Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024348.1 Corchorus olitorius cultivar O-4 contig24381, 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: 3241
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31


Found at i:1646 original size:33 final size:29

Alignment explanation


    Indices: 1607--1762  Score: 161
    Period size: 30  Copynumber: 5.0  Consensus size: 29

       1597 CAATCTTGGG

                                             
       1607 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
          1 ATGACAACTTCTGGTGTCAATAATTT--T-A-C

                                              *
       1640 ATGACAACTTCTGGTGTCAAGATAATAATTTTGAT
          1 ATGACAACTTCTGGTGTC-----AATAATTTT-AC

                                         
       1675 ATGACAACTTCTGGTGTCAATAATTTT-C
          1 ATGACAACTTCTGGTGTCAATAATTTTAC

                                        * *
       1703 ATGACAACTTCTGGTGTCAAGATAATTTAAT
          1 ATGACAACTTCTGGTGTC-A-ATAATTTTAC

                                         
       1734 ATGACAACTTCTGGTGTCAATTAATTTTA
          1 ATGACAACTTCTGGTGTCAA-TAATTTTA

       1763 AAATAAAATA


Statistics
Matches: 108,  Mismatches: 6, Indels: 21
        0.80            0.04        0.16

Matches are distributed among these distances:
  28   18  0.17
  29    2  0.02
  30   24  0.22
  31   18  0.17
  33   18  0.17
  35   18  0.17
  36    2  0.02
  38    8  0.07

ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37


Consensus pattern (29 bp):   
ATGACAACTTCTGGTGTCAATAATTTTAC

Found at i:1734 original size:68 final size:65

Alignment explanation


    Indices: 1607--1760  Score: 221
    Period size: 68  Copynumber: 2.4  Consensus size: 65

       1597 CAATCTTGGG

                                                                             
       1607 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTT
          1 ATGACAACTTCTGGTGTCAATAATTT-CT-A-CATGACAACTTCTGGTGTCAAGATAATAATTTT

               
       1672 GAT
         63 GAT

                                                                          *  
       1675 ATGACAACTTCTGGTGTCAATAATTT-T-CATGACAACTTCTGGTGTCAAG---ATAA-TTTAAT
          1 ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTTGAT

                                       
       1734 ATGACAACTTCTGGTGTCAATTAATTT
          1 ATGACAACTTCTGGTGTCAA-TAATTT

       1761 TAAAATAAAA


Statistics
Matches: 84,  Mismatches: 1, Indels: 10
        0.88            0.01        0.11

Matches are distributed among these distances:
  59   25  0.30
  60   10  0.12
  63   22  0.26
  66    1  0.01
  68   26  0.31

ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Consensus pattern (65 bp):   
ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAATAATTTTGAT

Found at i:1741 original size:31 final size:30

Alignment explanation


    Indices: 1640--1753  Score: 144
    Period size: 31  Copynumber: 3.7  Consensus size: 30

       1630 TTTCCTCAGC

                                               
       1640 ATGACAACTTCTGGTGTCAAGATAATAATTTTGAT
          1 ATGACAACTTCTGGTGTCAAG---ATAA-TTT-AT

                                          
       1675 ATGACAACTTCTGGTGTC-A-ATAATTT-T
          1 ATGACAACTTCTGGTGTCAAGATAATTTAT

                                            
       1702 CATGACAACTTCTGGTGTCAAGATAATTTAAT
          1 -ATGACAACTTCTGGTGTCAAGATAATTT-AT

                                
       1734 ATGACAACTTCTGGTGTCAA
          1 ATGACAACTTCTGGTGTCAA

       1754 TTAATTTTAA


Statistics
Matches: 74,  Mismatches: 0, Indels: 14
        0.84            0.00        0.16

Matches are distributed among these distances:
  27    1  0.01
  28   18  0.24
  29    4  0.05
  30   11  0.15
  31   20  0.27
  32    1  0.01
  34    1  0.01
  35   18  0.24

ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Consensus pattern (30 bp):   
ATGACAACTTCTGGTGTCAAGATAATTTAT
Done.