Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002047.1 Corchorus olitorius cultivar O-4 contig02047, 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: 2602
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:1258 original size:15 final size:15

Alignment explanation


    Indices: 1238--1269  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1228 AGAAAAAAGG

                  *        
       1238 AATATTTGCCAAGAA
          1 AATATTCGCCAAGAA

                           
       1253 AATATTCGCCAAGAA
          1 AATATTCGCCAAGAA

              
       1268 AA
          1 AA

       1270 AGGAATATTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22


Consensus pattern (15 bp):   
AATATTCGCCAAGAA

Found at i:1278 original size:20 final size:20

Alignment explanation


    Indices: 1226--1307  Score: 93
    Period size: 20  Copynumber: 4.3  Consensus size: 20

       1216 TTATCCATGA

                                 
       1226 CAAGAAAAAAGGAATATTTGC
          1 CAAG-AAAAAGGAATATTTGC

                             *  
       1247 CAAG---AA--AATATTCGC
          1 CAAGAAAAAGGAATATTTGC

                                
       1262 CAAGAAAAAGGAATATTTGC
          1 CAAGAAAAAGGAATATTTGC

                  *             
       1282 CAAGAACAAGGAATATTTGC
          1 CAAGAAAAAGGAATATTTGC

             *    
       1302 CGAGAA
          1 CAAGAA

       1308 CATTAAACTT


Statistics
Matches: 52,  Mismatches: 4, Indels: 11
        0.78            0.06        0.16

Matches are distributed among these distances:
  15   12  0.23
  17    2  0.04
  18    2  0.04
  20   32  0.62
  21    4  0.08

ACGTcount: A:0.49, C:0.13, G:0.20, T:0.18


Consensus pattern (20 bp):   
CAAGAAAAAGGAATATTTGC

Found at i:1958 original size:18 final size:17

Alignment explanation


    Indices: 1927--1961  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

       1917 ACATAACATT

                             
       1927 ATTAAATTGAATCAAAC
          1 ATTAAATTGAATCAAAC

                      *       
       1944 ATTAACATTGTATCAAAC
          1 ATTAA-ATTGAATCAAAC

       1962 GAGAAAACAA


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

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

ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31


Consensus pattern (17 bp):   
ATTAAATTGAATCAAAC
Done.