Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008174.1 Corchorus capsularis cultivar CVL-1 contig08195, 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: 10166
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34


Found at i:66 original size:33 final size:33

Alignment explanation


    Indices: 29--144  Score: 232
    Period size: 33  Copynumber: 3.5  Consensus size: 33

         19 GTGAAGCCGT

                                             
         29 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC
          1 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC

                                             
         62 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC
          1 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC

                                             
         95 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC
          1 CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC

                             
        128 CCCAGTGGGGCGGCTTC
          1 CCCAGTGGGGCGGCTTC

        145 GCCACGGTAA


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   83  1.00

ACGTcount: A:0.09, C:0.34, G:0.37, T:0.21


Consensus pattern (33 bp):   
CCCAGTGGGGCGGCTTCACCGTGGTTGAGCCTC

Found at i:747 original size:53 final size:53

Alignment explanation


    Indices: 670--867  Score: 378
    Period size: 53  Copynumber: 3.7  Consensus size: 53

        660 AAACTCCAAC

                   *                 *                           
        670 TAAATATAAATTAATTTTAGAAAAAACAAATATTCTATATGATTCATCACAAA
          1 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA

                                                                 
        723 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA
          1 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA

                                                                 
        776 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA
          1 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA

                                                   
        829 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATA
          1 TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATA

        868 ATGGTTAATC


Statistics
Matches: 143,  Mismatches: 2, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  53  143  1.00

ACGTcount: A:0.51, C:0.12, G:0.04, T:0.34


Consensus pattern (53 bp):   
TAAATATCAATTAATTTTAGAAAAACCAAATATTCTATATGATTCATCACAAA

Found at i:755 original size:26 final size:26

Alignment explanation


    Indices: 724--861  Score: 86
    Period size: 26  Copynumber: 5.2  Consensus size: 26

        714 CATCACAAAT

                                      
        724 AAATATCAATTAATTTTAGAAAAACC
          1 AAATATCAATTAATTTTAGAAAAACC

                    *    *    *  * *    *
        750 AAATATTCTATATGA-TTCATCACAAA-T
          1 AAATA-TCAAT-TAATTTTA-GAAAAACC

                                      
        777 AAATATCAATTAATTTTAGAAAAACC
          1 AAATATCAATTAATTTTAGAAAAACC

                    *    *    *  * *    *
        803 AAATATTCTATATGA-TTCATCACAAA-T
          1 AAATA-TCAAT-TAATTTTA-GAAAAACC

                                      
        830 AAATATCAATTAATTTTAGAAAAACC
          1 AAATATCAATTAATTTTAGAAAAACC

                  
        856 AAATAT
          1 AAATAT

        862 TCTATAATGG


Statistics
Matches: 78,  Mismatches: 24, Indels: 20
        0.64            0.20        0.16

Matches are distributed among these distances:
  25   12  0.15
  26   30  0.38
  27   24  0.31
  28   12  0.15

ACGTcount: A:0.51, C:0.12, G:0.04, T:0.33


Consensus pattern (26 bp):   
AAATATCAATTAATTTTAGAAAAACC

Found at i:782 original size:27 final size:27

Alignment explanation


    Indices: 697--835  Score: 92
    Period size: 27  Copynumber: 5.2  Consensus size: 27

        687 TAGAAAAAAC

                                       
        697 AAATATTCTATATGATTCATCACAAAT
          1 AAATATTCTATATGATTCATCACAAAT

                    *    *    *  * *    *
        724 AAATA-TCAAT-TAATT-TTAGAAAAACC
          1 AAATATTCTATATGATTCAT-CACAAA-T

                                       
        750 AAATATTCTATATGATTCATCACAAAT
          1 AAATATTCTATATGATTCATCACAAAT

                    *    *    *  * *    *
        777 AAATA-TCAAT-TAATT-TTAGAAAAACC
          1 AAATATTCTATATGATTCAT-CACAAA-T

                                       
        803 AAATATTCTATATGATTCATCACAAAT
          1 AAATATTCTATATGATTCATCACAAAT

                  
        830 AAATAT
          1 AAATAT

        836 CAATTAATTT


Statistics
Matches: 78,  Mismatches: 24, Indels: 20
        0.64            0.20        0.16

Matches are distributed among these distances:
  24    2  0.03
  25   16  0.21
  26   18  0.23
  27   24  0.31
  28   16  0.21
  29    2  0.03

ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35


Consensus pattern (27 bp):   
AAATATTCTATATGATTCATCACAAAT

Found at i:2813 original size:12 final size:13

Alignment explanation


    Indices: 2795--2827  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       2785 GTGGGTTTAG

                         
       2795 TAGTTTGTTTATT
          1 TAGTTTGTTTATT

                      *  
       2808 TA-TTTGTTTGTT
          1 TAGTTTGTTTATT

                    
       2820 TAGTTTGT
          1 TAGTTTGT

       2828 AATTAGTTTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  12   11  0.61
  13    7  0.39

ACGTcount: A:0.12, C:0.00, G:0.18, T:0.70


Consensus pattern (13 bp):   
TAGTTTGTTTATT
Done.