Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012612.1 Corchorus olitorius cultivar O-4 contig12645, 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: 19474
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:6280 original size:20 final size:19

Alignment explanation


    Indices: 6251--6294  Score: 61
    Period size: 20  Copynumber: 2.3  Consensus size: 19

       6241 ATGCATGTGG

                          *     
       6251 AAATGAAAAATGCTCATTGA
          1 AAATGAAAAATGCTAATT-A

                 *             
       6271 AAATGTAAAATGCTAATTA
          1 AAATGAAAAATGCTAATTA

                 
       6290 AAATG
          1 AAATG

       6295 CCACATACTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19    6  0.27
  20   16  0.73

ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27


Consensus pattern (19 bp):   
AAATGAAAAATGCTAATTA

Found at i:8528 original size:8 final size:8

Alignment explanation


    Indices: 8517--8554  Score: 51
    Period size: 8  Copynumber: 4.9  Consensus size: 8

       8507 GTTTTTCCAT

                    
       8517 TTTTTTCA
          1 TTTTTTCA

                   *
       8525 TTTTTTCC
          1 TTTTTTCA

               *    
       8533 TTTCTTC-
          1 TTTTTTCA

                    
       8540 TTTTTTCA
          1 TTTTTTCA

                   
       8548 TTTTTTC
          1 TTTTTTC

       8555 TTCAACTTTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
   7    6  0.23
   8   20  0.77

ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76


Consensus pattern (8 bp):   
TTTTTTCA

Found at i:9213 original size:40 final size:41

Alignment explanation


    Indices: 9116--9213  Score: 103
    Period size: 41  Copynumber: 2.4  Consensus size: 41

       9106 AAGTAGTAAC

                                   **           **   
       9116 TAAATCCTAAATCAGGGACTAAATTGCATATAATCATGAAA
          1 TAAATCCTAAATCAGGGACTAAACCGCATATAATCAAAAAA

                                  **                  
       9157 TAAAT-CTGAAATCAGGGACTAGGCCGCATA-AAT-AAAAAA
          1 TAAATCCT-AAATCAGGGACTAAACCGCATATAATCAAAAAA

                              
       9196 TGAAATCCTAAATCAGGG
          1 T-AAATCCTAAATCAGGG

       9214 GTAAATAAAT


Statistics
Matches: 48,  Mismatches: 6, Indels: 7
        0.79            0.10        0.11

Matches are distributed among these distances:
  39    5  0.10
  40   18  0.38
  41   25  0.52

ACGTcount: A:0.46, C:0.15, G:0.16, T:0.22


Consensus pattern (41 bp):   
TAAATCCTAAATCAGGGACTAAACCGCATATAATCAAAAAA

Found at i:12501 original size:19 final size:18

Alignment explanation


    Indices: 12477--12512  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      12467 TGAAGATTTA

                               
      12477 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      12496 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      12513 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:17952 original size:18 final size:18

Alignment explanation


    Indices: 17929--17965  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      17919 AAAGGGTAAT

                     *        
      17929 TAAAAAAAATTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

                  *           
      17947 TAAAAAGAAGTGTTTTCA
          1 TAAAAAAAAGTGTTTTCA

             
      17965 T
          1 T

      17966 GATAGAGGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38


Consensus pattern (18 bp):   
TAAAAAAAAGTGTTTTCA

Found at i:18834 original size:19 final size:18

Alignment explanation


    Indices: 18810--18845  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      18800 TGAAGATTTA

                               
      18810 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      18829 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      18846 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.