Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009677.1 Corchorus capsularis cultivar CVL-1 contig09698, 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: 21343
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:10718 original size:21 final size:20

Alignment explanation


    Indices: 10692--10738  Score: 58
    Period size: 20  Copynumber: 2.3  Consensus size: 20

      10682 ACTAACATGA

                                 
      10692 TTTGACAGTTAAAATTTGGGG
          1 TTTGACAG-TAAAATTTGGGG

                  *  *  *       
      10713 TTTGACCGTCAATTTTGGGG
          1 TTTGACAGTAAAATTTGGGG

                  
      10733 TTTGAC
          1 TTTGAC

      10739 CGTGAAATCA


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

Matches are distributed among these distances:
  20   16  0.70
  21    7  0.30

ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40


Consensus pattern (20 bp):   
TTTGACAGTAAAATTTGGGG

Found at i:14987 original size:21 final size:21

Alignment explanation


    Indices: 14934--14988  Score: 56
    Period size: 24  Copynumber: 2.5  Consensus size: 21

      14924 TTAAATTTTA

                     *  *  *     
      14934 ATAGTCAAAACCTAAGGTTTG
          1 ATAGTCAAACCCCAAAGTTTG

                                    
      14955 ATATTGGTCAAACCCCAAAGTTTG
          1 ATA---GTCAAACCCCAAAGTTTG

                      
      14979 ATAGTCAAAC
          1 ATAGTCAAAC

      14989 AATGTTAAAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 6
        0.76            0.08        0.16

Matches are distributed among these distances:
  21   10  0.36
  24   18  0.64

ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27


Consensus pattern (21 bp):   
ATAGTCAAACCCCAAAGTTTG

Found at i:16205 original size:194 final size:195

Alignment explanation


    Indices: 15874--16259  Score: 625
    Period size: 194  Copynumber: 2.0  Consensus size: 195

      15864 TGAAATTTTA

                                               *         *        * *        
      15874 AAAAAAAAGGCTATGAGAGACAAAAAAAATGACATTACATGAAATCTAAACCCTGAGTGAGATAA
          1 AAAAAAAAGGCTATGAGAGAC-AAAAAAATGACATGACATGAAATATAAACCCTAAATGAGATAA

                               *                  *                          
      15939 AATAAATGATATATAAACCCTAAGTGAGATAAAGAAATGCCCCAAAACTATATTAAACCCTAAGT
         65 AATAAATGATATATAAACCATAAGTGAGATAAAGAAATACCCCAAAACTATATTAAACCCTAAGT

                                                            *                
      16004 GAGATAGTCTAAATTTCAACATTCTATGTCAG-AAAAAGT-GCTGGAAGAGTCAAAATTTCAAAT
        130 GAGATAGTCTAAATTTCAACATTCTATGTC-GTAAAAAGTAG-TGGAAAAGTCAAAATTTCAAAT

               
      16067 TAT
        193 TAT

                                                                             
      16070 AAAAAAAAGGCTATGAGAGAC-AAAAAATGACATGACATGAAATATAAACCCTAAATGAGATAAA
          1 AAAAAAAAGGCTATGAGAGACAAAAAAATGACATGACATGAAATATAAACCCTAAATGAGATAAA

               *                         *                                   
      16134 ATACATGATATATAAACCATAAGTGAGATGAAGAAATACCCCAAAACTATATTAAACCCTAAGTG
         66 ATAAATGATATATAAACCATAAGTGAGATAAAGAAATACCCCAAAACTATATTAAACCCTAAGTG

                              *   *                                      
      16199 AGATAGTCTAAATTTCAATATTTTATGTCGTAAAAAGTAGTGGAAAAGTCAAAATTTCAAA
        131 AGATAGTCTAAATTTCAACATTCTATGTCGTAAAAAGTAGTGGAAAAGTCAAAATTTCAAA

      16260 AGTTGTGACA


Statistics
Matches: 177,  Mismatches: 11, Indels: 6
        0.91            0.06        0.03

Matches are distributed among these distances:
 193    1  0.01
 194  154  0.87
 195    1  0.01
 196   21  0.12

ACGTcount: A:0.49, C:0.13, G:0.15, T:0.24


Consensus pattern (195 bp):   
AAAAAAAAGGCTATGAGAGACAAAAAAATGACATGACATGAAATATAAACCCTAAATGAGATAAA
ATAAATGATATATAAACCATAAGTGAGATAAAGAAATACCCCAAAACTATATTAAACCCTAAGTG
AGATAGTCTAAATTTCAACATTCTATGTCGTAAAAAGTAGTGGAAAAGTCAAAATTTCAAATTAT

Found at i:16471 original size:13 final size:13

Alignment explanation


    Indices: 16455--16484  Score: 60
    Period size: 13  Copynumber: 2.3  Consensus size: 13

      16445 TATTATTTGT

                         
      16455 TATATTATATATA
          1 TATATTATATATA

                         
      16468 TATATTATATATA
          1 TATATTATATATA

                
      16481 TATA
          1 TATA

      16485 ATTTTAACCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (13 bp):   
TATATTATATATA

Found at i:17780 original size:2 final size:2

Alignment explanation


    Indices: 17722--17762  Score: 55
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      17712 TCAAAAATAC

                                        *           *     *              
      17722 AT AT AT AT AT AT AT AT AT AG AT AT AT AC AT AC AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      17763 ATTAACTAAG


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41


Consensus pattern (2 bp):   
AT

Found at i:18140 original size:2 final size:2

Alignment explanation


    Indices: 18135--18175  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      18125 AAAGAAAGAA

                                                                         
      18135 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      18176 AGAAACCGGT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.