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: Solexa-NF5889-16 (Length: 139)

Name: Solexa-NF5889-16
Description: NF5889
Algorithm: BLASTN 2.2.26 [Sep-21-2011]
Database: JCVI.Medtr.v4.20130313.fasta (1949 entries, 411831487 letters)


[»] Solexa-NF5889-16
Solexa-NF5889-16
[»] chr3 (5 HSPs)
chr3 (1-139)||(35443766-35443904)
chr3 (14-139)||(7315050-7315175)
chr3 (1-113)||(14013338-14013453)
chr3 (19-113)||(67567-67664)
chr3 (19-113)||(6501956-6502053)
[»] chr2 (4 HSPs)
chr2 (11-139)||(43668769-43668897)
chr2 (19-135)||(27732585-27732701)
chr2 (19-139)||(25613885-25614006)
chr2 (11-79)||(42808915-42808983)
[»] chr4 (3 HSPs)
chr4 (1-136)||(31599153-31599287)
chr4 (19-113)||(18579317-18579414)
chr4 (19-113)||(44050385-44050482)
[»] chr7 (1 HSPs)
chr7 (1-96)||(5732562-5732657)
[»] scaffold0219 (1 HSPs)
scaffold0219 (11-113)||(19226-19331)
[»] chr6 (2 HSPs)
chr6 (19-113)||(29286886-29286983)
chr6 (14-113)||(2259763-2259865)
[»] chr5 (1 HSPs)
chr5 (11-113)||(33994441-33994546)
[»] chr1 (3 HSPs)
chr1 (11-113)||(19495729-19495835)
chr1 (19-113)||(7966672-7966769)
chr1 (38-73)||(10165178-10165213)
[»] scaffold0169 (1 HSPs)
scaffold0169 (19-113)||(10556-10653)
[»] chr8 (1 HSPs)
chr8 (11-68)||(31281486-31281544)


Alignment Details
Target: chr3 (Bit Score: 127; Significance: 6e-66; HSPs: 5)
Name: chr3
Description:

Target: chr3; HSP #1
Raw Score: 127; E-Value: 6e-66
Query Start/End: Original strand, 1 - 139
Target Start/End: Original strand, 35443766 - 35443904
Alignment:
Q  1 agtatcagagacgacctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacata 100  Q
    ||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||    
T  35443766 agtatcagacacgaccttcaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacata 35443865  T
Q  101 ataactaataaattgacggaaacatatacatatatatca 139  Q
    |||||||||||||||||||||||||| ||||||||||||    
T  35443866 ataactaataaattgacggaaacatagacatatatatca 35443904  T

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Target: chr3; HSP #2
Raw Score: 78; E-Value: 1e-36
Query Start/End: Original strand, 14 - 139
Target Start/End: Original strand, 7315050 - 7315175
Alignment:
Q  14 acctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    |||| ||||||||||||||| ||||||||||||||| |||||||| ||||||| |||||||||||| | |||||||||||||||  | |||| |||||||    
T  7315050 accttcaatttgtgcaacctcagacatgtttaacttcacaaaagtgtatgaaatatcaaacactagaataaaattaaatgaaacgcagtaaccaataaat 7315149  T
Q  114 tgacggaaacatatacatatatatca 139  Q
    | ||||||||||||||||||||||||    
T  7315150 ttacggaaacatatacatatatatca 7315175  T

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Target: chr3; HSP #3
Raw Score: 37; E-Value: 0.000000000003
Query Start/End: Original strand, 1 - 113
Target Start/End: Complemental strand, 14013453 - 14013338
Alignment:
Q  1 agtatcagagacgacctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatg--aaaaatcaaacactaggacaaaattaaatgaaac 97  Q
    ||||||| | || |||| ||||||||||||||  | ||||||||||||||||||||| ||||||  |||||||| ||| ||| |  |||||||| |||||    
T  14013453 agtatcaaacacaaccttcaatttgtgcaaccacatacatgtttaactttacaaaagctttatgaaaaaaatcatacattagaatgaaattaaacgaaac 14013354  T
Q  98 ataataactaataaat 113  Q
    |||||||  |||||||    
T  14013353 ataataagcaataaat 14013338  T

