Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017709.1 Corchorus olitorius cultivar O-4 contig17742, 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: 35212
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:3241 original size:15 final size:15

Alignment explanation


    Indices: 3217--3259  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       3207 AATTGATCCG

                 *      *  
       3217 AAACCTAAAACCGGA
          1 AAACCCAAAACCCGA

                           
       3232 AAACCCAAAACCCGA
          1 AAACCCAAAACCCGA

                 *       
       3247 ATAACACAAAACC
          1 A-AACCCAAAACC

       3260 TGAGTGACCT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  15   14  0.58
  16   10  0.42

ACGTcount: A:0.56, C:0.33, G:0.07, T:0.05


Consensus pattern (15 bp):   
AAACCCAAAACCCGA

Found at i:4096 original size:85 final size:85

Alignment explanation


    Indices: 3906--4074  Score: 234
    Period size: 85  Copynumber: 2.0  Consensus size: 85

       3896 TAATTAAATT

                 *  *               * * *  *                                 
       3906 AGTAATATCGTAAAAATAAAATAGGTATGAGAATATTAGATTTAATCAAATAAAAATAGAGTTTT
          1 AGTAAAATGGTAAAAATAAAATAGTTTTAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTT

                   *     *      
       3971 TAGTTGAGTAAAATTATAAA
         66 TAGTTGACTAAAACTATAAA

                                                           **                
       3991 AGTAAAATGGTAAAAATAAAATAGTTTTAAGGATATTAGATTTAAT-TGA-AAAAATAGAGTTTT
          1 AGTAAAATGGTAAAAATAAAATAGTTTTAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTT

                                
       4054 TAGTTGACTAAAACTATAAA
         66 TAGTTGACTAAAACTATAAA

             
       4074 A
          1 A

       4075 ATTTAAACAA


Statistics
Matches: 74,  Mismatches: 10, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  83   33  0.45
  84    1  0.01
  85   40  0.54

ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33


Consensus pattern (85 bp):   
AGTAAAATGGTAAAAATAAAATAGTTTTAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTT
TAGTTGACTAAAACTATAAA

Found at i:6307 original size:2 final size:2

Alignment explanation


    Indices: 6300--6328  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       6290 CTCGTACTTT

                                                       
       6300 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 T

       6329 TCTTTAATAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:10246 original size:21 final size:21

Alignment explanation


    Indices: 10216--10260  Score: 72
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      10206 AACCCAATCG

                                 
      10216 TGGATAGTGATACGGATGAGA
          1 TGGATAGTGATACGGATGAGA

                 *     *         
      10237 TGGATTGTGATGCGGATGAGA
          1 TGGATAGTGATACGGATGAGA

               
      10258 TGG
          1 TGG

      10261 CGGACGAGAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.27, C:0.04, G:0.42, T:0.27


Consensus pattern (21 bp):   
TGGATAGTGATACGGATGAGA

Found at i:10529 original size:12 final size:12

Alignment explanation


    Indices: 10512--10536  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      10502 TGATGGTGCG

                        
      10512 TATGGTGATGCC
          1 TATGGTGATGCC

                        
      10524 TATGGTGATGCC
          1 TATGGTGATGCC

             
      10536 T
          1 T

      10537 TAGATCATGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36


Consensus pattern (12 bp):   
TATGGTGATGCC

Found at i:33074 original size:2 final size:2

Alignment explanation


    Indices: 33067--33099  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      33057 CAACTCGGGA

                                                             
      33067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      33100 AGTCATGTTT


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


Consensus pattern (2 bp):   
AT

Done.