Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022939.1 Corchorus olitorius cultivar O-4 contig22972, 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: 18211
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:615 original size:42 final size:41

Alignment explanation


    Indices: 556--675  Score: 169
    Period size: 42  Copynumber: 3.0  Consensus size: 41

        546 TAAACATATA

                                                      
        556 TACTAGCATTACTTTTCCATTACCATTGGCAAAGATCAAAAT
          1 TACTAGCATT-CTTTTCCATTACCATTGGCAAAGATCAAAAT

                                                      
        598 TACTAGCATTGCTTTTCCATTACCATTGGCAAAGATCAAAAT
          1 TACTAGCATT-CTTTTCCATTACCATTGGCAAAGATCAAAAT

            *            *                           
        640 GA--A--ATT-TTATCCATTACCATTGGCAAAGATCAAAAT
          1 TACTAGCATTCTTTTCCATTACCATTGGCAAAGATCAAAAT

        676 GAAATTTTAA


Statistics
Matches: 75,  Mismatches: 3, Indels: 6
        0.89            0.04        0.07

Matches are distributed among these distances:
  36   29  0.39
  38    3  0.04
  40    1  0.01
  42   42  0.56

ACGTcount: A:0.37, C:0.20, G:0.11, T:0.33


Consensus pattern (41 bp):   
TACTAGCATTCTTTTCCATTACCATTGGCAAAGATCAAAAT

Found at i:653 original size:36 final size:36

Alignment explanation


    Indices: 571--684  Score: 156
    Period size: 36  Copynumber: 3.0  Consensus size: 36

        561 GCATTACTTT

                                       *             *
        571 TCCATTACCATTGGCAAAGATCAAAATTACTAGCATTGCTTT
          1 TCCATTACCATTGGCAAAGATCAAAATGA--A--ATT--TTA

                                                
        613 TCCATTACCATTGGCAAAGATCAAAATGAAATTTTA
          1 TCCATTACCATTGGCAAAGATCAAAATGAAATTTTA

                                                
        649 TCCATTACCATTGGCAAAGATCAAAATGAAATTTTA
          1 TCCATTACCATTGGCAAAGATCAAAATGAAATTTTA

        685 AGGGTGGGAA


Statistics
Matches: 70,  Mismatches: 2, Indels: 6
        0.90            0.03        0.08

Matches are distributed among these distances:
  36   38  0.54
  38    3  0.04
  40    1  0.01
  42   28  0.40

ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32


Consensus pattern (36 bp):   
TCCATTACCATTGGCAAAGATCAAAATGAAATTTTA

Found at i:8620 original size:29 final size:29

Alignment explanation


    Indices: 8587--8646  Score: 120
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       8577 ATATATAATC

                                         
       8587 TATACTATATTAAAAAGTACGTTCACCTG
          1 TATACTATATTAAAAAGTACGTTCACCTG

                                         
       8616 TATACTATATTAAAAAGTACGTTCACCTG
          1 TATACTATATTAAAAAGTACGTTCACCTG

              
       8645 TA
          1 TA

       8647 AAACTTTTGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35


Consensus pattern (29 bp):   
TATACTATATTAAAAAGTACGTTCACCTG

Found at i:8911 original size:124 final size:126

Alignment explanation


    Indices: 8711--8967  Score: 337
    Period size: 124  Copynumber: 2.0  Consensus size: 126

       8701 CATTATTTAA

                   *                                                         
       8711 ACTTTTATAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT

                           *                                               
       8776 TTTTACCA-TTTTACTATTTTA-A-TTA-AAAAAACTTATATATATTAGAATTTTTTAAATAT
         66 TTTT--CATTTTTACCATTTTACATTTATAAAAAACTTATATATATTAGAATTTTTTAAATAT

                                            *                                
       8835 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTTAT-A
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATAT-CTTTATGA

                                               *  *                          
       8899 CCTATTTT-ATTTTTACCATTTTACTATTTTATTTTAAGAACTTATATATATTAGAATTTTTTAA
         65 --T-TTTTCATTTTTACCATTTTAC-A-TTTA--TAAAAAACTTATATATATTAGAATTTTTTAA

                
       8963 ATAT
        123 ATAT

             
       8967 A
          1 A

       8968 TTTCTTAAAT


Statistics
Matches: 116,  Mismatches: 5, Indels: 16
        0.85            0.04        0.12

Matches are distributed among these distances:
 124   56  0.48
 125   18  0.16
 126    1  0.01
 127    5  0.04
 129    3  0.03
 132   33  0.28

ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50


Consensus pattern (126 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCTTTATGAT
TTTTCATTTTTACCATTTTACATTTATAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:12037 original size:24 final size:24

Alignment explanation


    Indices: 12010--12060  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

      12000 TTTTCTCACG

                                  * 
      12010 TCTTCAAATCCATCAAAGTTTAGT
          1 TCTTCAAATCCATCAAAGTTTAAT

                      *             
      12034 TCTTCAAATCTATCAAAGTTTAAT
          1 TCTTCAAATCCATCAAAGTTTAAT

               
      12058 TCT
          1 TCT

      12061 CTTCTCGTTT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41


Consensus pattern (24 bp):   
TCTTCAAATCCATCAAAGTTTAAT
Done.