Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015401.1 Corchorus olitorius cultivar O-4 contig15434, 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: 23905
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:4393 original size:2 final size:2

Alignment explanation


    Indices: 4386--4428  Score: 77
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       4376 GGTCTTGATA

                                                               *          
       4386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
       4428 A
          1 A

       4429 AAGAAGCTGT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:4797 original size:34 final size:34

Alignment explanation


    Indices: 4758--4829  Score: 144
    Period size: 34  Copynumber: 2.1  Consensus size: 34

       4748 CGAAGCAGAG

                                              
       4758 TATATATATTTGCCTTCTGCACTAAGTCCTTAAT
          1 TATATATATTTGCCTTCTGCACTAAGTCCTTAAT

                                              
       4792 TATATATATTTGCCTTCTGCACTAAGTCCTTAAT
          1 TATATATATTTGCCTTCTGCACTAAGTCCTTAAT

                
       4826 TATA
          1 TATA

       4830 GCTGGAAAAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   38  1.00

ACGTcount: A:0.28, C:0.19, G:0.08, T:0.44


Consensus pattern (34 bp):   
TATATATATTTGCCTTCTGCACTAAGTCCTTAAT

Found at i:17225 original size:2 final size:2

Alignment explanation


    Indices: 17220--17251  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      17210 TGTTTTTCTT

                                                           
      17220 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

      17252 CAGTTTCCTC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:22473 original size:83 final size:79

Alignment explanation


    Indices: 22334--22514  Score: 254
    Period size: 83  Copynumber: 2.2  Consensus size: 79

      22324 GTATGGAGCA

                       *                              *      *           *   
      22334 CCTGTCTTCTCATGTTCCTTCGTGTCGGCGAGCCTCGACAGTTGGCGGCTGTTTTGAGAGCTTCA
          1 CCTGTCTTCTCGTGTTCCTTCGTGTCGGCGAGCCTCGACAGTCGGCGGCCGTTTTGAGAGCCTCA

                          
      22399 CTGCCTGAGAACTG
         66 CTGCCTGAGAACTG

                                         *  *        *                       
      22413 CCTGTCTTCTCGTGTTCCTTCGCTTTGTGTGGTGAGCCTCGGCAGTCGGCGGCCGTTTTGAGAGC
          1 CCTGTCTTCTCGTGTTCCTTCG---TGT-CGGCGAGCCTCGACAGTCGGCGGCCGTTTTGAGAGC

                          *   
      22478 CTCACTGCCTGAGAGCTG
         62 CTCACTGCCTGAGAACTG

                               
      22496 CCTGTCTTCTCGTGTTCCT
          1 CCTGTCTTCTCGTGTTCCT

      22515 AATTATATAT


Statistics
Matches: 90,  Mismatches: 8, Indels: 4
        0.88            0.08        0.04

Matches are distributed among these distances:
  79   21  0.23
  82    3  0.03
  83   66  0.73

ACGTcount: A:0.09, C:0.29, G:0.28, T:0.33


Consensus pattern (79 bp):   
CCTGTCTTCTCGTGTTCCTTCGTGTCGGCGAGCCTCGACAGTCGGCGGCCGTTTTGAGAGCCTCA
CTGCCTGAGAACTG

Found at i:22938 original size:99 final size:99

Alignment explanation


    Indices: 22814--23010  Score: 349
    Period size: 99  Copynumber: 2.0  Consensus size: 99

      22804 GTCTTTCTTA

                                                *                            
      22814 TTTTTTCAGAAATAATTTCTAATTAAATCGAAATCGGTTTTCTGATGCTCGTAAAAATAAACTCT
          1 TTTTTTCAGAAATAATTTCTAATTAAATCGAAATCGATTTTCTGATGCTCGTAAAAATAAACTCT

                                              
      22879 TAAATTAATAATGTTGAGATTTGCTCAGATGAAT
         66 TAAATTAATAATGTTGAGATTTGCTCAGATGAAT

                   **                                                        
      22913 TTTTTTCCTAAATAATTTCTAATTAAATCGAAATCGATTTTCTGATGCTCGTAAAAATAAACTCT
          1 TTTTTTCAGAAATAATTTCTAATTAAATCGAAATCGATTTTCTGATGCTCGTAAAAATAAACTCT

                      *            *         
      22978 TAAATTAATATTGTTGAGATTTGGTCAGATGAA
         66 TAAATTAATAATGTTGAGATTTGCTCAGATGAA

      23011 AATATATATT


Statistics
Matches: 93,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  99   93  1.00

ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40


Consensus pattern (99 bp):   
TTTTTTCAGAAATAATTTCTAATTAAATCGAAATCGATTTTCTGATGCTCGTAAAAATAAACTCT
TAAATTAATAATGTTGAGATTTGCTCAGATGAAT
Done.