Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001375.1 Corchorus olitorius cultivar O-4 contig01375, 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: 6345
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:278 original size:2 final size:2

Alignment explanation


    Indices: 271--309  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        261 CTACAATTGC

                                                                      
        271 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        310 CTTCTATATT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:317 original size:12 final size:12

Alignment explanation


    Indices: 302--336  Score: 52
    Period size: 12  Copynumber: 2.8  Consensus size: 12

        292 TATATATATA

                        
        302 TATATATACTTC
          1 TATATATACTTC

                 *      
        314 TATATTTACTTC
          1 TATATATACTTC

                       
        326 TATACTATACT
          1 TATA-TATACT

        337 ATAAAGAATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  12   15  0.75
  13    5  0.25

ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51


Consensus pattern (12 bp):   
TATATATACTTC

Found at i:802 original size:41 final size:41

Alignment explanation


    Indices: 745--823  Score: 133
    Period size: 41  Copynumber: 1.9  Consensus size: 41

        735 ATGGATTGAA

                       *                              
        745 TGAGTGAAGTCCACTCTTGAATT-AGGTGAGGTGTCACAGTT
          1 TGAGTGAAGTCAACTCTTG-ATTCAGGTGAGGTGTCACAGTT

                                                  
        786 TGAGTGAAGTCAACTCTTGATTCAGGTGAGGTGTCACA
          1 TGAGTGAAGTCAACTCTTGATTCAGGTGAGGTGTCACA

        824 ATTACTTGGT


Statistics
Matches: 36,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  40    3  0.08
  41   33  0.92

ACGTcount: A:0.25, C:0.15, G:0.29, T:0.30


Consensus pattern (41 bp):   
TGAGTGAAGTCAACTCTTGATTCAGGTGAGGTGTCACAGTT

Found at i:1293 original size:21 final size:21

Alignment explanation


    Indices: 1255--1294  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1245 CGCAAAAGAA

                         *       
       1255 TTAAAGTATGAAATAAAATGT
          1 TTAAAGTATGAAACAAAATGT

                                
       1276 TTAAAGTACT-AAACAAAAT
          1 TTAAAGTA-TGAAACAAAAT

       1295 ATAAAATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  21   16  0.94
  22    1  0.06

ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30


Consensus pattern (21 bp):   
TTAAAGTATGAAACAAAATGT

Found at i:4439 original size:184 final size:184

Alignment explanation


    Indices: 4130--4497  Score: 691
    Period size: 184  Copynumber: 2.0  Consensus size: 184

       4120 ATCACTAATC

                                                                             
       4130 ATTGTCTGTGCCCTAAAAGGCTTCAGATAATGTTTAGTGCACTTAGACTGGTCCATGCACGGAGC
          1 ATTGTCTGTGCCCTAAAAGGCTTCAGATAATGTTTAGTGCACTTAGACTGGTCCATGCACGGAGC

                               *                                          *  
       4195 GTTCAAGTTGTGTGATCCGTAGGGACCATGCATCATATACTGAACGACTGCATTATACCCAATGG
         66 GTTCAAGTTGTGTGATCCGCAGGGACCATGCATCATATACTGAACGACTGCATTATACCCAACGG

                                    *                             
       4260 GAGCAACTTCTTTGTCTGGTAATTTTGCATAAATGATTTCATTAATGGATTCTG
        131 GAGCAACTTCTTTGTCTGGTAATTCTGCATAAATGATTTCATTAATGGATTCTG

                                    *                                        
       4314 ATTGTCTGTGCCCTAAAAGGCTTCGGATAATGTTTAGTGCACTTAGACTGGTCCATGCACGGAGC
          1 ATTGTCTGTGCCCTAAAAGGCTTCAGATAATGTTTAGTGCACTTAGACTGGTCCATGCACGGAGC

                                                                             
       4379 GTTCAAGTTGTGTGATCCGCAGGGACCATGCATCATATACTGAACGACTGCATTATACCCAACGG
         66 GTTCAAGTTGTGTGATCCGCAGGGACCATGCATCATATACTGAACGACTGCATTATACCCAACGG

              *                                                   
       4444 GATCAACTTCTTTGTCTGGTAATTCTGCATAAATGATTTCATTAATGGATTCTG
        131 GAGCAACTTCTTTGTCTGGTAATTCTGCATAAATGATTTCATTAATGGATTCTG

       4498 GATCACGGCG


Statistics
Matches: 179,  Mismatches: 5, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 184  179  1.00

ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32


Consensus pattern (184 bp):   
ATTGTCTGTGCCCTAAAAGGCTTCAGATAATGTTTAGTGCACTTAGACTGGTCCATGCACGGAGC
GTTCAAGTTGTGTGATCCGCAGGGACCATGCATCATATACTGAACGACTGCATTATACCCAACGG
GAGCAACTTCTTTGTCTGGTAATTCTGCATAAATGATTTCATTAATGGATTCTG
Done.