Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020525.1 Corchorus olitorius cultivar O-4 contig20558, 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: 20791
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35


Found at i:70 original size:22 final size:23

Alignment explanation


    Indices: 26--70  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 23

         16 TTCTTTAAGG

                              *     
         26 GTAGAAAATGGGAGAAAGGCGATT
          1 GTAGAAAAT-GGAGAAAGCCGATT

                          *       
         50 GTAGAAAAT-GAGAGAGCCGAT
          1 GTAGAAAATGGAGAAAGCCGAT

         71 GATGAGGGGC


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22   10  0.53
  24    9  0.47

ACGTcount: A:0.42, C:0.07, G:0.36, T:0.16


Consensus pattern (23 bp):   
GTAGAAAATGGAGAAAGCCGATT

Found at i:1293 original size:11 final size:10

Alignment explanation


    Indices: 1277--1323  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       1267 AAACTCGTGT

                       
       1277 TTGAAGACTCA
          1 TTGAAGA-TCA

                    * 
       1288 TTGAAGATAA
          1 TTGAAGATCA

                       
       1298 TTTGAAGAT--
          1 -TTGAAGATCA

                      
       1307 TTGAAGATCA
          1 TTGAAGATCA

                   
       1317 TTGAAGA
          1 TTGAAGA

       1324 ATTATTTCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    8  0.25
  10    9  0.28
  11   15  0.47

ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32


Consensus pattern (10 bp):   
TTGAAGATCA

Found at i:1312 original size:19 final size:18

Alignment explanation


    Indices: 1288--1323  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1278 TGAAGACTCA

                               
       1288 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       1307 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       1324 ATTATTTCAA


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:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:7093 original size:39 final size:40

Alignment explanation


    Indices: 7031--7106  Score: 118
    Period size: 39  Copynumber: 1.9  Consensus size: 40

       7021 ATATATATAG

                      *                   *         
       7031 TACAAGGATAGCTAAACTGATAAGCTAAGAGTTTAAAGTT
          1 TACAAGGATAACTAAACTGATAAGCTAAGAATTTAAAGTT

                                       *         
       7071 TACAAGGATAACT-AACTGATAAGCTATGAATTTAAA
          1 TACAAGGATAACTAAACTGATAAGCTAAGAATTTAAA

       7107 TTATGAAGTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  39   21  0.64
  40   12  0.36

ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28


Consensus pattern (40 bp):   
TACAAGGATAACTAAACTGATAAGCTAAGAATTTAAAGTT

Found at i:10741 original size:9 final size:9

Alignment explanation


    Indices: 10727--10755  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

      10717 TGGACTTTTC

                     
      10727 AAAAATTAA
          1 AAAAATTAA

                     
      10736 AAAAATT-A
          1 AAAAATTAA

                     
      10744 AAAAATTAA
          1 AAAAATTAA

               
      10753 AAA
          1 AAA

      10756 TCAGAAAAAT


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

Matches are distributed among these distances:
   8    8  0.42
   9   11  0.58

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (9 bp):   
AAAAATTAA

Found at i:15216 original size:25 final size:23

Alignment explanation


    Indices: 15169--15220  Score: 68
    Period size: 23  Copynumber: 2.2  Consensus size: 23

      15159 ATTATATTAT

                            * *    
      15169 ATTATATATATAATTATTTTAAA
          1 ATTATATATATAATTAGTATAAA

                                     
      15192 ATTATATATATACATTGAGTATAAA
          1 ATTATATATATA-ATT-AGTATAAA

                
      15217 ATTA
          1 ATTA

      15221 AGAAAATAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23   12  0.48
  24    3  0.12
  25   10  0.40

ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46


Consensus pattern (23 bp):   
ATTATATATATAATTAGTATAAA

Found at i:19405 original size:2 final size:2

Alignment explanation


    Indices: 19400--19448  Score: 80
    Period size: 2  Copynumber: 24.5  Consensus size: 2

      19390 CATCACACAT

                                                          *           *   
      19400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TG TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                      
      19442 TA TA TA T
          1 TA TA TA T

      19449 GTATTCTTGG


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (2 bp):   
TA

Done.