Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015125.1 Corchorus capsularis cultivar CVL-1 contig15146, 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: 20280
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28


Found at i:28 original size:20 final size:20

Alignment explanation


    Indices: 3--40  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

          1 AT

                   *  *         
          3 AAAAAAATAATAAAAAAATC
          1 AAAAAAAAAAGAAAAAAATC

                              
         23 AAAAAAAAAAGAAAAAAA
          1 AAAAAAAAAAGAAAAAAA

         41 GAGTCTTTCA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.87, C:0.03, G:0.03, T:0.08


Consensus pattern (20 bp):   
AAAAAAAAAAGAAAAAAATC

Found at i:2115 original size:6 final size:6

Alignment explanation


    Indices: 2106--2138  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       2096 AAAGTAAAGC

                                                  
       2106 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
          1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA

       2139 GCAGATTATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30


Consensus pattern (6 bp):   
AAATCT

Found at i:2150 original size:12 final size:13

Alignment explanation


    Indices: 2135--2168  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       2125 AATCTAAATC

                   *     
       2135 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       2147 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       2160 TAAAGCAAA
          1 TAAAGCAAA

       2169 CAATAACTAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:6252 original size:16 final size:18

Alignment explanation


    Indices: 6231--6269  Score: 55
    Period size: 16  Copynumber: 2.3  Consensus size: 18

       6221 AGGGAGGAAG

                              
       6231 AAAGAAAGAA-AA-AGAA
          1 AAAGAAAGAAGAAGAGAA

                  *           
       6247 AAAGAACGAAGAAGAGAA
          1 AAAGAAAGAAGAAGAGAA

                 
       6265 AAAGA
          1 AAAGA

       6270 TTAAAAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  16    9  0.45
  17    2  0.10
  18    9  0.45

ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00


Consensus pattern (18 bp):   
AAAGAAAGAAGAAGAGAA

Found at i:20039 original size:21 final size:21

Alignment explanation


    Indices: 20015--20067  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      20005 CTTAAGAAAA

                     *            
      20015 CAATCTAAGGAAG-GAAACTCG
          1 CAAT-TAAGCAAGAGAAACTCG

                                  
      20036 CAA-TAAGCAAGATGAAACTCG
          1 CAATTAAGCAAGA-GAAACTCG

                        
      20057 CAA-TAAGCAAG
          1 CAATTAAGCAAG

      20068 GTGAAACCCG


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  19    7  0.24
  21   22  0.76

ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13


Consensus pattern (21 bp):   
CAATTAAGCAAGAGAAACTCG

Found at i:20072 original size:21 final size:21

Alignment explanation


    Indices: 20028--20089  Score: 88
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      20018 TCTAAGGAAG

                                 
      20028 GAAACTCGCAATAAGCAAGAT
          1 GAAACTCGCAATAAGCAAGAT

                               * 
      20049 GAAACTCGCAATAAGCAAGGT
          1 GAAACTCGCAATAAGCAAGAT

                 *    *   *     
      20070 GAAACCCGCACTAACCAAGA
          1 GAAACTCGCAATAAGCAAGA

      20090 CTGTTAGACG


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   36  1.00

ACGTcount: A:0.45, C:0.24, G:0.19, T:0.11


Consensus pattern (21 bp):   
GAAACTCGCAATAAGCAAGAT
Done.