Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016991.1 Corchorus olitorius cultivar O-4 contig17024, 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: 35610
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:6219 original size:21 final size:21

Alignment explanation


    Indices: 6195--6277  Score: 73
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       6185 TATCTTAGAT

                                  
       6195 ATAAT-ATATATTATTAAATAA
          1 ATAATAATATATT-TTAAATAA

                                  
       6216 ATAATAAATATATTTTAAAT-A
          1 ATAAT-AATATATTTTAAATAA

                           **      
       6237 ATAAATAATA-AGTTCAAAATAA
          1 AT-AATAATATA-TTTTAAATAA

                               
       6259 ATAAATAATATATATTTAA
          1 AT-AATAATATAT-TTTAA

       6278 TTACTAAACG


Statistics
Matches: 51,  Mismatches: 4, Indels: 12
        0.76            0.06        0.18

Matches are distributed among these distances:
  20    1  0.02
  21   18  0.35
  22   21  0.41
  23   11  0.22

ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39


Consensus pattern (21 bp):   
ATAATAATATATTTTAAATAA

Found at i:28257 original size:174 final size:174

Alignment explanation


    Indices: 28000--28319  Score: 525
    Period size: 174  Copynumber: 1.8  Consensus size: 174

      27990 ATAATTCTCT

                  *                     *                              *     
      28000 ATATATTGTGAGAAATCAATACACAAACTAAAAGAAAAAAAACTATCATAAATAGCTTATATACC
          1 ATATATAGTGAGAAATCAATACACAAACCAAAAGAAAAAAAACTATCATAAATAGCTTACATACC

              *                         *                   *              * 
      28065 TAGTAAGCAAACAAACCGACACAAATAAGCTAAATTTCCATTACGTGATATTTGAATTCAGGATT
         66 TAATAAGCAAACAAACCGACACAAATAAACTAAATTTCCATTACGTGAGATTTGAATTCAGGACT

                  *                                      
      28130 TCAAAATCCAGATCATTACAATTATATAATTTTCTATATATTCAA
        131 TCAAAACCCAGA-CATTACAATTATATAATTTTCTATATATTCAA

                                                                             
      28175 ATATATAGTGAGAAATCAATACACAAACCAAAAG-AAAAAAACTATCATAAATAGCTTACATACC
          1 ATATATAGTGAGAAATCAATACACAAACCAAAAGAAAAAAAACTATCATAAATAGCTTACATACC

                                                 *     *                     
      28239 TAATAAGCAAACAAACCGACACAAATAAACTAAATTTTCATTATGTGAGATTTGAATTCAGGACT
         66 TAATAAGCAAACAAACCGACACAAATAAACTAAATTTCCATTACGTGAGATTTGAATTCAGGACT

              *             
      28304 TCCAAACCCAGACATT
        131 TCAAAACCCAGACATT

      28320 GTATACTTAC


Statistics
Matches: 134,  Mismatches: 11, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
 173    4  0.03
 174   98  0.73
 175   32  0.24

ACGTcount: A:0.47, C:0.17, G:0.09, T:0.27


Consensus pattern (174 bp):   
ATATATAGTGAGAAATCAATACACAAACCAAAAGAAAAAAAACTATCATAAATAGCTTACATACC
TAATAAGCAAACAAACCGACACAAATAAACTAAATTTCCATTACGTGAGATTTGAATTCAGGACT
TCAAAACCCAGACATTACAATTATATAATTTTCTATATATTCAA

Found at i:30048 original size:6 final size:6

Alignment explanation


    Indices: 30039--30064  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      30029 AAAGCCTTCT

                                          
      30039 TCTCAA TCTCAA TCTCAA TCTCAA TC
          1 TCTCAA TCTCAA TCTCAA TCTCAA TC

      30065 CCTCCCTAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35


Consensus pattern (6 bp):   
TCTCAA

Found at i:34378 original size:3 final size:3

Alignment explanation


    Indices: 34370--34396  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      34360 TGTTGTATAG

                                               
      34370 TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT

      34397 ATAATCTTAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Done.