Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010415.1 Corchorus olitorius cultivar O-4 contig10447, 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: 2023
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39


Found at i:1431 original size:12 final size:12

Alignment explanation


    Indices: 1416--1443  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

       1406 AAATTTCAAA

                        
       1416 ATTATAAAAGAT
          1 ATTATAAAAGAT

                        
       1428 ATTATAAAAGAT
          1 ATTATAAAAGAT

                
       1440 ATTA
          1 ATTA

       1444 AAGATCCGAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36


Consensus pattern (12 bp):   
ATTATAAAAGAT

Found at i:1627 original size:215 final size:214

Alignment explanation


    Indices: 1243--1638  Score: 720
    Period size: 215  Copynumber: 1.8  Consensus size: 214

       1233 GCTTAATAAC

                 *                                                           
       1243 TTTATGAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                          *            *                                     
       1308 GATACAACACATTATTATTATTATATATAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTTG
         66 GATACAACACATTACTATTATTATATAGAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTTG

                                                                             
       1373 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTATAAAAG
        131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTATAAAAG

                               
       1438 ATATTAAAGATCCGATTTA
        196 ATATTAAAGATCCGATTTA

                                       *                                     
       1457 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
          1 TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA

                                                *        *                   
       1522 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAATTAGTTGAACATTAGTGGTT
         66 GATACAACACATTACTATTAT-TATATAGAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTT

                                             *                  
       1587 GATTTATTAAATTAAATTAGATCAATGTCAAACCAAATTTCAAAATTATAAA
        130 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAA

       1639 TTAAAAACAT


Statistics
Matches: 174,  Mismatches: 7, Indels: 1
        0.96            0.04        0.01

Matches are distributed among these distances:
 214   83  0.48
 215   91  0.52

ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36


Consensus pattern (214 bp):   
TTTATCAATGGTGAATGTTATTAATTTCTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATTATATAGAACTATAACAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTATAAAAG
ATATTAAAGATCCGATTTA

Found at i:1849 original size:21 final size:21

Alignment explanation


    Indices: 1783--1849  Score: 57
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       1773 TAAGAATTTA

                        *        
       1783 ATTAATGTAAGTGTTTTAGTT
          1 ATTAATGTAAGTATTTTAGTT

                       *    ** *  
       1804 ATT-ATAGT-ATTATTACATTT
          1 ATTAAT-GTAAGTATTTTAGTT

                                  
       1824 AATTAATGTAAGTATTTTAGTT
          1 -ATTAATGTAAGTATTTTAGTT

                
       1846 ATTA
          1 ATTA

       1850 TTTATATTAC


Statistics
Matches: 33,  Mismatches: 9, Indels: 8
        0.66            0.18        0.16

Matches are distributed among these distances:
  20    9  0.27
  21   14  0.42
  22   10  0.30

ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52


Consensus pattern (21 bp):   
ATTAATGTAAGTATTTTAGTT
Done.