Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020161.1 Corchorus olitorius cultivar O-4 contig20194, 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: 13975
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:6198 original size:38 final size:39

Alignment explanation


    Indices: 6150--6255  Score: 166
    Period size: 38  Copynumber: 2.8  Consensus size: 39

       6140 ATGTTTTTAA

                         *                         
       6150 TTAAG-TAATTCCGAAAGAAGATTTTGGAAAATAAAAGT
          1 TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

                                                    
       6188 TT-AGATAATTCCAAAAGAAGATTTTGGAGAAATAAAAGT
          1 TTAAGATAATTCCAAAAGAAGATTTTGGA-AAATAAAAGT

                                           
       6227 TTAAGA-AA-TCCAAAAGAAGATTTTGGAAA
          1 TTAAGATAATTCCAAAAGAAGATTTTGGAAA

       6256 TTGATAAAAT


Statistics
Matches: 64,  Mismatches: 1, Indels: 7
        0.89            0.01        0.10

Matches are distributed among these distances:
  37    4  0.06
  38   43  0.67
  39   14  0.22
  40    3  0.05

ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27


Consensus pattern (39 bp):   
TTAAGATAATTCCAAAAGAAGATTTTGGAAAATAAAAGT

Found at i:8778 original size:27 final size:27

Alignment explanation


    Indices: 8748--8800  Score: 70
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       8738 AGCTAAATTC

                                       
       8748 GGTGAAACCACCGAATTGCAAATCAGA
          1 GGTGAAACCACCGAATTGCAAATCAGA

                 * * *           *    
       8775 GGTGAGAGCTCCGAATTGCAATTCAG
          1 GGTGAAACCACCGAATTGCAAATCAG

       8801 GGCTCACACG


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   22  1.00

ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19


Consensus pattern (27 bp):   
GGTGAAACCACCGAATTGCAAATCAGA

Found at i:12420 original size:26 final size:27

Alignment explanation


    Indices: 12364--12426  Score: 67
    Period size: 26  Copynumber: 2.4  Consensus size: 27

      12354 CCCTAATCCG

                      *     *    *     
      12364 ATTTC-TTTTGCTTTTTTTTATTATTA
          1 ATTTCGTTTTCCTTTTCTTTACTATTA

            *                          
      12390 TTTTCGTTTTCCTTTTCTTTACT-TTA
          1 ATTTCGTTTTCCTTTTCTTTACTATTA

                  *    
      12416 ATTTCGATTTC
          1 ATTTCGTTTTC

      12427 TTAATTTTCC


Statistics
Matches: 30,  Mismatches: 6, Indels: 2
        0.79            0.16        0.05

Matches are distributed among these distances:
  26   16  0.53
  27   14  0.47

ACGTcount: A:0.13, C:0.14, G:0.05, T:0.68


Consensus pattern (27 bp):   
ATTTCGTTTTCCTTTTCTTTACTATTA
Done.