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: F9542H-LTR4-TNT-insertion-17 (Length: 595)

Name: F9542H-LTR4-TNT-insertion-17
Description: F9542H-LTR4
Algorithm: BLASTN 2.2.26 [Sep-21-2011]
Database: JCVI.Medtr.v4.20130313.fasta (1949 entries, 411831487 letters)


[»] F9542H-LTR4-TNT-insertion-17
F9542H-LTR4-TNT-insertion-17
[»] chr5 (2 HSPs)
chr5 (9-554)||(39184636-39185182)
chr5 (40-251)||(8730292-8730501)
[»] chr1 (3 HSPs)
chr1 (47-262)||(42373538-42373752)
chr1 (38-402)||(17032729-17033101)
chr1 (84-266)||(19597952-19598135)
[»] chr4 (3 HSPs)
chr4 (151-270)||(16501182-16501302)
chr4 (65-172)||(46699375-46699483)
chr4 (84-139)||(12295557-12295612)
[»] chr2 (4 HSPs)
chr2 (40-174)||(22885907-22886042)
chr2 (40-251)||(25505406-25505615)
chr2 (145-271)||(31902910-31903036)
chr2 (145-300)||(39339357-39339512)
[»] chr7 (2 HSPs)
chr7 (104-264)||(37792747-37792908)
chr7 (142-179)||(12480376-12480413)
[»] chr3 (3 HSPs)
chr3 (65-228)||(25595054-25595217)
chr3 (91-191)||(5556058-5556158)
chr3 (155-252)||(1653452-1653549)


Alignment Details
Target: chr5 (Bit Score: 512; Significance: 0; HSPs: 2)
Name: chr5
Description:

Target: chr5; HSP #1
Raw Score: 512; E-Value: 0
Query Start/End: Original strand, 9 - 554
Target Start/End: Original strand, 39184636 - 39185182
Alignment:
Q  9 caccacgcctcacccccaccaccaacaccaacaagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagcca 108  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  39184636 caccacgcctcacccccaccaccaacaccaacaagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagcca 39184735  T
Q  109 cgaagaatatacccacaagccaacgatagagccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaaacatatatataggaaga 208  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  39184736 cgaagaatatacccacaagccaacgatagagccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaaacatatatataggaaga 39184835  T
Q  209 cgaaacacaactacaaaacataggcaacgacgccagtttgaagcagaatcacaacctaaatcagagaaatgcagctgccggtgacatggagaaaacatat 308  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  39184836 cgaaacacaactacaaaacataggcaacgacgccagtttgaagcagaatcacaacctaaatcagagaaatgcagctgccggtgacatggagaaaacatat 39184935  T
Q  309 gtcgccggagtaaacaaccaaccccatgaacctgcggaactgaccgaatggaagctgatctcagcaacaaaatcaccaaaaccagtaccgaacgtgaaag 408  Q
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  39184936 gtcgccggagtaaacaaccaaccccatgaacctgcggaactgaccgaatggaagctgatctcagcaacaaaatcaccaaaaccagtaccgaacgtgaaag 39185035  T
Q  409 cacgtgagacacccagagaaaaaagtcgatatatacctaaaaccac-nnnnnnnnnccaagcaaccagcaccactacccaccgtgtatggccgtcggaaa 507  Q
    ||||||||||||||||||||||||||||||||||||||||||||||          ||||||||||||||||||||||||||||||||||||||||||||    
T  39185036 cacgtgagacacccagagaaaaaagtcgatatatacctaaaaccacaaaaaaaaaaccaagcaaccagcaccactacccaccgtgtatggccgtcggaaa 39185135  T
Q  508 gctggtgacaacaccaccaaacagtaacacaaaaacttaaacaaccc 554  Q
    |||||||||||||||||||||||||||||||||||||||||||||||    
T  39185136 gctggtgacaacaccaccaaacagtaacacaaaaacttaaacaaccc 39185182  T

