Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005709.1 Corchorus capsularis cultivar CVL-1 contig05727, 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: 4772
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28


Found at i:710 original size:17 final size:17

Alignment explanation


    Indices: 690--724  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        680 TAACGTTAGG

                             
        690 CATAGTTTAAAGGTAAA
          1 CATAGTTTAAAGGTAAA

                             
        707 CATAGTTTAAAGGTAAA
          1 CATAGTTTAAAGGTAAA

             
        724 C
          1 C

        725 GTTAGTAAAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29


Consensus pattern (17 bp):   
CATAGTTTAAAGGTAAA

Found at i:3582 original size:38 final size:38

Alignment explanation


    Indices: 3531--3631  Score: 130
    Period size: 38  Copynumber: 2.7  Consensus size: 38

       3521 ACCCAAATAA

                             ** *  *        *     
       3531 AATTAAGAGTCAAAGTATTAGTAGTCAATAAAGTTGAT
          1 AATTAAGAGTCAAAGTAAGAATAATCAATAAAATTGAT

                                       *          
       3569 AATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGAT
          1 AATTAAGAGTCAAAGTAAGAATAATCAATAAAATTGAT

               *              *      
       3607 AATCAAGAGTCAAAGTAAAAATAAT
          1 AATTAAGAGTCAAAGTAAGAATAAT

       3632 AATCAGTAAA


Statistics
Matches: 55,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  38   55  1.00

ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27


Consensus pattern (38 bp):   
AATTAAGAGTCAAAGTAAGAATAATCAATAAAATTGAT

Found at i:3733 original size:32 final size:32

Alignment explanation


    Indices: 3697--3783  Score: 129
    Period size: 32  Copynumber: 2.7  Consensus size: 32

       3687 GGGAGAGAGT

                  *                         
       3697 AAAAGAGTAATCAGTAATTAAGAAAGGAAGTA
          1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA

                  *                         
       3729 AAAAGATTAATCAGTAATTAAGAAAGGAAGTA
          1 AAAAGACTAATCAGTAATTAAGAAAGGAAGTA

                          *        
       3761 AAAAGGACTAATCAATAAATTAA
          1 AAAA-GACTAATCAGT-AATTAA

       3784 TAATTAAGAA


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  32   35  0.70
  33    9  0.18
  34    6  0.12

ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21


Consensus pattern (32 bp):   
AAAAGACTAATCAGTAATTAAGAAAGGAAGTA

Found at i:4055 original size:21 final size:21

Alignment explanation


    Indices: 4009--4054  Score: 76
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3999 AAAAGTTAGC

                                 
       4009 TAAAAGTAAACAGTAAAAAGG
          1 TAAAAGTAAACAGTAAAAAGG

                     *           
       4030 TAAAAGTAATCAGTAAAAA-G
          1 TAAAAGTAAACAGTAAAAAGG

                 
       4050 TAAAA
          1 TAAAA

       4055 ATGGCAAAGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  20    6  0.25
  21   18  0.75

ACGTcount: A:0.63, C:0.04, G:0.15, T:0.17


Consensus pattern (21 bp):   
TAAAAGTAAACAGTAAAAAGG

Found at i:4189 original size:16 final size:16

Alignment explanation


    Indices: 4170--4273  Score: 61
    Period size: 16  Copynumber: 6.2  Consensus size: 16

       4160 GTGTAGATTA

                            
       4170 AAAAATGGTATTAAGT
          1 AAAAATGGTATTAAGT

                        **  * 
       4186 -AAAA-GAGTAAAGAATT
          1 AAAAATG-GT-ATTAAGT

                     *        
       4202 AAAAATGGTGTTAAGGGT
          1 AAAAATGGTATTAA--GT

                              
       4220 CAAAAATGGTATCT-AGT
          1 -AAAAATGGTAT-TAAGT

                *          **
       4237 AAGAGATGGTATTAAAC
          1 AA-AAATGGTATTAAGT

                            
       4254 AAAAATGGTATTAAGT
          1 AAAAATGGTATTAAGT

                
       4270 AAAA
          1 AAAA

       4274 GAGTAAGAAA


Statistics
Matches: 64,  Mismatches: 14, Indels: 20
        0.65            0.14        0.20

Matches are distributed among these distances:
  14    1  0.02
  15    6  0.09
  16   24  0.38
  17   19  0.30
  18    2  0.03
  19   11  0.17
  20    1  0.02

ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26


Consensus pattern (16 bp):   
AAAAATGGTATTAAGT

Found at i:4301 original size:15 final size:15

Alignment explanation


    Indices: 4281--4311  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4271 AAAGAGTAAG

                   *       
       4281 AAAAATGGTAAAAGT
          1 AAAAATGATAAAAGT

                           
       4296 AAAAATGATAAAAGT
          1 AAAAATGATAAAAGT

             
       4311 A
          1 A

       4312 GTAAAAGTAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19


Consensus pattern (15 bp):   
AAAAATGATAAAAGT
Done.