Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016204.1 Corchorus capsularis cultivar CVL-1 contig16225, 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: 29272
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:473 original size:75 final size:71

Alignment explanation


    Indices: 319--473  Score: 195
    Period size: 75  Copynumber: 2.1  Consensus size: 71

        309 GAATATTTTC

                                                                 *           
        319 TAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAAAACAATAAAGTTGA
          1 TAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAAAAAAATAAAGTTGA

                    **
        384 GAATATTTTC
         66 G---A-TTAA

                                                                             
        394 TAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAAATAAATTATAAAG
          1 TAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAA-AAA-AAA--ATAAAG

                       
        459 ATTGAG-TTAA
         62 -TTGAGATTAA

                 
        469 TAAAT
          1 TAAAT

        474 AGAATATTTT


Statistics
Matches: 72,  Mismatches: 3, Indels: 10
        0.85            0.04        0.12

Matches are distributed among these distances:
  75   56  0.78
  76    3  0.04
  77    2  0.03
  79    6  0.08
  80    5  0.07

ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33


Consensus pattern (71 bp):   
TAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAAAAAAAAATAAAGTTGA
GATTAA

Found at i:649 original size:66 final size:66

Alignment explanation


    Indices: 579--703  Score: 166
    Period size: 66  Copynumber: 1.9  Consensus size: 66

        569 ATTCAATTAT

                                                         *                   
        579 AAAAATCATAATAAA-ATAAATAATTAAA-AGATAATTCT-AGATTTTGCCAATTTGTGGGAAGT
          1 AAAAATCATAA-AAACATAAATAATTAAATA-ATAATT-TGAGATCTTGCCAATTTGTGGGAAGT

                
        641 CTAG
         63 CTAG

                               *                  * *                  
        645 AAAAATCATAAAAACATAATTAATTAAATAATAATTTGGGGTCTTGCCAATTTGTGGGA
          1 AAAAATCATAAAAACATAAATAATTAAATAATAATTTGAGATCTTGCCAATTTGTGGGA

        704 GACTAAATAA


Statistics
Matches: 52,  Mismatches: 4, Indels: 6
        0.84            0.06        0.10

Matches are distributed among these distances:
  65    4  0.08
  66   47  0.90
  67    1  0.02

ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32


Consensus pattern (66 bp):   
AAAAATCATAAAAACATAAATAATTAAATAATAATTTGAGATCTTGCCAATTTGTGGGAAGTCTA
G

Found at i:777 original size:26 final size:25

Alignment explanation


    Indices: 714--769  Score: 94
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        704 GACTAAATAA

                                      
        714 TAAAGATATGATTAAAATTCAAAAAC
          1 TAAA-ATATGATTAAAATTCAAAAAC

                               *     
        740 TAAAATATGATTAAAATTCGAAAAC
          1 TAAAATATGATTAAAATTCAAAAAC

                 
        765 TAAAA
          1 TAAAA

        770 GTGAGATTTG


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  25   25  0.86
  26    4  0.14

ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27


Consensus pattern (25 bp):   
TAAAATATGATTAAAATTCAAAAAC

Found at i:3510 original size:17 final size:17

Alignment explanation


    Indices: 3464--3510  Score: 51
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       3454 AAGATTTAAG

                             
       3464 AAAT-ATTACTAGTACT
          1 AAATCATTACTAGTACT

               *   * *    *  
       3480 AAAACATGATTAGTCCT
          1 AAATCATTACTAGTACT

                          
       3497 AAATCATTACTAGT
          1 AAATCATTACTAGT

       3511 TCATGTGATA


Statistics
Matches: 23,  Mismatches: 7, Indels: 1
        0.74            0.23        0.03

Matches are distributed among these distances:
  16    3  0.13
  17   20  0.87

ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34


Consensus pattern (17 bp):   
AAATCATTACTAGTACT

Found at i:27155 original size:21 final size:21

Alignment explanation


    Indices: 27130--27169  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      27120 AAAAAGATCA

                    **           
      27130 CATGTGGTTCACCATGTAAGG
          1 CATGTGGTGAACCATGTAAGG

                               
      27151 CATGTGGTGAACCATGTAA
          1 CATGTGGTGAACCATGTAA

      27170 AATTTAGGTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28


Consensus pattern (21 bp):   
CATGTGGTGAACCATGTAAGG

Found at i:28059 original size:15 final size:14

Alignment explanation


    Indices: 28039--28081  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 14

      28029 TCTTAATTGC

                          
      28039 AATAAAGTAAATAG
          1 AATAAAGTAAATAG

                   *        
      28053 TAATAAAATGAAATAG
          1 -AATAAAGT-AAATAG

                         
      28069 AAGTAAAGTAAAT
          1 AA-TAAAGTAAAT

      28082 TTGTCTTGAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 4
        0.80            0.07        0.13

Matches are distributed among these distances:
  15   13  0.54
  16   11  0.46

ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23


Consensus pattern (14 bp):   
AATAAAGTAAATAG
Done.