Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001079.1 Corchorus capsularis cultivar CVL-1 contig01079, 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: 12723
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:2943 original size:13 final size:13

Alignment explanation


    Indices: 2925--2949  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2915 TCTATATGTA

                         
       2925 TATCTTATCTTAC
          1 TATCTTATCTTAC

                        
       2938 TATCTTATCTTA
          1 TATCTTATCTTA

       2950 TTACTATATA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56


Consensus pattern (13 bp):   
TATCTTATCTTAC

Found at i:4095 original size:87 final size:87

Alignment explanation


    Indices: 4004--4171  Score: 225
    Period size: 86  Copynumber: 1.9  Consensus size: 87

       3994 CATGCTTGGA

                            *             *    *                             
       4004 TTTTCTTAAAAATTGGGAGATTTGAAGATTTG-A-GTAATTGTTATATGAATTCATGACATGAGT
          1 TTTTCTTAAAAATT-GAAGATTTG-A-ATTAGTACATAATTGTTATATGAATTCATGACATGAGT

              *                      
       4067 AAGACAT-TTTTTTTAACCGATAAT
         63 AAAACATCTTTTTTTAACCGATAAT

                      *             *         *                              
       4091 TTTTCTTAAAGATTGAAGATTTGACTTAGTACATCATTGTTATATGAATTCATGACATGAGTAAA
          1 TTTTCTTAAAAATTGAAGATTTGAATTAGTACATAATTGTTATATGAATTCATGACATGAGTAAA

                            
       4156 ACATCTTTTTTTAACC
         66 ACATCTTTTTTTAACC

       4172 CTGCAAACCA


Statistics
Matches: 71,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  84    3  0.04
  85    2  0.03
  86   42  0.59
  87   24  0.34

ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42


Consensus pattern (87 bp):   
TTTTCTTAAAAATTGAAGATTTGAATTAGTACATAATTGTTATATGAATTCATGACATGAGTAAA
ACATCTTTTTTTAACCGATAAT

Found at i:5559 original size:21 final size:19

Alignment explanation


    Indices: 5535--5574  Score: 53
    Period size: 21  Copynumber: 2.0  Consensus size: 19

       5525 GTCTTCAATT

                                 
       5535 CAGGGAGACGACTTCCTCAAG
          1 CAGGGAGACGA--TCCTCAAG

                   *           
       5556 CAGGGAGTCGATCCTCAAG
          1 CAGGGAGACGATCCTCAAG

       5575 AAATTGCCAG


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

Matches are distributed among these distances:
  19    8  0.44
  21   10  0.56

ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15


Consensus pattern (19 bp):   
CAGGGAGACGATCCTCAAG

Found at i:7809 original size:3 final size:3

Alignment explanation


    Indices: 7796--7826  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       7786 GCTTTTCATC

                 *                                   
       7796 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA A
          1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A

       7827 ACCTTCAATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (3 bp):   
AGA

Found at i:9329 original size:282 final size:281

Alignment explanation


    Indices: 8826--9385  Score: 987
    Period size: 282  Copynumber: 2.0  Consensus size: 281

       8816 GAAATCATGT

                                                                             
       8826 GTTCCCTTCCTTTAATTTGTTTTTCTATCATGGTATCAGATAATAACCGTTTCTCTCAATTTTCT
          1 GTTCCCTTCCTTTAATTTGTTTTTCTATCATGGTATCAGATAATAACCGTTTCTCTCAATTTTCT

                                           *                                 
       8891 GTAGTTTTCCGCATTTTCTTTCTGTTTCCTATCTTTTCTCACTAGCCAAACAGAGTTCTTGGTCA
         66 GTAGTTTTCCGCATTTTCTTTCTGTTTCCTAGCTTTTCTCACTAGCCAAACAGAGTTCTTGGTCA

             *                                                         *     
       8956 GTTTTTTTGATCAAATCTCGACTGTATTTCCAGTCTTTCTTCGTCGACTGTATTTGCAGTTTCAA
        131 GATTTTTTGATCAAATCTCGACTGTATTTCCAGTCTTTCTTCGTCGACTGTATTTGCAGCTTCAA

                  *                                              *           
       9021 GCTTTCTCAGACAGTGATAGGGGAACATGTACTGATACTAGGAGATCAGTTACGGGATTTTGTGT
        196 GCTTTCGCAGACAGTGATAGGGGAACATGTACTGATACTAGGAGATCAGTTACAGGATTTTGTGT

                                 
       9086 CTTGCTAGGAGGAGCTTTTGC
        261 CTTGCTAGGAGGAGCTTTTGC

                    *                                *                       
       9107 GTTCCCTTTCTTTAATTTGTTTTTCTATCATGGTATCAGATGATAACCGTTTTTCTCTCAATTTT
          1 GTTCCCTTCCTTTAATTTGTTTTTCTATCATGGTATCAGATAATAACCG--TTTCTCTCAATTTT

              *                *                      *                      
       9172 CTTTAGTTTTCCGCATTTTGTTTCTGTTTCCTAGCTTTTCTCGCTAGCCAAACAGAGTTCTTGGT
         64 CTGTAGTTTTCCGCATTTTCTTTCTGTTTCCTAGCTTTTCTCACTAGCCAAACAGAGTTCTTGGT

                                   *                   *                     
       9237 CA-ATTTTTTGATCAAATCTCGATTGTATTTCCAGTCTTTCTTTGTCGACTGTATTTGCAGCTTC
        129 CAGATTTTTTGATCAAATCTCGACTGTATTTCCAGTCTTTCTTCGTCGACTGTATTTGCAGCTTC

                                                                             
       9301 AAGCTTTCGCAGACAGTGATAGGGGAACATGTACTGATACTAGGAGATCAGTTACAGGATTTTGT
        194 AAGCTTTCGCAGACAGTGATAGGGGAACATGTACTGATACTAGGAGATCAGTTACAGGATTTTGT

                                
       9366 GTCTTGCTAGGAGGAGCTTT
        259 GTCTTGCTAGGAGGAGCTTT

       9386 GGTTTCGTGG


Statistics
Matches: 265,  Mismatches: 12, Indels: 3
        0.95            0.04        0.01

Matches are distributed among these distances:
 281   47  0.18
 282  141  0.53
 283   77  0.29

ACGTcount: A:0.20, C:0.19, G:0.18, T:0.42


Consensus pattern (281 bp):   
GTTCCCTTCCTTTAATTTGTTTTTCTATCATGGTATCAGATAATAACCGTTTCTCTCAATTTTCT
GTAGTTTTCCGCATTTTCTTTCTGTTTCCTAGCTTTTCTCACTAGCCAAACAGAGTTCTTGGTCA
GATTTTTTGATCAAATCTCGACTGTATTTCCAGTCTTTCTTCGTCGACTGTATTTGCAGCTTCAA
GCTTTCGCAGACAGTGATAGGGGAACATGTACTGATACTAGGAGATCAGTTACAGGATTTTGTGT
CTTGCTAGGAGGAGCTTTTGC
Done.