Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001790.1 Corchorus olitorius cultivar O-4 contig01790, 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: 1778
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:74 original size:21 final size:21

Alignment explanation


    Indices: 44--83  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

         34 CTAAAAACAG

                 *               
         44 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
         65 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

         84 CTGGTCTGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:137 original size:71 final size:72

Alignment explanation


    Indices: 36--227  Score: 298
    Period size: 71  Copynumber: 2.7  Consensus size: 72

         26 ATTGAAGCCT

                     *                                             *        *
         36 AAAAA-CAGGACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGTTG-AAAG
          1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCAGTTGAAAAA

                   
         99 ACGGAAG
         66 ACGGAAG

                          *                                  *               
        106 AAAAATCAGAACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCAGTTGAAAAA
          1 AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCAGTTGAAAAA

                   
        171 ACGGAAG
         66 ACGGAAG

                *               *                             
        178 AAAATTCAGAACAAGTCCTGTCCAGGACTTGGACAACTCCTGCCCAGGAC
          1 AAAAATCAGAACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGAC

        228 TTGTTGCGGA


Statistics
Matches: 111,  Mismatches: 8, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  70    5  0.05
  71   50  0.45
  72   37  0.33
  73   19  0.17

ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17


Consensus pattern (72 bp):   
AAAAATCAGAACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCAGTTGAAAAA
ACGGAAG

Found at i:142 original size:21 final size:21

Alignment explanation


    Indices: 116--157  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        106 AAAAATCAGA

                                 
        116 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

                                 
        137 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        158 GTCAGTTGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19


Consensus pattern (21 bp):   
ACAACTCCTGCCCAGGACTTG

Found at i:218 original size:22 final size:22

Alignment explanation


    Indices: 188--230  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        178 AAAATTCAGA

                *     *           
        188 ACAAGTCCTGTCCAGGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

                                 
        210 ACAACTCCTGCCCAGGACTTG
          1 ACAACTCCTGCCCAGGACTTG

        231 TTGCGGAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21


Consensus pattern (22 bp):   
ACAACTCCTGCCCAGGACTTGG

Found at i:1298 original size:21 final size:21

Alignment explanation


    Indices: 1274--1314  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1264 TTGAAGCACT

                                  
       1274 ATTGGATAC-AAGTGGTACTAA
          1 ATTGGAT-CTAAGTGGTACTAA

                                
       1295 ATTGGATCTAAGTGGTACTA
          1 ATTGGATCTAAGTGGTACTA

       1315 GGGTTTCTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    1  0.05
  21   18  0.95

ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32


Consensus pattern (21 bp):   
ATTGGATCTAAGTGGTACTAA
Done.