Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010792.1 Corchorus olitorius cultivar O-4 contig10824, 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: 9581
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5658 original size:19 final size:18

Alignment explanation


    Indices: 5625--5660  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5615 TTGAAATAAT

                              
       5625 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       5643 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       5661 TGAGTCTTCA


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:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:5668 original size:11 final size:10

Alignment explanation


    Indices: 5625--5671  Score: 53
    Period size: 11  Copynumber: 4.7  Consensus size: 10

       5615 TTGAAATAAT

                      
       5625 TCTTCAATGA
          1 TCTTCAATGA

                      
       5635 TCTTCAA--A
          1 TCTTCAATGA

                     * 
       5643 TCTTCAAATTA
          1 TCTTC-AATGA

                      
       5654 TCTTCAATGA
          1 TCTTCAATGA

                    
       5664 GTCTTCAA
          1 -TCTTCAA

       5672 ACACGAACCT


Statistics
Matches: 32,  Mismatches: 1, Indels: 7
        0.80            0.03        0.17

Matches are distributed among these distances:
   8    6  0.19
   9    2  0.06
  10   11  0.34
  11   13  0.41

ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40


Consensus pattern (10 bp):   
TCTTCAATGA

Found at i:6509 original size:18 final size:18

Alignment explanation


    Indices: 6474--6508  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       6464 CTCCTCTATC

                     *        
       6474 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
       6492 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

       6509 TTTGTAATTA


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

Matches are distributed among these distances:
  17    5  0.31
  18   11  0.69

ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:7121 original size:43 final size:43

Alignment explanation


    Indices: 7060--7145  Score: 172
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       7050 TAAAATGCAT

                                                       
       7060 GATCAAAAACAAAAACAAACAACTCATTCATATCAAGGAAGCA
          1 GATCAAAAACAAAAACAAACAACTCATTCATATCAAGGAAGCA

                                                       
       7103 GATCAAAAACAAAAACAAACAACTCATTCATATCAAGGAAGCA
          1 GATCAAAAACAAAAACAAACAACTCATTCATATCAAGGAAGCA

       7146 ATAGAAGCAA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  43   43  1.00

ACGTcount: A:0.56, C:0.21, G:0.09, T:0.14


Consensus pattern (43 bp):   
GATCAAAAACAAAAACAAACAACTCATTCATATCAAGGAAGCA

Found at i:9552 original size:5 final size:6

Alignment explanation


    Indices: 9541--9568  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

       9531 CAAATCAAAT

                                            
       9541 AGAAAA AGAAAA AGAAAA AGAAAA AGAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AGAA

       9569 TACACAATTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Done.