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

Target: chr5; HSP #2
Raw Score: 44; E-Value: 9e-16
Query Start/End: Original strand, 40 - 251
Target Start/End: Complemental strand, 8730501 - 8730292
Alignment:
Q  40 caagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagag 139  Q
    |||||||||||||||||||| || ||||| ||||  | ||| ||||||||||||   |||| ||| |||| |  ||||||||||| | ||||||||||||    
T  8730501 caagacaacaaagttgaaagtctccaaggtaagcaacaacatcgccatagcattataaagaggcaaccacaataaatatacccaccaaccaacgatagag 8730402  T
Q  140 ccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaaacatatatataggaagacgaaacacaactacaaaacataggcaacgac 239  Q
     || |||||| | ||||||| | |||| || |||||||| |||||||| |||| | ||  | ||||||||||| |  ||| ||||||||  |||| ||||    
T  8730401 acagaactacactgccaaactgtctca-catgaaaacaggcagcaaca-aaaatagatccagaggaagacgaagccaaacaacaaaacacgggcagcgac 8730304  T
Q  240 gccagtttgaag 251  Q
    |||||| |||||    
T  8730303 gccagtctgaag 8730292  T

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

Target: chr1 (Bit Score: 100; Significance: 4e-49; HSPs: 3)
Name: chr1
Description:

Target: chr1; HSP #1
Raw Score: 100; E-Value: 4e-49
Query Start/End: Original strand, 47 - 262
Target Start/End: Complemental strand, 42373752 - 42373538
Alignment:
Q  47 acaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagagccaaaac 146  Q
    ||||||||||| | || |||||||| | || ||| ||||||||||||||||||||||||||||   |||||||||||||| |||| ||||||| ||||||    
T  42373752 acaaagttgaaggtctccaaggaaatcagcaacatcgccatagcattccgaagaagcagccacagtgaatatacccacaa-ccaaagatagagacaaaac 42373654  T
Q  147 tacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaaacatatatataggaagacgaaacacaactacaaaacataggcaacgacgccagtt 246  Q
    ||||||| |||||| ||||||||||||||||| ||| |||| | |||| ||  ||||||||||||||||||||| |||||||  ||||||||| || |||    
T  42373653 tacgccgtcaaaccacctcaccaagaaaacaggcagtaacatagaacagatcgataggaagacgaaacacaacttcaaaacacgggcaacgacaccggtt 42373554  T
Q  247 tgaagcagaatcacaa 262  Q
    |||||| |||||||||    
T  42373553 tgaagcggaatcacaa 42373538  T

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

Target: chr1; HSP #2
Raw Score: 89; E-Value: 1e-42
Query Start/End: Original strand, 38 - 402
Target Start/End: Complemental strand, 17033101 - 17032729
Alignment:
Q  38 aacaagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatag 137  Q
    |||||||||||||||||||| | ||  ||||||||| |||||| |||||||||||||||||||||||||||||  ||||| ||||||||  || ||||||    
T  17033101 aacaagacaacaaagttgaaggtctctaaggaaagcagccacatcgccatagcattccgaagaagcagccacgttgaataaacccacaaatcagcgatag 17033002  T
Q  138 ag-ccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaa---aacatatatataggaagacgaaacacaactac-aaaacatagg 232  Q
    || | |||||||| | ||||||||| |||||||||||||||  |||||||| ||    |||||| || ||||||||||||  |||| || |||||| |||    
T  17033001 agacaaaaactacactgccaaaccgtctcaccaagaaaacaagcagcaacataatatcacatatctagaggaagacgaaatccaacaacaaaaacacagg 17032902  T
Q  233 caacgacgccagtttgaagcagaatcacaacctaaatcagagaaatgcagctgccggtgacatggagaaaacatatgtcgccggagtaaac---aaccaa 329  Q
     |  ||| || || ||||||||||||||||||   |||| | |||||  || |||||||||| |||| | || |  |||| ||||||||||   ||||||    
T  17032901 tagtgaccccggtgtgaagcagaatcacaaccctgatcaaaaaaatgtggccgccggtgacaaggaggagacttccgtcgtcggagtaaacaaaaaccaa 17032802  T
Q  330 ccccatgaacctgcggaactgaccgaatggaagctgatctcagcaacaaaatcaccaaaaccagtaccgaacg 402  Q
      ||||||||||||  ||||||| |||| || ||  ||||||||||||| |  |||||||||||| |||||||    
T  17032801 gtccatgaacctgcaaaactgactgaatcgacgccaatctcagcaacaacacaaccaaaaccagttccgaacg 17032729  T

