Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021431.1 Corchorus olitorius cultivar O-4 contig21464, 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: 18361
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:5491 original size:27 final size:28

Alignment explanation


    Indices: 5461--5516  Score: 89
    Period size: 27  Copynumber: 2.0  Consensus size: 28

       5451 AAAAGTACTT

                                         
       5461 AAGAAAAATAAAC-AAAAAT-AAAAGAAA
          1 AAGAAAAAT-AACGAAAAATAAAAAGAAA

                                        
       5488 AAGAAAAATAACGAAAAATAAAAAGAAA
          1 AAGAAAAATAACGAAAAATAAAAAGAAA

             
       5516 A
          1 A

       5517 GGGTAAGAAA


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

Matches are distributed among these distances:
  26    3  0.11
  27   15  0.56
  28    9  0.33

ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07


Consensus pattern (28 bp):   
AAGAAAAATAACGAAAAATAAAAAGAAA

Found at i:5503 original size:16 final size:17

Alignment explanation


    Indices: 5474--5517  Score: 54
    Period size: 16  Copynumber: 2.6  Consensus size: 17

       5464 AAAAATAAAC

                             
       5474 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       5491 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 *     
       5507 AAAAAGAAAAG
          1 AAAAATAAAAG

       5518 GGTAAGAAAT


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  16   13  0.59
  17    9  0.41

ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG

Found at i:13554 original size:19 final size:18

Alignment explanation


    Indices: 13521--13556  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      13511 TTGAAATTAT

                              
      13521 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      13539 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      13557 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:14058 original size:2 final size:2

Alignment explanation


    Indices: 13986--14039  Score: 81
    Period size: 2  Copynumber: 27.0  Consensus size: 2

      13976 ACAATTCAAG

                            *     *     *                                 
      13986 CT CT CT CT CT CA CT CA CT CA CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

                             
      14028 CT CT CT CT CT CT
          1 CT CT CT CT CT CT

      14040 ACAAAACCTG


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   46  1.00

ACGTcount: A:0.06, C:0.50, G:0.00, T:0.44


Consensus pattern (2 bp):   
CT

Found at i:17515 original size:54 final size:54

Alignment explanation


    Indices: 17454--17625  Score: 265
    Period size: 54  Copynumber: 3.1  Consensus size: 54

      17444 AGAAAAATTG

                                                                   
      17454 TGAGCTATAGATGGATATATAATTGCT-TGTAAAAGGTTCTGTAATTGAAGCAAT
          1 TGAGCTATAGATGGATATATAATTG-TATGTAAAAGGTTCTGTAATTGAAGCAAT

                                                                    
      17508 TGAGCTATAGATGAAGATATATAATTGTATGTAAAAGGTTCTGTAATTGAAGCAAT
          1 TGAGCTATAGATG--GATATATAATTGTATGTAAAAGGTTCTGTAATTGAAGCAAT

                         * *                      *       *       
      17564 TGAGCTATAGATGCAGATATAATTGTATGTAAAAGGTTGTGTAATTAAAGCAAT
          1 TGAGCTATAGATGGATATATAATTGTATGTAAAAGGTTCTGTAATTGAAGCAAT

               *    
      17618 TGAACTAT
          1 TGAGCTAT

      17626 TAATGCACAA


Statistics
Matches: 110,  Mismatches: 5, Indels: 6
        0.91            0.04        0.05

Matches are distributed among these distances:
  54   57  0.52
  55    1  0.01
  56   52  0.47

ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34


Consensus pattern (54 bp):   
TGAGCTATAGATGGATATATAATTGTATGTAAAAGGTTCTGTAATTGAAGCAAT

Found at i:17666 original size:110 final size:110

Alignment explanation


    Indices: 17454--17673  Score: 243
    Period size: 110  Copynumber: 2.0  Consensus size: 110

      17444 AGAAAAATTG

                         * *                              *          *       
      17454 TGAGCTATAGATGGATATATAATTGCTTGTAAAAGGTTCTGTAATTGAAGCAATTGAGCTATAGA
          1 TGAGCTATAGATGCAGATATAATTGCTTGTAAAAGGTTCTGTAATTAAAGCAATTGAACTATAGA

                         *      *         ***            
      17519 TGAAGATATATAATTGTATGTAAAAGGTTCTGTAATTGAAGCAAT
         66 TGAAGATATATAAGTGTATGCAAAAGGTTCCAAAATTGAAGCAAT

                                                   *                         
      17564 TGAGCTATAGATGCAGATATAATTG-TATGTAAAAGGTTGTGTAATTAAAGCAATTGAACTATTA
          1 TGAGCTATAGATGCAGATATAATTGCT-TGTAAAAGGTTCTGTAATTAAAGCAATTGAACTA-TA

                                     *     *           *      
      17628 -ATGCACA-ATATA-AAGTGTA-GCGAAAGCTTTCCAAAATTGCAGCAAT
         64 GATG-A-AGATATATAAGTGTATGCAAAAG-GTTCCAAAATTGAAGCAAT

      17674 ACTTTTCCAT


Statistics
Matches: 92,  Mismatches: 13, Indels: 10
        0.80            0.11        0.09

Matches are distributed among these distances:
 109    6  0.07
 110   77  0.84
 111    8  0.09
 112    1  0.01

ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32


Consensus pattern (110 bp):   
TGAGCTATAGATGCAGATATAATTGCTTGTAAAAGGTTCTGTAATTAAAGCAATTGAACTATAGA
TGAAGATATATAAGTGTATGCAAAAGGTTCCAAAATTGAAGCAAT
Done.