Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024153.1 Corchorus olitorius cultivar O-4 contig24186, 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: 17679
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1430 original size:2 final size:2

Alignment explanation


    Indices: 1423--1451  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1413 TATATCTTAC

                                                        
       1423 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       1452 AAATCACGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

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


Consensus pattern (2 bp):   
TA

Found at i:1443 original size:13 final size:13

Alignment explanation


    Indices: 1425--1450  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1415 TATCTTACTA

                         
       1425 TATATATATATAT
          1 TATATATATATAT

                         
       1438 TATATATATATAT
          1 TATATATATATAT

       1451 AAAATCACGA


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

Matches are distributed among these distances:
  13   13  1.00

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


Consensus pattern (13 bp):   
TATATATATATAT

Found at i:1443 original size:15 final size:15

Alignment explanation


    Indices: 1423--1451  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

       1413 TATATCTTAC

                           
       1423 TATATATATATATAT
          1 TATATATATATATAT

                          
       1438 TATATATATATATA
          1 TATATATATATATA

       1452 AAATCACGAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

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


Consensus pattern (15 bp):   
TATATATATATATAT

Found at i:1563 original size:16 final size:16

Alignment explanation


    Indices: 1544--1593  Score: 64
    Period size: 17  Copynumber: 3.0  Consensus size: 16

       1534 CTTTTTGGTC

                  *         
       1544 ATTATACTTTATTAAT
          1 ATTATATTTTATTAAT

                  *           
       1560 ATTAATTTTTTAATTAAT
          1 ATT-ATATTTT-ATTAAT

                            
       1578 ATTATATTTTATTAAT
          1 ATTATATTTTATTAAT

       1594 TTTTTTTGGT


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  16    9  0.31
  17   11  0.38
  18    9  0.31

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (16 bp):   
ATTATATTTTATTAAT

Found at i:1577 original size:18 final size:20

Alignment explanation


    Indices: 1554--1594  Score: 68
    Period size: 18  Copynumber: 2.1  Consensus size: 20

       1544 ATTATACTTT

                                
       1554 ATTAATATTA-ATTTT-TTA
          1 ATTAATATTATATTTTATTA

                                
       1572 ATTAATATTATATTTTATTA
          1 ATTAATATTATATTTTATTA

               
       1592 ATT
          1 ATT

       1595 TTTTTTGGTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  18   10  0.48
  19    5  0.24
  20    6  0.29

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (20 bp):   
ATTAATATTATATTTTATTA

Found at i:13772 original size:25 final size:25

Alignment explanation


    Indices: 13738--13807  Score: 115
    Period size: 25  Copynumber: 2.8  Consensus size: 25

      13728 TCTCTCGATC

                                 *   
      13738 CAAATCTTTCTTCTTCGATCATATT
          1 CAAATCTTTCTTCTTCGATCAGATT

                                     
      13763 CAAATCTTTCTTCTTCGATCAGATT
          1 CAAATCTTTCTTCTTCGATCAGATT

                                 
      13788 CAAAT-TCTTCTTCTTCGATC
          1 CAAATCT-TTCTTCTTCGATC

      13808 CTATCATGGC


Statistics
Matches: 43,  Mismatches: 1, Indels: 2
        0.93            0.02        0.04

Matches are distributed among these distances:
  24    1  0.02
  25   42  0.98

ACGTcount: A:0.23, C:0.26, G:0.06, T:0.46


Consensus pattern (25 bp):   
CAAATCTTTCTTCTTCGATCAGATT

Done.