Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024362.1 Corchorus olitorius cultivar O-4 contig24395, 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: 7067
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:542 original size:51 final size:50

Alignment explanation


    Indices: 441--542  Score: 134
    Period size: 51  Copynumber: 2.0  Consensus size: 50

        431 GTTCTTCATA

                                                     * **     
        441 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                         *                 *                    
        491 TTTTCTCTTGTTTCGATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
        542 T
          1 T

        543 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 5, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  50    7  0.16
  51   38  0.84

ACGTcount: A:0.21, C:0.24, G:0.15, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:953 original size:27 final size:27

Alignment explanation


    Indices: 918--970  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        908 CTACAATCAT

                                       
        918 ATATCTCTTTATATTCTCAAACAAATG
          1 ATATCTCTTTATATTCTCAAACAAATG

                                      
        945 ATATCTCTTTATATTCTCAAACAAAT
          1 ATATCTCTTTATATTCTCAAACAAAT

        971 CTAATAAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42


Consensus pattern (27 bp):   
ATATCTCTTTATATTCTCAAACAAATG

Found at i:2754 original size:17 final size:18

Alignment explanation


    Indices: 2728--2762  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

       2718 TATTTATATA

                       *      
       2728 TAATTAATTAATATAATT
          1 TAATTAATTAAAATAATT

                              
       2746 TAATT-ATTAAAATAATT
          1 TAATTAATTAAAATAATT

       2763 ATTAAAAAAA


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

Matches are distributed among these distances:
  17   11  0.69
  18    5  0.31

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (18 bp):   
TAATTAATTAAAATAATT

Found at i:5811 original size:20 final size:20

Alignment explanation


    Indices: 5786--5824  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5776 CTTATAAAAT

                          *     
       5786 AATAATAACTAATTTTTAAA
          1 AATAATAACTAATTATTAAA

                               
       5806 AATAATAACTAATTATTAA
          1 AATAATAACTAATTATTAA

       5825 TTTTAAAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38


Consensus pattern (20 bp):   
AATAATAACTAATTATTAAA
Done.