Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008282.1 Corchorus capsularis cultivar CVL-1 contig08303, 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: 5928
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29


Found at i:2215 original size:2 final size:2

Alignment explanation


    Indices: 2210--2239  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2200 TCTCTCTCTC

                                                        
       2210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2240 AGTGAAAGCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4399 original size:29 final size:29

Alignment explanation


    Indices: 4348--4404  Score: 80
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       4338 TAATGAAACG

                         *               
       4348 TGGAGAAGGAGAAGGGAAGACGTGGAGAC
          1 TGGAGAAGGAGAAAGGAAGACGTGGAGAC

                           *             
       4377 TGGAGAAGGAGAACATGAA-ACGTGGAGA
          1 TGGAGAAGGAGAA-AGGAAGACGTGGAGA

       4405 AGGGAGAGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   22  0.88
  30    3  0.12

ACGTcount: A:0.40, C:0.07, G:0.44, T:0.09


Consensus pattern (29 bp):   
TGGAGAAGGAGAAAGGAAGACGTGGAGAC

Found at i:4410 original size:29 final size:29

Alignment explanation


    Indices: 4349--4411  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       4339 AATGAAACGT

                        *              **
       4349 GGAGAAGGAGAAGGGAAGACGTGGAGACT
          1 GGAGAAGGAGAAAGGAAGACGTGGAGAAG

                          *               
       4378 GGAGAAGGAGAACATGAA-ACGTGGAGAAG
          1 GGAGAAGGAGAA-AGGAAGACGTGGAGAAG

                 
       4407 GGAGA
          1 GGAGA

       4412 GAAAGAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  29   26  0.90
  30    3  0.10

ACGTcount: A:0.41, C:0.06, G:0.46, T:0.06


Consensus pattern (29 bp):   
GGAGAAGGAGAAAGGAAGACGTGGAGAAG

Found at i:4736 original size:16 final size:18

Alignment explanation


    Indices: 4715--4749  Score: 56
    Period size: 16  Copynumber: 2.1  Consensus size: 18

       4705 AAAATCATAA

                              
       4715 TCAATTAAT-AT-ATTAT
          1 TCAATTAATCATAATTAT

                              
       4731 TCAATTAATCATAATTAT
          1 TCAATTAATCATAATTAT

             
       4749 T
          1 T

       4750 ATATTCATCA


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

Matches are distributed among these distances:
  16    9  0.53
  17    2  0.12
  18    6  0.35

ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49


Consensus pattern (18 bp):   
TCAATTAATCATAATTAT
Done.