Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014531.1 Corchorus olitorius cultivar O-4 contig14564, 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: 16453
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:3560 original size:89 final size:89

Alignment explanation


    Indices: 3437--3637  Score: 323
    Period size: 89  Copynumber: 2.3  Consensus size: 89

       3427 CCTGTTGGCT

                                 *   *                                       
       3437 GTTTATGGCTATACCAACGCCCCCCGCTGTTGGTATACATTCTACAGCAACGTAAGCCGTAGG-T
          1 GTTTATGGCTATACCAACGCCACCCACTGTTGGTATACATTCTACAGCAACGTAAGCCGT-GGAT

                *                    
       3501 ATATTTCCAATCATACCATTTTTTG
         65 ATATCTCCAATCATACCATTTTTTG

                *                     *                 *           *        
       3526 GTTTGTGGCTATACCAACGCCACCCATTGTTGGTATACATTCTATAGCAACGTAAGTCGTGGATA
          1 GTTTATGGCTATACCAACGCCACCCACTGTTGGTATACATTCTACAGCAACGTAAGCCGTGGATA

                                    
       3591 TATCTCCAATCATACCATTTTTTG
         66 TATCTCCAATCATACCATTTTTTG

                                   
       3615 GTTTATGGCTATACCAACGCCAC
          1 GTTTATGGCTATACCAACGCCAC

       3638 AGGTCGTTTG


Statistics
Matches: 103,  Mismatches: 8, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  88    2  0.02
  89  101  0.98

ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33


Consensus pattern (89 bp):   
GTTTATGGCTATACCAACGCCACCCACTGTTGGTATACATTCTACAGCAACGTAAGCCGTGGATA
TATCTCCAATCATACCATTTTTTG

Found at i:3824 original size:40 final size:40

Alignment explanation


    Indices: 3780--3856  Score: 120
    Period size: 40  Copynumber: 1.9  Consensus size: 40

       3770 GTCATTCACA

                           *                         
       3780 TTAAAAAT-ATAATCCAAAACAATTTGTTCTAATCCACACG
          1 TTAAAAATGA-AATCAAAAACAATTTGTTCTAATCCACACG

                         *                       
       3820 TTAAAAATGAAATTAAAAACAATTTGTTCTAATCCAC
          1 TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCAC

       3857 TCATGTAACA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  40   33  0.97
  41    1  0.03

ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31


Consensus pattern (40 bp):   
TTAAAAATGAAATCAAAAACAATTTGTTCTAATCCACACG

Found at i:4017 original size:17 final size:17

Alignment explanation


    Indices: 3981--4018  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       3971 GAAGCAGTGG

                           * 
       3981 GAATATTGAACTTAGGA
          1 GAATATTGAACTTAGAA

                              
       3998 GAATATTGAA-TTATGAA
          1 GAATATTGAACTTA-GAA

                
       4015 GAAT
          1 GAAT

       4019 GTTTGAAAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  16    3  0.16
  17   16  0.84

ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32


Consensus pattern (17 bp):   
GAATATTGAACTTAGAA

Found at i:13543 original size:20 final size:20

Alignment explanation


    Indices: 13520--13561  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      13510 CCTTATCATC

                     *          
      13520 TGTAATGGTTTTATTAAGTT
          1 TGTAATGGTATTATTAAGTT

                                
      13540 TGTAATGGTATTATTAAGTT
          1 TGTAATGGTATTATTAAGTT

              
      13560 TG
          1 TG

      13562 AGTAATTACT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52


Consensus pattern (20 bp):   
TGTAATGGTATTATTAAGTT
Done.