Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007572.1 Corchorus olitorius cultivar O-4 contig07597, 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, 747

Length: 1246
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:206 original size:90 final size:90

Alignment explanation


    Indices: 55--408  Score: 609
    Period size: 90  Copynumber: 3.9  Consensus size: 90

         45 GCAGTTGCTG

                                      *   *     *              *             
         55 AACTTTGAGATGTTGCCTAAAGGTGTACCGGTTCCTTCATCGGGGCCAAGCGCTCGTACATCAGC
          1 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC

                                  * *
        120 AGATGTTCCACCACCTCCTTCGTTG
         66 AGATGTTCCACCACCTCCTTCGCTA

                                                  *                          
        145 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCCTCGGGGCCAAGCACTCGTACATCAGC
          1 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC

                           *         
        210 AGATGTTCCACCACCACCTTCGCTA
         66 AGATGTTCCACCACCTCCTTCGCTA

                                                                    *        
        235 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGAACATCAGC
          1 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC

                                     
        300 AGATGTTCCACCACCTCCTTCGCTA
         66 AGATGTTCCACCACCTCCTTCGCTA

                                         *                                   
        325 AACTTTGAGATGTTGCCTAAAGGTGTGCCAATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC
          1 AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC

                         *     
        390 AGATGTTCCACCATCTCCT
         66 AGATGTTCCACCACCTCCT

        409 ATGCTAGCAT


Statistics
Matches: 250,  Mismatches: 14, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  90  250  1.00

ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26


Consensus pattern (90 bp):   
AACTTTGAGATGTTGCCTAAAGGTGTGCCGATTCCTCCATCGGGGCCAAGCACTCGTACATCAGC
AGATGTTCCACCACCTCCTTCGCTA

Found at i:1163 original size:7 final size:7

Alignment explanation


    Indices: 1136--1199  Score: 64
    Period size: 7  Copynumber: 9.4  Consensus size: 7

       1126 TAATATCTAG

                   
       1136 TATATA-
          1 TATATAT

                   
       1142 TATATAT
          1 TATATAT

                     
       1149 ATATTATAT
          1 -TA-TATAT

                   
       1158 TATATAT
          1 TATATAT

                   
       1165 TATATAT
          1 TATATAT

                   
       1172 TATATA-
          1 TATATAT

                   
       1178 TAT-T-T
          1 TATATAT

               * * 
       1183 TATTTTT
          1 TATATAT

                   
       1190 TATATAT
          1 TATATAT

               
       1197 TAT
          1 TAT

       1200 TTGAAACACC


Statistics
Matches: 50,  Mismatches: 2, Indels: 11
        0.79            0.03        0.17

Matches are distributed among these distances:
   5    4  0.08
   6   10  0.20
   7   27  0.54
   8    4  0.08
   9    5  0.10

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (7 bp):   
TATATAT

Found at i:1196 original size:2 final size:2

Alignment explanation


    Indices: 1136--1180  Score: 62
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       1126 TAATATCTAG

                                                                          
       1136 TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA T- TA TA TA T- TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                      
       1174 TA TA TA T
          1 TA TA TA T

       1181 TTTATTTTTT


Statistics
Matches: 39,  Mismatches: 0, Indels: 8
        0.83            0.00        0.17

Matches are distributed among these distances:
   1    4  0.10
   2   35  0.90

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (2 bp):   
TA
Done.