Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014670.1 Corchorus capsularis cultivar CVL-1 contig14691, 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: 14726
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27


Found at i:1170 original size:55 final size:55

Alignment explanation


    Indices: 1057--1226  Score: 243
    Period size: 55  Copynumber: 3.1  Consensus size: 55

       1047 TCAAGAAAAG

                         *           *                    *       *
       1057 AGTAATCAGTAAATCAGTAATTAAGAAAAAAG-GATTAATCAGAGTTAAAGTAAT
          1 AGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAAC

                                                                *  
       1111 AGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTGAC
          1 AGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAAC

                                          *  *            *  *    *
       1166 AGTAATCAGTAAACCAGTAATTAAGTAAAAGGAAATTAATCAGAGTTAAGGTAAT
          1 AGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAAC

                  
       1221 AGTAAT
          1 AGTAAT

       1227 AGCAAATAGG


Statistics
Matches: 104,  Mismatches: 11, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  54   30  0.29
  55   74  0.71

ACGTcount: A:0.50, C:0.08, G:0.18, T:0.25


Consensus pattern (55 bp):   
AGTAATCAGTAAACCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAAC

Found at i:5524 original size:3 final size:3

Alignment explanation


    Indices: 5516--5554  Score: 51
    Period size: 3  Copynumber: 12.3  Consensus size: 3

       5506 ATATATATAT

                                                    *          
       5516 ATA ATA ATA ATA ATAA ATA ATA ATA ATA AGTG ATA ATA A
          1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA A-TA ATA ATA A

       5555 CAATTTTTGA


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   3   27  0.84
   4    5  0.16

ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31


Consensus pattern (3 bp):   
ATA

Found at i:5536 original size:13 final size:13

Alignment explanation


    Indices: 5518--5554  Score: 56
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       5508 ATATATATAT

                         
       5518 AATAATAATAATA
          1 AATAATAATAATA

                         
       5531 AATAATAATAATA
          1 AATAATAATAATA

             * *       
       5544 AGTGATAATAA
          1 AATAATAATAA

       5555 CAATTTTTGA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  13   22  1.00

ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30


Consensus pattern (13 bp):   
AATAATAATAATA
Done.