Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007694.1 Corchorus capsularis cultivar CVL-1 contig07715, 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: 12114
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29


Found at i:823 original size:3 final size:3

Alignment explanation


    Indices: 815--853  Score: 51
    Period size: 3  Copynumber: 12.0  Consensus size: 3

        805 TGCAACAATA

                                                              
        815 ATT ATT ATTT ATTT ATTT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT A-TT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT

        854 TTGGGCCTTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   3   24  0.69
   4   11  0.31

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
ATT

Found at i:3063 original size:10 final size:10

Alignment explanation


    Indices: 3050--3075  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

       3040 AAATCTCGAT

                      
       3050 ATATCCGTAA
          1 ATATCCGTAA

                      
       3060 ATATCCGTAA
          1 ATATCCGTAA

                  
       3070 ATATCC
          1 ATATCC

       3076 ATATTAAATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31


Consensus pattern (10 bp):   
ATATCCGTAA

Found at i:5293 original size:20 final size:20

Alignment explanation


    Indices: 5277--5317  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5267 AAATCAAAGT

                             *  
       5277 AAAACCAAGATAATCAATCC
          1 AAAACCAAGATAATCAAACC

                       *  *     
       5297 AAAACCAAGATTATAAAACC
          1 AAAACCAAGATAATCAAACC

             
       5317 A
          1 A

       5318 GATCAGTCAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.59, C:0.22, G:0.05, T:0.15


Consensus pattern (20 bp):   
AAAACCAAGATAATCAAACC

Found at i:6211 original size:23 final size:23

Alignment explanation


    Indices: 6184--6232  Score: 66
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       6174 TATTTCCCCT

                                     
       6184 TTTCTTTTTCCTTT-T-TTCTTTCC
          1 TTTC-TTTTCCTTTCTCTT-TTTCC

                                   
       6207 TTTCTTTTCCTTTCTCTTTTTCC
          1 TTTCTTTTCCTTTCTCTTTTTCC

               
       6230 TTT
          1 TTT

       6233 TACCCTTTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  22    9  0.38
  23   13  0.54
  24    2  0.08

ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73


Consensus pattern (23 bp):   
TTTCTTTTCCTTTCTCTTTTTCC

Found at i:6366 original size:14 final size:14

Alignment explanation


    Indices: 6347--6373  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       6337 CCTATGGCCC

                          
       6347 TTTTCCTTCTTTTT
          1 TTTTCCTTCTTTTT

                         
       6361 TTTTCCTTCTTTT
          1 TTTTCCTTCTTTT

       6374 CTTCTTTTCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78


Consensus pattern (14 bp):   
TTTTCCTTCTTTTT

Found at i:6625 original size:14 final size:14

Alignment explanation


    Indices: 6603--6638  Score: 54
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       6593 TAAACACTTA

                *       * 
       6603 CCAAGCTCCAAAGT
          1 CCAATCTCCAAACT

                          
       6617 CCAATCTCCAAACT
          1 CCAATCTCCAAACT

                    
       6631 CCAATCTC
          1 CCAATCTC

       6639 TTATCCAATT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.33, C:0.42, G:0.06, T:0.19


Consensus pattern (14 bp):   
CCAATCTCCAAACT

Found at i:11461 original size:20 final size:20

Alignment explanation


    Indices: 11445--11485  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      11435 AAATCAAAGT

                             *  
      11445 AAAACCAAGATAATCAATCC
          1 AAAACCAAGATAATCAAACC

                       *  *     
      11465 AAAACCAAGATTATAAAACC
          1 AAAACCAAGATAATCAAACC

             
      11485 A
          1 A

      11486 GATCAGTCAA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.59, C:0.22, G:0.05, T:0.15


Consensus pattern (20 bp):   
AAAACCAAGATAATCAAACC
Done.