Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009745.1 Corchorus olitorius cultivar O-4 contig09777, 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: 2371
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:219 original size:20 final size:20

Alignment explanation


    Indices: 189--234  Score: 65
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        179 TTCTAATTTT

                       *         
        189 TATATTTAAAATTATTATAAA
          1 TATA-TTAAAAATATTATAAA

                              * 
        210 TATATTAAAAATATTATATA
          1 TATATTAAAAATATTATAAA

                 
        230 TATAT
          1 TATAT

        235 ATATTAGGCG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   19  0.83
  21    4  0.17

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (20 bp):   
TATATTAAAAATATTATAAA

Found at i:862 original size:133 final size:128

Alignment explanation


    Indices: 472--904  Score: 447
    Period size: 131  Copynumber: 3.3  Consensus size: 128

        462 CCAAAGCATG

                              *            **         *                * *   
        472 ATTACTTTTGAAACGACAGATTAAGTCGTTGAAAAATCTTAAACTTTCCACAATGACTTTTGTTA
          1 ATTACTTTTGAAACGACAAATTAAGTCGTTGTGAAATCTT-ATCTTT-CACAATGACTTCTATTA

                      **               *                       *    *        
        537 GTCGTTGCTTGGTATATTTTACAAATTGTTTTTCGCAGCGACCTTGAAAGTCGCTACAAAAACAT
         64 GTCGTTGCTTAATATATTTTACAAATTATTTTT-GCAGCGACCTTGAAAGTTGCTAAAAAAACAT

             
        602 A
        128 A

                        * *             *                        *     *   * 
        603 ATTACTTTTGAAGCCACAAATTAAGTCGCTGTGAAATCTTACTCTTTTCACAACGACTAAC-AAT
          1 ATTACTTTTGAAACGACAAATTAAGTCGTTGTGAAATCTTA-TC-TTTCACAATGACT-TCTATT

                             **    *          *           *                  
        667 AGTCGTTGCTTAATATAGGTTACTAATTGATTTTCGCAGCGACCTTAAAAGTTGCTACAAAAAAA
         63 AGTCGTTGCTTAATATATTTTACAAATT-ATTTTTGCAGCGACCTTGAAAGTTGCT--AAAAAAA

                *
        732 TCATG
        125 -CATA

              *                                             *           *    
        737 ATCACTTTTGAAACGACAAATTAAGTCGTTGTGAAATCTTATCTATTCGCAATGACTTCTCTTAG
          1 ATTACTTTTGAAACGACAAATTAAGTCGTTGTGAAATCTTATCT-TTCACAATGACTTCTATTAG

                        *      *                 *               *           
        802 TCGTTGCTTAATGTATTTTCCAAATTAATTTTTGCAGTGACAC-TGAAAGTTGATAAAAAAACAT
         65 TCGTTGCTTAATATATTTTACAAATT-ATTTTTGCAGCGAC-CTTGAAAGTTGCTAAAAAAACAT

             
        866 A
        128 A

                  *    *                          
        867 ATTACTGTTGAGACGACAAATTAAGTCGTTGTGAAATC
          1 ATTACTTTTGAAACGACAAATTAAGTCGTTGTGAAATC

        905 CTATTATGTT


Statistics
Matches: 246,  Mismatches: 46, Indels: 21
        0.79            0.15        0.07

Matches are distributed among these distances:
 130   39  0.16
 131   94  0.38
 132    9  0.04
 133   63  0.26
 134   41  0.17

ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Consensus pattern (128 bp):   
ATTACTTTTGAAACGACAAATTAAGTCGTTGTGAAATCTTATCTTTCACAATGACTTCTATTAGT
CGTTGCTTAATATATTTTACAAATTATTTTTGCAGCGACCTTGAAAGTTGCTAAAAAAACATA

Found at i:1231 original size:144 final size:144

Alignment explanation


    Indices: 971--1238  Score: 373
    Period size: 144  Copynumber: 1.9  Consensus size: 144

        961 ACGAGTGGCA

                            *                     *               *          
        971 AAGTTTTGGTGTAGATTTGGGCAAGTCTCAAACTTATAGTTAGGCAACTTCCACTAGGTTACATC
          1 AAGTTTTGGTGTAGATCTGGGCAAGTCTCAAACTTATACTTAGGCAACTTCCACCAGGTTACATC

              *                  *  *               *            *           
       1036 TTTGACAAGTTGCATTCAAGACCTGGCCAAGTGTTTTCCTGATTTTTTCCTACTCTATTCATCCG
         66 TTGGACAAGTTGCATTCAAGAACTAGCCAAGTGTTTTCCTAATTTTTTCCTACCCTATTCATCCG

                          
       1101 AATCAACTCTAGCC
        131 AATCAACTCTAGCC

                        *                                                    
       1115 AAGTTTTGGTGTGGATCTGGGCAAGTCTCGAAA-TTATACTTAGGCGAA-TTCCACCAGGTTA-A
          1 AAGTTTTGGTGTAGATCTGGGCAAGTCTC-AAACTTATACTTAGGC-AACTTCCACCAGGTTACA

                           *                 *                             
       1177 GTCTTGGACAAGTTGTATTC-AGCAACTAGCCATGTGTTTTCCTAATTTTTTCCTACCCTATT
         64 -TCTTGGACAAGTTGCATTCAAG-AACTAGCCAAGTGTTTTCCTAATTTTTTCCTACCCTATT

       1239 TGACTAAATC


Statistics
Matches: 109,  Mismatches: 11, Indels: 8
        0.85            0.09        0.06

Matches are distributed among these distances:
 143    3  0.03
 144  101  0.93
 145    5  0.05

ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36


Consensus pattern (144 bp):   
AAGTTTTGGTGTAGATCTGGGCAAGTCTCAAACTTATACTTAGGCAACTTCCACCAGGTTACATC
TTGGACAAGTTGCATTCAAGAACTAGCCAAGTGTTTTCCTAATTTTTTCCTACCCTATTCATCCG
AATCAACTCTAGCC

Done.