Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011963.1 Corchorus olitorius cultivar O-4 contig11996, 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: 15993
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:1712 original size:128 final size:130

Alignment explanation


    Indices: 1500--1762  Score: 404
    Period size: 128  Copynumber: 2.0  Consensus size: 130

       1490 CATTGTTTAA

                     *          *           *  *     *  *      *             
       1500 ATTTTTATAGTTTTACTCAATTAAAAACTCTAGTTTTATTTGATTAAATCTGATATCCTTATAAC
          1 ATTTTTATAATTTTACTCAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC

                                    *                                  *     
       1565 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTT-ATATATTAGAAATTTT-TAATAT
         66 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATAT

                                                                     *     * 
       1628 ATTTTTATAATTTTACTCAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCTTTATACC
          1 ATTTTTATAATTTTACTCAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC

                                                                             
       1693 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATA
         66 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAAATTTTAAAATA

             
       1758 T
        130 T

                
       1759 ATTT
          1 ATTT

       1763 CTTAAATGGC


Statistics
Matches: 121,  Mismatches: 11, Indels: 3
        0.90            0.08        0.02

Matches are distributed among these distances:
 128   96  0.79
 130   16  0.13
 131    9  0.07

ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49


Consensus pattern (130 bp):   
ATTTTTATAATTTTACTCAACTAAAAACTCTACTTCTATTTAATAAAATCTAATATCCTTATAAC
TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATAT

Found at i:3829 original size:22 final size:22

Alignment explanation


    Indices: 3789--3830  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       3779 GTTTATAATA

                *         *       
       3789 TTCTTGGGTCATTCGGGTTAAC
          1 TTCTCGGGTCATTCAGGTTAAC

                         *      
       3811 TTCTCGGGTCATTTAGGTTA
          1 TTCTCGGGTCATTCAGGTTA

       3831 TGAATTTGCC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43


Consensus pattern (22 bp):   
TTCTCGGGTCATTCAGGTTAAC

Found at i:6919 original size:33 final size:33

Alignment explanation


    Indices: 6881--6943  Score: 81
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       6871 GAACAAAAAT

                                    *        
       6881 GTTTCTAACAATCAGACACGGAATTAGAGAAAC
          1 GTTTCTAACAATCAGACACGGAATCAGAGAAAC

                  *  **     *             
       6914 GTTTCTGACTGTCAGAGACGGAATCAGAGA
          1 GTTTCTAACAATCAGACACGGAATCAGAGA

       6944 CGTTCCACTA


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  33   25  1.00

ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22


Consensus pattern (33 bp):   
GTTTCTAACAATCAGACACGGAATCAGAGAAAC

Found at i:7891 original size:19 final size:19

Alignment explanation


    Indices: 7869--7920  Score: 54
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       7859 GGGCTGAAAT

                               
       7869 TAATTAATTATTAAATAAA
          1 TAATTAATTATTAAATAAA

                         * * *  
       7888 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAAATAAA

                           
       7907 TAATT-ATTATTAAA
          1 TAATTAATTATTAAA

       7921 AATCCCACTT


Statistics
Matches: 26,  Mismatches: 5, Indels: 5
        0.72            0.14        0.14

Matches are distributed among these distances:
  18    9  0.35
  19   16  0.62
  20    1  0.04

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (19 bp):   
TAATTAATTATTAAATAAA
Done.