Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014331.1 Corchorus capsularis cultivar CVL-1 contig14352, 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: 26647
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32


Found at i:269 original size:2 final size:2

Alignment explanation


    Indices: 262--286  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        252 TGAGGAAAAT

                                                 
        262 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        287 TAATAGTAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7158 original size:22 final size:22

Alignment explanation


    Indices: 7130--7173  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7120 AAGCAGCTTG

                                  
       7130 AAGAGAATTTTCCAGTATCATA
          1 AAGAGAATTTTCCAGTATCATA

                                  
       7152 AAGAGAATTTTCCAGTATCATA
          1 AAGAGAATTTTCCAGTATCATA

       7174 GATTCCTTGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32


Consensus pattern (22 bp):   
AAGAGAATTTTCCAGTATCATA

Found at i:8805 original size:27 final size:28

Alignment explanation


    Indices: 8770--8837  Score: 95
    Period size: 27  Copynumber: 2.5  Consensus size: 28

       8760 ATCCTAGGGA

                *                   *   
       8770 ACTACCTTTGAATGGGA-AACTGTTTTG
          1 ACTAACTTTGAATGGGAGAACTGTCTTG

                                        
       8797 ACTAACTTTGAAT-GGAGAACTGTCTTG
          1 ACTAACTTTGAATGGGAGAACTGTCTTG

                    *     
       8824 ACTAACTTGGAATG
          1 ACTAACTTTGAATG

       8838 AGAGTCTGAC


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  26    3  0.08
  27   33  0.92

ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34


Consensus pattern (28 bp):   
ACTAACTTTGAATGGGAGAACTGTCTTG

Found at i:13248 original size:27 final size:27

Alignment explanation


    Indices: 13215--13282  Score: 109
    Period size: 27  Copynumber: 2.5  Consensus size: 27

      13205 AATCTAGGGA

                                   *   
      13215 ACTAACTTTGAATGGAAAACTGTTTTG
          1 ACTAACTTTGAATGGAAAACTGTCTTG

                            *          
      13242 ACTAACTTTGAATGGAGAACTGTCTTG
          1 ACTAACTTTGAATGGAAAACTGTCTTG

                    *     
      13269 ACTAACTTGGAATG
          1 ACTAACTTTGAATG

      13283 AGAGTCTGAC


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34


Consensus pattern (27 bp):   
ACTAACTTTGAATGGAAAACTGTCTTG

Done.