Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023031.1 Corchorus olitorius cultivar O-4 contig23064, 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: 11422
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30


Found at i:150 original size:15 final size:15

Alignment explanation


    Indices: 118--147  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        108 TAAATTTCAA

                           
        118 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
        133 TAAAATAAAA-ATAT
          1 TAAAATAAAATATAT

             
        147 T
          1 T

        148 TAATTTTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

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


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:1339 original size:26 final size:26

Alignment explanation


    Indices: 1304--1353  Score: 100
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       1294 ATAATTTTTG

                                      
       1304 AAAAATAATAAAAAAAACTTGTGACA
          1 AAAAATAATAAAAAAAACTTGTGACA

                                    
       1330 AAAAATAATAAAAAAAACTTGTGA
          1 AAAAATAATAAAAAAAACTTGTGA

       1354 TGGGTGTCGT


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

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.66, C:0.06, G:0.08, T:0.20


Consensus pattern (26 bp):   
AAAAATAATAAAAAAAACTTGTGACA

Found at i:1554 original size:21 final size:21

Alignment explanation


    Indices: 1489--1554  Score: 57
    Period size: 21  Copynumber: 3.1  Consensus size: 21

       1479 GGGGTTTTTG

                    *              
       1489 AATTAAAGAAACAATAA-AAATA
          1 AATT-AAGCAACAA-AATAAATA

                  *   *           
       1511 AA-TAAACAAGAAAAT-AATAA
          1 AATTAAGCAACAAAATAAAT-A

                                 
       1531 AATTAAGCAACAAAATAAATA
          1 AATTAAGCAACAAAATAAATA

               
       1552 AAT
          1 AAT

       1555 ACTCCAATTC


Statistics
Matches: 35,  Mismatches: 5, Indels: 9
        0.71            0.10        0.18

Matches are distributed among these distances:
  19    5  0.14
  20    9  0.26
  21   16  0.46
  22    5  0.14

ACGTcount: A:0.71, C:0.06, G:0.05, T:0.18


Consensus pattern (21 bp):   
AATTAAGCAACAAAATAAATA

Found at i:5028 original size:22 final size:22

Alignment explanation


    Indices: 5003--5048  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       4993 AAGTTGTTGT

                      *            
       5003 TTCGACCTCTAC-GAAGGTTGAA
          1 TTCGACCTCTCCAG-AGGTTGAA

                                  
       5025 TTCGACCTCTCCAGAGGTTGAA
          1 TTCGACCTCTCCAGAGGTTGAA

              
       5047 TT
          1 TT

       5049 AGGAGATTTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   21  0.95
  23    1  0.05

ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30


Consensus pattern (22 bp):   
TTCGACCTCTCCAGAGGTTGAA
Done.