Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012944.1 Corchorus olitorius cultivar O-4 contig12977, 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: 7792
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Found at i:350 original size:198 final size:199

Alignment explanation


    Indices: 4--459  Score: 736
    Period size: 198  Copynumber: 2.3  Consensus size: 199

          1 ATT

                                                  *                          
          4 TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTATACTGACAGTGTATTGTATAACAATCT
          1 TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCT

                                            * *               *      *       
         69 TATAAAAAAAATTATACAATACACCGTCAGTGGAGTTTAGCAGACTGCACGCGCAGGGCTTAAGG
         66 TATAAAAAAAATTATACAATACACCGTCAGTGAAATTTAGCAGACTGCACACGCAGGACTTAAGG

                                                   *                         
        134 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTTTATATTTAATTAATTATGAAA-TAGA
        131 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTTAATATTTAATTAATTATGAAACTAG-

                 
        198 GTATG
        195 GTATG

                                                      * *                    
        203 TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACACTAATAGTGTATTGTATAACAATCT
          1 TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCT

                                                               *   *  *      
        268 TAT-AAAAAAATTATACAATACACCGTCAGTGAAATTTAGCAGACTGCACATGCATGATTTAAGG
         66 TATAAAAAAAATTATACAATACACCGTCAGTGAAATTTAGCAGACTGCACACGCAGGACTTAAGG

                                       *                      *              
        332 GTTGACATGTGTCCCCTTAGGGAATATTTATTAATATTTAATATTTAATTTATTATGAAACTAGG
        131 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTTAATATTTAATTAATTATGAAACTAGG

                
        397 TATG
        196 TATG

                  *                *    *           *                  
        401 TGTCAATTTCTTAACCCGCTTATGGAGTCCAAAATTTACATTGACAGTGTATTGTATAA
          1 TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACACTGACAGTGTATTGTATAA

        460 TGATCCTTAT


Statistics
Matches: 237,  Mismatches: 19, Indels: 3
        0.92            0.07        0.01

Matches are distributed among these distances:
 198  169  0.71
 199   68  0.29

ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Consensus pattern (199 bp):   
TGTCAACTTCTTAACCCGCTTATAGAGTTCAAAATTTACACTGACAGTGTATTGTATAACAATCT
TATAAAAAAAATTATACAATACACCGTCAGTGAAATTTAGCAGACTGCACACGCAGGACTTAAGG
GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTTAATATTTAATTAATTATGAAACTAGG
TATG

Found at i:4120 original size:2 final size:2

Alignment explanation


    Indices: 4067--4107  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       4057 TGGAGCATTG

                                                                         
       4067 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

       4108 CTTTGTAGAG


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00


Consensus pattern (2 bp):   
GA

Found at i:4506 original size:16 final size:16

Alignment explanation


    Indices: 4481--4511  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4471 TCTACATATT

                            
       4481 ATAAAGATTTAGTAAA
          1 ATAAAGATTTAGTAAA

                 *         
       4497 ATAAATATTTAGTAA
          1 ATAAAGATTTAGTAA

       4512 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:0.00, G:0.10, T:0.35


Consensus pattern (16 bp):   
ATAAAGATTTAGTAAA

Found at i:7200 original size:2 final size:2

Alignment explanation


    Indices: 7193--7228  Score: 56
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       7183 CATTTCTATC

                                                                  
       7193 AT AT AT AT -T AT AT CAT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT

       7229 TGATAACAAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    1  0.03
   2   29  0.91
   3    2  0.06

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7208 original size:14 final size:14

Alignment explanation


    Indices: 7189--7229  Score: 66
    Period size: 14  Copynumber: 2.9  Consensus size: 14

       7179 CCTACATTTC

                          
       7189 TATCATATATATTA
          1 TATCATATATATTA

                           
       7203 TATCATATATATATA
          1 TATCATATATAT-TA

                         
       7218 TAT-ATATATATT
          1 TATCATATATATT

       7230 GATAACAATG


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13    1  0.04
  14   20  0.77
  15    5  0.19

ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51


Consensus pattern (14 bp):   
TATCATATATATTA

Done.