Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021080.1 Corchorus olitorius cultivar O-4 contig21113, 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: 12663
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:65 original size:20 final size:21

Alignment explanation


    Indices: 40--85  Score: 60
    Period size: 20  Copynumber: 2.2  Consensus size: 21

         30 TTAAGGAAAG

                                  
         40 AATTAAAAA-TATTAATTAA-A
          1 AATTAAAAATTA-TAATTAAGA

                   *             
         60 AATTAAATATTATAATTAAGA
          1 AATTAAAAATTATAATTAAGA

                 
         81 AATTA
          1 AATTA

         86 TTATTTATAC


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  20   15  0.65
  21    8  0.35

ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37


Consensus pattern (21 bp):   
AATTAAAAATTATAATTAAGA

Found at i:588 original size:2 final size:2

Alignment explanation


    Indices: 578--607  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

        568 ATCGTGAGGT

                                                          
        578 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        608 TAGTTTTAAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   26  0.96

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:4294 original size:2 final size:2

Alignment explanation


    Indices: 4281--4337  Score: 73
    Period size: 2  Copynumber: 28.5  Consensus size: 2

       4271 ACTAAAAATA

                                               *                            
       4281 AT AT AT AGT AT AT AGT AT AT AT AT GT AT A- AT AT AT AT AT AT AT
          1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                  
       4324 AT AT AT AT -T AT AT A
          1 AT AT AT AT AT AT AT A

       4338 GTAATACGGG


Statistics
Matches: 49,  Mismatches: 2, Indels: 8
        0.83            0.03        0.14

Matches are distributed among these distances:
   1    2  0.04
   2   43  0.88
   3    4  0.08

ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:4316 original size:17 final size:16

Alignment explanation


    Indices: 4281--4336  Score: 71
    Period size: 15  Copynumber: 3.5  Consensus size: 16

       4271 ACTAAAAATA

                             
       4281 ATATATA-GTATATAGT
          1 ATATATATGTATATA-T

                            
       4297 ATATATATGTATA-AT
          1 ATATATATGTATATAT

                    *       
       4312 ATATATATATATATAT
          1 ATATATATGTATATAT

                     
       4328 ATATTATAT
          1 ATA-TATAT

       4337 AGTAATACGG


Statistics
Matches: 36,  Mismatches: 1, Indels: 5
        0.86            0.02        0.12

Matches are distributed among these distances:
  15   13  0.36
  16   13  0.36
  17   10  0.28

ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48


Consensus pattern (16 bp):   
ATATATATGTATATAT

Found at i:10430 original size:21 final size:20

Alignment explanation


    Indices: 10384--10426  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      10374 CTCTCACAAG

                        *    *  
      10384 TTTCTAGCCGTTGGAGCTCT
          1 TTTCTAGCCGTTAGAGCACT

                         *      
      10404 TTTCTAGCCGTTATAGCACT
          1 TTTCTAGCCGTTAGAGCACT

               
      10424 TTT
          1 TTT

      10427 TCTACTTTTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44


Consensus pattern (20 bp):   
TTTCTAGCCGTTAGAGCACT
Done.