 4864
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:317 original size:16 final size:16

Alignment explanation


    Indices: 298--353  Score: 51
    Period size: 16  Copynumber: 3.6  Consensus size: 16

        288 AGACCGAGCA

                            
        298 GACTCGAGACCCAAAT
          1 GACTCGAGACCCAAAT

                *    *      
        314 GACTTGA-ATCCAAAT
          1 GACTCGAGACCCAAAT

              *    *    *   
        329 GAGTCGAAACCCGAAT
          1 GACTCGAGACCCAAAT

               *     
        345 GACCCGAGA
          1 GACTCGAGA

        354 AAATTACCTG


Statistics
Matches: 30,  Mismatches: 9, Indels: 2
        0.73            0.22        0.05

Matches are distributed among these distances:
  15   12  0.40
  16   18  0.60

ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14


Consensus pattern (16 bp):   
GACTCGAGACCCAAAT

Found at i:974 original size:131 final size:131

Alignment explanation


    Indices: 796--1058  Score: 397
    Period size: 131  Copynumber: 2.0  Consensus size: 131

        786 ATTTAATAAA

                                    *    *       *    *     *                
        796 TATACTTTAAAAATTCTAATATATCTAAATTTTTTAATTAAATTAGTAGAATGATAAAAATAAAA
          1 TATACTTTAAAAATTCTAATATATATAAAGTTTTTAAATAAAATAGTAAAATGATAAAAATAAAA

                                                                             
        861 TAG-GTATAAGGATATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAAATATAA
         66 T-GTGTATAAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAAATATAA

               
        925 AAG
        129 AAG

                              *                                   *       *  
        928 TATA-TTTAAAAAATTCTGATATATAT-AAGTTTTTAAATAAAATAGTAAAATGGTAAAAATTAA
          1 TATACTTT-AAAAATTCTAATATATATAAAGTTTTTAAATAAAATAGTAAAATGATAAAAATAAA

                *                                                            
        991 ATGTTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAA
         65 ATGTGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAA

              
       1056 AG
        130 AG

             
       1058 T
          1 T

       1059 TTAAACAATG


Statistics
Matches: 120,  Mismatches: 9, Indels: 6
        0.89            0.07        0.04

Matches are distributed among these distances:
 130   38  0.32
 131   62  0.52
 132   20  0.17

ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38


Consensus pattern (131 bp):   
TATACTTTAAAAATTCTAATATATATAAAGTTTTTAAATAAAATAGTAAAATGATAAAAATAAAA
TGTGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAAATATAAAA
G

Found at i:3976 original size:32 final size:32

Alignment explanation


    Indices: 3933--4086  Score: 227
    Period size: 32  Copynumber: 4.8  Consensus size: 32

       3923 GATGCACACG

                                            
       3933 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT

                  *       *         * *     
       3965 ACTCAGCTAGATCGGGCATCCCTCTATCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT

                                            
       3997 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT

                  *       *         * *     
       4029 ACTCAGCTAGATCGGGCATCCCTCTATCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAAT

                        *             
       4061 ACTCAGTTAGATTGAGCATCCCTCGA
          1 ACTCAGTTAGATCGAGCATCCCTCGA

       4087 TCGTATGACA


Statistics
Matches: 106,  Mismatches: 16, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32  106  1.00

ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24


Consensus pattern (32 bp):   
ACTCAGTTAGATCGAGCATCCCTCGACCGAAT

Found at i:4034 original size:64 final size:64

Alignment explanation


    Indices: 3933--4086  Score: 299
    Period size: 64  Copynumber: 2.4  Consensus size: 64

       3923 GATGCACACG

                                                                            
       3933 ACTCAGTTAGATCGAGCATCCCTCGACCGAATACTCAGCTAGATCGGGCATCCCTCTATCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAATACTCAGCTAGATCGGGCATCCCTCTATCGAAT

                                                                            
       3997 ACTCAGTTAGATCGAGCATCCCTCGACCGAATACTCAGCTAGATCGGGCATCCCTCTATCGAAT
          1 ACTCAGTTAGATCGAGCATCCCTCGACCGAATACTCAGCTAGATCGGGCATCCCTCTATCGAAT

                        *             
       4061 ACTCAGTTAGATTGAGCATCCCTCGA
          1 ACTCAGTTAGATCGAGCATCCCTCGA

       4087 TCGTATGACA


Statistics
Matches: 89,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  64   89  1.00

ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24


Consensus pattern (64 bp):   
ACTCAGTTAGATCGAGCATCCCTCGACCGAATACTCAGCTAGATCGGGCATCCCTCTATCGAAT

Found at i:4321 original size:18 final size:18

Alignment explanation


    Indices: 4276--4322  Score: 51
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       4266 AAAAAAGCGG

                    *  *      
       4276 AGAGCACAAGACGCCATA
          1 AGAGCACACGAAGCCATA

                  *            
       4294 A-AGGCGCACGAAGCCATA
          1 AGA-GCACACGAAGCCATA

                       
       4312 AGAGCACACGA
          1 AGAGCACACGA

       4323 TATGCCACGC


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  17    1  0.04
  18   21  0.91
  19    1  0.04

ACGTcount: A:0.43, C:0.28, G:0.26, T:0.04


Consensus pattern (18 bp):   
AGAGCACACGAAGCCATA
Done.