Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021743.1 Corchorus olitorius cultivar O-4 contig21776, 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: 6773
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:549 original size:15 final size:16

Alignment explanation


    Indices: 516--555  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        506 TTACTTTGTT

                            
        516 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
        532 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
        547 TTGCTTTCT
          1 TTGTTTTCT

        556 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:5834 original size:21 final size:21

Alignment explanation


    Indices: 5809--5849  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5799 GAAATTTAAA

                                 
       5809 AAAAAAAC-AAAAAATCAAAT
          1 AAAAAAACAAAAAAATCAAAT

                                 
       5829 AAAAAAACAAAAAAATCAAAT
          1 AAAAAAACAAAAAAATCAAAT

       5850 CAAATCATAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    8  0.40
  21   12  0.60

ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10


Consensus pattern (21 bp):   
AAAAAAACAAAAAAATCAAAT

Found at i:5849 original size:26 final size:23

Alignment explanation


    Indices: 5805--5854  Score: 64
    Period size: 26  Copynumber: 2.0  Consensus size: 23

       5795 TTAAGAAATT

                       *           
       5805 TAAAAAAAAAACAAAAAATCAAA
          1 TAAAAAAAAAAAAAAAAATCAAA

                                      
       5828 TAAAAAAACAAAAAAATCAAATCAAA
          1 TAAAAAAA-AAAAAAA--AAATCAAA

             
       5854 T
          1 T

       5855 CATATCAAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  23    8  0.35
  24    6  0.26
  26    9  0.39

ACGTcount: A:0.78, C:0.10, G:0.00, T:0.12


Consensus pattern (23 bp):   
TAAAAAAAAAAAAAAAAATCAAA

Found at i:5881 original size:6 final size:5

Alignment explanation


    Indices: 5841--5880  Score: 53
    Period size: 5  Copynumber: 7.6  Consensus size: 5

       5831 AAAAACAAAA

                               *                           
       5841 AAATC AAATC AAATC ATATC AAATC AAAATC AAAATC AAA
          1 AAATC AAATC AAATC AAATC AAATC -AAATC -AAATC AAA

       5881 AGAGAATTGA


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   5   21  0.66
   6   11  0.34

ACGTcount: A:0.62, C:0.17, G:0.00, T:0.20


Consensus pattern (5 bp):   
AAATC

Found at i:6200 original size:8 final size:8

Alignment explanation


    Indices: 6183--6213  Score: 53
    Period size: 8  Copynumber: 3.9  Consensus size: 8

       6173 AAAAAAAAGG

                 *  
       6183 AAAGAAAA
          1 AAAGAGAA

                    
       6191 AAAGAGAA
          1 AAAGAGAA

                    
       6199 AAAGAGAA
          1 AAAGAGAA

                   
       6207 AAAGAGA
          1 AAAGAGA

       6214 GAGAGCTCTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   8   22  1.00

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (8 bp):   
AAAGAGAA

Done.