Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000407.1 Corchorus capsularis cultivar CVL-1 contig00407, 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: 24210
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1186 original size:3 final size:3

Alignment explanation


    Indices: 1178--1233  Score: 94
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1168 TATCACATCT

                                                                         
       1178 TTA TTA TTA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA

                       
       1225 TTA TTA TTA
          1 TTA TTA TTA

       1234 ATTTTAAAAA


Statistics
Matches: 51,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
   3   45  0.88
   4    6  0.12

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:3886 original size:6 final size:6

Alignment explanation


    Indices: 3877--3915  Score: 60
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       3867 CACACCCACA

                          *      *                       
       3877 AGGCGG AGGCGG TGGCGG TGGCGG AGGCGG AGGCGG AGG
          1 AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGGCGG AGG

       3916 ATTCGATATG


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   31  1.00

ACGTcount: A:0.13, C:0.15, G:0.67, T:0.05


Consensus pattern (6 bp):   
AGGCGG

Found at i:17739 original size:7 final size:7

Alignment explanation


    Indices: 17727--17772  Score: 74
    Period size: 7  Copynumber: 6.6  Consensus size: 7

      17717 GTCTTACGAA

                  *
      17727 TTCTCAG
          1 TTCTCAC

                   
      17734 TTCTCAC
          1 TTCTCAC

             *     
      17741 TCCTCAC
          1 TTCTCAC

                   
      17748 TTCTCAC
          1 TTCTCAC

                   
      17755 TTCTCAC
          1 TTCTCAC

                   
      17762 TTCTCAC
          1 TTCTCAC

                
      17769 TTCT
          1 TTCT

      17773 TATGAGTTTG


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   7   36  1.00

ACGTcount: A:0.13, C:0.41, G:0.02, T:0.43


Consensus pattern (7 bp):   
TTCTCAC

Found at i:17949 original size:15 final size:15

Alignment explanation


    Indices: 17929--17957  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      17919 TAACTCTCCG

                           
      17929 TGGGAGAGTGATTTT
          1 TGGGAGAGTGATTTT

                          
      17944 TGGGAGAGTGATTT
          1 TGGGAGAGTGATTT

      17958 CAGGGAAAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38


Consensus pattern (15 bp):   
TGGGAGAGTGATTTT

Found at i:17963 original size:15 final size:15

Alignment explanation


    Indices: 17930--17963  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      17920 AACTCTCCGT

                         **
      17930 GGGAGAGTGATTTTT
          1 GGGAGAGTGATTTCA

                           
      17945 GGGAGAGTGATTTCA
          1 GGGAGAGTGATTTCA

                
      17960 GGGA
          1 GGGA

      17964 AAGTAGCACT


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

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.24, C:0.03, G:0.44, T:0.29


Consensus pattern (15 bp):   
GGGAGAGTGATTTCA

Found at i:18281 original size:16 final size:17

Alignment explanation


    Indices: 18251--18284  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      18241 GCACTCTTAT

                             
      18251 CTACATCATTAAAAAAA
          1 CTACATCATTAAAAAAA

                              
      18268 CTAC-TCATTTAAAAAAA
          1 CTACATCA-TTAAAAAAA

      18285 TTATTGTGCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    3  0.19
  17   13  0.81

ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26


Consensus pattern (17 bp):   
CTACATCATTAAAAAAA
Done.