Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014225.1 Corchorus olitorius cultivar O-4 contig14258, 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: 51864
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:7452 original size:17 final size:19

Alignment explanation


    Indices: 7420--7457  Score: 62
    Period size: 17  Copynumber: 2.1  Consensus size: 19

       7410 TTTTATATGA

                               
       7420 ATATATGAAAGCCAAGCCT
          1 ATATATGAAAGCCAAGCCT

                               
       7439 ATAT-TGAAAG-CAAGCCT
          1 ATATATGAAAGCCAAGCCT

              
       7456 AT
          1 AT

       7458 GGGGTTTTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17    9  0.47
  18    6  0.32
  19    4  0.21

ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24


Consensus pattern (19 bp):   
ATATATGAAAGCCAAGCCT

Found at i:7509 original size:17 final size:18

Alignment explanation


    Indices: 7474--7509  Score: 65
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       7464 TTTTTTAATA

                              
       7474 TGAAAGCCAAGCCTATAT
          1 TGAAAGCCAAGCCTATAT

                              
       7492 TGAAAG-CAAGCCTATAT
          1 TGAAAGCCAAGCCTATAT

             
       7509 T
          1 T

       7510 CATGCATAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17   12  0.67
  18    6  0.33

ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25


Consensus pattern (18 bp):   
TGAAAGCCAAGCCTATAT

Found at i:7524 original size:49 final size:48

Alignment explanation


    Indices: 7419--7524  Score: 117
    Period size: 49  Copynumber: 2.2  Consensus size: 48

       7409 TTTTTATATG

                                                      *   *** 
       7419 AATATATGAAAGCCAAGCCTATATTGAAAGCAAGCCTATGGGGTTTTTTT
          1 AATATATGAAAGCCAAGCCTATATTGAAAGCAAGCCTAT--GATTTGCAT

            *                                                 
       7469 TA-ATATGAAAGCCAAGCCTATATTGAAAGCAAGCCTAT-ATTCATGCAT
          1 AATATATGAAAGCCAAGCCTATATTGAAAGCAAGCCTATGATT--TGCAT

                    
       7517 AATATATG
          1 AATATATG

       7525 CTTTATTAAG


Statistics
Matches: 47,  Mismatches: 6, Indels: 7
        0.78            0.10        0.12

Matches are distributed among these distances:
  46    2  0.04
  48    3  0.06
  49   41  0.87
  50    1  0.02

ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30


Consensus pattern (48 bp):   
AATATATGAAAGCCAAGCCTATATTGAAAGCAAGCCTATGATTTGCAT

Found at i:7809 original size:3 final size:3

Alignment explanation


    Indices: 7801--7849  Score: 91
    Period size: 3  Copynumber: 16.7  Consensus size: 3

       7791 GGTAACAAAT

                                                                           
       7801 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

              
       7848 TA
          1 TA

       7850 TTATTATTAT


Statistics
Matches: 45,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2    2  0.04
   3   43  0.96

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


Consensus pattern (3 bp):   
TAA

Found at i:17114 original size:22 final size:20

Alignment explanation


    Indices: 17065--17116  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 20

      17055 AAATTTAAAA

                                
      17065 GGAA-GGAAGGAGGCGCGTG
          1 GGAAGGGAAGGAGGCGCGTG

             *                     
      17084 GTAAGGGGAACGGAGGCGCGTGG
          1 GGAA-GGGAA-GGAGGCGCGT-G

                      
      17107 GGAAGGGAAG
          1 GGAAGGGAAG

      17117 AGAAGCAGCC


Statistics
Matches: 27,  Mismatches: 2, Indels: 6
        0.77            0.06        0.17

Matches are distributed among these distances:
  19    3  0.11
  21    5  0.19
  22   15  0.56
  23    4  0.15

ACGTcount: A:0.27, C:0.10, G:0.58, T:0.06


Consensus pattern (20 bp):   
GGAAGGGAAGGAGGCGCGTG

Found at i:28738 original size:29 final size:29

Alignment explanation


    Indices: 28696--28753  Score: 107
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      28686 GTTCGAATCA

                                         
      28696 TTGGATCGTTTCATGTAATATCATAGTAT
          1 TTGGATCGTTTCATGTAATATCATAGTAT

                               *         
      28725 TTGGATCGTTTCATGTAATGTCATAGTAT
          1 TTGGATCGTTTCATGTAATATCATAGTAT

      28754 ATCAATTTCC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45


Consensus pattern (29 bp):   
TTGGATCGTTTCATGTAATATCATAGTAT

Found at i:28963 original size:53 final size:53

Alignment explanation


    Indices: 28883--28988  Score: 212
    Period size: 53  Copynumber: 2.0  Consensus size: 53

      28873 AAGAGAAGAA

                                                                 
      28883 CCACTGATTTTGTTTTTAATCAAACACTTGCCAATTTCAGATGTAATTTTCCG
          1 CCACTGATTTTGTTTTTAATCAAACACTTGCCAATTTCAGATGTAATTTTCCG

                                                                 
      28936 CCACTGATTTTGTTTTTAATCAAACACTTGCCAATTTCAGATGTAATTTTCCG
          1 CCACTGATTTTGTTTTTAATCAAACACTTGCCAATTTCAGATGTAATTTTCCG

      28989 TTTAAATGAA


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  53   53  1.00

ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42


Consensus pattern (53 bp):   
CCACTGATTTTGTTTTTAATCAAACACTTGCCAATTTCAGATGTAATTTTCCG
Done.