Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009046.1 Corchorus capsularis cultivar CVL-1 contig09067, 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: 10352
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:1194 original size:15 final size:15

Alignment explanation


    Indices: 1156--1199  Score: 56
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1146 TGGTACGGAG

                           
       1156 GAAATGGGAAGGAAA
          1 GAAATGGGAAGGAAA

                             
       1171 GAAGA-GGGACA-GAAA
          1 GAA-ATGGGA-AGGAAA

                          
       1186 GAAATGGGAAGGAA
          1 GAAATGGGAAGGAA

       1200 GGAAGACTTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
  14    2  0.08
  15   21  0.84
  16    2  0.08

ACGTcount: A:0.52, C:0.02, G:0.41, T:0.05


Consensus pattern (15 bp):   
GAAATGGGAAGGAAA

Found at i:2277 original size:15 final size:15

Alignment explanation


    Indices: 2257--2302  Score: 58
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       2247 TGTAAGTTAC

                           
       2257 TTTCCTTCCTCTCTA
          1 TTTCCTTCCTCTCTA

                             
       2272 TTTCCTTTCCT-TCCTA
          1 TTTCC-TTCCTCT-CTA

                *          
       2288 TTTCTTTCCTCTCTA
          1 TTTCCTTCCTCTCTA

       2303 CCAAACACAC


Statistics
Matches: 27,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  15   14  0.52
  16   13  0.48

ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57


Consensus pattern (15 bp):   
TTTCCTTCCTCTCTA

Found at i:5442 original size:12 final size:12

Alignment explanation


    Indices: 5425--5456  Score: 64
    Period size: 12  Copynumber: 2.7  Consensus size: 12

       5415 ACCTGGCAAT

                        
       5425 TCGTGTTTCGTG
          1 TCGTGTTTCGTG

                        
       5437 TCGTGTTTCGTG
          1 TCGTGTTTCGTG

                    
       5449 TCGTGTTT
          1 TCGTGTTT

       5457 ACATAGGGTA


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

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.00, C:0.16, G:0.31, T:0.53


Consensus pattern (12 bp):   
TCGTGTTTCGTG

Found at i:5685 original size:14 final size:14

Alignment explanation


    Indices: 5666--5695  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       5656 TTAACTAAAC

                          
       5666 TATATATATATAAT
          1 TATATATATATAAT

                          
       5680 TATATATATATAAT
          1 TATATATATATAAT

              
       5694 TA
          1 TA

       5696 AAGATAATTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

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


Consensus pattern (14 bp):   
TATATATATATAAT

Found at i:5935 original size:42 final size:43

Alignment explanation


    Indices: 5865--5947  Score: 134
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       5855 CTTAAACGTG

                                                       
       5865 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC
          1 TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC

                                            *         
       5908 TTAATCGTGTC-TGACACGATT-CAGACACGAGACACGATAA
          1 TTAATCGTGTCTTGACACGATTAC-GACACGAAACACGATAA

       5948 GTCAAACACG


Statistics
Matches: 38,  Mismatches: 1, Indels: 3
        0.90            0.02        0.07

Matches are distributed among these distances:
  41    1  0.03
  42   26  0.68
  43   11  0.29

ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24


Consensus pattern (43 bp):   
TTAATCGTGTCTTGACACGATTACGACACGAAACACGATAATC

Found at i:9481 original size:22 final size:22

Alignment explanation


    Indices: 9450--9491  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       9440 TCTTTCTACT

                 *                
       9450 TTTTTGCTTCAATTTAGTCATA
          1 TTTTTACTTCAATTTAGTCATA

                      *         
       9472 TTTTTACTTCTATTTAGTCA
          1 TTTTTACTTCAATTTAGTCA

       9492 ATTGAGAGAG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57


Consensus pattern (22 bp):   
TTTTTACTTCAATTTAGTCATA
Done.