Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008586.1 Corchorus olitorius cultivar O-4 contig08613, 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: 10456
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:4270 original size:161 final size:161

Alignment explanation


    Indices: 4048--4371  Score: 648
    Period size: 161  Copynumber: 2.0  Consensus size: 161

       4038 CCTTCTAATC

                                                                             
       4048 GATACTTTGATTCGAAACACCTAAATCAGAGATATTTGGAACAAAAAACTCTATAATATTAAGTA
          1 GATACTTTGATTCGAAACACCTAAATCAGAGATATTTGGAACAAAAAACTCTATAATATTAAGTA

                                                                             
       4113 GACCATCTATTCAAACTAATAATATTTCAGGAGTATTTTTTATACTCGAAACATCAAATTTAGCT
         66 GACCATCTATTCAAACTAATAATATTTCAGGAGTATTTTTTATACTCGAAACATCAAATTTAGCT

                                           
       4178 TTTGAATCCTTCATAAAGTTTGTAGATTATG
        131 TTTGAATCCTTCATAAAGTTTGTAGATTATG

                                                                             
       4209 GATACTTTGATTCGAAACACCTAAATCAGAGATATTTGGAACAAAAAACTCTATAATATTAAGTA
          1 GATACTTTGATTCGAAACACCTAAATCAGAGATATTTGGAACAAAAAACTCTATAATATTAAGTA

                                                                             
       4274 GACCATCTATTCAAACTAATAATATTTCAGGAGTATTTTTTATACTCGAAACATCAAATTTAGCT
         66 GACCATCTATTCAAACTAATAATATTTCAGGAGTATTTTTTATACTCGAAACATCAAATTTAGCT

                                           
       4339 TTTGAATCCTTCATAAAGTTTGTAGATTATG
        131 TTTGAATCCTTCATAAAGTTTGTAGATTATG

              
       4370 GA
          1 GA

       4372 ACAATTTGTT


Statistics
Matches: 163,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 161  163  1.00

ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35


Consensus pattern (161 bp):   
GATACTTTGATTCGAAACACCTAAATCAGAGATATTTGGAACAAAAAACTCTATAATATTAAGTA
GACCATCTATTCAAACTAATAATATTTCAGGAGTATTTTTTATACTCGAAACATCAAATTTAGCT
TTTGAATCCTTCATAAAGTTTGTAGATTATG

Found at i:4641 original size:72 final size:71

Alignment explanation


    Indices: 4509--4652  Score: 270
    Period size: 72  Copynumber: 2.0  Consensus size: 71

       4499 CAAGTCCTAC

                                                                             
       4509 ATGAAAGTTGAAGATCACGAAACAGCCTTTTAATAGACACTTAAATCACCTCAATTGGACATCTG
          1 ATGAAAGTTGAAGATCACGAAACAGCCTTTTAATAGACACTTAAATCACCTCAATTGGACATCTG

                  
       4574 GAGCAA
         66 GAGCAA

                            *                                                
       4580 ATGAAAGTTGAAGATCTCGAAACAGCCTTTTGAATAGACACTTAAATCACCTCAATTGGACATCT
          1 ATGAAAGTTGAAGATCACGAAACAGCCTTTT-AATAGACACTTAAATCACCTCAATTGGACATCT

                   
       4645 GGAGCAA
         65 GGAGCAA

             
       4652 A
          1 A

       4653 AAGTATGTAT


Statistics
Matches: 71,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  71   30  0.42
  72   41  0.58

ACGTcount: A:0.39, C:0.19, G:0.17, T:0.24


Consensus pattern (71 bp):   
ATGAAAGTTGAAGATCACGAAACAGCCTTTTAATAGACACTTAAATCACCTCAATTGGACATCTG
GAGCAA

Found at i:5071 original size:12 final size:12

Alignment explanation


    Indices: 5054--5080  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       5044 CCATTTATAA

                        
       5054 ATATATTATATT
          1 ATATATTATATT

                        
       5066 ATATATTATATT
          1 ATATATTATATT

               
       5078 ATA
          1 ATA

       5081 ATTTAAAATG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (12 bp):   
ATATATTATATT

Found at i:6876 original size:66 final size:67

Alignment explanation


    Indices: 6735--6890  Score: 253
    Period size: 66  Copynumber: 2.4  Consensus size: 67

       6725 TTGCCCAAAA

                              *        *            *                        
       6735 AATACTAGCAAACTCCCACGTGAGACATCTAGAGACTTGTGTAAGAATTGATGGGCAATTCAGAT
          1 AATACTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT

              
       6800 AT
         66 AT

                                                                             
       6802 AATA-TAGCAAACTCCCATGTGAGACACCTA-AGACTTGTCTAAGAATTGATGGGCAATTCAGAT
          1 AATACTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT

              
       6865 AT
         66 AT

                      * *           
       6867 AATACTAGCAGAGTCCCATGTGAG
          1 AATACTAGCAAACTCCCATGTGAG

       6891 TTGTGACACC


Statistics
Matches: 83,  Mismatches: 5, Indels: 3
        0.91            0.05        0.03

Matches are distributed among these distances:
  65   38  0.46
  66   41  0.49
  67    4  0.05

ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25


Consensus pattern (67 bp):   
AATACTAGCAAACTCCCATGTGAGACACCTAGAGACTTGTCTAAGAATTGATGGGCAATTCAGAT
AT
Done.