Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023382.1 Corchorus olitorius cultivar O-4 contig23415, 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: 7351
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:2377 original size:7 final size:7

Alignment explanation


    Indices: 2365--2403  Score: 53
    Period size: 7  Copynumber: 5.4  Consensus size: 7

       2355 TATGTTCATT

                   
       2365 TATATTA
          1 TATATTA

                   
       2372 TATATTA
          1 TATATTA

                   
       2379 TATATTA
          1 TATATTA

                   
       2386 TATA-TA
          1 TATATTA

                     
       2392 TAATAATTA
          1 T-AT-ATTA

               
       2401 TAT
          1 TAT

       2404 TTTTATTTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   6    3  0.10
   7   20  0.69
   8    3  0.10
   9    3  0.10

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (7 bp):   
TATATTA

Found at i:3441 original size:48 final size:49

Alignment explanation


    Indices: 3335--3438  Score: 158
    Period size: 48  Copynumber: 2.1  Consensus size: 49

       3325 TCTATGTCAC

                                                              
       3335 TTTCATTTGGGCCTTTTCCTTTTATCTTTGGCCAAATGGGTCAACTTCCT
          1 TTTC-TTTGGGCCTTTTCCTTTTATCTTTGGCCAAATGGGTCAACTTCCT

                                  * *      *                 
       3385 TTTCTTTGGGCCTTTT-CTTTTCTTTTTGGCTAAATGGGTCAACTT-CT
          1 TTTCTTTGGGCCTTTTCCTTTTATCTTTGGCCAAATGGGTCAACTTCCT

                   
       3432 TTTCTTT
          1 TTTCTTT

       3439 TGGTTTCGGG


Statistics
Matches: 51,  Mismatches: 3, Indels: 3
        0.89            0.05        0.05

Matches are distributed among these distances:
  47    9  0.18
  48   26  0.51
  49   12  0.24
  50    4  0.08

ACGTcount: A:0.12, C:0.21, G:0.15, T:0.52


Consensus pattern (49 bp):   
TTTCTTTGGGCCTTTTCCTTTTATCTTTGGCCAAATGGGTCAACTTCCT

Found at i:4466 original size:10 final size:10

Alignment explanation


    Indices: 4444--4473  Score: 53
    Period size: 10  Copynumber: 3.1  Consensus size: 10

       4434 CGACCGTTGG

                      
       4444 GTGTTCTTG-
          1 GTGTTCTTGA

                      
       4453 GTGTTCTTGA
          1 GTGTTCTTGA

                      
       4463 GTGTTCTTGA
          1 GTGTTCTTGA

             
       4473 G
          1 G

       4474 AAAAAGGGGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    9  0.45
  10   11  0.55

ACGTcount: A:0.07, C:0.10, G:0.33, T:0.50


Consensus pattern (10 bp):   
GTGTTCTTGA
Done.