Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007872.1 Corchorus capsularis cultivar CVL-1 contig07893, 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: 10149
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:1370 original size:33 final size:33

Alignment explanation


    Indices: 1333--1409  Score: 100
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       1323 TGTCCATGTT

                              *         *    
       1333 GCGTGGCCGGTGATGGCCGGGCATCTCCGAGTC
          1 GCGTGGCCGGTGATGGCCAGGCATCTCCAAGTC

                        *         *          
       1366 GCGTGGCCGGTGTTGGCCAGGCTTCTCCAAGTC
          1 GCGTGGCCGGTGATGGCCAGGCATCTCCAAGTC

            * *        
       1399 ACATGGCCGGT
          1 GCGTGGCCGGT

       1410 CATTCGCGCC


Statistics
Matches: 38,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  33   38  1.00

ACGTcount: A:0.10, C:0.30, G:0.39, T:0.21


Consensus pattern (33 bp):   
GCGTGGCCGGTGATGGCCAGGCATCTCCAAGTC

Found at i:6770 original size:5 final size:5

Alignment explanation


    Indices: 6760--6784  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       6750 CTGGTCGAAA

                                         
       6760 TTTAT TTTAT TTTAT TTTAT TTTAT
          1 TTTAT TTTAT TTTAT TTTAT TTTAT

       6785 ATTTTTCGAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (5 bp):   
TTTAT

Found at i:7913 original size:33 final size:33

Alignment explanation


    Indices: 7871--7955  Score: 116
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       7861 GCCAGACATG

                *                            
       7871 TCCATGTCGCGTGGCCGGTGATGGCCGGGCATC
          1 TCCAAGTCGCGTGGCCGGTGATGGCCGGGCATC

               *                *    *    *  
       7904 TCCGAGTCGCGTGGCCGGTGTTGGCTGGGCTTC
          1 TCCAAGTCGCGTGGCCGGTGATGGCCGGGCATC

                      *        
       7937 TCCAAGTCGCATGGCCGGT
          1 TCCAAGTCGCGTGGCCGGT

       7956 CACTCGCGCC


Statistics
Matches: 45,  Mismatches: 7, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  33   45  1.00

ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24


Consensus pattern (33 bp):   
TCCAAGTCGCGTGGCCGGTGATGGCCGGGCATC

Found at i:10034 original size:88 final size:85

Alignment explanation


    Indices: 9905--10149  Score: 266
    Period size: 76  Copynumber: 3.0  Consensus size: 85

       9895 ATTATCATTA

                                         *                                   
       9905 TTAAATATATCTCCTAAATCTCCCACAATCTGGCAAGATTTAAAAGAAATATTCTCATTACTATT
          1 TTAAA-ATATCTCCTAAATCTCCCACAATTTGGCAAGATTT--AAGAAATATTCTCATTACTATT

                                    
       9970 CAATTTTTATTATTTATTTGTTTC
         63 C-ATTTTTATTATTTATTTGTTTC

                                *          *                    *            
       9994 TTAAAATATCTCCTAAATCTTCCACAATTTGACAAGATTT-AGAAAATATTCCCA--ACT-TT-A
          1 TTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAAG-AAATATTCTCATTACTATTCA

                            *    
      10054 ---TTATTA--T-TTTATTTC
         65 TTTTTATTATTTATTTGTTTC

                                                                      *      
      10069 TTAAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTT-AGAAATATTCTCATTATTAATTC
          1 TT-AAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAAGAAATATTCTCATTACT-ATTC

                               
      10133 TATTTTTA--ATTTATTTG
         64 -ATTTTTATTATTTATTTG


Statistics
Matches: 132,  Mismatches: 10, Indels: 32
        0.76            0.06        0.18

Matches are distributed among these distances:
  75   19  0.14
  76   39  0.30
  77    2  0.02
  78    6  0.05
  79    2  0.02
  81    2  0.02
  82    1  0.01
  83    2  0.02
  84    7  0.05
  85    5  0.04
  86   10  0.08
  88   32  0.24
  89    5  0.04

ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44


Consensus pattern (85 bp):   
TTAAAATATCTCCTAAATCTCCCACAATTTGGCAAGATTTAAGAAATATTCTCATTACTATTCAT
TTTTATTATTTATTTGTTTC

Done.