Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009619.1 Corchorus capsularis cultivar CVL-1 contig09640, 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: 37838
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:6757 original size:2 final size:2

Alignment explanation


    Indices: 6750--6781  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       6740 ATTGATGTTG

                                                           
       6750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       6782 CCAAGCTCTT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:29216 original size:23 final size:23

Alignment explanation


    Indices: 29184--29230  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      29174 GAAAAAAAAA

                                    
      29184 AAAAAAAAAAAGCGATATA-ATTG
          1 AAAAAAAAAAA-CGATATATATTG

                 *         *       
      29207 AAAAAGAAAAACGATTTATATTG
          1 AAAAAAAAAAACGATATATATTG

             
      29230 A
          1 A

      29231 GCTGATGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  22    6  0.29
  23   15  0.71

ACGTcount: A:0.62, C:0.04, G:0.13, T:0.21


Consensus pattern (23 bp):   
AAAAAAAAAAACGATATATATTG

Found at i:32286 original size:29 final size:29

Alignment explanation


    Indices: 32243--32314  Score: 83
    Period size: 28  Copynumber: 2.5  Consensus size: 29

      32233 GTAGTAACTG

                  *           **          
      32243 AAAGTCTGAAACTCTTCTGGCCAAAAAAAA
          1 AAAGTCCGAAACTCTT-TCACCAAAAAAAA

                                        *
      32273 AAAGTCCG-AACTCTTTCACCAAAAAAAG
          1 AAAGTCCGAAACTCTTTCACCAAAAAAAA

                  *       
      32301 AAAGTCTGAAACTC
          1 AAAGTCCGAAACTC

      32315 AATATTTAAA


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  28   17  0.47
  29   12  0.33
  30    7  0.19

ACGTcount: A:0.46, C:0.22, G:0.12, T:0.19


Consensus pattern (29 bp):   
AAAGTCCGAAACTCTTTCACCAAAAAAAA

Found at i:36491 original size:3 final size:3

Alignment explanation


    Indices: 36483--36521  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

      36473 ATGTTTGCAC

                                                               
      36483 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

      36522 TTGCTACTCA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Done.