Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021049.1 Corchorus olitorius cultivar O-4 contig21082, 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: 5201
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:1156 original size:29 final size:29

Alignment explanation


    Indices: 1107--1176  Score: 88
    Period size: 30  Copynumber: 2.4  Consensus size: 29

       1097 TTAAAATTTA

                            *            
       1107 TCAGGGGCATTTTGGTCA-TTTTTTCGCC
          1 TCAGGGGCATTTTGGTAATTTTTTTCGCC

             *             *            * 
       1135 TTAGGGGCACTTTTGTTAATTTTTTTCGTC
          1 TCAGGGGCA-TTTTGGTAATTTTTTTCGCC

                        
       1165 TCAGGGGCATTT
          1 TCAGGGGCATTT

       1177 AGGTCAAAAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  28    8  0.23
  29   10  0.29
  30   17  0.49

ACGTcount: A:0.13, C:0.17, G:0.24, T:0.46


Consensus pattern (29 bp):   
TCAGGGGCATTTTGGTAATTTTTTTCGCC

Found at i:1915 original size:17 final size:18

Alignment explanation


    Indices: 1888--1921  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       1878 CAAACAAATA

                        *     
       1888 AAAGAAAACATGCAAGAC
          1 AAAGAAAACATGAAAGAC

                             
       1906 AAAG-AAACATGAAAGA
          1 AAAGAAAACATGAAAGA

       1922 AATGGAACCA


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

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06


Consensus pattern (18 bp):   
AAAGAAAACATGAAAGAC

Found at i:4659 original size:47 final size:47

Alignment explanation


    Indices: 4596--4775  Score: 201
    Period size: 47  Copynumber: 4.0  Consensus size: 47

       4586 ATTAAACTAA

                                                           
       4596 AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG
          1 AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG

             *               *              *              
       4643 AGGAAG--A--A-TTTAGTT-TAGGTAATTAAGCTAAGTAGTAAAAG
          1 AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG

                 *       *                       *         
       4684 AAGAAAAAATTAGCTTAATTCTAGGTAATTAAACTAAATAGTAAAAG
          1 AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG

               **   **  *      *       *                 
       4731 AAGTCGAACCTATTTTAATCCTAGGTAGTTAAACTAAGTAGTAAA
          1 AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA

       4776 GAGTAGTCAA


Statistics
Matches: 108,  Mismatches: 19, Indels: 12
        0.78            0.14        0.09

Matches are distributed among these distances:
  41   29  0.27
  42    6  0.06
  43    2  0.02
  45    2  0.02
  46    5  0.05
  47   64  0.59

ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29


Consensus pattern (47 bp):   
AAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG
Done.