Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010622.1 Corchorus capsularis cultivar CVL-1 contig10643, 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: 33854
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33


Found at i:1348 original size:15 final size:16

Alignment explanation


    Indices: 1320--1349  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       1310 CCACAGAGAA

                            
       1320 TAATTAATTTCTATCG
          1 TAATTAATTTCTATCG

                           
       1336 TAATTAA-TTCTATC
          1 TAATTAATTTCTATC

       1350 AGGAAGGAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.33, C:0.13, G:0.03, T:0.50


Consensus pattern (16 bp):   
TAATTAATTTCTATCG

Found at i:7861 original size:49 final size:48

Alignment explanation


    Indices: 7762--7892  Score: 160
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       7752 AGCGTGCCAA

                       *               *      *          *  
       7762 TCAATTTTGTTCAAAAATTGA-AAAAAAATGCAATGAAAGATAAATAT
          1 TCAATTTTGTTTAAAAATTGAGAAAAAGATGCAAGGAAAGATAAAGAT

                                         *                  * 
       7809 TCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCAAGGAAA-ATTAAAGGT
          1 TCAATTTTGT-TTAAAAATTGAGAAAAAGATGCAAGGAAAGA-TAAAGAT

                                                
       7858 TCAATTTTGTTGTAAAAATTGAGAAAAAGA-GCAAG
          1 TCAATTTTGTT-TAAAAATTGAGAAAAAGATGCAAG

       7893 AAATGTAAAA


Statistics
Matches: 73,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  47   10  0.14
  48   17  0.23
  49   46  0.63

ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29


Consensus pattern (48 bp):   
TCAATTTTGTTTAAAAATTGAGAAAAAGATGCAAGGAAAGATAAAGAT

Found at i:14652 original size:16 final size:16

Alignment explanation


    Indices: 14631--14678  Score: 53
    Period size: 16  Copynumber: 3.0  Consensus size: 16

      14621 AAACCTGAAT

                            
      14631 CCGAACCTAAAAATAC
          1 CCGAACCTAAAAATAC

                     * *     
      14647 CCGAACCT-GACATAAC
          1 CCGAACCTAAAAAT-AC

                   *        
      14663 CCGAACCCAAAAATAC
          1 CCGAACCTAAAAATAC

      14679 TGAACCTACT


Statistics
Matches: 25,  Mismatches: 5, Indels: 4
        0.74            0.15        0.12

Matches are distributed among these distances:
  15    3  0.12
  16   19  0.76
  17    3  0.12

ACGTcount: A:0.46, C:0.35, G:0.08, T:0.10


Consensus pattern (16 bp):   
CCGAACCTAAAAATAC

Found at i:15021 original size:26 final size:26

Alignment explanation


    Indices: 14985--15054  Score: 140
    Period size: 26  Copynumber: 2.7  Consensus size: 26

      14975 GAAAGCTACT

                                      
      14985 TAATTATTTGCTATTTTTTTTTGAAA
          1 TAATTATTTGCTATTTTTTTTTGAAA

                                      
      15011 TAATTATTTGCTATTTTTTTTTGAAA
          1 TAATTATTTGCTATTTTTTTTTGAAA

                              
      15037 TAATTATTTGCTATTTTT
          1 TAATTATTTGCTATTTTT

      15055 ATGCTACTTA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   44  1.00

ACGTcount: A:0.26, C:0.04, G:0.07, T:0.63


Consensus pattern (26 bp):   
TAATTATTTGCTATTTTTTTTTGAAA

Found at i:23578 original size:21 final size:21

Alignment explanation


    Indices: 23554--23620  Score: 62
    Period size: 21  Copynumber: 3.2  Consensus size: 21

      23544 ATGTTTAGAG

                           *     
      23554 CAAGAATATTCCAATTGATTC
          1 CAAGAATATTCCAATCGATTC

                ** *  *          
      23575 CAAGCTTCTTACAATCGATTC
          1 CAAGAATATTCCAATCGATTC

            * *           *      
      23596 TAGGAATATTCCAACCGATTC
          1 CAAGAATATTCCAATCGATTC

                
      23617 CAAG
          1 CAAG

      23621 TTATGCACAT


Statistics
Matches: 32,  Mismatches: 14, Indels: 0
        0.70            0.30        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30


Consensus pattern (21 bp):   
CAAGAATATTCCAATCGATTC

Found at i:33820 original size:2 final size:2

Alignment explanation


    Indices: 33815--33854  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      33805 TTAGTGTGTG

                                                                       
      33815 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Done.