Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021461.1 Corchorus olitorius cultivar O-4 contig21494, 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: 14191
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:2854 original size:21 final size:20

Alignment explanation


    Indices: 2809--2866  Score: 82
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       2799 CTGTTTAGCA

                                
       2809 ACTGTACAGATGAGATT-AC
          1 ACTGTACAGATGAGATTAAC

                       *        *
       2828 ACTGTACAGATTAGATTAGAT
          1 ACTGTACAGATGAGATTA-AC

                              
       2849 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       2867 TTAGAGCAGC


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  19   16  0.47
  21   18  0.53

ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAAC

Found at i:3334 original size:30 final size:31

Alignment explanation


    Indices: 3294--3358  Score: 123
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       3284 ACTTTAGAAA

                                           
       3294 ATAAAGTTTGAGATTAGAAGTGTTCCATATT
          1 ATAAAGTTTGAGATTAGAAGTGTTCCATATT

                                           
       3325 ATAAA-TTTGAGATTAGAAGTGTTCCATATT
          1 ATAAAGTTTGAGATTAGAAGTGTTCCATATT

                
       3355 ATAA
          1 ATAA

       3359 GTATTTAGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   29  0.85
  31    5  0.15

ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38


Consensus pattern (31 bp):   
ATAAAGTTTGAGATTAGAAGTGTTCCATATT

Found at i:3360 original size:16 final size:16

Alignment explanation


    Indices: 3306--3360  Score: 51
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       3296 AAAGTTTGAG

                            
       3306 ATTAGAAGTGTTCCAT
          1 ATTAGAAGTGTTCCAT

                *  *     * *
       3322 ATTATAAAT-TT-GAG
          1 ATTAGAAGTGTTCCAT

                            
       3336 ATTAGAAGTGTTCCAT
          1 ATTAGAAGTGTTCCAT

                *    
       3352 ATTATAAGT
          1 ATTAGAAGT

       3361 ATTTAGGGGA


Statistics
Matches: 28,  Mismatches: 9, Indels: 4
        0.68            0.22        0.10

Matches are distributed among these distances:
  14    8  0.29
  15    4  0.14
  16   16  0.57

ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40


Consensus pattern (16 bp):   
ATTAGAAGTGTTCCAT

Found at i:12419 original size:38 final size:38

Alignment explanation


    Indices: 12322--12470  Score: 219
    Period size: 38  Copynumber: 3.9  Consensus size: 38

      12312 GGCTGTGCAT

                                           *        
      12322 AGTGGACCCGTACCTCAGGGGGGTTAAACTGATGGTAAAG
          1 AGTGGACCCGTACCTCA-GGGGGTTAAACTGTTGGT-AAG

                     *    *                       
      12362 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                       *                          
      12400 AGTGGACCCGTGCCTCAGGGGGTTAAACTGTTGGTAAG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

                  *    *                      
      12438 AGTGGATCCGTGCCTCAGGGGGTT-AACTGTTGG
          1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG

      12471 CTAGACTTGA


Statistics
Matches: 102,  Mismatches: 7, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  37    9  0.09
  38   61  0.60
  39   17  0.17
  40   15  0.15

ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23


Consensus pattern (38 bp):   
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAG

Found at i:12510 original size:6 final size:6

Alignment explanation


    Indices: 12500--12548  Score: 73
    Period size: 6  Copynumber: 8.3  Consensus size: 6

      12490 CGTTAACGGA

                 *      *                                          
      12500 TGATTA TGATTA TG-TTG TGATTG TGATTG TGATTG TGATTG TGATTG
          1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG

              
      12547 TG
          1 TG

      12549 GTGCAGCCTG


Statistics
Matches: 41,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
   5    4  0.10
   6   37  0.90

ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51


Consensus pattern (6 bp):   
TGATTG

Done.