Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010938.1 Corchorus capsularis cultivar CVL-1 contig10959, 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: 8756
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:4073 original size:21 final size:22

Alignment explanation


    Indices: 4038--4081  Score: 72
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       4028 TTGAAAAAGT

                      *           
       4038 GGAAAAAGGTGTCCAACGGCTA
          1 GGAAAAAGGTCTCCAACGGCTA

                                  
       4060 GGAAAAAGG-CTCCAACGGCTA
          1 GGAAAAAGGTCTCCAACGGCTA

             
       4081 G
          1 G

       4082 AATGATGTGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.36, C:0.20, G:0.32, T:0.11


Consensus pattern (22 bp):   
GGAAAAAGGTCTCCAACGGCTA

Found at i:4239 original size:16 final size:17

Alignment explanation


    Indices: 4214--4246  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       4204 TCTACTATTT

                             
       4214 TTGAGATAAAA-TTGTA
          1 TTGAGATAAAACTTGTA

                 *           
       4230 TTGAGTTAAAACTTGTA
          1 TTGAGATAAAACTTGTA

       4247 CTTGGGATCT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39


Consensus pattern (17 bp):   
TTGAGATAAAACTTGTA

Found at i:6253 original size:30 final size:31

Alignment explanation


    Indices: 6164--6261  Score: 153
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       6154 TAATCGTCAT

                  *                *      *
       6164 TGACACTAGAAGTTGTCAATGGTGTTACAAT
          1 TGACACCAGAAGTTGTCAATGGTCTTACAAA

                                 *         
       6195 TGACACCAGAAGTTGTCAATGATCTTACAAA
          1 TGACACCAGAAGTTGTCAATGGTCTTACAAA

                                           
       6226 TGACACCAGAAGTTGTC-ATGGTCTTACAAA
          1 TGACACCAGAAGTTGTCAATGGTCTTACAAA

                  
       6256 TGACAC
          1 TGACAC

       6262 ACAAATGACA


Statistics
Matches: 62,  Mismatches: 5, Indels: 1
        0.91            0.07        0.01

Matches are distributed among these distances:
  30   18  0.29
  31   44  0.71

ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Consensus pattern (31 bp):   
TGACACCAGAAGTTGTCAATGGTCTTACAAA

Found at i:6301 original size:30 final size:30

Alignment explanation


    Indices: 6267--6432  Score: 162
    Period size: 30  Copynumber: 5.6  Consensus size: 30

       6257 GACACACAAA

                               *          
       6267 TGACACCAAAAGTTGTCATCATTTTGAAAT
          1 TGACACCAAAAGTTGTCATGATTTTGAAAT

                    *                 * * 
       6297 TGACACCATAAGTTGTCATGATTTTGTAGT
          1 TGACACCAAAAGTTGTCATGATTTTGAAAT

                  **    *             *   
       6327 TGACACTTAAAGATGTCATGATTTTGCAAT
          1 TGACACCAAAAGTTGTCATGATTTTGAAAT

                *   *    *                 
       6357 TGACGCCAGAAGTCGTCATGATTTT-ACAAT
          1 TGACACCAAAAGTTGTCATGATTTTGA-AAT

                                  *   *   
       6387 TGACA-C--AAGTTGTCATGATCTTGCAAT
          1 TGACACCAAAAGTTGTCATGATTTTGAAAT

                                
       6414 TGACA-CAAGAAGTTGTCAT
          1 TGACACCAA-AAGTTGTCAT

       6433 ATACACTATT


Statistics
Matches: 110,  Mismatches: 21, Indels: 10
        0.78            0.15        0.07

Matches are distributed among these distances:
  27   23  0.21
  29    1  0.01
  30   86  0.78

ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Consensus pattern (30 bp):   
TGACACCAAAAGTTGTCATGATTTTGAAAT

Found at i:6360 original size:60 final size:58

Alignment explanation


    Indices: 6275--6432  Score: 192
    Period size: 60  Copynumber: 2.7  Consensus size: 58

       6265 AATGACACCA

                       *      *           *                ** *       
       6275 AAAGTTGTCATCATTTTGAAATTGACACCATAAGTTGTCATGATTTTGTAGTTGACAC
          1 AAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAATTGACAC

                  *                     *        *                      
       6333 TTAAAGATGTCATGATTTTGCAATTGACGCCAGAAGTCGTCATGATTTTACAATTGACAC
          1 --AAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAATTGACAC

                          *             *            
       6393 -AAGTTGTCATGATCTTGCAATTGACACAAGAAGTTGTCAT
          1 AAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCAT

       6433 ATACACTATT


Statistics
Matches: 84,  Mismatches: 14, Indels: 3
        0.83            0.14        0.03

Matches are distributed among these distances:
  57   35  0.42
  60   49  0.58

ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35


Consensus pattern (58 bp):   
AAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTACAATTGACAC

Done.