Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021671.1 Corchorus olitorius cultivar O-4 contig21704, 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: 7143
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:917 original size:43 final size:42

Alignment explanation


    Indices: 848--929  Score: 103
    Period size: 43  Copynumber: 1.9  Consensus size: 42

        838 AAAAAAAATG

                         *                             
        848 CCGCCTATTTTTTGTTTAACAAAATTTTCCCACTCAAATAAAC
          1 CCGCCTATTTTTTATTTAACAAAATTTTCCCACT-AAATAAAC

                             **             *       
        891 CCGCCTA-TTTTTATTTCCCAATAATTTTCCCTCTAAATA
          1 CCGCCTATTTTTTATTTAACAA-AATTTTCCCACTAAATA

        930 CTTGTTACAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  42   16  0.47
  43   18  0.53

ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40


Consensus pattern (42 bp):   
CCGCCTATTTTTTATTTAACAAAATTTTCCCACTAAATAAAC

Found at i:1340 original size:16 final size:14

Alignment explanation


    Indices: 1308--1334  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       1298 AATGACCAAG

                          
       1308 TTTTGTAACAGAAT
          1 TTTTGTAACAGAAT

                         
       1322 TTTTGTAACAGAA
          1 TTTTGTAACAGAA

       1335 AATTTTCCCA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41


Consensus pattern (14 bp):   
TTTTGTAACAGAAT

Found at i:1377 original size:2 final size:2

Alignment explanation


    Indices: 1370--1396  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1360 TTTCTGATAG

                                                    
       1370 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1397 TCAATTTAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2405 original size:18 final size:19

Alignment explanation


    Indices: 2378--2414  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

       2368 TTGCATGGAG

                               
       2378 GCATGAAGAC-ATGGAGAT
          1 GCATGAAGACTATGGAGAT

                 *             
       2396 GCATGGAGACTATGGAGAT
          1 GCATGAAGACTATGGAGAT

       2415 AACGATGGAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    9  0.53
  19    8  0.47

ACGTcount: A:0.35, C:0.11, G:0.35, T:0.19


Consensus pattern (19 bp):   
GCATGAAGACTATGGAGAT

Found at i:5204 original size:19 final size:18

Alignment explanation


    Indices: 5171--5206  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5161 TGGAAATAAT

                              
       5171 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       5189 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       5207 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:6731 original size:30 final size:29

Alignment explanation


    Indices: 6686--6742  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       6676 GTTTATTAAT

                                           
       6686 GAAACTTGAAAATTAAAGACATAAGATAAAG
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAG

                    *                  
       6717 GAAA-TTGCAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

       6743 CTAATCCTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  28    4  0.16
  29    5  0.20
  30   12  0.48
  31    4  0.16

ACGTcount: A:0.58, C:0.07, G:0.14, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAG
Done.