Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023574.1 Corchorus olitorius cultivar O-4 contig23607, 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: 5608
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:262 original size:19 final size:20

Alignment explanation


    Indices: 217--272  Score: 69
    Period size: 21  Copynumber: 2.8  Consensus size: 20

        207 GCTGCTCTAA

                                 
        217 TAATCTCATATGTACAGTACC
          1 TAATCTCATATGTACAGTA-C

                  *            *
        238 TAATCTAATATGTACAGT-G
          1 TAATCTCATATGTACAGTAC

                     *      
        257 TAATCTCATCTGTACA
          1 TAATCTCATATGTACA

        273 ATTACTAAAC


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  19   14  0.45
  21   17  0.55

ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36


Consensus pattern (20 bp):   
TAATCTCATATGTACAGTAC

Found at i:3141 original size:23 final size:25

Alignment explanation


    Indices: 3099--3146  Score: 73
    Period size: 23  Copynumber: 2.0  Consensus size: 25

       3089 TAGTGGATTA

                    *                
       3099 AATTAAAATATTAAATAAATTTAAG
          1 AATTAAAACATTAAATAAATTTAAG

                                     
       3124 AATT-AAACATTAAA-AAATTTAAG
          1 AATTAAAACATTAAATAAATTTAAG

       3147 GCTGACCCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    9  0.41
  24    9  0.41
  25    4  0.18

ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33


Consensus pattern (25 bp):   
AATTAAAACATTAAATAAATTTAAG

Found at i:3823 original size:70 final size:70

Alignment explanation


    Indices: 3744--3886  Score: 250
    Period size: 70  Copynumber: 2.0  Consensus size: 70

       3734 TAAAATAGTT

                      * *                                        *           
       3744 AAATGGTAAACTGAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATATAGTTTTTAGTT
          1 AAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTT

                 
       3809 GAGTA
         66 GAGTA

                                             *                               
       3814 AAATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTT
          1 AAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTT

                 
       3879 GAGTA
         66 GAGTA

               
       3884 AAA
          1 AAA

       3887 CTATAAATCT


Statistics
Matches: 69,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  70   69  1.00

ACGTcount: A:0.50, C:0.01, G:0.13, T:0.36


Consensus pattern (70 bp):   
AAATGGTAAAATAAAATAGTTATAAAGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTT
GAGTA

Found at i:4226 original size:3 final size:3

Alignment explanation


    Indices: 4220--4254  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       4210 TAAATAATAA

                                         *    *           
       4220 ATT ATT ATT ATT ATT ATT ATT ACT ATA ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT

       4255 ATGATTTATC


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60


Consensus pattern (3 bp):   
ATT

Done.