Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022629.1 Corchorus olitorius cultivar O-4 contig22662, 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: 25368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:4308 original size:19 final size:20

Alignment explanation


    Indices: 4264--4321  Score: 82
    Period size: 19  Copynumber: 2.9  Consensus size: 20

       4254 GCTGCTCTAA

                          *      
       4264 TAATCTCATCTGTAGAGTACC
          1 TAATCTCATCTGTACAGTA-C

                  *             
       4285 TAATCTAATCTGTACAGT-C
          1 TAATCTCATCTGTACAGTAC

                              
       4304 TAATCTCATCTGTACAGT
          1 TAATCTCATCTGTACAGT

       4322 TGCTAAACAG


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

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

ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36


Consensus pattern (20 bp):   
TAATCTCATCTGTACAGTAC

Found at i:11691 original size:13 final size:13

Alignment explanation


    Indices: 11673--11697  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      11663 GTGTGTGTAT

                         
      11673 ATATATATATAAA
          1 ATATATATATAAA

                        
      11686 ATATATATATAA
          1 ATATATATATAA

      11698 TAAGGAAAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (13 bp):   
ATATATATATAAA

Found at i:16328 original size:27 final size:27

Alignment explanation


    Indices: 16298--16366  Score: 111
    Period size: 27  Copynumber: 2.6  Consensus size: 27

      16288 TAATTTAGTT

                                       
      16298 TTATTCATGAATCAATTAATAACGTGA
          1 TTATTCATGAATCAATTAATAACGTGA

                        *        **    
      16325 TTATTCATGAATTAATTAATATTGTGA
          1 TTATTCATGAATCAATTAATAACGTGA

                           
      16352 TTATTCATGAATCAA
          1 TTATTCATGAATCAA

      16367 GAGTTGTCTT


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42


Consensus pattern (27 bp):   
TTATTCATGAATCAATTAATAACGTGA

Found at i:17961 original size:18 final size:18

Alignment explanation


    Indices: 17938--17973  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      17928 ATATTCATTC

                              
      17938 GTGTTACATGAGAAATAA
          1 GTGTTACATGAGAAATAA

                              
      17956 GTGTTACATGAGAAATAA
          1 GTGTTACATGAGAAATAA

      17974 ATGTCTTGTG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28


Consensus pattern (18 bp):   
GTGTTACATGAGAAATAA

Found at i:21036 original size:93 final size:93

Alignment explanation


    Indices: 20877--21062  Score: 336
    Period size: 93  Copynumber: 2.0  Consensus size: 93

      20867 TTTAACACTA

                                   *        **                               
      20877 AAAATTGCGGTTTAATCTGCGGATACCGACAATTTTCGTTAAGATTTTAAGGTATATATACACTA
          1 AAAATTGCGGTTTAATCTGCGGACACCGACAACCTTCGTTAAGATTTTAAGGTATATATACACTA

                                        
      20942 ATTGAAAGTTTAAATCGAGAGATACCTT
         66 ATTGAAAGTTTAAATCGAGAGATACCTT

                                *                                            
      20970 AAAATTGCGGTTTAATCTGCTGACACCGACAACCTTCGTTAAGATTTTAAGGTATATATACACTA
          1 AAAATTGCGGTTTAATCTGCGGACACCGACAACCTTCGTTAAGATTTTAAGGTATATATACACTA

                                        
      21035 ATTGAAAGTTTAAATCGAGAGATACCTT
         66 ATTGAAAGTTTAAATCGAGAGATACCTT

      21063 CTTGTATTCA


Statistics
Matches: 89,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  93   89  1.00

ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Consensus pattern (93 bp):   
AAAATTGCGGTTTAATCTGCGGACACCGACAACCTTCGTTAAGATTTTAAGGTATATATACACTA
ATTGAAAGTTTAAATCGAGAGATACCTT

Found at i:21251 original size:27 final size:27

Alignment explanation


    Indices: 21221--21283  Score: 99
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      21211 GAATAATGTG

                                       
      21221 ATGAATCAATTAATAATGTGATTATTC
          1 ATGAATCAATTAATAATGTGATTATTC

                  *        *    *      
      21248 ATGAATTAATTAATATTGTGTTTATTC
          1 ATGAATCAATTAATAATGTGATTATTC

                     
      21275 ATGAATCAA
          1 ATGAATCAA

      21284 GAGTTGTCTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   32  1.00

ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43


Consensus pattern (27 bp):   
ATGAATCAATTAATAATGTGATTATTC

Found at i:22997 original size:17 final size:19

Alignment explanation


    Indices: 22965--22999  Score: 56
    Period size: 17  Copynumber: 1.9  Consensus size: 19

      22955 CTAAGTTTGC

                               
      22965 GGTTTGTCTGCAATTTTTT
          1 GGTTTGTCTGCAATTTTTT

                              
      22984 GGTTTGT-T-CAATTTTT
          1 GGTTTGTCTGCAATTTTT

      23000 GAGTCTGGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    8  0.50
  18    1  0.06
  19    7  0.44

ACGTcount: A:0.11, C:0.09, G:0.20, T:0.60


Consensus pattern (19 bp):   
GGTTTGTCTGCAATTTTTT
Done.