Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014169.1 Corchorus olitorius cultivar O-4 contig14202, 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: 8397
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33


Found at i:119 original size:40 final size:40

Alignment explanation


    Indices: 4--123  Score: 168
    Period size: 40  Copynumber: 3.0  Consensus size: 40

          1 TTG

                                    *       ** *    
          4 AAACAACACCTTCCGGTGGGGAAGAGCAAACTAAGAATTT
          1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT

                 *                                  
         44 AAACAGCACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT
          1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT

             *             *              *         
         84 AGACAACACCTTCCGATGGGGAAGGGCAAATTGGGTATTT
          1 AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT

        124 GGACTAGACA


Statistics
Matches: 71,  Mismatches: 9, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  40   71  1.00

ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20


Consensus pattern (40 bp):   
AAACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTT

Found at i:693 original size:18 final size:16

Alignment explanation


    Indices: 650--681  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        640 ATCTTGATTT

                 *          
        650 TTCAGGGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

                            
        666 TTCAGAGCTTTTCTGC
          1 TTCAGAGCTTTTCTGC

        682 CTTGTAGAGC


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44


Consensus pattern (16 bp):   
TTCAGAGCTTTTCTGC

Found at i:2277 original size:38 final size:38

Alignment explanation


    Indices: 2230--2454  Score: 317
    Period size: 38  Copynumber: 5.9  Consensus size: 38

       2220 ACTTTCAACA

                *                     **  *        
       2230 AAGCTATCAAATTT-ATTATTCGCTTTTGATCAAGACCC
          1 AAGCGATC-AATTTCATTATTCGCTTAGGACCAAGACCC

                                     *           *
       2268 AAGCGATCAATTTCATTATTCGCTTGGGACCAAGACCT
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                                                  
       2306 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                          *          *   *      **
       2344 AAGCGATCAATTTCTTTATTCGCTTGGGATCAAGACAT
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                                                  
       2382 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

                          *          *         
       2420 AAGCGATCAATTTCTTTATTCGCTTGGGACCAAGA
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGA

       2455 TTAATAAATT


Statistics
Matches: 167,  Mismatches: 19, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
  37    5  0.03
  38  162  0.97

ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Consensus pattern (38 bp):   
AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCC

Found at i:2326 original size:76 final size:76

Alignment explanation


    Indices: 2230--2454  Score: 371
    Period size: 76  Copynumber: 3.0  Consensus size: 76

       2220 ACTTTCAACA

                *                     **  *                      *           
       2230 AAGCTATCAAATTT-ATTATTCGCTTTTGATCAAGACCCAAGCGATCAATTTCATTATTCGCTTG
          1 AAGCGATC-AATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTG

                      * 
       2294 GGACCAAGACCT
         65 GGACCAAGACAT

                                                                             
       2306 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG

              *        
       2371 GATCAAGACAT
         66 GACCAAGACAT

                                                                             
       2382 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG
          1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG

                    
       2447 GACCAAGA
         66 GACCAAGA

       2455 TTAATAAATT


Statistics
Matches: 140,  Mismatches: 8, Indels: 2
        0.93            0.05        0.01

Matches are distributed among these distances:
  75    5  0.04
  76  135  0.96

ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Consensus pattern (76 bp):   
AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCCAAGCGATCAATTTCTTTATTCGCTTGG
GACCAAGACAT

Found at i:3521 original size:57 final size:57

Alignment explanation


    Indices: 3447--3563  Score: 198
    Period size: 57  Copynumber: 2.1  Consensus size: 57

       3437 CTTTGGTTTT

                *                                          *         
       3447 TTTTTTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAATTTAGCGAAC
          1 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC

                                                        *          * 
       3504 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
          1 TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC

               
       3561 TTT
          1 TTT

       3564 GTAAGTAGTT


Statistics
Matches: 56,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  57   56  1.00

ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42


Consensus pattern (57 bp):   
TTTTGTGCTCTAACTTTTGCCTAAGCCGTCCTTTGCAGGATTTTAAACTTAGCGAAC
Done.