Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017287.1 Corchorus olitorius cultivar O-4 contig17320, 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: 11139
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:1197 original size:21 final size:21

Alignment explanation


    Indices: 1171--1212  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1161 GCACAAAGAA

                                 
       1171 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

                                 
       1192 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCGGAGTTG

       1213 CCTAGGATGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCGGAGTTG

Found at i:4122 original size:14 final size:15

Alignment explanation


    Indices: 4096--4125  Score: 53
    Period size: 14  Copynumber: 2.1  Consensus size: 15

       4086 CTAAGTCCAA

                           
       4096 TCCTTGCTTATTTAT
          1 TCCTTGCTTATTTAT

                           
       4111 TCCTTG-TTATTTAT
          1 TCCTTGCTTATTTAT

             
       4125 T
          1 T

       4126 TTTCCTAATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    9  0.60
  15    6  0.40

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (15 bp):   
TCCTTGCTTATTTAT

Found at i:4976 original size:19 final size:18

Alignment explanation


    Indices: 4938--4976  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4928 GGTTCTTGTT

                         *    
       4938 TTTGTGCAATTGATCTAA
          1 TTTGTGCAATTGACCTAA

                         *     
       4956 TTTGTGCAATTAGCCCTAA
          1 TTTGTGCAATT-GACCTAA

              
       4975 TT
          1 TT

       4977 GGAGATATTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   11  0.61
  19    7  0.39

ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44


Consensus pattern (18 bp):   
TTTGTGCAATTGACCTAA

Found at i:11000 original size:43 final size:43

Alignment explanation


    Indices: 10948--11139  Score: 282
    Period size: 43  Copynumber: 4.5  Consensus size: 43

      10938 TAAGGAAAAA

                *     *                                
      10948 TGCCTCTGTGCTATATATGTGTTTGAGGACTTTGTAATAGAAT
          1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAT

                                     *                  
      10991 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTG-ATATAG-A-
          1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAAT

                *                              *       *
      11032 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAA
          1 TGCCCCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAAT

                                     *                 
      11076 TGCCCCTGTGTTATATATGTGTTTGGGGACTTTGTAATAGAAT
          1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAT

                                 
      11119 TGCCCCTGTGTTATATATGTG
          1 TGCCCCTGTGTTATATATGTG


Statistics
Matches: 135,  Mismatches: 9, Indels: 10
        0.88            0.06        0.06

Matches are distributed among these distances:
  41   28  0.21
  42   10  0.07
  43   69  0.51
  44   28  0.21

ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42


Consensus pattern (43 bp):   
TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAAT

Found at i:11101 original size:85 final size:85

Alignment explanation


    Indices: 10946--11139  Score: 311
    Period size: 85  Copynumber: 2.3  Consensus size: 85

      10936 CATAAGGAAA

                        *                       *       *                    
      10946 AATGCCTCTGTGCTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGT
          1 AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATGT

                                 
      11011 GTTTGGGGACTTTG-ATATAG
         66 GTTTGGGGACTTTGTA-ATAG

                                                                             
      11031 -ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAAATGCCCCTGTGTTATATATG
          1 AATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGGAATAGAAATGCCCCTGTGTTATATATG

                                 
      11095 TGTTTGGGGACTTTGTAATAG
         65 TGTTTGGGGACTTTGTAATAG

                   *                
      11116 AATTGCCCCTGTGTTATATATGTG
          1 AA-TGCCTCTGTGTTATATATGTG


Statistics
Matches: 101,  Mismatches: 4, Indels: 6
        0.91            0.04        0.05

Matches are distributed among these distances:
  84   30  0.30
  85   49  0.49
  86    2  0.02
  87   20  0.20

ACGTcount: A:0.22, C:0.12, G:0.25, T:0.41


Consensus pattern (85 bp):   
AATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGGAATAGAAATGCCCCTGTGTTATATATGT
GTTTGGGGACTTTGTAATAG
Done.