Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018082.1 Corchorus olitorius cultivar O-4 contig18115, 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: 12830
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33


Found at i:1182 original size:15 final size:15

Alignment explanation


    Indices: 1162--1192  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1152 AGACTGAAGC

                           
       1162 GACTTTTATTATAGG
          1 GACTTTTATTATAGG

                           
       1177 GACTTTTATTATAGG
          1 GACTTTTATTATAGG

             
       1192 G
          1 G

       1193 GCTCCTACAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45


Consensus pattern (15 bp):   
GACTTTTATTATAGG

Found at i:9606 original size:174 final size:174

Alignment explanation


    Indices: 9278--9619  Score: 497
    Period size: 174  Copynumber: 1.9  Consensus size: 174

       9268 AAATATATAC

                                           *     ***                         
       9278 TATATATTATTTTTAGTGACTATGGAAATTATTTAAATGTCAAATTGAGGATTAATGTGGTGCCT
          1 TATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAAATTGAGGATTAATGTGGTGCCT

            *            *                        *                          
       9343 TCTTTTGGTAATTTTTTTTTTAATCTTTTCGCACTTTTTAGGTGACTAAAAAGACCCTCAATGAA
         66 CCTTTTGG----TCTTTTTTTAATCTTTTCGCACTTTTCAGGTGACTAAAAAGACCCTCAATGAA

                             *                               
       9408 TTTCCTCCCTTACTTTTGCTGCTGCCCTTTTTTTGTAATACTATAATAA
        127 TTTCCTCCCTTACTTTTCCTGCTGCCC-TTTTTTGTAATACTATAATAA

                                                                          *  
       9457 TATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAAATTGAGGATTAATGTGGTGTCT
          1 TATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAAATTGAGGATTAATGTGGTGCCT

                             **        *       *       *           *         
       9522 CCTTTTGG-CTTTTTTTGGTCTTTTCGTACTTTTCGGGTGACTTAAAAGACCCTCGATGAATTTC
         66 CCTTTTGGTCTTTTTTTAATCTTTTCGCACTTTTCAGGTGACTAAAAAGACCCTCAATGAATTTC

                                              
       9586 CTCCCTTACTTTTCCTGCTGCCCTTTTTTGTAAT
        131 CTCCCTTACTTTTCCTGCTGCCCTTTTTTGTAAT

       9620 TTACTATTTT


Statistics
Matches: 148,  Mismatches: 15, Indels: 6
        0.88            0.09        0.04

Matches are distributed among these distances:
 173   11  0.07
 174   70  0.47
 179   67  0.45

ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45


Consensus pattern (174 bp):   
TATATATTATTTTTAGTGACTATGGAAATTACTTAAAAACCAAATTGAGGATTAATGTGGTGCCT
CCTTTTGGTCTTTTTTTAATCTTTTCGCACTTTTCAGGTGACTAAAAAGACCCTCAATGAATTTC
CTCCCTTACTTTTCCTGCTGCCCTTTTTTGTAATACTATAATAA

Found at i:11695 original size:19 final size:20

Alignment explanation


    Indices: 11667--11704  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      11657 TTTATCCTCT

                                
      11667 AATGGATAG-TTTTATTTTA
          1 AATGGATAGTTTTTATTTTA

                 *             
      11686 AATGGGTAGTTTTTATTTT
          1 AATGGATAGTTTTTATTTT

      11705 GTTTTGAATT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    8  0.47
  20    9  0.53

ACGTcount: A:0.26, C:0.00, G:0.18, T:0.55


Consensus pattern (20 bp):   
AATGGATAGTTTTTATTTTA

Done.