Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013111.1 Corchorus olitorius cultivar O-4 contig13144, 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: 24610
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:280 original size:13 final size:13

Alignment explanation


    Indices: 262--294  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

        252 TTTAGTAAAT

                         
        262 TATATATATATAC
          1 TATATATATATAC

                         
        275 TATATATATATAC
          1 TATATATATATAC

              *    
        288 TACATAT
          1 TATATAT

        295 TATTTGAAAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45


Consensus pattern (13 bp):   
TATATATATATAC

Found at i:1431 original size:31 final size:31

Alignment explanation


    Indices: 1393--1470  Score: 149
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       1383 CTCAAATAAG

                                           
       1393 AGTTTGATATGATTGTTTTTTTTTTCCCAGA
          1 AGTTTGATATGATTGTTTTTTTTTTCCCAGA

                                           
       1424 AGTTTGATATGATTG-TTTTTTTTTCCCAGA
          1 AGTTTGATATGATTGTTTTTTTTTTCCCAGA

                             
       1454 AGTTTGATATGATTGTT
          1 AGTTTGATATGATTGTT

       1471 AACCATTGAA


Statistics
Matches: 46,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  30   30  0.65
  31   16  0.35

ACGTcount: A:0.21, C:0.08, G:0.18, T:0.54


Consensus pattern (31 bp):   
AGTTTGATATGATTGTTTTTTTTTTCCCAGA

Found at i:4926 original size:12 final size:12

Alignment explanation


    Indices: 4909--4935  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4899 CTTCTAGTAT

                        
       4909 GAATAAAAGAAA
          1 GAATAAAAGAAA

                        
       4921 GAATAAAAGAAA
          1 GAATAAAAGAAA

               
       4933 GAA
          1 GAA

       4936 AGAAAAAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07


Consensus pattern (12 bp):   
GAATAAAAGAAA

Found at i:4964 original size:13 final size:13

Alignment explanation


    Indices: 4925--4966  Score: 50
    Period size: 14  Copynumber: 3.1  Consensus size: 13

       4915 AAGAAAGAAT

                          
       4925 AAAAGAAAG-AAAG
          1 AAAA-AAAGAAAAG

                           
       4938 AAAAAAAAGAAAAAG
          1 -AAAAAAAG-AAAAG

                         
       4953 AAAAAAAGAAAAG
          1 AAAAAAAGAAAAG

             
       4966 A
          1 A

       4967 TGGTAGTTTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  13   10  0.38
  14   12  0.46
  15    4  0.15

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (13 bp):   
AAAAAAAGAAAAG

Found at i:6420 original size:3 final size:3

Alignment explanation


    Indices: 6412--6441  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       6402 GTGCAATATT

                                                   
       6412 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

       6442 TTTTTATGGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:18632 original size:53 final size:53

Alignment explanation


    Indices: 18569--18677  Score: 209
    Period size: 53  Copynumber: 2.1  Consensus size: 53

      18559 CAAAAACCAA

                                                                 
      18569 CTCTACTTCAAGCATAATTCAAGTTAGAGGGAAAAATAGAAAGAAGGAAAAGC
          1 CTCTACTTCAAGCATAATTCAAGTTAGAGGGAAAAATAGAAAGAAGGAAAAGC

                                *                                
      18622 CTCTACTTCAAGCATAATTCGAGTTAGAGGGAAAAATAGAAAGAAGGAAAAGC
          1 CTCTACTTCAAGCATAATTCAAGTTAGAGGGAAAAATAGAAAGAAGGAAAAGC

               
      18675 CTC
          1 CTC

      18678 CTGGAGTACA


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  53   55  1.00

ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19


Consensus pattern (53 bp):   
CTCTACTTCAAGCATAATTCAAGTTAGAGGGAAAAATAGAAAGAAGGAAAAGC

Found at i:20417 original size:42 final size:42

Alignment explanation


    Indices: 20370--20453  Score: 150
    Period size: 42  Copynumber: 2.0  Consensus size: 42

      20360 CCCCTGTGAA

                                                      
      20370 TGGATTCCACAAGTAAATGTCCTCGCAACTTCGAAAAGCTAG
          1 TGGATTCCACAAGTAAATGTCCTCGCAACTTCGAAAAGCTAG

                                   *       *          
      20412 TGGATTCCACAAGTAAATGTCCTTGCAACTTGGAAAAGCTAG
          1 TGGATTCCACAAGTAAATGTCCTCGCAACTTCGAAAAGCTAG

      20454 GCACAACAAG


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25


Consensus pattern (42 bp):   
TGGATTCCACAAGTAAATGTCCTCGCAACTTCGAAAAGCTAG
Done.