Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006270.1 Corchorus capsularis cultivar CVL-1 contig06289, 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: 2759
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27


Found at i:1238 original size:6 final size:6

Alignment explanation


    Indices: 1227--1288  Score: 69
    Period size: 6  Copynumber: 11.0  Consensus size: 6

       1217 GGGATCACTA

                                          *      *                 
       1227 ACTAAT ACTAAT -CTAAT ACTAAT A-GAAT A-GAAT ACTAAT -CTAAT
          1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT

                   *            
       1271 ACTAAT TCTAAT ACTAAT
          1 ACTAAT ACTAAT ACTAAT

       1289 GGAATAGAAA


Statistics
Matches: 49,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
   5   19  0.39
   6   30  0.61

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34


Consensus pattern (6 bp):   
ACTAAT

Found at i:1244 original size:11 final size:11

Alignment explanation


    Indices: 1223--1288  Score: 62
    Period size: 11  Copynumber: 5.5  Consensus size: 11

       1213 AGCCGGGATC

                       
       1223 ACTAA-CTAAT
          1 ACTAATCTAAT

                       
       1233 ACTAATCTAAT
          1 ACTAATCTAAT

                     *      
       1244 ACTAATAGAATAGAAT
          1 ACTAAT---CT--AAT

                       
       1260 ACTAATCTAAT
          1 ACTAATCTAAT

                        
       1271 ACTAATTCTAAT
          1 ACTAA-TCTAAT

                  
       1283 ACTAAT
          1 ACTAAT

       1289 GGAATAGAAA


Statistics
Matches: 47,  Mismatches: 2, Indels: 13
        0.76            0.03        0.21

Matches are distributed among these distances:
  10    5  0.11
  11   20  0.43
  12   11  0.23
  13    1  0.02
  14    1  0.02
  16    9  0.19

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33


Consensus pattern (11 bp):   
ACTAATCTAAT

Found at i:1287 original size:39 final size:37

Alignment explanation


    Indices: 1223--1297  Score: 123
    Period size: 39  Copynumber: 2.0  Consensus size: 37

       1213 AGCCGGGATC

                                                 
       1223 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT
          1 ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

                                         *        
       1260 ACTAATCTAATACTAATTCTAATACTAATGGAATAGAA
          1 ACTAA-CTAATACTAA-TCTAATACTAATAGAATAGAA

       1298 AAAATAGAAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  37    5  0.14
  38   10  0.29
  39   20  0.57

ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31


Consensus pattern (37 bp):   
ACTAACTAATACTAATCTAATACTAATAGAATAGAAT

Found at i:1323 original size:18 final size:18

Alignment explanation


    Indices: 1280--1330  Score: 65
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       1270 TACTAATTCT

                     *        
       1280 AATACTAATGGAATAG-A
          1 AATACTAATAGAATAGAA

                              
       1297 AA-A--AATAGAATAGAA
          1 AATACTAATAGAATAGAA

                              
       1312 AATACTAATAGAATAGAA
          1 AATACTAATAGAATAGAA

             
       1330 A
          1 A

       1331 GAAAAGAACT


Statistics
Matches: 29,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  14    9  0.31
  15    3  0.10
  16    2  0.07
  17    2  0.07
  18   13  0.45

ACGTcount: A:0.63, C:0.04, G:0.14, T:0.20


Consensus pattern (18 bp):   
AATACTAATAGAATAGAA
Done.