Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013380.1 Corchorus olitorius cultivar O-4 contig13413, 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: 20970
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31


Found at i:3261 original size:15 final size:15

Alignment explanation


    Indices: 3233--3274  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3223 TTACTTTGTT

                   *        
       3233 TTGTTTTTTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       3249 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       3264 TTGTTTTCTGT
          1 TTGTTTTCTGT

       3275 CAACCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   17  0.68
  16    8  0.32

ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:9437 original size:24 final size:24

Alignment explanation


    Indices: 9372--9437  Score: 105
    Period size: 25  Copynumber: 2.7  Consensus size: 24

       9362 GAGTACCAAC

                *                   
       9372 CAAATGTATACCGTAAACACCCAT
          1 CAAAGGTATACCGTAAACACCCAT

                                     
       9396 CAAAGGGTATACCGTAAACACCCAT
          1 CAAA-GGTATACCGTAAACACCCAT

                        *    
       9421 CAAAGGTATACCATAAA
          1 CAAAGGTATACCGTAAA

       9438 TACACCCACC


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  24   16  0.41
  25   23  0.59

ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18


Consensus pattern (24 bp):   
CAAAGGTATACCGTAAACACCCAT

Found at i:9506 original size:16 final size:16

Alignment explanation


    Indices: 9482--9527  Score: 83
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       9472 CCTCATTAAT

                *           
       9482 CCACATTCTTGAAAAA
          1 CCACGTTCTTGAAAAA

                            
       9498 CCACGTTCTTGAAAAA
          1 CCACGTTCTTGAAAAA

                          
       9514 CCACGTTCTTGAAA
          1 CCACGTTCTTGAAA

       9528 TAAGAACGTG


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  16   29  1.00

ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26


Consensus pattern (16 bp):   
CCACGTTCTTGAAAAA

Found at i:11545 original size:36 final size:36

Alignment explanation


    Indices: 11505--11637  Score: 149
    Period size: 36  Copynumber: 3.7  Consensus size: 36

      11495 TGGTTGTAAT

                   *    *  *   *                
      11505 GCCGCTGACCTTGGTTGCCTAATACTTGGCTATAAC
          1 GCCGCTGGCCTTAGTCGCCCAATACTTGGCTATAAC

                       *           *           *
      11541 GCCGCTGGCCTCAGTCGCCCAATGCTTGGCTATAAT
          1 GCCGCTGGCCTTAGTCGCCCAATACTTGGCTATAAC

                    *              **    *      
      11577 GCCGCTGGTCTTAGTCGCCCAATGTTTGGTTATAAC
          1 GCCGCTGGCCTTAGTCGCCCAATACTTGGCTATAAC

                       *       *     
      11613 GCCGCTGGCCTAAGTCGCCTAATAC
          1 GCCGCTGGCCTTAGTCGCCCAATAC

      11638 ATAATTGGCT


Statistics
Matches: 80,  Mismatches: 17, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  36   80  1.00

ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28


Consensus pattern (36 bp):   
GCCGCTGGCCTTAGTCGCCCAATACTTGGCTATAAC

Found at i:13264 original size:29 final size:31

Alignment explanation


    Indices: 13208--13273  Score: 84
    Period size: 30  Copynumber: 2.2  Consensus size: 31

      13198 AGGTAAAATA

                                           
      13208 TCCAAAATTGAGAGTTCAAGGGGC-AAAACG
          1 TCCAAAATTGAGAGTTCAAGGGGCAAAAACG

                             **             
      13238 TCCAAAATTGA-AGTT-TTGGGGACAAAAACG
          1 TCCAAAATTGAGAGTTCAAGGGG-CAAAAACG

                  
      13268 TCCAAA
          1 TCCAAA

      13274 CGCCACAAAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  28    4  0.12
  29    5  0.16
  30   23  0.72

ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20


Consensus pattern (31 bp):   
TCCAAAATTGAGAGTTCAAGGGGCAAAAACG

Found at i:17628 original size:21 final size:21

Alignment explanation


    Indices: 17602--17641  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      17592 AGGGTCTAAT

                     *           
      17602 CTCATATTATCCATGGCTGTG
          1 CTCATATTACCCATGGCTGTG

                               
      17623 CTCATATTACCCATGGCTG
          1 CTCATATTACCCATGGCTG

      17642 CGCTGTTGAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35


Consensus pattern (21 bp):   
CTCATATTACCCATGGCTGTG
Done.