Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010677.1 Corchorus capsularis cultivar CVL-1 contig10698, 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: 11434
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:2581 original size:16 final size:17

Alignment explanation


    Indices: 2551--2585  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       2541 TTGTAAATTT

                      *      
       2551 TTTTCAAAAATTTTTGC
          1 TTTTCAAAAACTTTTGC

                             
       2568 TTTTC-AAAACTTTTGC
          1 TTTTCAAAAACTTTTGC

              
       2584 TT
          1 TT

       2586 CTCTGGTTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54


Consensus pattern (17 bp):   
TTTTCAAAAACTTTTGC

Found at i:4303 original size:33 final size:33

Alignment explanation


    Indices: 4266--4342  Score: 100
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       4256 AGCACTTGTG

                             *               
       4266 ACCGGCCACGCAACTTGGAGATGCCCGACCATC
          1 ACCGGCCACGCAACTTGAAGATGCCCGACCATC

                    *  *    *   *      *     
       4299 ACCGGCCATGCGACTTTAAGTTGCCCGGCCATC
          1 ACCGGCCACGCAACTTGAAGATGCCCGACCATC

                       
       4332 ACCGGCCACGC
          1 ACCGGCCACGC

       4343 GATAAGGACA


Statistics
Matches: 37,  Mismatches: 7, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  33   37  1.00

ACGTcount: A:0.21, C:0.40, G:0.25, T:0.14


Consensus pattern (33 bp):   
ACCGGCCACGCAACTTGAAGATGCCCGACCATC

Found at i:7158 original size:14 final size:14

Alignment explanation


    Indices: 7141--7169  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       7131 AAGATCTAAT

                          
       7141 AAGAAAGTAGGGGA
          1 AAGAAAGTAGGGGA

                          
       7155 AAGAAAGTAGGGGA
          1 AAGAAAGTAGGGGA

             
       7169 A
          1 A

       7170 GTAGCTACAG


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:0.52, C:0.00, G:0.41, T:0.07


Consensus pattern (14 bp):   
AAGAAAGTAGGGGA

Found at i:11397 original size:2 final size:2

Alignment explanation


    Indices: 11390--11434  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

      11380 GTGCATTCTA

                                                                          
      11390 AT AT AT AT 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 AT AT AT AT

                
      11432 AT A
          1 AT A


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.