Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007063.1 Corchorus capsularis cultivar CVL-1 contig07084, 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: 18910
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1095 original size:20 final size:20

Alignment explanation


    Indices: 1070--1108  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1060 AAAAAGAACA

                  *             
       1070 CCAATTTGCAAATCAAATGT
          1 CCAATTCGCAAATCAAATGT

                    *          
       1090 CCAATTCGTAAATCAAATG
          1 CCAATTCGCAAATCAAATG

       1109 CCTTGTATTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28


Consensus pattern (20 bp):   
CCAATTCGCAAATCAAATGT

Found at i:1265 original size:14 final size:14

Alignment explanation


    Indices: 1242--1275  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1232 TAACTGTGAT

                 *        
       1242 ACTAATCTAAATGG
          1 ACTAAACTAAATGG

                          
       1256 ACTAAACTAAATGG
          1 ACTAAACTAAATGG

                  
       1270 ACTAAA
          1 ACTAAA

       1276 GTTAATATGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.50, C:0.15, G:0.12, T:0.24


Consensus pattern (14 bp):   
ACTAAACTAAATGG

Found at i:4874 original size:162 final size:162

Alignment explanation


    Indices: 4607--4939  Score: 632
    Period size: 162  Copynumber: 2.1  Consensus size: 162

       4597 TACTTATAAT

                                                                             
       4607 TTTGTGTTAAGTTCTTGATGATAGTAGTCAAAACCCTGTTTTAATTTTATGATTCTGAATCTTAT
          1 TTTGTGTTAAGTTCTTGATGATAGTAGTCAAAACCCTGTTTTAATTTTATGATTCTGAATCTTAT

                                                                             
       4672 TTGAGTTATGTGGCCACTAACGATGTAAGAGGAAGATCTATGGCTAGATCAGGCTTAGAATTAAT
         66 TTGAGTTATGTGGCCACTAACGATGTAAGAGGAAGATCTATGGCTAGATCAGGCTTAGAATTAAT

                                           *
       4737 CACTCAAGTTTGATTGTATATAGCAAATTAGG
        131 CACTCAAGTTTGATTGTATATAGCAAATTAGA

                     *                                                       
       4769 TTTGTGTTAGGTTCTTGATGATAGTAGTCAAAACCCTGTTTTAATTTTATGATTCTGAATCTTAT
          1 TTTGTGTTAAGTTCTTGATGATAGTAGTCAAAACCCTGTTTTAATTTTATGATTCTGAATCTTAT

                                                                             
       4834 TTGAGTTATGTGGCCACTAACGATGTAAGAGGAAGATCTATGGCTAGATCAGGCTTAGAATTAAT
         66 TTGAGTTATGTGGCCACTAACGATGTAAGAGGAAGATCTATGGCTAGATCAGGCTTAGAATTAAT

                               *            
       4899 CACTCAAGTTTGATTGTATGTAGCAAATTAGA
        131 CACTCAAGTTTGATTGTATATAGCAAATTAGA

                      
       4931 TTTGT-TTAA
          1 TTTGTGTTAA

       4940 TCGCTGCTTA


Statistics
Matches: 167,  Mismatches: 4, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
 161    3  0.02
 162  164  0.98

ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38


Consensus pattern (162 bp):   
TTTGTGTTAAGTTCTTGATGATAGTAGTCAAAACCCTGTTTTAATTTTATGATTCTGAATCTTAT
TTGAGTTATGTGGCCACTAACGATGTAAGAGGAAGATCTATGGCTAGATCAGGCTTAGAATTAAT
CACTCAAGTTTGATTGTATATAGCAAATTAGA

Found at i:5292 original size:6 final size:6

Alignment explanation


    Indices: 5281--5307  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       5271 ATTAATCTGC

                                           
       5281 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       5308 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Done.