Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005456.1 Corchorus capsularis cultivar CVL-1 contig05474, 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: 12868
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:3043 original size:33 final size:33

Alignment explanation


    Indices: 2984--3050  Score: 98
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2974 GGTATAATGT

                             *   *           
       2984 AAGTTAAGATCTCCTTTTTATTGCCAAAAAAAA
          1 AAGTTAAGATCTCCTTTGTATGGCCAAAAAAAA

                               *         *   
       3017 AAGTTAAGATCTCCTTTGTGTGGCCAAAAGAAA
          1 AAGTTAAGATCTCCTTTGTATGGCCAAAAAAAA

             
       3050 A
          1 A

       3051 GGGGAAAAAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   30  1.00

ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30


Consensus pattern (33 bp):   
AAGTTAAGATCTCCTTTGTATGGCCAAAAAAAA

Found at i:6392 original size:10 final size:10

Alignment explanation


    Indices: 6379--6408  Score: 60
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       6369 CCCCGCCCCG

                      
       6379 TCCCGCTCCA
          1 TCCCGCTCCA

                      
       6389 TCCCGCTCCA
          1 TCCCGCTCCA

                      
       6399 TCCCGCTCCA
          1 TCCCGCTCCA

       6409 CTAAATATAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.10, C:0.60, G:0.10, T:0.20


Consensus pattern (10 bp):   
TCCCGCTCCA

Found at i:6393 original size:20 final size:20

Alignment explanation


    Indices: 6370--6408  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       6360 GGTTATTTGC

                    *           
       6370 CCCGCCCCGTCCCGCTCCAT
          1 CCCGCCCCATCCCGCTCCAT

                 *             
       6390 CCCGCTCCATCCCGCTCCA
          1 CCCGCCCCATCCCGCTCCA

       6409 CTAAATATAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.08, C:0.64, G:0.13, T:0.15


Consensus pattern (20 bp):   
CCCGCCCCATCCCGCTCCAT

Found at i:7029 original size:13 final size:13

Alignment explanation


    Indices: 7011--7035  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       7001 ACGGTTAATC

                         
       7011 ACTAAATTTTATT
          1 ACTAAATTTTATT

                        
       7024 ACTAAATTTTAT
          1 ACTAAATTTTAT

       7036 AAATTTGTAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52


Consensus pattern (13 bp):   
ACTAAATTTTATT

Found at i:12780 original size:2 final size:2

Alignment explanation


    Indices: 12773--12797  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      12763 TGCTTCCTGT

                                                 
      12773 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      12798 GACTGTTAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Done.