Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005108.1 Corchorus capsularis cultivar CVL-1 contig05126, 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: 24264
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34


Found at i:2216 original size:35 final size:34

Alignment explanation


    Indices: 2175--2250  Score: 102
    Period size: 35  Copynumber: 2.3  Consensus size: 34

       2165 GGTCGAGTTA

                                      *        
       2175 AATTTGGGTCAGATTGATTCGGGTTCGGGTTAAAT
          1 AATTTGGGTCAGATTGATTCGGGTTCAGG-TAAAT

                        *      *              
       2210 AATTTGGGTCAGGTTGATTTGGGTTCAGGTAAAT
          1 AATTTGGGTCAGATTGATTCGGGTTCAGGTAAAT

                     
       2244 --TTTGGGT
          1 AATTTGGGT

       2251 TATAAGTTAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  32    7  0.18
  34    5  0.13
  35   26  0.68

ACGTcount: A:0.21, C:0.07, G:0.33, T:0.39


Consensus pattern (34 bp):   
AATTTGGGTCAGATTGATTCGGGTTCAGGTAAAT

Found at i:2245 original size:16 final size:16

Alignment explanation


    Indices: 2210--2251  Score: 50
    Period size: 17  Copynumber: 2.6  Consensus size: 16

       2200 CGGGTTAAAT

                           *
       2210 AATTTGGG-TCAGGTT
          1 AATTTGGGTTCAGGTA

            *               
       2225 GATTTGGGTTCAGGTA
          1 AATTTGGGTTCAGGTA

                       
       2241 AATTTTGGGTT
          1 AA-TTTGGGTT

       2252 ATAAGTTAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  15    7  0.32
  16    7  0.32
  17    8  0.36

ACGTcount: A:0.19, C:0.05, G:0.33, T:0.43


Consensus pattern (16 bp):   
AATTTGGGTTCAGGTA

Found at i:4254 original size:31 final size:32

Alignment explanation


    Indices: 4219--4280  Score: 92
    Period size: 31  Copynumber: 2.0  Consensus size: 32

       4209 CTTTTAGAAT

                                             
       4219 TTTCCAAAGGTG-CATCA-TTTTATTTTTTTTG
          1 TTTCCAAAGG-GACATCACTTTTATTTTTTTTG

                 *                         
       4250 TTTCCTAAGGGACATCACTTTTATTTTTTTT
          1 TTTCCAAAGGGACATCACTTTTATTTTTTTT

       4281 AGTGTTCCCC


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  30    1  0.04
  31   14  0.50
  32   13  0.46

ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55


Consensus pattern (32 bp):   
TTTCCAAAGGGACATCACTTTTATTTTTTTTG

Found at i:17055 original size:6 final size:6

Alignment explanation


    Indices: 17044--17075  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      17034 GGTAAATTCA

                                                 
      17044 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT
          1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT

      17076 ATGGAATAAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (6 bp):   
TTTAAT

Found at i:18393 original size:14 final size:14

Alignment explanation


    Indices: 18374--18400  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      18364 AGACGTGTTT

                          
      18374 CTTTTTTTTTTTTC
          1 CTTTTTTTTTTTTC

                         
      18388 CTTTTTTTTTTTT
          1 CTTTTTTTTTTTT

      18401 TGAAAGGCAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89


Consensus pattern (14 bp):   
CTTTTTTTTTTTTC

Found at i:19400 original size:11 final size:11

Alignment explanation


    Indices: 19384--19408  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      19374 TGAAGCGGAA

                       
      19384 AGAAGAAAAAG
          1 AGAAGAAAAAG

                       
      19395 AGAAGAAAAAG
          1 AGAAGAAAAAG

               
      19406 AGA
          1 AGA

      19409 CAAGATTTGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (11 bp):   
AGAAGAAAAAG

Found at i:20254 original size:115 final size:115

Alignment explanation


    Indices: 20052--20274  Score: 410
    Period size: 115  Copynumber: 1.9  Consensus size: 115

      20042 TTTGGGTCAT

                                                                             
      20052 TTGCATATGGCCGAATATGTTTAAAGTAAAAAGTTATTAAAATAATTGAAATTAATTATAATTAT
          1 TTGCATATGGCCGAATATGTTTAAAGTAAAAAGTTATTAAAATAATTGAAATTAATTATAATTAT

                                                              
      20117 TATTCAAAGCATCCAATTTTTGTAATCTAACCTAATTGAATTGACGTGTG
         66 TATTCAAAGCATCCAATTTTTGTAATCTAACCTAATTGAATTGACGTGTG

                  *   *                                                      
      20167 TTGCATGTGGTCGAATATGTTTAAAGTAAAAAGTTATTAAAATAATTGAAATTAATTATAATTAT
          1 TTGCATATGGCCGAATATGTTTAAAGTAAAAAGTTATTAAAATAATTGAAATTAATTATAATTAT

                        *                 *            
      20232 TATTCAAAGCATTCAATTTTTGTAATCTAAGCTAATTGAATTG
         66 TATTCAAAGCATCCAATTTTTGTAATCTAACCTAATTGAATTG

      20275 CTGGAAAAAA


Statistics
Matches: 104,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 115  104  1.00

ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39


Consensus pattern (115 bp):   
TTGCATATGGCCGAATATGTTTAAAGTAAAAAGTTATTAAAATAATTGAAATTAATTATAATTAT
TATTCAAAGCATCCAATTTTTGTAATCTAACCTAATTGAATTGACGTGTG
Done.