Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018814.1 Corchorus olitorius cultivar O-4 contig18847, 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: 12250
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:938 original size:2 final size:2

Alignment explanation


    Indices: 931--969  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        921 ATAATTTTCC

                                                      *        *       
        931 TA TA TA TA TA TA TA TA TA TA T- TA TA TA AA TA TA AA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        970 GGAATGCGGT


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:1493 original size:20 final size:22

Alignment explanation


    Indices: 1470--1509  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1460 TATTTCACAT

                           *      
       1470 AAAT-ATTC-CATATCAAATTC
          1 AAATAATTCACATATAAAATTC

                                
       1490 AAATAATTCACATATAAAAT
          1 AAATAATTCACATATAAAAT

       1510 ATTGATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    4  0.24
  21    4  0.24
  22    9  0.53

ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33


Consensus pattern (22 bp):   
AAATAATTCACATATAAAATTC

Found at i:3035 original size:109 final size:109

Alignment explanation


    Indices: 2844--3061  Score: 373
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       2834 TATACTTGTA

                                                           *                 
       2844 TATTATTACTAATTGTGTGGTTTATTCAATTGAACCGATTAAATAAGTACACATACCAAACAATA
          1 TATTATTACTAATTGTGTGGTTTATTCAATTGAACCGATTAAATAAGCACACATACCAAACAATA

                                                        
       2909 AAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
         66 AAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC

                    *  *      *                 *                            
       2953 TATTATTATTAGTTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
          1 TATTATTACTAATTGTGTGGTTTATTCAATTGAACCGATTAAATAAGCACACATACCAAACAATA

            *   *                                       
       3018 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
         66 AAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC

       3062 AAAATGACTG


Statistics
Matches: 102,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 109  102  1.00

ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30


Consensus pattern (109 bp):   
TATTATTACTAATTGTGTGGTTTATTCAATTGAACCGATTAAATAAGCACACATACCAAACAATA
AAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC

Found at i:7937 original size:61 final size:61

Alignment explanation


    Indices: 7831--8007  Score: 232
    Period size: 61  Copynumber: 2.9  Consensus size: 61

       7821 GTGGTATGCG

                           *  *       *                                   
       7831 TTCGAATAAAATATACGGTAAGTTGGAAATTTTTTATTTTCTTTTATGTGTTGGGTATTGTA
          1 TTCGAATAAAATATATGGAAAGTTGGTAA-TTTTTATTTTCTTTTATGTGTTGGGTATTGTA

                    *                              *               *     
       7893 TTCGAATAGAATATATGGAAAGTTGGTAATTTTTATTTTGTTTTATGTGTTGGGTTTTGTA
          1 TTCGAATAAAATATATGGAAAGTTGGTAATTTTTATTTTCTTTTATGTGTTGGGTATTGTA

                    *         *                 *       *           
       7954 TTCGAATATAATATATGGGAAGTTGGTCAA-TTTT-CTTTCTTTAATGTGTTGGGT
          1 TTCGAATAAAATATATGGAAAGTTGGT-AATTTTTATTTTCTTTTATGTGTTGGGT

       8008 TTCTGACTTG


Statistics
Matches: 103,  Mismatches: 11, Indels: 4
        0.87            0.09        0.03

Matches are distributed among these distances:
  60   17  0.17
  61   59  0.57
  62   27  0.26

ACGTcount: A:0.25, C:0.05, G:0.21, T:0.49


Consensus pattern (61 bp):   
TTCGAATAAAATATATGGAAAGTTGGTAATTTTTATTTTCTTTTATGTGTTGGGTATTGTA

Found at i:10622 original size:29 final size:30

Alignment explanation


    Indices: 10570--10629  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

      10560 GAAATTCGTG

                               *      *    
      10570 TTTGAAGACTCATTGAAGACTTATTTGAAGA
          1 TTTGAAGACT-ATTGAAGAATTATTTCAAGA

                                          
      10601 TTTGAAGACT-TTGAAGAATTATTTCAAGA
          1 TTTGAAGACTATTGAAGAATTATTTCAAGA

      10630 GGAAAGAATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   17  0.63
  31   10  0.37

ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37


Consensus pattern (30 bp):   
TTTGAAGACTATTGAAGAATTATTTCAAGA
Done.