Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020299.1 Corchorus olitorius cultivar O-4 contig20332, 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: 4993
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33


Found at i:2078 original size:10 final size:10

Alignment explanation


    Indices: 2055--2100  Score: 51
    Period size: 10  Copynumber: 4.7  Consensus size: 10

       2045 CGAACTCATC

                      
       2055 TTGAAGAC--
          1 TTGAAGACAA

                      
       2063 TTGAAGACAA
          1 TTGAAGACAA

                   *   
       2073 TTGAAGTTCAA
          1 TTGAAG-ACAA

                     *
       2084 TTGAAGACAT
          1 TTGAAGACAA

                   
       2094 TTGAAGA
          1 TTGAAGA

       2101 TGATTTGAGC


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
   8    8  0.25
  10   15  0.47
  11    9  0.28

ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28


Consensus pattern (10 bp):   
TTGAAGACAA

Found at i:2186 original size:21 final size:21

Alignment explanation


    Indices: 2156--2216  Score: 113
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       2146 CTAAAAACAG

                 *               
       2156 GACAAGTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                                 
       2177 GACAACTCCTGCCCAGGACTT
          1 GACAACTCCTGCCCAGGACTT

                               
       2198 GACAACTCCTGCCCAGGAC
          1 GACAACTCCTGCCCAGGAC

       2217 CTGGTCTGTT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  21   39  1.00

ACGTcount: A:0.25, C:0.38, G:0.21, T:0.16


Consensus pattern (21 bp):   
GACAACTCCTGCCCAGGACTT

Found at i:2274 original size:50 final size:50

Alignment explanation


    Indices: 2199--2320  Score: 181
    Period size: 50  Copynumber: 2.4  Consensus size: 50

       2189 CCAGGACTTG

                              *             *                 
       2199 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

                                                        *     
       2249 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAATTCAGA
          1 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

                *  *  *   *       
       2299 ACAAGTCATGTCCAAGACTTGG
          1 ACAACTCCTGCCCAGGACTTGG

       2321 ACAACTCCTG


Statistics
Matches: 65,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  50   65  1.00

ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19


Consensus pattern (50 bp):   
ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGA

Found at i:4551 original size:65 final size:66

Alignment explanation


    Indices: 4475--4600  Score: 173
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       4465 AGTAATTCTG

                          **      *                        *                 
       4475 AACCTAATTTGAGTGTTGTTTGTAATGA-ACGAAATCTGTTTTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTACTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT

             
       4539 A
         66 A

                                   *       *             *       *       
       4540 AACCTAATTTGAGTACTGTTTGCGATGACACTAAATCTGTTTTAGGTATTGTTTGTGATGA
          1 AACCTAATTTGAGTACTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGA

       4601 AACAAATTCT


Statistics
Matches: 52,  Mismatches: 8, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  65   24  0.46
  66   28  0.54

ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41


Consensus pattern (66 bp):   
AACCTAATTTGAGTACTGTTTGCAATGACACGAAATCTGTTTTAGATATTGTTAGTGATGATACT
A

Found at i:4593 original size:33 final size:33

Alignment explanation


    Indices: 4490--4615  Score: 105
    Period size: 33  Copynumber: 3.8  Consensus size: 33

       4480 AATTTGAGTG

                    *       *             * *
       4490 TTGTTTGTAATG-AACGAAATCTGTTTTAGATG
          1 TTGTTTGTGATGAAACTAAATCTGTTTTAGGTA

                 *       *      *  **         
       4522 TTGTTAGTGATGATACTAAACCTAATTT-GAGTA
          1 TTGTTTGTGATGAAACTAAATCTGTTTTAG-GTA

            *      *     *                   
       4555 CTGTTTGCGATGACACTAAATCTGTTTTAGGTA
          1 TTGTTTGTGATGAAACTAAATCTGTTTTAGGTA

                                         
       4588 TTGTTTGTGATGAAAC-AAATTCTGTTTT
          1 TTGTTTGTGATGAAACTAAA-TCTGTTTT

       4616 GGATGCTAAT


Statistics
Matches: 71,  Mismatches: 19, Indels: 7
        0.73            0.20        0.07

Matches are distributed among these distances:
  32   14  0.20
  33   56  0.79
  34    1  0.01

ACGTcount: A:0.28, C:0.10, G:0.20, T:0.43


Consensus pattern (33 bp):   
TTGTTTGTGATGAAACTAAATCTGTTTTAGGTA

Done.