View Alignment

This page shows all the targets hit by the same query that passed the project filter. Click a track to view the detailed alignment.

Legend
 Query
 Query hiting target  Query hiting target's complemental strand
 Query's complemental strand hiting target  Query's complemental strand hiting target's complemental strand

Alignment Overview

Query: F9045J-LTR4-TNT-insertion-1 (Length: 581)

Name: F9045J-LTR4-TNT-insertion-1
Description: F9045J-LTR4
Algorithm: BLASTN 2.2.26 [Sep-21-2011]
Database: JCVI.Medtr.v4.20130313.fasta (1949 entries, 411831487 letters)


[»] F9045J-LTR4-TNT-insertion-1
F9045J-LTR4-TNT-insertion-1
[»] chr3 (2 HSPs)
chr3 (40-496)||(46682418-46682874)
chr3 (40-121)||(46655238-46655321)
[»] chr7 (1 HSPs)
chr7 (493-572)||(6932361-6932440)
[»] chr4 (1 HSPs)
chr4 (493-572)||(508425-508504)
[»] chr6 (1 HSPs)
chr6 (493-572)||(14544911-14544990)
[»] chr5 (1 HSPs)
chr5 (493-572)||(26291035-26291114)
[»] chr2 (2 HSPs)
chr2 (522-572)||(18290825-18290875)
chr2 (7-45)||(42691734-42691772)
[»] scaffold0002 (1 HSPs)
scaffold0002 (518-571)||(169930-169983)


Alignment Details
Target: chr3 (Bit Score: 453; Significance: 0; HSPs: 2)
Name: chr3
Description:

Target: chr3; HSP #1
Raw Score: 453; E-Value: 0
Query Start/End: Original strand, 40 - 496
Target Start/End: Original strand, 46682418 - 46682874
Alignment:
Q  40 gaattcttagtttttctccttaacataattcccattctttcaatgtaattttacaaaatttgttaacttcatttattttttaaagtatgcattgtactct 139  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  46682418 gaattcttagtttttctccttaacataattcccattctttcaatgtaattttacaaaatttgttaacttcatttattttttaaagtatgcattgtactct 46682517  T
Q  140 attgatgtaataaagaaaaagtgtatttgtttgttcattaactgtaagattcaatttaatgatattctctaaaccaaatagttaaatttaacctgcaatt 239  Q
    ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  46682518 attgatgtaataaagaaaaagtgtaattgtttgttcattaactgtaagattcaatttaatgatattctctaaaccaaatagttaaatttaacctgcaatt 46682617  T
Q  240 cttttgacaatgctattagtttagtaatctctttatctcgatgatattgtgggtgaaaattacaaacaactacaattctcccaagtcctagtaataaata 339  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  46682618 cttttgacaatgctattagtttagtaatctctttatctcgatgatattgtgggtgaaaattacaaacaactacaattctcccaagtcctagtaataaata 46682717  T
Q  340 cgaagacaactttcatgtaaaacaaacaaccctatatgaaagactatttactttaaatatgatcatatatatatccaaattgtaattgtaataatctaaa 439  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  46682718 cgaagacaactttcatgtaaaacaaacaaccctatatgaaagactatttactttaaatatgatcatatatatatccaaattgtaattgtaataatctaaa 46682817  T
Q  440 ttttattaggtagatattaatgagttctaaactctagtttcacccaataaaacaatt 496  Q
    |||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  46682818 ttttattaggtagatattaatgagttctaaactctagtttcacccaataaaacaatt 46682874  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr3; HSP #2
Raw Score: 33; E-Value: 0.000000003
Query Start/End: Original strand, 40 - 121
Target Start/End: Complemental strand, 46655321 - 46655238
Alignment:
Q  40 gaattcttagtttttctccttaac--ataattcccattctttcaatgtaattttacaaaatttgttaacttcatttatttttta 121  Q
    ||||||||||||||| ||||||||  ||| |||| || |||| |||| | |||||| ||||||||| | |||||||||||||||    
T  46655321 gaattcttagtttttgtccttaacatatatttccgatgctttgaatgcatttttacgaaatttgttgatttcatttatttttta 46655238  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr7 (Bit Score: 59; Significance: 1e-24; HSPs: 1)
Name: chr7
Description:

