Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021798.1 Corchorus olitorius cultivar O-4 contig21831, 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: 14027
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:683 original size:36 final size:36

Alignment explanation


    Indices: 636--705  Score: 113
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        626 TTCAATAACC

                         *      *               
        636 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

                  *                           
        672 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

        706 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:1608 original size:205 final size:202

Alignment explanation


    Indices: 1219--1630  Score: 725
    Period size: 205  Copynumber: 2.0  Consensus size: 202

       1209 GCTTAATAAC

                      *                                                      
       1219 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                          *                                                  
       1284 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAAGTAGTTGAACATTAGTGGTT
         66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAAGTAGTTGAACATTAGTGGTT

                    *                                                        
       1349 GATTTATTGAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
        131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGAT

             **     
       1414 CTGATTTA
        195 CCAATTTA

                                                                             
       1422 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                                           *      *        *                 
       1487 GATACAACACATTACTATTATATATATAGAATTATACCTAAAAAAAATTAGTTGAACATTAGTGG
         66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAAGTAGTTGAACATTAGTGG

                                                                             
       1552 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
        129 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGA

                     
       1617 TCCAATTTA
        194 TCCAATTTA

                 
       1626 TTTAT
          1 TTTAT

       1631 TATTAAGGAA


Statistics
Matches: 199,  Mismatches: 8, Indels: 3
        0.95            0.04        0.01

Matches are distributed among these distances:
 203   89  0.45
 204   17  0.09
 205   93  0.47

ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37


Consensus pattern (202 bp):   
TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATC
CAATTTA

Found at i:4072 original size:23 final size:23

Alignment explanation


    Indices: 4042--4100  Score: 66
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       4032 TTATAAAACT

                                  * 
       4042 AAACTAACAACAAGAC-TTTTATC
          1 AAACTAACAACAA-ACATTTTACC

                     **  *         
       4065 AAACTAACAGTAACCATTTTACC
          1 AAACTAACAACAAACATTTTACC

                         
       4088 AAACTAACAACAA
          1 AAACTAACAACAA

       4101 TTTAACCATA


Statistics
Matches: 29,  Mismatches: 6, Indels: 2
        0.78            0.16        0.05

Matches are distributed among these distances:
  22    1  0.03
  23   28  0.97

ACGTcount: A:0.51, C:0.24, G:0.03, T:0.22


Consensus pattern (23 bp):   
AAACTAACAACAAACATTTTACC

Found at i:4956 original size:45 final size:45

Alignment explanation


    Indices: 4889--4977  Score: 142
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       4879 ATTACCTAAA

                             *     *                     
       4889 TTCTACTCCATCTATAGGTAATTTATCAAAATAAAGCTAATATTC
          1 TTCTACTCCATCTATAGATAATTCATCAAAATAAAGCTAATATTC

                *        *                              
       4934 TTCTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
          1 TTCTACTCCATCTATAGATAATTCATCAAAATAAAGCTAATATT

       4978 AATTGTTGTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   40  1.00

ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37


Consensus pattern (45 bp):   
TTCTACTCCATCTATAGATAATTCATCAAAATAAAGCTAATATTC
Done.