Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014849.1 Corchorus olitorius cultivar O-4 contig14882, 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: 2875
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39


Found at i:423 original size:132 final size:123

Alignment explanation


    Indices: 175--434  Score: 387
    Period size: 124  Copynumber: 2.0  Consensus size: 123

        165 CATTGTTTAA

                   *                                                         
        175 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT

                                                                       
        240 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTTAAATAT
         66 TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAA-TTTTTTAAATAT

                                            *                                
        299 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-C-T-T---

                 *                       *  *                                
        364 TATTTTATTTTTACCATTTTACTATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATA
         60 TA--TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA

             
        429 T
        123 T

                  
        430 A-TTTT
          1 ACTTTT

        435 CTTAAATGAA


Statistics
Matches: 123,  Mismatches: 5, Indels: 10
        0.89            0.04        0.07

Matches are distributed among these distances:
 124   54  0.44
 125    1  0.01
 126    1  0.01
 127    1  0.01
 130    6  0.05
 131   13  0.11
 132   47  0.38

ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51


Consensus pattern (123 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:454 original size:15 final size:14

Alignment explanation


    Indices: 418--456  Score: 51
    Period size: 15  Copynumber: 2.7  Consensus size: 14

        408 TATATTAGAA

                       *  
        418 TTTTTTAAATATAT
          1 TTTTTTAAATAAAT

               *           
        432 TTTCTTAAATGAAAT
          1 TTTTTTAAAT-AAAT

                      
        447 TTTTTTAAAT
          1 TTTTTTAAAT

        457 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  14    9  0.43
  15   12  0.57

ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59


Consensus pattern (14 bp):   
TTTTTTAAATAAAT

Found at i:959 original size:17 final size:16

Alignment explanation


    Indices: 919--969  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

        909 CATGTAATCT

                    **      
        919 TTGATCACCGGTGATC
          1 TTGATCACTAGTGATC

                             
        935 TTGCATCACTAGTGATC
          1 TTG-ATCACTAGTGATC

                             
        952 TTAGATCACTAGTGATC
          1 TT-GATCACTAGTGATC

             
        969 T
          1 T

        970 GGGGGGTGAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35


Consensus pattern (16 bp):   
TTGATCACTAGTGATC

Found at i:2148 original size:2 final size:2

Alignment explanation


    Indices: 2141--2188  Score: 78
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       2131 CTTAATACGC

                                                                            
       2141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT ACT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT

                 
       2185 AT AT
          1 AT AT

       2189 TATTTTTAGT


Statistics
Matches: 44,  Mismatches: 0, Indels: 4
        0.92            0.00        0.08

Matches are distributed among these distances:
   2   40  0.91
   3    4  0.09

ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.