Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016448.1 Corchorus olitorius cultivar O-4 contig16481, 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: 12217
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1288 original size:112 final size:112

Alignment explanation


    Indices: 1138--1359  Score: 374
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       1128 TTGAAGTTAA

                          *               *                     *         *  
       1138 TGTTTTTAAGCTATTTCACATCCAAAAGTCTTATATACGTTTGAAAATAACTGGACTTTGCCGTA
          1 TGTTTTTAAGCTATATCACATCCAAAAGTCATATATACGTTTGAAAATAACTAGACTTTGCCATA

                                                           
       1203 GCTTGATGTTAAATTTTCCAACTTTAATTCGGTTTTACAGAATTTAG
         66 GCTTGATGTTAAATTTTCCAACTTTAATTCGGTTTTACAGAATTTAG

                                                              *              
       1250 TGTTTTTAAGCTATATCACATCCAGAAA-TCATATATACGTTTGAAAATAGCTAGACTTTGCCAT
          1 TGTTTTTAAGCTATATCACATCCA-AAAGTCATATATACGTTTGAAAATAACTAGACTTTGCCAT

                                                  *       
       1314 AGCTTGATGTTAAATTTTCCAACTTTAATTCGGTTTTATAGAATTT
         65 AGCTTGATGTTAAATTTTCCAACTTTAATTCGGTTTTACAGAATTT

       1360 TGCTGCTGAC


Statistics
Matches: 103,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
 112  100  0.97
 113    3  0.03

ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41


Consensus pattern (112 bp):   
TGTTTTTAAGCTATATCACATCCAAAAGTCATATATACGTTTGAAAATAACTAGACTTTGCCATA
GCTTGATGTTAAATTTTCCAACTTTAATTCGGTTTTACAGAATTTAG

Found at i:9629 original size:32 final size:33

Alignment explanation


    Indices: 9570--9637  Score: 86
    Period size: 32  Copynumber: 2.1  Consensus size: 33

       9560 ACTAGACGCG

                                ***          
       9570 AAACTAATATCTAATCAAACCTCAAAAA-AAAA
          1 AAACTAATATCTAATCAAACAGAAAAAAGAAAA

                                              
       9602 AAACTAATATCTAATCTAAA-AGAAAAAAGAAAA
          1 AAACTAATATCTAATC-AAACAGAAAAAAGAAAA

               
       9635 AAA
          1 AAA

       9638 AAATCAGGAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  32   21  0.68
  33   10  0.32

ACGTcount: A:0.66, C:0.13, G:0.03, T:0.18


Consensus pattern (33 bp):   
AAACTAATATCTAATCAAACAGAAAAAAGAAAA

Found at i:11337 original size:30 final size:30

Alignment explanation


    Indices: 11303--11365  Score: 126
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      11293 AAAGCCTCAA

                                          
      11303 AAACCGAAGAACTTGCTTTGAAATCGGATT
          1 AAACCGAAGAACTTGCTTTGAAATCGGATT

                                          
      11333 AAACCGAAGAACTTGCTTTGAAATCGGATT
          1 AAACCGAAGAACTTGCTTTGAAATCGGATT

               
      11363 AAA
          1 AAA

      11366 AGAAATGACC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   33  1.00

ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25


Consensus pattern (30 bp):   
AAACCGAAGAACTTGCTTTGAAATCGGATT
Done.