Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022809.1 Corchorus olitorius cultivar O-4 contig22842, 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: 18073
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:286 original size:12 final size:13

Alignment explanation


    Indices: 268--297  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        258 GTTTTCTTTA

                         
        268 ATTTTCTTGATTG
          1 ATTTTCTTGATTG

                         
        281 -TTTTCTTGATTG
          1 ATTTTCTTGATTG

                 
        293 ATTTT
          1 ATTTT

        298 AATTGCTAGT


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

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67


Consensus pattern (13 bp):   
ATTTTCTTGATTG

Found at i:11490 original size:25 final size:25

Alignment explanation


    Indices: 11456--11504  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      11446 TCAAACAATC

                       *             
      11456 TTGAGCACTCTTGCTCGGACTCTAT
          1 TTGAGCACTCTCGCTCGGACTCTAT

                              *     
      11481 TTGAGCACTCTCGCTCGGTCTCTA
          1 TTGAGCACTCTCGCTCGGACTCTA

      11505 CAAACCAATC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.14, C:0.31, G:0.20, T:0.35


Consensus pattern (25 bp):   
TTGAGCACTCTCGCTCGGACTCTAT

Found at i:14388 original size:2 final size:2

Alignment explanation


    Indices: 14335--14373  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      14325 CTTGGAATAC

                                    *                                 
      14335 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      14374 GGACGACGGA


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:17114 original size:104 final size:103

Alignment explanation


    Indices: 16984--17182  Score: 310
    Period size: 105  Copynumber: 1.9  Consensus size: 103

      16974 AGATTTCTTC

                                 *            *                           *  
      16984 TTTATTTTAATTTTGCAATAGTGTAAAAATGTT-CTACGAATGAAATTATCCCTTAATTATATTT
          1 TTTATTTTAATTTTGCAATAGAGTAAAAATGTTAATACGAATGAAATTATCCCTTAATTATACTT

                        *                           
      17048 TGTCCAAAATCTGGAAAAAAAACCTTAGTCATAAGATTTT
         66 TGTCCAAAATC-AG-AAAAAAACCTTAGTCATAAGATTTT

                                                                   **        
      17088 TTTATTTTAATTTTGCAATAGAGTAAAAATGTTAATACGAATGAAATTATCCCTTGGTTATACTT
          1 TTTATTTTAATTTTGCAATAGAGTAAAAATGTTAATACGAATGAAATTATCCCTTAATTATACTT

                             *            
      17153 TGTCCAAAATCAGAAAATAACCTTAGTCAT
         66 TGTCCAAAATCAGAAAAAAACCTTAGTCAT

      17183 CTAAATAGAA


Statistics
Matches: 87,  Mismatches: 7, Indels: 3
        0.90            0.07        0.03

Matches are distributed among these distances:
 103   16  0.18
 104   33  0.38
 105   38  0.44

ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39


Consensus pattern (103 bp):   
TTTATTTTAATTTTGCAATAGAGTAAAAATGTTAATACGAATGAAATTATCCCTTAATTATACTT
TGTCCAAAATCAGAAAAAAACCTTAGTCATAAGATTTT
Done.