Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015115.1 Corchorus olitorius cultivar O-4 contig15148, 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: 8083
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:1727 original size:24 final size:25

Alignment explanation


    Indices: 1698--1748  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       1688 ATAGAGTAAC

                       *             
       1698 AATAAAATAAATAAACAAGA-AAAT
          1 AATAAAATAAAGAAACAAGATAAAT

                    *                
       1722 AATAAAATTAAGAAACAAGATAAAT
          1 AATAAAATAAAGAAACAAGATAAAT

              
       1747 AA
          1 AA

       1749 ATACTCCAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   18  0.75
  25    6  0.25

ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18


Consensus pattern (25 bp):   
AATAAAATAAAGAAACAAGATAAAT

Found at i:2226 original size:27 final size:28

Alignment explanation


    Indices: 2176--2228  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       2166 AAATCAATTA

                           *            
       2176 GAAATCATAAAAACATAAAGATAAATCT
          1 GAAATCATAAAAACACAAAGATAAATCT

                                       
       2204 GAAATCATAAAATAC-CAAA-ATAAAT
          1 GAAATCATAAAA-ACACAAAGATAAAT

       2229 AATCAGATTA


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27    6  0.26
  28   15  0.65
  29    2  0.09

ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21


Consensus pattern (28 bp):   
GAAATCATAAAAACACAAAGATAAATCT

Found at i:2684 original size:22 final size:22

Alignment explanation


    Indices: 2659--2700  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2649 GCGTTCCTGA

                  *               
       2659 GGGTACCCGGGGCCGGGTAGGG
          1 GGGTACACGGGGCCGGGTAGGG

                                
       2681 GGGTACACGGGGCCGGGTAG
          1 GGGTACACGGGGCCGGGTAG

       2701 CCTCAGAACT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.12, C:0.21, G:0.57, T:0.10


Consensus pattern (22 bp):   
GGGTACACGGGGCCGGGTAGGG

Found at i:3677 original size:125 final size:125

Alignment explanation


    Indices: 3409--3691  Score: 381
    Period size: 125  Copynumber: 2.3  Consensus size: 125

       3399 AGGATTATAT

                             *              *                                
       3409 ATAGCGGCGTTTGT-CAAGAGAAACGCCACTACTCATAACAAAGAAATGGTGTTTTCAGTTTCAC
          1 ATAGCGGCGTTT-TCCATGAGAAACGCCACTATTCATAACAAAGAAATGGTGTTTTCAGTTTCAC

               *           * * * *               *               *       
       3473 CAACTTTCTATTCTTTGTAGAGGATTATATATAGCGGTGTTTACTATAGAAACGCCACTAA
         65 CAAATTTCTATTCTTGGGAAAAGATTATATATAGCGGCGTTTACTATAGAAACACCACTAA

                *  *            *                                            
       3534 ATAGTGGAG-TTTCTCATGAAAAACGCCACTATTCATAACAAAGAAATGGTGTTTTCAGTTTCAC
          1 ATAGCGGCGTTTTC-CATGAGAAACGCCACTATTCATAACAAAGAAATGGTGTTTTCAGTTTCAC

                                               *         *              *
       3598 CAAATTTCTATTCTTGGGAAAAGATTATATATAGCTGCGTTTACTTTAGAAACACCACTAT
         65 CAAATTTCTATTCTTGGGAAAAGATTATATATAGCGGCGTTTACTATAGAAACACCACTAA

            *                          *     
       3659 TTAGCGGCGTTTTCCATGAGAAACGCCGCTATT
          1 ATAGCGGCGTTTTCCATGAGAAACGCCACTATT

       3692 TTATTTAGAA


Statistics
Matches: 135,  Mismatches: 20, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 123    1  0.01
 124    2  0.01
 125  128  0.95
 126    4  0.03

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


Consensus pattern (125 bp):   
ATAGCGGCGTTTTCCATGAGAAACGCCACTATTCATAACAAAGAAATGGTGTTTTCAGTTTCACC
AAATTTCTATTCTTGGGAAAAGATTATATATAGCGGCGTTTACTATAGAAACACCACTAA

Found at i:5843 original size:28 final size:28

Alignment explanation


    Indices: 5803--5862  Score: 120
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       5793 GCTCTATTCA

                                        
       5803 CATTAAGATTGTAGTTCCTTCAGTCTTG
          1 CATTAAGATTGTAGTTCCTTCAGTCTTG

                                        
       5831 CATTAAGATTGTAGTTCCTTCAGTCTTG
          1 CATTAAGATTGTAGTTCCTTCAGTCTTG

                
       5859 CATT
          1 CATT

       5863 TCATTTCCTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   32  1.00

ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43


Consensus pattern (28 bp):   
CATTAAGATTGTAGTTCCTTCAGTCTTG
Done.