Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014882.1 Corchorus olitorius cultivar O-4 contig14915, 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: 2488
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.42


Found at i:868 original size:28 final size:32

Alignment explanation


    Indices: 828--887  Score: 83
    Period size: 29  Copynumber: 2.0  Consensus size: 32

        818 GTATGCAAAC

                       *                    
        828 GAAAGTG-TTTTGGAATG-G-AAAT-TGTTTT
          1 GAAAGTGATTTGGGAATGTGAAAATGTGTTTT

                                            
        856 GAAAGTGATTTGGGAATGTGAAAATGTGTTTT
          1 GAAAGTGATTTGGGAATGTGAAAATGTGTTTT

        888 AATGTCCTTG


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  28    7  0.26
  29    9  0.33
  30    1  0.04
  31    4  0.15
  32    6  0.22

ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40


Consensus pattern (32 bp):   
GAAAGTGATTTGGGAATGTGAAAATGTGTTTT

Found at i:988 original size:28 final size:28

Alignment explanation


    Indices: 943--998  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        933 TTAAACTGAT

                         *    **        
        943 TGGTAAGAGTGAATTCGTGTCTCAGGGG
          1 TGGTAAGAGTGAACTCGTACCTCAGGGG

                                         
        971 TGGTAAGAGT-AGACTCGTACCTCAGGGG
          1 TGGTAAGAGTGA-ACTCGTACCTCAGGGG

        999 GTTAAACTGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  27    1  0.04
  28   23  0.96

ACGTcount: A:0.23, C:0.14, G:0.38, T:0.25


Consensus pattern (28 bp):   
TGGTAAGAGTGAACTCGTACCTCAGGGG

Found at i:1032 original size:38 final size:37

Alignment explanation


    Indices: 971--1049  Score: 113
    Period size: 38  Copynumber: 2.1  Consensus size: 37

        961 GTCTCAGGGG

                    *     *                       
        971 TGGTAAGAGTAGACTCGTACCTCAGGGGGTTAAACTGT
          1 TGGTAAGAATAGACCCGTACCTCAGGGGGTT-AACTGT

                      *       *                  
       1009 TGGTAAGAATGGACCCGTGCCTCAGGGGGTTAACTGT
          1 TGGTAAGAATAGACCCGTACCTCAGGGGGTTAACTGT

                
       1046 TGGT
          1 TGGT

       1050 TAGACTCGAG


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  37   10  0.27
  38   27  0.73

ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27


Consensus pattern (37 bp):   
TGGTAAGAATAGACCCGTACCTCAGGGGGTTAACTGT

Found at i:1089 original size:6 final size:6

Alignment explanation


    Indices: 1078--1120  Score: 86
    Period size: 6  Copynumber: 7.2  Consensus size: 6

       1068 CGTTAACGGA

                                                              
       1078 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG T
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG T

       1121 AGTGCAGCCT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   37  1.00

ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51


Consensus pattern (6 bp):   
TGATTG

Found at i:2200 original size:19 final size:21

Alignment explanation


    Indices: 2176--2233  Score: 59
    Period size: 20  Copynumber: 2.9  Consensus size: 21

       2166 TAGAGATCTT

                     *           
       2176 AATTATAAGGT-TTTT-TTAA
          1 AATTATAAGCTATTTTATTAA

                                  
       2195 AATTATTAAGCTATTTTATTAA
          1 AATTA-TAAGCTATTTTATTAA

            *      *          
       2217 TATTATAGGCT-TTTTAT
          1 AATTATAAGCTATTTTAT

       2234 ATACTAACCT


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  19    5  0.15
  20   11  0.33
  21    9  0.27
  22    8  0.24

ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53


Consensus pattern (21 bp):   
AATTATAAGCTATTTTATTAA

Found at i:2233 original size:20 final size:20

Alignment explanation


    Indices: 2176--2233  Score: 57
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       2166 TAGAGATCTT

                                 
       2176 AATTATAAGG-TTTTT-TTAA
          1 AATTAT-AGGCTTTTTATTAA

                    *             
       2195 AATTATTAAGCTATTTTATTAA
          1 AATTA-TAGGCT-TTTTATTAA

            *                
       2217 TATTATAGGCTTTTTAT
          1 AATTATAGGCTTTTTAT

       2234 ATACTAACCT


Statistics
Matches: 32,  Mismatches: 3, Indels: 7
        0.76            0.07        0.17

Matches are distributed among these distances:
  19    7  0.22
  20    8  0.25
  21    9  0.28
  22    8  0.25

ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53


Consensus pattern (20 bp):   
AATTATAGGCTTTTTATTAA
Done.