Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015628.1 Corchorus olitorius cultivar O-4 contig15661, 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: 18567
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30


Found at i:1097 original size:22 final size:22

Alignment explanation


    Indices: 1072--1148  Score: 73
    Period size: 22  Copynumber: 3.4  Consensus size: 22

       1062 TTGCCTTCTT

                   *       *      
       1072 GTCGACACTTGCTTCTTCTTAA
          1 GTCGACAATTGCTTCCTCTTAA

                 *                
       1094 GTCGATAATTGCTTCCTCTTAA
          1 GTCGACAATTGCTTCCTCTTAA

                    *  **           
       1116 GTCGACTATTTTTTTCCTCTTTAA
          1 GTCGAC-AATTGCTTCCTC-TTAA

                *    
       1140 GTCGCCAAT
          1 GTCGACAAT

       1149 CCCTTTGTCG


Statistics
Matches: 44,  Mismatches: 9, Indels: 3
        0.79            0.16        0.05

Matches are distributed among these distances:
  22   24  0.55
  23   11  0.25
  24    9  0.20

ACGTcount: A:0.19, C:0.25, G:0.13, T:0.43


Consensus pattern (22 bp):   
GTCGACAATTGCTTCCTCTTAA

Found at i:1136 original size:23 final size:22

Alignment explanation


    Indices: 1080--1143  Score: 74
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       1070 TTGTCGACAC

                   *              
       1080 TTGCTTCTTCTTAAGTCGATAA
          1 TTGCTTCCTCTTAAGTCGATAA

                                  *
       1102 TTGCTTCCTCTTAAGTCGACTAT
          1 TTGCTTCCTCTTAAGTCGA-TAA

              **               
       1125 TTTTTTCCTCTTTAAGTCG
          1 TTGCTTCCTC-TTAAGTCG

       1144 CCAATCCCTT


Statistics
Matches: 36,  Mismatches: 4, Indels: 2
        0.86            0.10        0.05

Matches are distributed among these distances:
  22   18  0.50
  23   10  0.28
  24    8  0.22

ACGTcount: A:0.17, C:0.22, G:0.12, T:0.48


Consensus pattern (22 bp):   
TTGCTTCCTCTTAAGTCGATAA

Found at i:9058 original size:6 final size:6

Alignment explanation


    Indices: 9042--9073  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       9032 ATCAAATAGG

                                                  
       9042 AAAAG- AAAAGA AAAAGA AAAAGA AAAAGA AAA
          1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA

       9074 TAATAAACAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5    5  0.19
   6   21  0.81

ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00


Consensus pattern (6 bp):   
AAAAGA

Found at i:18226 original size:69 final size:69

Alignment explanation


    Indices: 18063--18290  Score: 343
    Period size: 67  Copynumber: 3.3  Consensus size: 69

      18053 ATTTCCCGCA

                *   *                                               *        
      18063 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGCTCCTC-A
          1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCACTCCTCAA

                
      18127 -AGC
         66 CAGC

                                          *                             *    
      18130 ACAAGTCCGGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTAATTTGCACTCTTCAA
          1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCACTCCTCAA

                
      18195 CAGC
         66 CAGC

                                                *              *      *      
      18199 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCATGTCTTGTCCTGTATTTTTGCATTCCTCA
          1 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCACTCCTCA

                 
      18264 ACAGC
         65 ACAGC

            *       *             
      18269 CCAAGTCCTGGACAGGACTTGG
          1 ACAAGTCCGGGACAGGACTTGG

      18291 CCAAGATCTG


Statistics
Matches: 146,  Mismatches: 12, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  67   58  0.40
  68    1  0.01
  69   51  0.35
  70   36  0.25

ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26


Consensus pattern (69 bp):   
ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCACTCCTCAA
CAGC
Done.