Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013794.1 Corchorus olitorius cultivar O-4 contig13827, 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: 5483
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34


Found at i:1737 original size:69 final size:65

Alignment explanation


    Indices: 1565--1754  Score: 258
    Period size: 67  Copynumber: 2.8  Consensus size: 65

       1555 AATTAAATGA

                 *            *     *                                        
       1565 CATTAATACTAATTGATTTTAATTTGATC-A-ATATTCAAATCAAGCAATCAATCAATCAATTTA
          1 CATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAAT----CAATCAATCAATCAATTTA

                
       1628 ATAT
         62 ATAT

                                                                             
       1632 CATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATCAATTTAATAT
          1 CATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATCAATTTAATAT

                                               *                      
       1697 CATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCAAATCAATCAATCAAT
          1 CA--TTAGTACTAATTGATTCTAATTGGATC--AAGATATTCAAATCAATCAATCAAT

       1755 TTAATATATA


Statistics
Matches: 113,  Mismatches: 4, Indels: 10
        0.89            0.03        0.08

Matches are distributed among these distances:
  65   25  0.22
  67   53  0.47
  68    1  0.01
  69   34  0.30

ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38


Consensus pattern (65 bp):   
CATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATCAATTTAATAT

Found at i:1871 original size:2 final size:2

Alignment explanation


    Indices: 1864--1902  Score: 60
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       1854 TACAGTTTTA

                                                                     
       1864 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT GAT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT -AT AT A

       1903 CACACACTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   2   31  0.89
   3    4  0.11

ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:4659 original size:111 final size:113

Alignment explanation


    Indices: 4515--4722  Score: 348
    Period size: 111  Copynumber: 1.8  Consensus size: 113

       4505 ATTGTAAATT

                                 *                          *         *      
       4515 CTCTATGTGGCTTGTGGCATATCCTAACCTTGAATTAGAACAGCCTCCTTAACCTAAATTTTATA
          1 CTCTATGTGGCTTGTGGCATACCCTAACCTTGAATTAGAACAGCCTCCCTAACCTAAACTTTATA

                      *                                     
       4580 GT-AAAA-AAGAAAAAAAAACTAGGAATCTAGGAACCCACAGATTCAC
         66 GTAAAAAGAAAAAAAAAAAACTAGGAATCTAGGAACCCACAGATTCAC

                                                   *                         
       4626 CTCTATGTGGCTTGTGGCATACCCTAACCTTGAATTAGAGCAGCCTCCCTAACCTAAACTTTATA
          1 CTCTATGTGGCTTGTGGCATACCCTAACCTTGAATTAGAACAGCCTCCCTAACCTAAACTTTATA

                                            
       4691 GTAGAAAAGAAAAAAAAAAAACTAGGAATCTA
         66 GTA-AAAAGAAAAAAAAAAAACTAGGAATCTA

       4723 TATATGTTCC


Statistics
Matches: 89,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
 111   63  0.71
 113    4  0.04
 114   22  0.25

ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25


Consensus pattern (113 bp):   
CTCTATGTGGCTTGTGGCATACCCTAACCTTGAATTAGAACAGCCTCCCTAACCTAAACTTTATA
GTAAAAAGAAAAAAAAAAAACTAGGAATCTAGGAACCCACAGATTCAC
Done.