Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014491.1 Corchorus capsularis cultivar CVL-1 contig14512, 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: 33061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:973 original size:18 final size:19

Alignment explanation


    Indices: 938--977  Score: 55
    Period size: 18  Copynumber: 2.2  Consensus size: 19

        928 TTATTGTCTC

                        **     
        938 CATCATTGATCATTACCAT
          1 CATCATTGATCACCACCAT

                               
        957 CATCATT-ATCACCACCAT
          1 CATCATTGATCACCACCAT

               
        975 CAT
          1 CAT

        978 GTAACATTAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18   12  0.63
  19    7  0.37

ACGTcount: A:0.33, C:0.33, G:0.03, T:0.33


Consensus pattern (19 bp):   
CATCATTGATCACCACCAT

Found at i:1499 original size:31 final size:31

Alignment explanation


    Indices: 1461--1525  Score: 112
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       1451 TTGGGTTATC

                         *                 
       1461 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

                               *           
       1492 AGTCTCCAGATCTCTAGATTTTGGATGTTTG
          1 AGTCTCCAGATCTCTAGATCTTGGATGTTTG

               
       1523 AGT
          1 AGT

       1526 TAGTTCAGTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42


Consensus pattern (31 bp):   
AGTCTCCAGATCTCTAGATCTTGGATGTTTG

Found at i:3340 original size:3 final size:3

Alignment explanation


    Indices: 3332--3357  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       3322 AAAACAATTC

                                              
       3332 ATT ATT ATT ATT ATT ATT ATT ATT AT
          1 ATT ATT ATT ATT ATT ATT ATT ATT AT

       3358 AGTAATGATA


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

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
ATT

Found at i:9540 original size:100 final size:100

Alignment explanation


    Indices: 9404--9584  Score: 247
    Period size: 100  Copynumber: 1.8  Consensus size: 100

       9394 GAATGTTCTG

                                     *              * *           ****       
       9404 ATATTAAACGTGATACATACCGTTACTTAACTAATACAATGCTAATGATTGAATGTGGAGTGATC
          1 ATATTAAACGTGATACATACCGTTAATTAACTAATACAATACAAATGATTGAATAACAAGTGATC

                      *                        
       9469 GATCGTGTATTAATTATTTCAAGTCAAATCATTGA
         66 GATCGTGTATCAATTATTTCAAGTCAAATCATTGA

                  * *                                            *           
       9504 ATATTAGATGTGATACATACCGTTAATTAA-TAAATACAATACAAATGATTGATTAACAAGTGAT
          1 ATATTAAACGTGATACATACCGTTAATTAACT-AATACAATACAAATGATTGAATAACAAGTGAT

                             
       9568 CGATCGTGTATCAATTA
         65 CGATCGTGTATCAATTA

       9585 CTGAATCAAT


Statistics
Matches: 69,  Mismatches: 11, Indels: 2
        0.84            0.13        0.02

Matches are distributed among these distances:
  99    1  0.01
 100   68  0.99

ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34


Consensus pattern (100 bp):   
ATATTAAACGTGATACATACCGTTAATTAACTAATACAATACAAATGATTGAATAACAAGTGATC
GATCGTGTATCAATTATTTCAAGTCAAATCATTGA
Done.