Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009506.1 Corchorus olitorius cultivar O-4 contig09538, 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: 7904
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Found at i:1225 original size:17 final size:18

Alignment explanation


    Indices: 1199--1238  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1189 TCCAAATTTG

                 *            
       1199 GAAAACATGA-AAAAAAT
          1 GAAAAAATGAGAAAAAAT

                              
       1216 GAAAAAATGAGAAAAAAT
          1 GAAAAAATGAGAAAAAAT

            *    
       1234 CAAAA
          1 GAAAA

       1239 GTGTTTTCCA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17    9  0.45
  18   11  0.55

ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10


Consensus pattern (18 bp):   
GAAAAAATGAGAAAAAAT

Found at i:1252 original size:13 final size:13

Alignment explanation


    Indices: 1234--1259  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1224 GAGAAAAAAT

                         
       1234 CAAAAGTGTTTTC
          1 CAAAAGTGTTTTC

                         
       1247 CAAAAGTGTTTTC
          1 CAAAAGTGTTTTC

       1260 AAGTATGTTC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Consensus pattern (13 bp):   
CAAAAGTGTTTTC

Found at i:6702 original size:2 final size:2

Alignment explanation


    Indices: 6695--6724  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       6685 AGTTATATTC

                                          *             
       6695 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       6725 GAAAAACACA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:6832 original size:2 final size:2

Alignment explanation


    Indices: 6825--6855  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       6815 TAACTTGAGG

                                                          
       6825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       6856 ACTCTTTAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.