Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021059.1 Corchorus olitorius cultivar O-4 contig21092, 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: 21371
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34


Found at i:3271 original size:30 final size:30

Alignment explanation


    Indices: 3204--3272  Score: 129
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       3194 CTAATATATA

                   *                      
       3204 TTGACACCAGAAGTTGTCATGATTTTGCAG
          1 TTGACACTAGAAGTTGTCATGATTTTGCAG

                                          
       3234 TTGACACTAGAAGTTGTCATGATTTTGCAG
          1 TTGACACTAGAAGTTGTCATGATTTTGCAG

                     
       3264 TTGACACTA
          1 TTGACACTA

       3273 AAATTATTAT


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   38  1.00

ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35


Consensus pattern (30 bp):   
TTGACACTAGAAGTTGTCATGATTTTGCAG

Found at i:4326 original size:3 final size:3

Alignment explanation


    Indices: 4318--4343  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       4308 TTAGAAAGTT

                                              
       4318 TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TT

       4344 TACTCTATCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTA

Found at i:4608 original size:2 final size:2

Alignment explanation


    Indices: 4601--4627  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4591 TTCCTGCTGG

                                                    
       4601 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4628 GCATCTGTTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:7570 original size:123 final size:123

Alignment explanation


    Indices: 7425--7669  Score: 356
    Period size: 123  Copynumber: 2.0  Consensus size: 123

       7415 TACCCTATTC

                                                   *                         
       7425 GACTCAACATTCTTCTTTTTTATCTTT-ACAAATTTATCGTTTCC-AAAAGCTTTTCCCATATAA
          1 GACTCAACATTCTTCTTTTTTAT-TTTCACAAATTTATCATTTCCGAAAA-CTTTTCCCATATAA

               *       *                   *                               
       7488 ATTGCATTTCCCATCTAAC-TTTTCTCTACACTCCACGAATTT-TACTCTTCCCACTACTTTT
         64 A-TACATTTCCAATCTAACTTTTTC-CTACAATCCACG-ATTTCTACTCTTCCCACTACTTTT

                                                                             
       7549 GACT-AACATTCTTCTTTTTTATTTTCACAAATTTATCATTTCCGAAAACTTTTCCCATATAAAT
          1 GACTCAACATTCTTCTTTTTTATTTTCACAAATTTATCATTTCCGAAAACTTTTCCCATATAAAT

                                    **                               
       7613 ACATTTCCAATCTAACTTTTTCCTGGAATCCACGATTTCTACTCTTCCCACTACTTT
         66 ACATTTCCAATCTAACTTTTTCCTACAATCCACGATTTCTACTCTTCCCACTACTTT

       7670 CCACCTTATA


Statistics
Matches: 111,  Mismatches: 6, Indels: 10
        0.87            0.05        0.08

Matches are distributed among these distances:
 121    4  0.04
 122   45  0.41
 123   54  0.49
 124    8  0.07

ACGTcount: A:0.26, C:0.27, G:0.04, T:0.43


Consensus pattern (123 bp):   
GACTCAACATTCTTCTTTTTTATTTTCACAAATTTATCATTTCCGAAAACTTTTCCCATATAAAT
ACATTTCCAATCTAACTTTTTCCTACAATCCACGATTTCTACTCTTCCCACTACTTTT

Found at i:14167 original size:21 final size:20

Alignment explanation


    Indices: 14143--14194  Score: 50
    Period size: 21  Copynumber: 2.5  Consensus size: 20

      14133 AAAAAACTTT

                                *
      14143 TAAAATAATTTATAAAGTTAG
          1 TAAAATAATTTA-AAAGTTAA

                 *  *            
      14164 TAAAACATCTTTAAAAGTTAA
          1 TAAAATA-ATTTAAAAGTTAA

              *       
      14185 TATAATAATT
          1 TAAAATAATT

      14195 AACAAAAGCT


Statistics
Matches: 24,  Mismatches: 6, Indels: 3
        0.73            0.18        0.09

Matches are distributed among these distances:
  20    2  0.08
  21   18  0.75
  22    4  0.17

ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38


Consensus pattern (20 bp):   
TAAAATAATTTAAAAGTTAA

Found at i:17660 original size:3 final size:3

Alignment explanation


    Indices: 17652--17791  Score: 253
    Period size: 3  Copynumber: 46.7  Consensus size: 3

      17642 CCCAAATTTT

                        *                                 *                
      17652 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

            *                                                              
      17700 GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                                                                      
      17748 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

      17792 TTACTTCAAA


Statistics
Matches: 131,  Mismatches: 6, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3  131  1.00

ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66


Consensus pattern (3 bp):   
TTA

Done.