Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017410.1 Corchorus olitorius cultivar O-4 contig17443, 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: 15169
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30


Found at i:4313 original size:33 final size:33

Alignment explanation


    Indices: 4276--4338  Score: 99
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       4266 CCCTAATTTC

                 *             *             
       4276 ATAATTAAACCCAAAGGCCGAATAATGCTTTTG
          1 ATAATCAAACCCAAAGGCCCAATAATGCTTTTG

                                   *      
       4309 ATAATCAAACCCAAAGGCCCAATCATGCTT
          1 ATAATCAAACCCAAAGGCCCAATAATGCTT

       4339 AATTTTATTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  33   27  1.00

ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24


Consensus pattern (33 bp):   
ATAATCAAACCCAAAGGCCCAATAATGCTTTTG

Found at i:4367 original size:2 final size:2

Alignment explanation


    Indices: 4360--4426  Score: 61
    Period size: 2  Copynumber: 34.5  Consensus size: 2

       4350 GCATGACCAT

                        *     *                                       *   
       4360 TA TA TA TA AA TA AA TA TA TA TA TA TA TA T- TA T- TA TA TT TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                                      
       4400 T- TA TA TA TA TA TA GTA GTA -A TA TA TA T
          1 TA TA TA TA TA TA TA -TA -TA TA TA TA TA T

       4427 GTGGTCAATA


Statistics
Matches: 54,  Mismatches: 6, Indels: 10
        0.77            0.09        0.14

Matches are distributed among these distances:
   1    4  0.07
   2   45  0.83
   3    5  0.09

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:5217 original size:41 final size:41

Alignment explanation


    Indices: 5154--5238  Score: 120
    Period size: 41  Copynumber: 2.1  Consensus size: 41

       5144 AATCCTGCGC

                     *                               
       5154 AAACCCTAACAAACAATATAAACCCTAAGTGAGAT-AAAAG
          1 AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG

                                         *             
       5194 AAACCCTCAAAAAACACAT-TAAACCCTAGGTGAGATAAAAAG
          1 AAACCCT-AAAAAACA-ATATAAACCCTAAGTGAGATAAAAAG

               
       5236 AAA
          1 AAA

       5239 AAACATGAAC


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  40    7  0.17
  41   23  0.57
  42   10  0.25

ACGTcount: A:0.55, C:0.20, G:0.11, T:0.14


Consensus pattern (41 bp):   
AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAAG

Found at i:7301 original size:21 final size:22

Alignment explanation


    Indices: 7276--7324  Score: 73
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       7266 AAAGTTATTA

                                   
       7276 AAAAAGCTACAA-TGATTATTCT
          1 AAAAAG-TACAAGTGATTATTCT

                    *             
       7298 AAAAAGTATAAGTGATTATTCT
          1 AAAAAGTACAAGTGATTATTCT

                 
       7320 AAAAA
          1 AAAAA

       7325 CAATATTATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  21    4  0.16
  22   21  0.84

ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31


Consensus pattern (22 bp):   
AAAAAGTACAAGTGATTATTCT

Found at i:8699 original size:24 final size:24

Alignment explanation


    Indices: 8656--8701  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       8646 AATAATTATT

                         *          
       8656 ATTATAATAAGAATAAGTTTAATA
          1 ATTATAATAAGAAGAAGTTTAATA

                      *    *      
       8680 ATTATAATAATAAGATGTTTAA
          1 ATTATAATAAGAAGAAGTTTAA

       8702 CGTAAATTTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39


Consensus pattern (24 bp):   
ATTATAATAAGAAGAAGTTTAATA

Found at i:13659 original size:32 final size:32

Alignment explanation


    Indices: 13617--13686  Score: 81
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      13607 GCAAGCCCAA

                 *                            
      13617 GCCTGCTGCGCTAGCCCAGCAGG-C-GCTGGCCT
          1 GCCTGGTGCGC-AGCCCAG-AGGCCTGCTGGCCT

                         *                * 
      13649 GCCTGGTGCGCAGGCCAGAGGCCTGCTGGCTT
          1 GCCTGGTGCGCAGCCCAGAGGCCTGCTGGCCT

                  
      13681 GCCTGG
          1 GCCTGG

      13687 CCGGCCAGGC


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  30    3  0.09
  31    7  0.21
  32   23  0.70

ACGTcount: A:0.09, C:0.36, G:0.39, T:0.17


Consensus pattern (32 bp):   
GCCTGGTGCGCAGCCCAGAGGCCTGCTGGCCT
Done.