Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014240.1 Corchorus capsularis cultivar CVL-1 contig14261, 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: 12761
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:3147 original size:3 final size:3

Alignment explanation


    Indices: 3139--3174  Score: 63
    Period size: 3  Copynumber: 12.0  Consensus size: 3

       3129 TAAAAGAAGG

                                                 *         
       3139 GAA GAA GAA GAA GAA GAA GAA GAA GAA GTA GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA

       3175 ACCATTACCT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03


Consensus pattern (3 bp):   
GAA

Found at i:5306 original size:14 final size:15

Alignment explanation


    Indices: 5279--5308  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       5269 TGTTATTGAC

                           
       5279 TGTAAAAGTTAATTA
          1 TGTAAAAGTTAATTA

                           
       5294 TGTAAAA-TTAATTA
          1 TGTAAAAGTTAATTA

             
       5308 T
          1 T

       5309 TAATTAATTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    8  0.53
  15    7  0.47

ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43


Consensus pattern (15 bp):   
TGTAAAAGTTAATTA

Found at i:7763 original size:108 final size:108

Alignment explanation


    Indices: 7546--7748  Score: 354
    Period size: 108  Copynumber: 1.9  Consensus size: 108

       7536 TATTCACGAA

                 *                                                           
       7546 ATCATAATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGCTATGGCTTGAT
          1 ATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGCTATGGCTTGAT

                                                       
       7611 CACCATTATCGACACAGACTTGCAATTGTTTCAAGCCGACGTG
         66 CACCATTATCGACACAGACTTGCAATTGTTTCAAGCCGACGTG

                                  *         *                    *           
       7654 ATCATCATCATCATCAGGGACATGGGCATCAATAAGCCCAGATTGTTCTTCGGGTATGGCTTGAT
          1 ATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGCTATGGCTTGAT

                                           
       7719 CACCATTA-CTGACACAGACTTGCAATTGTT
         66 CACCATTATC-GACACAGACTTGCAATTGTT

       7749 CTAAGTCGTC


Statistics
Matches: 90,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
 107    1  0.01
 108   89  0.99

ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28


Consensus pattern (108 bp):   
ATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGCTATGGCTTGAT
CACCATTATCGACACAGACTTGCAATTGTTTCAAGCCGACGTG

Found at i:8942 original size:107 final size:108

Alignment explanation


    Indices: 8755--8976  Score: 365
    Period size: 107  Copynumber: 2.1  Consensus size: 108

       8745 TATTCACGAA

                            *                                    *           
       8755 ATCATCATCATCATCAGGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGCTATGGCTTGAT
          1 ATCATCATCATCATCAAGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGATATGGCTTGAT

                *           *                   *      
       8820 CACCGTTACCGACACAGACTTGCAATTGTTTCAAGCTGTCGTG
         66 CACCATTACCGACACACACTTGCAATTGTTTCAAGCCGTCGTG

                                                                             
       8863 ATCATCATCATCATCAAGGACA-GGGCATCAACAAGCCCAGATTGTTCTTCGGATATGGCTTGAT
          1 ATCATCATCATCATCAAGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGATATGGCTTGAT

                    *                      *           
       8927 CACCATTATCGACACACACTTGCAATTGTTTTAAGCCGTCGTG
         66 CACCATTACCGACACACACTTGCAATTGTTTCAAGCCGTCGTG

              *    
       8970 ATGATCA
          1 ATCATCA

       8977 CGATCACCAA


Statistics
Matches: 106,  Mismatches: 8, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
 107   85  0.80
 108   21  0.20

ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27


Consensus pattern (108 bp):   
ATCATCATCATCATCAAGGACAGGGGCATCAACAAGCCCAGATTGTTCTTCGGATATGGCTTGAT
CACCATTACCGACACACACTTGCAATTGTTTCAAGCCGTCGTG

Found at i:10193 original size:114 final size:114

Alignment explanation


    Indices: 9994--10225  Score: 365
    Period size: 114  Copynumber: 2.0  Consensus size: 114

       9984 TATTCACGAA

                  *          *          *          *                *        
       9994 ATCATCTTCATCATCATTAGGGACAGGGGCATCAACAAGTCCAGATTGTGCTTCGGCTATGGCTT
          1 ATCATCATCATCATCATCAGGGACAGGGACATCAACAAGCCCAGATTGTGCTTCGGATATGGCTT

                       *                                     
      10059 GATCACCATTATCGACACAGACTTGCAATTGTTTCAAGCCGTCGTGATC
         66 GATCACCATTACCGACACAGACTTGCAATTGTTTCAAGCCGTCGTGATC

                                                             *               
      10108 ATCATCATCATCATCATCAGGGACAGGGACATCAACAAGCCCAGATTGTTCTTCGGATATGGCTT
          1 ATCATCATCATCATCATCAGGGACAGGGACATCAACAAGCCCAGATTGTGCTTCGGATATGGCTT

                           *                  *   *         *
      10173 GATCACCATTACCGATACAGACTTGCAATTGTTTTAAGTCGTCGTGATG
         66 GATCACCATTACCGACACAGACTTGCAATTGTTTCAAGCCGTCGTGATC

                
      10222 ATCA
          1 ATCA

      10226 CGATCACCAA


Statistics
Matches: 107,  Mismatches: 11, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
 114  107  1.00

ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29


Consensus pattern (114 bp):   
ATCATCATCATCATCATCAGGGACAGGGACATCAACAAGCCCAGATTGTGCTTCGGATATGGCTT
GATCACCATTACCGACACAGACTTGCAATTGTTTCAAGCCGTCGTGATC

Found at i:12661 original size:6 final size:6

Alignment explanation


    Indices: 12645--12678  Score: 52
    Period size: 6  Copynumber: 5.8  Consensus size: 6

      12635 TAGAAAGATA

                                         *          
      12645 ATATA- ATATAG ATATAG ATATAG ACATAG ATATA
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

      12679 TGATCCAGAG


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   5    5  0.19
   6   21  0.81

ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32


Consensus pattern (6 bp):   
ATATAG

Done.