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Target: chr1; HSP #3
Raw Score: 37; E-Value: 0.00000000001
Query Start/End: Original strand, 84 - 266
Target Start/End: Complemental strand, 19598135 - 19597952
Alignment:
Q  84 ccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagagccaaa-actacgccgccaaaccgcctcaccaagaaaacagacag 182  Q
    ||||||||||| |||||| || |||| |||||||||| ||||| ||| ||| |||| ||||  ||||||| ||||||| |||| ||||| |||||| |||    
T  19598135 ccatagcattctgaagaatcaaccacaaagaatatactcacaaaccatcgaaagagacaaaggctacgcctccaaaccacctcgccaag-aaacaggcag 19598037  T
Q  183 caacacaaa-acatatatataggaagacgaaacacaactacaaaacataggcaacgacgccagtttgaagcagaatcacaaccta 266  Q
    |||| |||| ||| |   | ||||||| ||||| |||| ||| ||||  |||||||||||| || |||||  ||| |||||||||    
T  19598036 caacccaaacacaaaccaaaaggaagatgaaacccaacaacagaacacgggcaacgacgccggtctgaagtggaaacacaaccta 19597952  T

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Target: chr4 (Bit Score: 49; Significance: 1e-18; HSPs: 3)
Name: chr4
Description:

Target: chr4; HSP #1
Raw Score: 49; E-Value: 1e-18
Query Start/End: Original strand, 151 - 270
Target Start/End: Complemental strand, 16501302 - 16501182
Alignment:
Q  151 ccgccaaaccgcctcaccaagaaaacagacagcaacacaaa-acatatatataggaagacgaaacacaactacaaaacataggcaacgacgccagtttga 249  Q
    |||||||||||||||||||||||||||||| || ||||||| ||| || || |||||||| |||  |||| ||| ||||| |||| ||||||| ||||||    
T  16501302 ccgccaaaccgcctcaccaagaaaacagacggccacacaaacacaaatttagaggaagactaaaaccaacaacacaacatgggcagcgacgccggtttga 16501203  T
Q  250 agcagaatcacaacctaaatc 270  Q
    ||  ||||||||||| |||||    
T  16501202 agtggaatcacaacccaaatc 16501182  T

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

Target: chr4; HSP #2
Raw Score: 41; E-Value: 0.00000000000006
Query Start/End: Original strand, 65 - 172
Target Start/End: Original strand, 46699375 - 46699483
Alignment:
Q  65 aaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagagcca-aaactacgccgccaaaccgcc 163  Q
    ||||||||| || ||| | ||||| ||||||||||||||||||| |  |||| ||||||||| ||| ||||| ||  | |||||||||||||||||| ||    
T  46699375 aaggaaagcagcaacatcaccataacattccgaagaagcagccatggtgaatttacccacaaaccagcgataaagatataaactacgccgccaaaccacc 46699474  T
Q  164 tcaccaaga 172  Q
    |||||||||    
T  46699475 tcaccaaga 46699483  T

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

Target: chr4; HSP #3
Raw Score: 32; E-Value: 0.00000001
Query Start/End: Original strand, 84 - 139
Target Start/End: Complemental strand, 12295612 - 12295557
Alignment:
Q  84 ccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagag 139  Q
    ||||||||||| |||||||||||||||  |||||||||||||| ||| | ||||||    
T  12295612 ccatagcattctgaagaagcagccacggtgaatatacccacaaaccatcaatagag 12295557  T

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

Target: chr2 (Bit Score: 44; Significance: 9e-16; HSPs: 4)
Name: chr2
Description:

