Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010887.1 Corchorus olitorius cultivar O-4 contig10919, 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: 5062
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28


Found at i:520 original size:22 final size:22

Alignment explanation


    Indices: 495--539  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        485 CAAACTAAGA

                                  
        495 AGTAAGAAGGCATACTAGACGG
          1 AGTAAGAAGGCATACTAGACGG

                                  
        517 AGTAAGAAGGCATACTAGACGG
          1 AGTAAGAAGGCATACTAGACGG

             
        539 A
          1 A

        540 CTACTCGCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.42, C:0.13, G:0.31, T:0.13


Consensus pattern (22 bp):   
AGTAAGAAGGCATACTAGACGG

Found at i:987 original size:19 final size:19

Alignment explanation


    Indices: 963--1019  Score: 114
    Period size: 19  Copynumber: 3.0  Consensus size: 19

        953 TCGAGCAGAA

                               
        963 GTTATCTTTCTGACTTTAC
          1 GTTATCTTTCTGACTTTAC

                               
        982 GTTATCTTTCTGACTTTAC
          1 GTTATCTTTCTGACTTTAC

                               
       1001 GTTATCTTTCTGACTTTAC
          1 GTTATCTTTCTGACTTTAC

       1020 TTAGAATTAG


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   38  1.00

ACGTcount: A:0.16, C:0.21, G:0.11, T:0.53


Consensus pattern (19 bp):   
GTTATCTTTCTGACTTTAC

Found at i:2205 original size:22 final size:22

Alignment explanation


    Indices: 2177--2220  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2167 CTATCGGCAA

                                  
       2177 TAATCAGCTCTTTCATCCCCTG
          1 TAATCAGCTCTTTCATCCCCTG

                                  
       2199 TAATCAGCTCTTTCATCCCCTG
          1 TAATCAGCTCTTTCATCCCCTG

       2221 ATTGATGTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.18, C:0.36, G:0.09, T:0.36


Consensus pattern (22 bp):   
TAATCAGCTCTTTCATCCCCTG

Found at i:2850 original size:22 final size:22

Alignment explanation


    Indices: 2825--2868  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2815 CATCCCTAGG

                                  
       2825 CTATTGGGAGCCTTAAGAGGCA
          1 CTATTGGGAGCCTTAAGAGGCA

                                  
       2847 CTATTGGGAGCCTTAAGAGGCA
          1 CTATTGGGAGCCTTAAGAGGCA

       2869 AAGGAAAATG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23


Consensus pattern (22 bp):   
CTATTGGGAGCCTTAAGAGGCA
Done.