Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005096.1 Corchorus capsularis cultivar CVL-1 contig05114, 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: 6707
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40


Found at i:2303 original size:19 final size:19

Alignment explanation


    Indices: 2279--2317  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2269 AAGACACCAT

                               
       2279 TACACCAAATGTTGATCAA
          1 TACACCAAATGTTGATCAA

                               
       2298 TACACCAAATGTTGATCAA
          1 TACACCAAATGTTGATCAA

             
       2317 T
          1 T

       2318 CTTTCACATA


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

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28


Consensus pattern (19 bp):   
TACACCAAATGTTGATCAA

Found at i:5862 original size:178 final size:186

Alignment explanation


    Indices: 5555--5919  Score: 543
    Period size: 178  Copynumber: 2.0  Consensus size: 186

       5545 GATTATTCAA

                                 *                              *     *      
       5555 TTTGAAGTTAGTGAAGTCACGGGTAAACAAGTAAGTAGTTTAGCATTAGAATTTATGATCTTATA
          1 TTTGAAGTTAGTGAAGTCACGCGTAAACAAGTAAGTAGTTTAGCATTAGAATATATGAGCTTATA

                                                 *                           
       5620 CTTTCCACTAATTGAACTATAATTCATTGGATTTGAAGACAAGGATGACTAATTCTTGATATCCT
         66 CTTTCCACTAATTGAACTATAATTCATTGGATTTGAAAACAAGGATGACTAATTCTTGATATCCT

                                                                     
       5685 TGGCTGTTTTCACAGGCACTTAAAAAGATGTCAAACCACCT-TGCGTTGATGCAAGC
        131 TGGCTGTTTTCACAGGCACTTAAAAAGATGTCAAACCACCTAT-CGTTGATGCAAGC

                               *                                     *       
       5741 TTTGAAGTTAGTGAAGTCATGCG--AA-AA-T-AGTAGATTTAGCATTAGAATATATTAGC-T-T
          1 TTTGAAGTTAGTGAAGTCACGCGTAAACAAGTAAGTAG-TTTAGCATTAGAATATATGAGCTTAT

                                                                             
       5799 ACTTTCCACTAATTGAACTA-AA-TCATTGGATTTGAAAACAAGGATGACTAATTCTTGATATCC
         65 ACTTTCCACTAATTGAACTATAATTCATTGGATTTGAAAACAAGGATGACTAATTCTTGATATCC

                              *   **            *            *       
       5862 TTGGCTGTTTTCACAGGCTCTTGGAAAGATGTCAAAGCACCTATCGTTGGTGCAAGC
        130 TTGGCTGTTTTCACAGGCACTTAAAAAGATGTCAAACCACCTATCGTTGATGCAAGC

             
       5919 T
          1 T

       5920 ATACTTAAGA


Statistics
Matches: 166,  Mismatches: 11, Indels: 12
        0.88            0.06        0.06

Matches are distributed among these distances:
 178   91  0.55
 179    3  0.02
 180   21  0.13
 181    6  0.04
 182   20  0.12
 183    2  0.01
 184    2  0.01
 186   21  0.13

ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33


Consensus pattern (186 bp):   
TTTGAAGTTAGTGAAGTCACGCGTAAACAAGTAAGTAGTTTAGCATTAGAATATATGAGCTTATA
CTTTCCACTAATTGAACTATAATTCATTGGATTTGAAAACAAGGATGACTAATTCTTGATATCCT
TGGCTGTTTTCACAGGCACTTAAAAAGATGTCAAACCACCTATCGTTGATGCAAGC

Found at i:6667 original size:2 final size:2

Alignment explanation


    Indices: 6660--6705  Score: 92
    Period size: 2  Copynumber: 23.0  Consensus size: 2

       6650 ACATACCTAG

                                                                          
       6660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                 
       6702 TA TA
          1 TA TA

       6706 GT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   44  1.00

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


Consensus pattern (2 bp):   
TA

Done.