Target: chr2; HSP #1
Raw Score: 44; E-Value: 9e-16
Query Start/End: Original strand, 40 - 174
Target Start/End: Original strand, 22885907 - 22886042
Alignment:
Q  40 caagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagag 139  Q
    |||||||||||  ||||||| ||  ||||||||| |  ||| |||| ||||||| ||||||||||||||| | |||||||||||||| | |  |||||||    
T  22885907 caagacaacaagattgaaagtctctaaggaaagcaggaacatcgccttagcatttcgaagaagcagccacaacgaatatacccacaaactagtgatagag 22886006  T
Q  140 cca-aaactacgccgccaaaccgcctcaccaagaaa 174  Q
      | |||| ||||||||||||| |||||||||||||    
T  22886007 atagaaaccacgccgccaaaccacctcaccaagaaa 22886042  T

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

Target: chr2; HSP #2
Raw Score: 44; E-Value: 9e-16
Query Start/End: Original strand, 40 - 251
Target Start/End: Original strand, 25505406 - 25505615
Alignment:
Q  40 caagacaacaaagttgaaagacttcaaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagag 139  Q
    |||||||||||||||||||| || ||||| ||||  | ||| ||||||||||||   |||| ||| |||| |  ||||||||||| | ||||||||||||    
T  25505406 caagacaacaaagttgaaagtctccaaggtaagcaacaacatcgccatagcattataaagaggcaaccacaataaatatacccaccaaccaacgatagag 25505505  T
Q  140 ccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaaacatatatataggaagacgaaacacaactacaaaacataggcaacgac 239  Q
     || |||||| | ||||||| | |||| || |||||||| |||||||| |||| | ||  | ||||||||||| |  ||| ||||||||  |||| ||||    
T  25505506 acagaactacactgccaaactgtctca-catgaaaacaggcagcaaca-aaaatagatccagaggaagacgaagccaaacaacaaaacacgggcagcgac 25505603  T
Q  240 gccagtttgaag 251  Q
    |||||| |||||    
T  25505604 gccagtctgaag 25505615  T

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

Target: chr2; HSP #3
Raw Score: 40; E-Value: 0.0000000000002
Query Start/End: Original strand, 145 - 271
Target Start/End: Original strand, 31902910 - 31903036
Alignment:
Q  145 actacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaa-acatatatataggaagacgaaacacaactacaaaacataggcaacgacgcca 243  Q
    ||||||||||||||  |||||| ||||||| || |||||||||| || | | || || ||||||||||||| |||| ||||||||  |||| |||||||     
T  31902910 actacgccgccaaatagcctcagcaagaaa-caaacagcaacactaacatagatctagaggaagacgaaacccaacaacaaaacacgggcagcgacgccg 31903008  T
Q  244 gtttgaagcagaatcacaacctaaatca 271  Q
    ||||||||| ||| ||||||||| ||||    
T  31903009 gtttgaagcggaaacacaacctagatca 31903036  T

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

Target: chr2; HSP #4
Raw Score: 37; E-Value: 0.00000000001
Query Start/End: Original strand, 145 - 300
Target Start/End: Original strand, 39339357 - 39339512
Alignment:
Q  145 actacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaa-acatatatataggaagacgaaacacaactacaaaacataggcaacgacgcca 243  Q
    |||||||||||||||  |||||||||| ||||||||||||||||||| | | || || ||||||| ||||  |||| ||||||||   ||| ||||| |     
T  39339357 actacgccgccaaacatcctcaccaag-aaacagacagcaacacaaatatagatctagaggaagaggaaatccaacaacaaaacacgagcagcgacgtcg 39339455  T
Q  244 gtttgaagcagaatcacaacctaaatcagagaaatgcagctgccggtgacatggaga 300  Q
    ||||||||   || ||||||| |||||| ||||| || || |||||||||| |||||    
T  39339456 gtttgaagtgaaaacacaaccaaaatcatagaaaggcggccgccggtgacaaggaga 39339512  T

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

Target: chr7 (Bit Score: 39; Significance: 0.0000000000009; HSPs: 2)
Name: chr7
Description:

