Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024159.1 Corchorus olitorius cultivar O-4 contig24192, 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: 23036
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:11980 original size:59 final size:59

Alignment explanation


    Indices: 11916--12053  Score: 215
    Period size: 59  Copynumber: 2.3  Consensus size: 59

      11906 AGAATTAACA

                     *                                                  
      11916 TACACGGCCAGCATTCATTTTGCCCAAAAT-AACAATATACATTTGGTCCAATCAAATAT
          1 TACACGGCCTGCATTCATTTTGCCC-AAATCAACAATATACATTTGGTCCAATCAAATAT

                           *  *             *      *                   
      11975 TACACGGCCTGCATTAATCTTGCCCAAATCAAGAATATATATTTGGTCCAATCAAATAT
          1 TACACGGCCTGCATTCATTTTGCCCAAATCAACAATATACATTTGGTCCAATCAAATAT

                                
      12034 TACACGGCCTGCATTCATTT
          1 TACACGGCCTGCATTCATTT

      12054 GGTCCAATCA


Statistics
Matches: 71,  Mismatches: 7, Indels: 2
        0.89            0.09        0.03

Matches are distributed among these distances:
  58    4  0.06
  59   67  0.94

ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30


Consensus pattern (59 bp):   
TACACGGCCTGCATTCATTTTGCCCAAATCAACAATATACATTTGGTCCAATCAAATAT

Found at i:12459 original size:54 final size:54

Alignment explanation


    Indices: 12377--12486  Score: 220
    Period size: 54  Copynumber: 2.0  Consensus size: 54

      12367 TACAAGTGAC

                                                                  
      12377 CTGACGGGTCAATAGGTAACCTTTTCTCAACTTTTCTACATCATAACAGCTCAT
          1 CTGACGGGTCAATAGGTAACCTTTTCTCAACTTTTCTACATCATAACAGCTCAT

                                                                  
      12431 CTGACGGGTCAATAGGTAACCTTTTCTCAACTTTTCTACATCATAACAGCTCAT
          1 CTGACGGGTCAATAGGTAACCTTTTCTCAACTTTTCTACATCATAACAGCTCAT

              
      12485 CT
          1 CT

      12487 TTCCCCCCTA


Statistics
Matches: 56,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  54   56  1.00

ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34


Consensus pattern (54 bp):   
CTGACGGGTCAATAGGTAACCTTTTCTCAACTTTTCTACATCATAACAGCTCAT

Found at i:22076 original size:8 final size:8

Alignment explanation


    Indices: 22065--22095  Score: 53
    Period size: 8  Copynumber: 3.8  Consensus size: 8

      22055 TAAGAAATTT

                    
      22065 AAAAAATA
          1 AAAAAATA

                    
      22073 AAAAAATA
          1 AAAAAATA

                     
      22081 ATAAAAATA
          1 A-AAAAATA

                  
      22090 AAAAAA
          1 AAAAAA

      22096 GAAAGAAAGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   8   14  0.64
   9    8  0.36

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (8 bp):   
AAAAAATA

Found at i:22855 original size:107 final size:107

Alignment explanation


    Indices: 22669--22889  Score: 415
    Period size: 107  Copynumber: 2.1  Consensus size: 107

      22659 TTCATTTCCA

                 *                                                *          
      22669 CTCCAATTGTCATCTCCATTCTCTAAAAATATCCTTGCTTTATTGACACATGTTGTGTCACTACC
          1 CTCCACTTGTCATCTCCATTCTCTAAAAATATCCTTGCTTTATTGACACATGTTCTGTCACTACC

                                                      
      22734 TAGTTTCTTTGATATTTTTGGAGATGGAAAATGGAGAATGTT
         66 TAGTTTCTTTGATATTTTTGGAGATGGAAAATGGAGAATGTT

                                            *                                
      22776 CTCCACTTGTCATCTCCATTCTCTAAAAATATGCTTGCTTTATTGACACATGTTCTGTCACTACC
          1 CTCCACTTGTCATCTCCATTCTCTAAAAATATCCTTGCTTTATTGACACATGTTCTGTCACTACC

                                                      
      22841 TAGTTTCTTTGATATTTTTGGAGATGGAAAATGGAGAATGTT
         66 TAGTTTCTTTGATATTTTTGGAGATGGAAAATGGAGAATGTT

                   
      22883 CTCCACT
          1 CTCCACT

      22890 ACCTAGTTTC


Statistics
Matches: 111,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 107  111  1.00

ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40


Consensus pattern (107 bp):   
CTCCACTTGTCATCTCCATTCTCTAAAAATATCCTTGCTTTATTGACACATGTTCTGTCACTACC
TAGTTTCTTTGATATTTTTGGAGATGGAAAATGGAGAATGTT
Done.