Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000589.1 Corchorus capsularis cultivar CVL-1 contig00589, 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, 998

Length: 1664
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31


Found at i:540 original size:21 final size:21

Alignment explanation


    Indices: 486--540  Score: 60
    Period size: 21  Copynumber: 2.6  Consensus size: 21

        476 CATTTTGATG

                                  
        486 ATTTGT-TTAATTTAATACTTA
          1 ATTTGTATTAATTTAATAC-TA

                  *        *     
        507 ATTTGTTTTAATTTACTAC-A
          1 ATTTGTATTAATTTAATACTA

                          
        527 ATTTAGTATTAATT
          1 ATTT-GTATTAATT

        541 AGCATTAAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  20    5  0.17
  21   14  0.47
  22   11  0.37

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


Consensus pattern (21 bp):   
ATTTGTATTAATTTAATACTA

Found at i:1064 original size:16 final size:16

Alignment explanation


    Indices: 1043--1083  Score: 73
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1033 CGATCCGAGT

                            
       1043 CCGAACCCGAAAATAC
          1 CCGAACCCGAAAATAC

                            
       1059 CCGAACCCGAAAATAC
          1 CCGAACCCGAAAATAC

             *       
       1075 CTGAACCCG
          1 CCGAACCCG

       1084 CCCGAACCCA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.39, C:0.39, G:0.15, T:0.07


Consensus pattern (16 bp):   
CCGAACCCGAAAATAC

Found at i:1522 original size:21 final size:21

Alignment explanation


    Indices: 1489--1558  Score: 86
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       1479 AATTATGTAC

                    *     *  *   
       1489 ATGTACATGTCATAGAATATT
          1 ATGTACATATCATACAAAATT

                 *               
       1510 ATGTATATATCATACAAAATT
          1 ATGTACATATCATACAAAATT

                    *   *        
       1531 ATGTACATGTCAAACAAAATT
          1 ATGTACATATCATACAAAATT

                   
       1552 ATGTACA
          1 ATGTACA

       1559 CAGGTGCATG


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   42  1.00

ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34


Consensus pattern (21 bp):   
ATGTACATATCATACAAAATT

Found at i:1540 original size:27 final size:27

Alignment explanation


    Indices: 1475--1540  Score: 63
    Period size: 21  Copynumber: 2.7  Consensus size: 27

       1465 ATGATACCAA

                                  *    
       1475 ACAAAATTATGTACATGTACATGTCAT
          1 ACAAAATTATGTACATGTACATATCAT

               *               *       
       1502 --AGAA-TAT-T--ATGTATATATCAT
          1 ACAAAATTATGTACATGTACATATCAT

                              
       1523 ACAAAATTATGTACATGT
          1 ACAAAATTATGTACATGT

       1541 CAAACAAAAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 12
        0.64            0.09        0.27

Matches are distributed among these distances:
  21   11  0.38
  23    4  0.14
  24    6  0.21
  25    4  0.14
  27    4  0.14

ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36


Consensus pattern (27 bp):   
ACAAAATTATGTACATGTACATATCAT
Done.