Target: chr7; HSP #1
Raw Score: 59; E-Value: 1e-24
Query Start/End: Original strand, 493 - 572
Target Start/End: Original strand, 6932361 - 6932440
Alignment:
Q  493 aattcatttatcaaccgannnnnnncttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 572  Q
    ||||||||||||||||||       |||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  6932361 aattcatttatcaaccgatttttttcttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 6932440  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr4 (Bit Score: 59; Significance: 1e-24; HSPs: 1)
Name: chr4
Description:

Target: chr4; HSP #1
Raw Score: 59; E-Value: 1e-24
Query Start/End: Original strand, 493 - 572
Target Start/End: Original strand, 508425 - 508504
Alignment:
Q  493 aattcatttatcaaccgannnnnnncttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 572  Q
    ||||||||||||||||||       |||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  508425 aattcatttatcaaccgatttttttcttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 508504  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr6 (Bit Score: 55; Significance: 2e-22; HSPs: 1)
Name: chr6
Description:

Target: chr6; HSP #1
Raw Score: 55; E-Value: 2e-22
Query Start/End: Original strand, 493 - 572
Target Start/End: Original strand, 14544911 - 14544990
Alignment:
Q  493 aattcatttatcaaccgannnnnnncttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 572  Q
    ||||||||||||||||||       ||| |||||||||||||||||||||||||||||||||||||||||||||||||||    
T  14544911 aattcatttatcaaccgatttttttctttcatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 14544990  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr5 (Bit Score: 55; Significance: 2e-22; HSPs: 1)
Name: chr5
Description:

Target: chr5; HSP #1
Raw Score: 55; E-Value: 2e-22
Query Start/End: Original strand, 493 - 572
Target Start/End: Original strand, 26291035 - 26291114
Alignment:
Q  493 aattcatttatcaaccgannnnnnncttccatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 572  Q
    ||||||||||||||||||       ||| |||||||||||||||||||||||||||||||||||||||||||||||||||    
T  26291035 aattcatttatcaaccgatttttttctttcatttgaactaatttcaataattcttttagttgctttgataggtgcaattg 26291114  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr2 (Bit Score: 43; Significance: 0.000000000000004; HSPs: 2)
Name: chr2
Description:

Target: chr2; HSP #1
Raw Score: 43; E-Value: 0.000000000000004
Query Start/End: Original strand, 522 - 572
Target Start/End: Complemental strand, 18290875 - 18290825
Alignment:
Q  522 catttgaactaatttcaataattcttttagttgctttgataggtgcaattg 572  Q
    ||||||||||||||||||||||| ||||||||||||||||| |||||||||    
T  18290875 catttgaactaatttcaataattattttagttgctttgatatgtgcaattg 18290825  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: chr2; HSP #2
Raw Score: 39; E-Value: 0.0000000000009
Query Start/End: Original strand, 7 - 45
Target Start/End: Original strand, 42691734 - 42691772
Alignment:
Q  7 accatagacctcttcagatagagatactattaggaattc 45  Q
    |||||||||||||||||||||||||||||||||||||||    
T  42691734 accatagacctcttcagatagagatactattaggaattc 42691772  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]

Target: scaffold0002 (Bit Score: 30; Significance: 0.0000002; HSPs: 1)
Name: scaffold0002
Description:

Target: scaffold0002; HSP #1
Raw Score: 30; E-Value: 0.0000002
Query Start/End: Original strand, 518 - 571
Target Start/End: Original strand, 169930 - 169983
Alignment:
Q  518 cttccatttgaactaatttcaataattcttttagttgctttgataggtgcaatt 571  Q
    ||||| |||||||| ||||| ||||||||| ||||| |||| ||||||||||||    
T  169930 cttccgtttgaactcatttccataattcttctagtttctttaataggtgcaatt 169983  T

Back To: [ HSP Overview ] [ Target Overview ] [ Alignment Overview ]



© Oklahoma State University

This website was viewed 24702 times since January 2019
Visitors: 3697