Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014647.1 Corchorus capsularis cultivar CVL-1 contig14668, 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: 4165
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34


Found at i:1190 original size:46 final size:46

Alignment explanation


    Indices: 1055--1197  Score: 171
    Period size: 46  Copynumber: 3.1  Consensus size: 46

       1045 TTATATATAT

                       *                    *              
       1055 TATATTATATACGTTTTTATTATATATAAATACATATAAATTTAAAA
          1 TATATTATATATGTTTTTATTATATATAAATAAATA-AAATTTAAAA

                        *  * * *      * **        *        
       1102 TATATTATATATATTATAAATATATTTTCTATAAAT-ATATTTAAAA
          1 TATATTATATATGTTTTTATTATA-TATAAATAAATAAAATTTAAAA

                                                          
       1148 TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA
          1 TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA

                
       1194 TATA
          1 TATA

       1198 GTTTAAATAT


Statistics
Matches: 76,  Mismatches: 18, Indels: 5
        0.77            0.18        0.05

Matches are distributed among these distances:
  45    8  0.11
  46   42  0.55
  47   19  0.25
  48    7  0.09

ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48


Consensus pattern (46 bp):   
TATATTATATATGTTTTTATTATATATAAATAAATAAAATTTAAAA

Found at i:3668 original size:107 final size:105

Alignment explanation


    Indices: 3553--3827  Score: 412
    Period size: 107  Copynumber: 2.6  Consensus size: 105

       3543 TTTTAGAAAT

                                                              *              
       3553 AAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTGTATTTTTATTTTAA
          1 AAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTATATTTTTATTTTAA

                                                      
       3618 GGGTAAATTTCAAAATTAATAATTTATTGTTATAGGGTTTTA
         66 GGGTAAATTTCAAAATTAATAA--TATTGTTATAGGGTTTTA

                       *                                       *          *  
       3660 AAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCT-AATTAAAATTTTATTTTTATTCTA
          1 AAAATAAAATATAAAACTAATTTCACTAAGTTTAG-CCCTAAATTAAAATTATATTTTTATTTTA

               *         *                           
       3724 AGGTTAAATTTCATAATTAATAATATTGTTATAGGGTTTTA
         65 AGGGTAAATTTCAAAATTAATAATATTGTTATAGGGTTTTA

            *            *                                     * *           
       3765 GAAATAAAATATATAACTAA-TTCACTAAGTTTAGCCC-AAATTAAAATTAAAATTTTATTTTAA
          1 AAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTATATTTTTATTTTAA

       3828 AGGTTAGAAA


Statistics
Matches: 154,  Mismatches: 12, Indels: 8
        0.89            0.07        0.05

Matches are distributed among these distances:
 103   24  0.16
 104   14  0.09
 105   35  0.23
 107   77  0.50
 108    4  0.03

ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41


Consensus pattern (105 bp):   
AAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCTAAATTAAAATTATATTTTTATTTTAA
GGGTAAATTTCAAAATTAATAATATTGTTATAGGGTTTTA

Found at i:4140 original size:2 final size:2

Alignment explanation


    Indices: 4133--4165  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       4123 CTTCAACTTT

                                                             
       4133 TA TA TA TA 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 TA TA TA TA T


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Done.