Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009556.1 Corchorus capsularis cultivar CVL-1 contig09577, 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: 3434
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37


Found at i:1819 original size:2 final size:2

Alignment explanation


    Indices: 1812--1838  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1802 CTTTAACTAG

                                                    
       1812 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 T

       1839 TTGCCAGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3167 original size:3 final size:3

Alignment explanation


    Indices: 3159--3261  Score: 54
    Period size: 3  Copynumber: 32.3  Consensus size: 3

       3149 CATGGCTCGT

                                             *                             
       3159 TTC TTC TTC TTC TTC TT- TATC -TC CTC TTCC TTC -TC TTC TCTC TTTC
          1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC TT-C TTC TTC TTC T-TC -TTC

             *                                                            
       3205 TCC TCTC TTCC ATT- TTC TTTC TCTC ATTC -TC TTC TTTC TTC TTC TTC
          1 TTC T-TC TT-C -TTC TTC -TTC T-TC -TTC TTC TTC -TTC TTC TTC TTC

                         
       3252 TTC TTC TTC T
          1 TTC TTC TTC T

       3262 CTTTTTCTAA


Statistics
Matches: 81,  Mismatches: 3, Indels: 32
        0.70            0.03        0.28

Matches are distributed among these distances:
   2    9  0.11
   3   48  0.59
   4   20  0.25
   5    4  0.05

ACGTcount: A:0.03, C:0.36, G:0.00, T:0.61


Consensus pattern (3 bp):   
TTC

Found at i:3261 original size:27 final size:27

Alignment explanation


    Indices: 3158--3269  Score: 85
    Period size: 27  Copynumber: 4.2  Consensus size: 27

       3148 CCATGGCTCG

                                     *  
       3158 TTTCTTCTTCTTCTTCTT-TATCTCCTC
          1 TTTCTTCTTCTTCTTCTTCT-TCTCTTC

              *                      * 
       3185 TTCCTTC-TCTTC-TC-TCTT-TCTCC
          1 TTTCTTCTTCTTCTTCTTCTTCTCTTC

             *                              
       3208 TCTCTTCCATT-TTCTTTCTCTCATTCTCTTC
          1 TTTCTT-C-TTCTTC-TTCT-TC-TTCTCTTC

                                       
       3239 TTTCTTCTTCTTCTTCTTCTTCTCTT-
          1 TTTCTTCTTCTTCTTCTTCTTCTCTTC

                 
       3265 TTTCT
          1 TTTCT

       3270 AATTCTCTTC


Statistics
Matches: 67,  Mismatches: 7, Indels: 23
        0.69            0.07        0.24

Matches are distributed among these distances:
  23    7  0.10
  24    3  0.04
  25    6  0.09
  26   11  0.16
  27   15  0.22
  28    2  0.03
  29    8  0.12
  30    6  0.09
  31    9  0.13

ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62


Consensus pattern (27 bp):   
TTTCTTCTTCTTCTTCTTCTTCTCTTC
Done.