Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015504.1 Corchorus olitorius cultivar O-4 contig15537, 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: 12353
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36


Found at i:263 original size:15 final size:15

Alignment explanation


    Indices: 245--291  Score: 51
    Period size: 15  Copynumber: 3.2  Consensus size: 15

        235 TATTAATCAA

                           
        245 TATTTTAATTAATAT
          1 TATTTTAATTAATAT

                 *   *  * *
        260 TATTTCAA-AAAAAA
          1 TATTTTAATTAATAT

                           
        274 TATTTTAATTAATAT
          1 TATTTTAATTAATAT

               
        289 TAT
          1 TAT

        292 ACTATAAGGG


Statistics
Matches: 23,  Mismatches: 8, Indels: 2
        0.70            0.24        0.06

Matches are distributed among these distances:
  14   10  0.43
  15   13  0.57

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51


Consensus pattern (15 bp):   
TATTTTAATTAATAT

Found at i:1525 original size:13 final size:14

Alignment explanation


    Indices: 1509--1549  Score: 50
    Period size: 13  Copynumber: 3.0  Consensus size: 14

       1499 TAGCAAATAA

                       *  
       1509 CAATATTAAT-TTT
          1 CAATATTAATACTT

                           
       1522 CAATTATTAATACTT
          1 CAA-TATTAATACTT

                          
       1537 CAA-ATTAATACTT
          1 CAATATTAATACTT

       1550 ATGGTCAATC


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  13   13  0.52
  14    7  0.28
  15    5  0.20

ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46


Consensus pattern (14 bp):   
CAATATTAATACTT

Found at i:3803 original size:21 final size:21

Alignment explanation


    Indices: 3774--3826  Score: 58
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       3764 TAAAACTATC

                                  
       3774 TAAGATTACTATAAA-GCTTAA
          1 TAAG-TTACTATAAATGCTTAA

                                 *
       3795 TAAAGTTACTA-AAATGCTTAC
          1 T-AAGTTACTATAAATGCTTAA

                        
       3816 TAAGTTA-TATA
          1 TAAGTTACTATA

       3827 TTAAAAAGTT


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  19    2  0.07
  20   10  0.36
  21   13  0.46
  22    3  0.11

ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36


Consensus pattern (21 bp):   
TAAGTTACTATAAATGCTTAA

Found at i:4127 original size:22 final size:22

Alignment explanation


    Indices: 4083--4134  Score: 70
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4073 GCTTACAAGA

                        *   *     
       4083 TTACT-AAAATTTTAATAAAGG
          1 TTACTAAAAATTGTAACAAAGG

                               *  
       4104 TTACTAAAAATTGTAACAAGGG
          1 TTACTAAAAATTGTAACAAAGG

                     
       4126 TTACTAAAA
          1 TTACTAAAA

       4135 CCTTTAGTAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21    5  0.19
  22   22  0.81

ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33


Consensus pattern (22 bp):   
TTACTAAAAATTGTAACAAAGG

Found at i:4810 original size:16 final size:16

Alignment explanation


    Indices: 4789--4819  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4779 ATAATTAATC

                            
       4789 ATAAAGACTTAGTAAA
          1 ATAAAGACTTAGTAAA

                   *       
       4805 ATAAAGATTTAGTAA
          1 ATAAAGACTTAGTAA

       4820 TATTTTTCAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29


Consensus pattern (16 bp):   
ATAAAGACTTAGTAAA

Found at i:10918 original size:18 final size:19

Alignment explanation


    Indices: 10879--10918  Score: 55
    Period size: 21  Copynumber: 2.1  Consensus size: 19

      10869 GTGCTCTCAT

                                 
      10879 TGTGATGCTCCCATTTTTCAA
          1 TGTGATGCTCCCA--TTTCAA

                               
      10900 TGTGATGCTCCCA-TTCAA
          1 TGTGATGCTCCCATTTCAA

             
      10918 T
          1 T

      10919 TCTGACTATT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    6  0.32
  21   13  0.68

ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40


Consensus pattern (19 bp):   
TGTGATGCTCCCATTTCAA
Done.