Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009879.1 Corchorus olitorius cultivar O-4 contig09911, 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: 2531
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Found at i:2098 original size:5 final size:5

Alignment explanation


    Indices: 2084--2121  Score: 53
    Period size: 5  Copynumber: 7.8  Consensus size: 5

       2074 GGTCCATTCA

                                                           
       2084 TTTTC TTTTTC TTTTC TTTTC TTTT- TTTTC TTTT- TTTT
          1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT

       2122 TTAAACTTGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   4    8  0.26
   5   18  0.58
   6    5  0.16

ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87


Consensus pattern (5 bp):   
TTTTC

Found at i:2105 original size:10 final size:9

Alignment explanation


    Indices: 2089--2121  Score: 57
    Period size: 9  Copynumber: 3.6  Consensus size: 9

       2079 ATTCATTTTC

                     
       2089 TTTTTCTTT
          1 TTTTTCTTT

                      
       2098 TCTTTTCTTT
          1 T-TTTTCTTT

                     
       2108 TTTTTCTTT
          1 TTTTTCTTT

                 
       2117 TTTTT
          1 TTTTT

       2122 TTAAACTTGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   9   14  0.61
  10    9  0.39

ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88


Consensus pattern (9 bp):   
TTTTTCTTT

Found at i:2232 original size:37 final size:37

Alignment explanation


    Indices: 2165--2279  Score: 187
    Period size: 37  Copynumber: 3.1  Consensus size: 37

       2155 GGGCCATACG

                       *                      *  
       2165 CTGGCCCGCGCACCAGGCCTGGGCGC-TGGGCCGTGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                    *                            
       2201 CTGGCCCGTGCGCCAGGCCTGGGCGCTTGGGCCGCGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                  *                              
       2238 CTGGCCTGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
          1 CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC

                 
       2275 CTGGC
          1 CTGGC

       2280 TGGCCCAAGT


Statistics
Matches: 73,  Mismatches: 5, Indels: 1
        0.92            0.06        0.01

Matches are distributed among these distances:
  36   24  0.33
  37   49  0.67

ACGTcount: A:0.03, C:0.41, G:0.43, T:0.13


Consensus pattern (37 bp):   
CTGGCCCGCGCGCCAGGCCTGGGCGCTTGGGCCGCGC
Done.