Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010548.1 Corchorus capsularis cultivar CVL-1 contig10569, 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: 59124
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:7912 original size:14 final size:15

Alignment explanation


    Indices: 7895--7928  Score: 52
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       7885 TTGGTTTTCT

                           
       7895 TTTTCTTTTC-TTTA
          1 TTTTCTTTTCATTTA

                          *
       7909 TTTTCTTTTCATTTC
          1 TTTTCTTTTCATTTA

                 
       7924 TTTTC
          1 TTTTC

       7929 ATTAAGTAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   10  0.56
  15    8  0.44

ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76


Consensus pattern (15 bp):   
TTTTCTTTTCATTTA

Found at i:7917 original size:19 final size:20

Alignment explanation


    Indices: 7889--7926  Score: 60
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       7879 TTTTTTTTGG

                       *        
       7889 TTTTCTTTTTCTTTTCTTTA
          1 TTTTCTTTTTCATTTCTTTA

                               
       7909 TTTTC-TTTTCATTTCTTT
          1 TTTTCTTTTTCATTTCTTT

       7927 TCATTAAGTA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   12  0.71
  20    5  0.29

ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79


Consensus pattern (20 bp):   
TTTTCTTTTTCATTTCTTTA

Found at i:20186 original size:2 final size:2

Alignment explanation


    Indices: 20179--20204  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      20169 GATTCTTAGA

                                                  
      20179 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

      20205 TTATTTATTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:27803 original size:3 final size:3

Alignment explanation


    Indices: 27795--27823  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      27785 TTAGAGTATA

                                                  
      27795 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

      27824 GACTTTTTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
ATT

Found at i:28610 original size:2 final size:2

Alignment explanation


    Indices: 28603--28631  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      28593 AATCAAAATT

                                                       
      28603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      28632 TTAGAGAACC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:58275 original size:71 final size:72

Alignment explanation


    Indices: 58154--58290  Score: 190
    Period size: 71  Copynumber: 1.9  Consensus size: 72

      58144 TAATCTCTCA

                                           *  *  *                           
      58154 AGAATTTCCATGCAAATATCATTCGGGAAATTACTCTGACAAAGCGCCATA-TTTTTTTCTTCTA
          1 AGAATTTCCATGCAAATATCATTCGGGAAATGACCCTAACAAAGCGCCATATTTTTTTTCTTCTA

                   
      58218 GGACTCG
         66 GGACTCG

                             *                             *                 
      58225 AGAATTTCCATGCAAATTTCATTC-GGAAACTGACCCTAAC-AAGCTTCCATATTTTTTTTCTTC
          1 AGAATTTCCATGCAAATATCATTCGGGAAA-TGACCCTAACAAAGC-GCCATATTTTTTTTCTTC

               
      58288 TAG
         64 TAG

      58291 CTTAGATGGA


Statistics
Matches: 58,  Mismatches: 5, Indels: 5
        0.85            0.07        0.07

Matches are distributed among these distances:
  70    9  0.16
  71   35  0.60
  72   14  0.24

ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36


Consensus pattern (72 bp):   
AGAATTTCCATGCAAATATCATTCGGGAAATGACCCTAACAAAGCGCCATATTTTTTTTCTTCTA
GGACTCG

Found at i:58972 original size:2 final size:2

Alignment explanation


    Indices: 58920--58953  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      58910 CTTGCATGTG

                                                              
      58920 AT 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 AT

      58954 GGCAGAAAGA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT
Done.