Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010243.1 Corchorus capsularis cultivar CVL-1 contig10264, 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: 6707
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:4910 original size:134 final size:133

Alignment explanation


    Indices: 4517--4919  Score: 788
    Period size: 133  Copynumber: 3.0  Consensus size: 133

       4507 TCAAACCACT

                  *                                                          
       4517 ATAGAAATAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG
          1 ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG

                                                                             
       4582 GTCCAAAAGTACCAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCTT
         66 GTCCAAAAGTACCAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCTT

               
       4647 CAC
        131 CAC

                                                                             
       4650 ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG
          1 ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG

                                                                             
       4715 GTCCAAAAGTACCAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCTT
         66 GTCCAAAAGTACCAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCTT

               
       4780 CAC
        131 CAC

                                                                             
       4783 ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG
          1 ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG

                                                                             
       4848 GTCCAAAAGTACCAAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCT
         66 GTCCAAAAGTACC-AAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCT

                
       4913 TCAC
        130 TCAC

               
       4917 ATA
          1 ATA

       4920 TGAAAATCCC


Statistics
Matches: 268,  Mismatches: 1, Indels: 1
        0.99            0.00        0.00

Matches are distributed among these distances:
 133  210  0.78
 134   58  0.22

ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28


Consensus pattern (133 bp):   
ATAGAAGTAATTTTTTTTGGCTATATTAAGAACGAAACACAATTAAAAGATAGGCATCAACTAAG
GTCCAAAAGTACCAAGTCTAAACCGGTCTTCATCCATCAGGTCGATAAGTTGACTAGGGGTTCTT
CAC

Found at i:5378 original size:13 final size:13

Alignment explanation


    Indices: 5347--5371  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5337 ATAACAGTTG

                         
       5347 TTTTAAATATTTC
          1 TTTTAAATATTTC

                        
       5360 TTTTAAATATTT
          1 TTTTAAATATTT

       5372 TTGTTAATTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64


Consensus pattern (13 bp):   
TTTTAAATATTTC
Done.