Target: chr7; HSP #1
Raw Score: 39; E-Value: 0.0000000000009
Query Start/End: Original strand, 104 - 264
Target Start/End: Complemental strand, 37792908 - 37792747
Alignment:
Q  104 agccacgaagaatatacccacaagccaacgatagagcca-aaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaaa-acatatatat 201  Q
    |||||||| ||||| |||||||| ||||||| |||| || ||||||||||||||||||  |  ||||||||| |||||||||||||||| ||  ||  |     
T  37792908 agccacgatgaataaacccacaaaccaacgacagagacagaaactacgccgccaaaccagccaaccaagaaa-cagacagcaacacaaacacggatcaag 37792810  T
Q  202 aggaagacgaaacacaactacaaaacataggcaacgacgccagtttgaagcagaatcacaacc 264  Q
    || |||| ||||| ||||  |||||||  | |||||||||| ||||||||| ||| |||||||    
T  37792809 agaaagatgaaacccaacagcaaaacacggacaacgacgccggtttgaagcggaaacacaacc 37792747  T

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

Target: chr7; HSP #2
Raw Score: 30; E-Value: 0.0000002
Query Start/End: Original strand, 142 - 179
Target Start/End: Complemental strand, 12480413 - 12480376
Alignment:
Q  142 aaaactacgccgccaaaccgcctcaccaagaaaacaga 179  Q
    |||||||  |||||||||||||||||||||||||||||    
T  12480413 aaaactattccgccaaaccgcctcaccaagaaaacaga 12480376  T

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

Target: chr3 (Bit Score: 37; Significance: 0.00000000001; HSPs: 3)
Name: chr3
Description:

Target: chr3; HSP #1
Raw Score: 37; E-Value: 0.00000000001
Query Start/End: Original strand, 65 - 228
Target Start/End: Original strand, 25595054 - 25595217
Alignment:
Q  65 aaggaaagcggccacaacgccatagcattccgaagaagcagccacgaagaatatacccacaagccaacgatagagccaaaactacgccgccaaaccgcct 164  Q
    ||||||||| || ||| |||||| || |||| || | |||||||||   || ||||||| || | | |||||||| | ||||||||  ||||||||||||    
T  25595054 aaggaaagcagcaacatcgccattgccttccaaaaatgcagccacggttaaaatacccataaacgagcgatagagacgaaactacgttgccaaaccgcct 25595153  T
Q  165 caccaagaaaacagacagcaacac-aaaacatatatataggaagacgaaacacaactacaaaaca 228  Q
    ||||||| |||||  ||||||||| |||||| || || |||| ||||||||| ||| ||||||||    
T  25595154 caccaag-aaacaagcagcaacacaaaaacaaatctagaggatgacgaaacataacaacaaaaca 25595217  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, 91 - 191
Target Start/End: Complemental strand, 5556158 - 5556058
Alignment:
Q  91 attccgaagaagcagccacgaagaatatacccacaagccaacgatagagccaaaactacgccgccaaaccgcctcaccaagaaaacagacagcaacacaa 190  Q
    |||||||||||||| |||    |||||||||||||| ||| ||| |||| |||||| | || ||| ||||||| ||||| |||||||  |||||||||||    
T  5556158 attccgaagaagcaaccatagtgaatatacccacaaaccagcgacagagacaaaacaatgcagcctaaccgccacaccatgaaaacaagcagcaacacaa 5556059  T
Q  191 a 191  Q
    |    
T  5556058 a 5556058  T

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

Target: chr3; HSP #3
Raw Score: 29; E-Value: 0.0000008
Query Start/End: Original strand, 155 - 252
Target Start/End: Original strand, 1653452 - 1653549
Alignment:
Q  155 caaaccgcctcaccaagaaaacagacagcaacacaaaacatatatat--aggaagacgaaacacaactacaaaacataggcaacgacgccagtttgaagc 252  Q
    |||||| |||||| |||||| ||| |||||||||||| |||| ||||  ||||||||||||  |||| ||||||||  |||| ||||||| |||||||||    
T  1653452 caaacctcctcacgaagaaa-caggcagcaacacaaa-cataaatatggaggaagacgaaatccaacaacaaaacacgggcatcgacgccggtttgaagc 1653549  T

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



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