Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002091.1 Corchorus olitorius cultivar O-4 contig02091, 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: 2676
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.41


Found at i:231 original size:29 final size:30

Alignment explanation


    Indices: 194--261  Score: 77
    Period size: 29  Copynumber: 2.3  Consensus size: 30

        184 AACGTAAGGA

                *     *  *                
        194 ATTAATTTGTCCCGAAA-AAAACATAACGG
          1 ATTATTTTGTACCAAAACAAAACATAACGG

                                        *  
        223 ATTATTTTGTACCAAAAGCAAAACATAAGGG
          1 ATTATTTTGTACCAAAA-CAAAACATAACGG

                     
        254 ATT-TTTTG
          1 ATTATTTTG

        262 GGGTATTTAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  29   14  0.42
  30    5  0.15
  31   14  0.42

ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31


Consensus pattern (30 bp):   
ATTATTTTGTACCAAAACAAAACATAACGG

Found at i:1788 original size:39 final size:40

Alignment explanation


    Indices: 1732--1812  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       1722 TTTAATTCCT

                                       *            
       1732 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACCTACATTAATTAA

                     *          *                   
       1772 ATGTAATA-CTATAATAACTGAAATACCTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACCTACATTAATTAA

              
       1811 AT
          1 AT

       1813 TCTTAGGCAT


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.51, C:0.10, G:0.04, T:0.36


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACCTACATTAATTAA

Found at i:2171 original size:205 final size:199

Alignment explanation


    Indices: 1923--2331  Score: 658
    Period size: 205  Copynumber: 2.0  Consensus size: 199

       1913 TTCCTTAATA

                      *                                                      
       1923 ATAAATAAATGGGATCTTAATATCTTTTATAATTTTCAAATTTTGTTTGACATTGATCTAATTTA
          1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTCAAATTTTGTTTGACATTGATCTAATTTA

                                                *             *             *
       1988 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATACA-AATAG
         66 ATTTAATAAATCAACCACTAATGTTCAACT-A----CTTTTGGTATAGTTATATATACATAATAA

                                                                    *        
       2052 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAATCTTAGACTTAAAAAAATTAATAACA
        126 TAATGTGTTGTATCTTATTCACTACAACTTTGATAGTAATCTTAGACTT-AAAAAACTAATAACA

                      
       2117 TTCACCATTG
        190 TTCACCATTG

                  *                              *                           
       2127 ATAAATTAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
          1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTCAAATTTTGTTTGACATTGATCTAATTT

                                                                 *           
       2192 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTGGTATAGTTATATATATATAATAATAAT
         65 AATTTAATAAATCAACCACTAATGTTCAACTACTTTTGGTATAGTTATATATACATAATAATAAT

                                        *                                    
       2257 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAACTAATAACATTCAC
        130 GTGTTGTATCTTATTCACTACAACTTTGATAGTAATCTTAGACTTAAAAAACTAATAACATTCAC

                *
       2322 CATTT
        195 CATTG

                 
       2327 ATAAA
          1 ATAAA

       2332 GTTATTAAGC


Statistics
Matches: 193,  Mismatches: 10, Indels: 8
        0.91            0.05        0.04

Matches are distributed among these distances:
 200   48  0.25
 201   52  0.27
 204   15  0.08
 205   78  0.40

ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43


Consensus pattern (199 bp):   
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTCAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACTAATGTTCAACTACTTTTGGTATAGTTATATATACATAATAATAATG
TGTTGTATCTTATTCACTACAACTTTGATAGTAATCTTAGACTTAAAAAACTAATAACATTCACC
ATTG
Done.