Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000750.1 Corchorus olitorius cultivar O-4 contig00750, 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, 673

Length: 1122
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35


Found at i:288 original size:171 final size:166

Alignment explanation


    Indices: 1--372  Score: 582
    Period size: 171  Copynumber: 2.2  Consensus size: 166

                       *                    *                                
          1 GTTCAATAATTAATTTTTTTTGGTAACATAATCACTAATTGATTTATTTATTTATGTTAATTTTT
          1 GTTCAATAATTTA-TTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGTTAATTTTT

                                           *                                 
         66 TTGGTAGCGATTTATGGTAAAAATAAATAATTATCAATCAATTAAAACTTTGATTGACAAAATTA
         65 TTGGTAGCGATTTATGGTAAAAATAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTA

                                *   *             
        131 ACTAACGACTAACTTGGATTTATTTATTTATTTACCAT
        130 ACTAACGACTAACTT-GATTCATTCATTTATTTACCAT

                                                                             
        169 GTTCAATAATTTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATTTATGTTAATT
          1 GTTCAATAATTTATTTTTTTGGTAACATAATTACTAATTG----ATTTATTTATTTATGTTAATT

                                     *                     *                 
        234 TTTTTGGTAGCGATTTATGGTAAAATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAA
         62 TTTTTGGTAGCGATTTATGGTAAAAATAAATAATCATCAATCAATTAAAACTTTGATTGACAAAA

                                                *   
        299 TTAACTAACGACTAACTTGATTCATTCATTTATTTAGCAT
        127 TTAACTAACGACTAACTTGATTCATTCATTTATTTACCAT

                                   *    *     
        339 GTTCAATCAATTTTATTTTTTTGCTAACGTAATT
          1 GTTCAAT-AA-TTTATTTTTTTGGTAACATAATT

        373 GATTCGTTTA


Statistics
Matches: 188,  Mismatches: 10, Indels: 8
        0.91            0.05        0.04

Matches are distributed among these distances:
 167   26  0.14
 168   12  0.06
 170   26  0.14
 171  103  0.55
 172   21  0.11

ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46


Consensus pattern (166 bp):   
GTTCAATAATTTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGTTAATTTTTT
TGGTAGCGATTTATGGTAAAAATAAATAATCATCAATCAATTAAAACTTTGATTGACAAAATTAA
CTAACGACTAACTTGATTCATTCATTTATTTACCAT

Found at i:806 original size:15 final size:15

Alignment explanation


    Indices: 786--924  Score: 77
    Period size: 15  Copynumber: 9.1  Consensus size: 15

        776 CTAATTGAAT

                           
        786 AATATACAAAGTAAA
          1 AATATACAAAGTAAA

                  *    *    *
        801 AATATATATAATTGAAT
          1 AATATACA-AAGT-AAA

                           
        818 AATATACAAAGTAAA
          1 AATATACAAAGTAAA

                   ** *    *
        833 AATATA-TGATTGAAT
          1 AATATACAAAGT-AAA

                          *
        848 AATATACAAAGTAAC
          1 AATATACAAAGTAAA

                   *  *    *
        863 AATATA-TAATTGAAT
          1 AATATACAAAGT-AAA

                  *        
        878 AATATATAAAGTAAA
          1 AATATACAAAGTAAA

                   *  *    *
        893 AATATA-TAATTGAAT
          1 AATATACAAAGT-AAA

                           
        908 AATATACAAAGTAAA
          1 AATATACAAAGTAAA

              
        923 AA
          1 AA

        925 AAACACAATT


Statistics
Matches: 90,  Mismatches: 26, Indels: 16
        0.68            0.20        0.12

Matches are distributed among these distances:
  14    8  0.09
  15   59  0.66
  16   14  0.16
  17    9  0.10

ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29


Consensus pattern (15 bp):   
AATATACAAAGTAAA

Found at i:845 original size:30 final size:30

Alignment explanation


    Indices: 777--924  Score: 251
    Period size: 30  Copynumber: 4.9  Consensus size: 30

        767 AAAGTTTGTC

                                            
        777 TAATTGAATAATATACAAAGTAAAAATATATA
          1 TAATTGAATAATATACAAAGT-AAAA-ATATA

                                          
        809 TAATTGAATAATATACAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

             *                     *      
        839 TGATTGAATAATATACAAAGTAACAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

                           *              
        869 TAATTGAATAATATATAAAGTAAAAATATA
          1 TAATTGAATAATATACAAAGTAAAAATATA

                                      
        899 TAATTGAATAATATACAAAGTAAAAA
          1 TAATTGAATAATATACAAAGTAAAAA

        925 AAACACAATT


Statistics
Matches: 110,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  30   85  0.77
  31    4  0.04
  32   21  0.19

ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30


Consensus pattern (30 bp):   
TAATTGAATAATATACAAAGTAAAAATATA

Done.