Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014675.1 Corchorus olitorius cultivar O-4 contig14708, 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: 8753
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27


Found at i:944 original size:19 final size:20

Alignment explanation


    Indices: 903--944  Score: 52
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        893 TGATTAAATG

                       *        
        903 AACTCTAGAAAGTGTATTCA
          1 AACTCTAGAAACTGTATTCA

                                 
        923 AACTCT-GAAACTCGTATT-A
          1 AACTCTAGAAACT-GTATTCA

               
        942 AAC
          1 AAC

        945 CCTATAAGAC


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  19    9  0.45
  20   11  0.55

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29


Consensus pattern (20 bp):   
AACTCTAGAAACTGTATTCA

Found at i:1324 original size:14 final size:12

Alignment explanation


    Indices: 1281--1325  Score: 54
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       1271 ATTTTATTAC

                         
       1281 TGTTTTATTAAAT
          1 TGTTTTA-TAAAT

                        
       1294 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
       1306 GGTTTTAAGTAAAT
          1 TGTTTT-A-TAAAT

                  
       1320 TGTTTT
          1 TGTTTT

       1326 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    8  0.29
  14   10  0.36

ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:6673 original size:172 final size:172

Alignment explanation


    Indices: 6380--6708  Score: 552
    Period size: 172  Copynumber: 1.9  Consensus size: 172

       6370 TAGGGACCAT

                  *                                                          
       6380 GTGATCTGTCGTCAGCAAATCATAAAAATAAAAATCCCAACAATTACTAACTAACAATAGCTAGG
          1 GTGATCGGTCGTCAGCAAATCATAAAAATAAAAATCCCAACAATTACTAACTAACAATAGCTAGG

                           *            *        *                           
       6445 GCAAGTAGGGGTCGATCCCACAGAGAGATAGGTTATTGTTCTTTTTCTTAAAACAAACAAACAAA
         66 GCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTATTCTTTTTCTTAAAACAAACAAACAAA

                                 *                    
       6510 ATAAAGAAGATTTTGAAAGTAGAATTAAATCAAATCAAACTA
        131 ATAAAGAAGATTTTGAAAGTAAAATTAAATCAAATCAAACTA

                                                                     *   *   
       6552 GTGATCGGTCGTCAGCAAATCATAAAAATAAAAATCCCAACAATTACTAACTAA-AGGTAGTTAG
          1 GTGATCGGTCGTCAGCAAATCATAAAAATAAAAATCCCAACAATTACTAACTAACA-ATAGCTAG

                                           *                              *  
       6616 GGCAAGTAGGGGTCGAACCCACAGAGAGAAATGTTATTATTCTTTTTCTTAAAACAAACAAATAA
         65 GGCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTATTCTTTTTCTTAAAACAAACAAACAA

                             *          
       6681 AATAAAGAAGATTTTGAGAGTAAAATTA
        130 AATAAAGAAGATTTTGAAAGTAAAATTA

       6709 GGTTAAACCA


Statistics
Matches: 146,  Mismatches: 10, Indels: 2
        0.92            0.06        0.01

Matches are distributed among these distances:
 171    1  0.01
 172  145  0.99

ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25


Consensus pattern (172 bp):   
GTGATCGGTCGTCAGCAAATCATAAAAATAAAAATCCCAACAATTACTAACTAACAATAGCTAGG
GCAAGTAGGGGTCGAACCCACAGAGAGAAAGGTTATTATTCTTTTTCTTAAAACAAACAAACAAA
ATAAAGAAGATTTTGAAAGTAAAATTAAATCAAATCAAACTA
Done.