Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015359.1 Corchorus capsularis cultivar CVL-1 contig15380, 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: 3374
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:2197 original size:12 final size:13

Alignment explanation


    Indices: 2156--2200  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2146 TTAATTTGTT

                         
       2156 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       2169 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       2182 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       2194 TGCTTTA
          1 TGCTTTA

       2201 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:2208 original size:6 final size:6

Alignment explanation


    Indices: 2197--2223  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       2187 TATAATCTGC

                                           
       2197 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       2224 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:2272 original size:14 final size:15

Alignment explanation


    Indices: 2244--2276  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       2234 ATTTTTAGTT

                    *      
       2244 TAATTGTTTTCTTCA
          1 TAATTGTTATCTTCA

                           
       2259 TAATTGTTAT-TTCA
          1 TAATTGTTATCTTCA

                
       2273 TAAT
          1 TAAT

       2277 CCCTGTTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58


Consensus pattern (15 bp):   
TAATTGTTATCTTCA

Found at i:2949 original size:19 final size:18

Alignment explanation


    Indices: 2916--2952  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       2906 TTGAAATAAT

                              
       2916 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *         
       2934 TCTTCAAATTATCTTCAAA
          1 TCTTC-AATGATCTTCAAA

       2953 AAATCTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.35, C:0.22, G:0.03, T:0.41


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.