Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005900.1 Corchorus olitorius cultivar O-4 contig05925, 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: 10648
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32


Found at i:1206 original size:53 final size:53

Alignment explanation


    Indices: 1126--1230  Score: 183
    Period size: 53  Copynumber: 2.0  Consensus size: 53

       1116 ACGGAAGGAG

                             *                                   
       1126 TATTTTGTTAGTGAAAGTTCAATCTTTTTATTAAGATTCAAATATTTAGGATA
          1 TATTTTGTTAGTGAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGATA

                     *                   *                      
       1179 TATTTTGTTGGTGAAAGCTCAATCTTTTTGTTAAGATTCAAATATTTAGGAT
          1 TATTTTGTTAGTGAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGAT

       1231 TTGCTTGGTT


Statistics
Matches: 49,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  53   49  1.00

ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47


Consensus pattern (53 bp):   
TATTTTGTTAGTGAAAGCTCAATCTTTTTATTAAGATTCAAATATTTAGGATA

Found at i:2474 original size:2 final size:2

Alignment explanation


    Indices: 2469--2498  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2459 GTATTTTTTA

                                                          
       2469 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2499 ATCAAATAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7127 original size:167 final size:167

Alignment explanation


    Indices: 6851--7178  Score: 557
    Period size: 167  Copynumber: 2.0  Consensus size: 167

       6841 TCACTCAGCC

                                                                             
       6851 ATAAATCAAGCAATCTGGCTCAAGAAGTTGATGATTGAAGTGAATGAAGAACCAGAAAGAGCTAT
          1 ATAAATCAAGCAATCTGGCTCAAGAAGTTGATGATTGAAGTGAATGAAGAACCAGAAAGAGCTAT

                                   *                        *                
       6916 TCTTATCTATTGTGACAATCAGGTAGTTGTACCATTGCTAAAAATCCAGTTTGTCATGGTCGAAC
         66 TCTTATCTATTGTGACAATCAGGCAGTTGTACCATTGCTAAAAATCCACTTTGTCATGGTCGAAC

                                                 
       6981 CAAGCATTTTAAAATCAAGTTTCACATTTTCTCAACA
        131 CAAGCATTTTAAAATCAAGTTTCACATTTTCTCAACA

                                                               **    * *     
       7018 ATAAATCAAGCAATCTGGCTCAAGAAGTTGATGATTGAAGTGAATGAAGAATTAGAAGGGGCTAT
          1 ATAAATCAAGCAATCTGGCTCAAGAAGTTGATGATTGAAGTGAATGAAGAACCAGAAAGAGCTAT

             *                            *                          *      *
       7083 TGTTATCTATTGTGACAATCAGGCAGTTGTGCCATTGCTAAAAATCCACTTTGTCATTGTCGAAT
         66 TCTTATCTATTGTGACAATCAGGCAGTTGTACCATTGCTAAAAATCCACTTTGTCATGGTCGAAC

                        *                  
       7148 CAAGCATTTTAAGATCAAGTTTCACATTTTC
        131 CAAGCATTTTAAAATCAAGTTTCACATTTTC

       7179 AGAGAAGCTC


Statistics
Matches: 150,  Mismatches: 11, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 167  150  1.00

ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31


Consensus pattern (167 bp):   
ATAAATCAAGCAATCTGGCTCAAGAAGTTGATGATTGAAGTGAATGAAGAACCAGAAAGAGCTAT
TCTTATCTATTGTGACAATCAGGCAGTTGTACCATTGCTAAAAATCCACTTTGTCATGGTCGAAC
CAAGCATTTTAAAATCAAGTTTCACATTTTCTCAACA

Found at i:9584 original size:12 final size:12

Alignment explanation


    Indices: 9550--9602  Score: 63
    Period size: 12  Copynumber: 4.3  Consensus size: 12

       9540 CGAGCAAGGT

                      * 
       9550 TCTGCTTATTAC
          1 TCTGCTTATTCC

                  *      
       9562 TCCTGCGTATTCC
          1 T-CTGCTTATTCC

                        
       9575 TCTGCTTATT-C
          1 TCTGCTTATTCC

                         
       9586 TCCTGCTTATTCC
          1 T-CTGCTTATTCC

                
       9599 TCTG
          1 TCTG

       9603 TTAGTATTAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  11    2  0.06
  12   21  0.60
  13   12  0.34

ACGTcount: A:0.09, C:0.32, G:0.11, T:0.47


Consensus pattern (12 bp):   
TCTGCTTATTCC

Found at i:9596 original size:24 final size:25

Alignment explanation


    Indices: 9550--9602  Score: 90
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       9540 CGAGCAAGGT

                                     
       9550 TCTGCTTATTACTCCTGCGTATTCC
          1 TCTGCTTATTACTCCTGCGTATTCC

                              *      
       9575 TCTGCTTATT-CTCCTGCTTATTCC
          1 TCTGCTTATTACTCCTGCGTATTCC

                
       9599 TCTG
          1 TCTG

       9603 TTAGTATTAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  24   17  0.63
  25   10  0.37

ACGTcount: A:0.09, C:0.32, G:0.11, T:0.47


Consensus pattern (25 bp):   
TCTGCTTATTACTCCTGCGTATTCC
Done.