Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015688.1 Corchorus olitorius cultivar O-4 contig15721, 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: 11436
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1306 original size:14 final size:13

Alignment explanation


    Indices: 1286--1325  Score: 62
    Period size: 14  Copynumber: 2.9  Consensus size: 13

       1276 ACCTATGTCT

                         
       1286 ATAATTATTATAC
          1 ATAATTATTATAC

                          
       1299 ATTAATTATTATAC
          1 A-TAATTATTATAC

                         
       1313 ATAATCTATTATA
          1 ATAAT-TATTATA

       1326 TTTACAGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    5  0.20
  14   20  0.80

ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47


Consensus pattern (13 bp):   
ATAATTATTATAC

Found at i:1526 original size:26 final size:26

Alignment explanation


    Indices: 1497--1550  Score: 81
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       1487 TAAGTCCTAA

                    *         *   *   
       1497 ATCATGAATTTTTACAAAGATTGAGC
          1 ATCATGAACTTTTACAAAAATTAAGC

                                      
       1523 ATCATGAACTTTTACAAAAATTAAGC
          1 ATCATGAACTTTTACAAAAATTAAGC

              
       1549 AT
          1 AT

       1551 TTATTTGAAC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  26   25  1.00

ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33


Consensus pattern (26 bp):   
ATCATGAACTTTTACAAAAATTAAGC

Found at i:1924 original size:50 final size:50

Alignment explanation


    Indices: 1860--1972  Score: 210
    Period size: 50  Copynumber: 2.3  Consensus size: 50

       1850 TTCAGTAACG

                                                              
       1860 AATGATT-ATTGAATTCATTACTGAAGTTGTTTACAAAATTACTTATGAA
          1 AATGATTAATTGAATTCATTACTGAAGTTGTTTACAAAATTACTTATGAA

                                                              
       1909 AATGATTAATTGAATTCATTACTGAAGTTGTTTACAAAATTACTTATGAA
          1 AATGATTAATTGAATTCATTACTGAAGTTGTTTACAAAATTACTTATGAA

                    *     
       1959 AATGATTATTTGAA
          1 AATGATTAATTGAA

       1973 ATTGTTGATA


Statistics
Matches: 62,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  49    7  0.11
  50   55  0.89

ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41


Consensus pattern (50 bp):   
AATGATTAATTGAATTCATTACTGAAGTTGTTTACAAAATTACTTATGAA

Found at i:10170 original size:50 final size:51

Alignment explanation


    Indices: 10077--10174  Score: 135
    Period size: 51  Copynumber: 1.9  Consensus size: 51

      10067 ATTATTTCTC

                                                  *            
      10077 TTCAATCTCGTCTCAGGACGTTAAATCAACTATCTCATGTTTCTCTCCTCT
          1 TTCAATCTCGTCTCAGGACGTTAAATCAACTATCTCATATTTCTCTCCTCT

                           *  *         **     *            
      10128 TTCAATCTCGTCTCATGATGTTAAA-CATTTATCTTATATTTCTCTCC
          1 TTCAATCTCGTCTCAGGACGTTAAATCAACTATCTCATATTTCTCTCC

      10175 CATAAATAAC


Statistics
Matches: 41,  Mismatches: 6, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  50   18  0.44
  51   23  0.56

ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43


Consensus pattern (51 bp):   
TTCAATCTCGTCTCAGGACGTTAAATCAACTATCTCATATTTCTCTCCTCT
Done.