Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012768.1 Corchorus olitorius cultivar O-4 contig12801, 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: 5838
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33


Found at i:437 original size:16 final size:16

Alignment explanation


    Indices: 416--449  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        406 AAATGGTCAC

                            
        416 TGATATGTATTCTTAT
          1 TGATATGTATTCTTAT

                    *       
        432 TGATATGTGTTCTTAT
          1 TGATATGTATTCTTAT

              
        448 TG
          1 TG

        450 GTTTTTTTCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56


Consensus pattern (16 bp):   
TGATATGTATTCTTAT

Found at i:496 original size:19 final size:19

Alignment explanation


    Indices: 472--510  Score: 78
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        462 AATGGTGCAT

                               
        472 GCTCTGTTTCTGGAAAATA
          1 GCTCTGTTTCTGGAAAATA

                               
        491 GCTCTGTTTCTGGAAAATA
          1 GCTCTGTTTCTGGAAAATA

             
        510 G
          1 G

        511 GCAGTAGTGC


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

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36


Consensus pattern (19 bp):   
GCTCTGTTTCTGGAAAATA

Found at i:4304 original size:58 final size:58

Alignment explanation


    Indices: 4201--4315  Score: 178
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       4191 ATAGCATCAT

                      *                                               
       4201 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
          1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA

                                       *             *           *    
       4259 GCCTCGGTCCGAAAACGTCTTTTTTTATGCATCTAAT-AAAGAACATGTCACTTGATA
          1 GCCTCGGTCCGAAAACGTC-TTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATA

       4316 TTTGATTAAT


Statistics
Matches: 52,  Mismatches: 4, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  58   36  0.69
  59   16  0.31

ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31


Consensus pattern (58 bp):   
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
Done.