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Target: chr3; HSP #4
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Original strand, 67567 - 67664
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaa--atcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    |||||| |||||||| |||||||||| |||| ||||||| |||| |||||  |||| ||| ||| ||||||||||||| ||  ||||||| |||||||    
T  67567 caatttttgcaacctcagacatgtttcacttgacaaaagctttaagaaaagaatcatacattagaacaaaattaaatggaatgtaataacgaataaat 67664  T

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Target: chr3; HSP #5
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Original strand, 6501956 - 6502053
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaa--aatcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    ||||||||||||||| |||||||| | |||| ||||||| |||| ||||  ||||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  6501956 caatttgtgcaacctcagacatgtctcacttgacaaaagctttaagaaaagaatcatatattagaacaaaattaaatgaaatgtaataacgaataaat 6502053  T

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Target: chr2 (Bit Score: 81; Significance: 2e-38; HSPs: 4)
Name: chr2
Description:

Target: chr2; HSP #1
Raw Score: 81; E-Value: 2e-38
Query Start/End: Original strand, 11 - 139
Target Start/End: Original strand, 43668769 - 43668897
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacataataactaata 110  Q
    ||||||| | ||||||||||||| |||||| |||||||| ||||||||||||||||||||||||||||| | ||||| ||||||||| || |||| ||||    
T  43668769 acgaccttcgatttgtgcaacctcagacatatttaacttcacaaaagtttatgaaaaatcaaacactagaataaaatgaaatgaaacgtagtaacaaata 43668868  T
Q  111 aattgacggaaacatatacatatatatca 139  Q
    |||||||||||||||| ||||||||||||    
T  43668869 aattgacggaaacatagacatatatatca 43668897  T

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Target: chr2; HSP #2
Raw Score: 61; E-Value: 1e-26
Query Start/End: Original strand, 19 - 135
Target Start/End: Complemental strand, 27732701 - 27732585
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacataataactaataaattgacg 118  Q
    ||||||||||||||| | |||||| |||||| |||||||||||||||| |||| |||  || | ||||||||||| ||| ||||||| ||||||||||||    
T  27732701 caatttgtgcaacctcaaacatgtctaacttcacaaaagtttatgaaatatcagacatcagaataaaattaaatgtaacgtaataaccaataaattgacg 27732602  T
Q  119 gaaacatatacatatat 135  Q
    |||||||| ||||||||    
T  27732601 gaaacatagacatatat 27732585  T

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Target: chr2; HSP #3
Raw Score: 46; E-Value: 1e-17
Query Start/End: Original strand, 19 - 139
Target Start/End: Original strand, 25613885 - 25614006
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaaatcaaacactaggacaaaattaaatgaaacataataactaataaattgac 117  Q
    |||||||| ||||||  |||||||||||||| ||||||| ||||| |||||||| ||| ||| |  |  |||||  |||| ||||||| |||||||||||    
T  25613885 caatttgtacaacctcggacatgtttaacttcacaaaagctttataaaaaatcatacattagaatgaggttaaacaaaacgtaataaccaataaattgac 25613984  T
Q  118 ggaaacatatacatatatatca 139  Q
    ||||||||| ||||||||||||    
T  25613985 ggaaacatacacatatatatca 25614006  T

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Target: chr2; HSP #4
Raw Score: 45; E-Value: 5e-17
Query Start/End: Original strand, 11 - 79
Target Start/End: Complemental strand, 42808983 - 42808915
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactag 79  Q
    ||||||| ||||||||||||| | | ||||||||||||| |||||| ||||||||||||||||||||||    
T  42808983 acgaccttcaatttgtgcaacatcaaacatgtttaacttcacaaaaatttatgaaaaatcaaacactag 42808915  T

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Target: chr4 (Bit Score: 52; Significance: 3e-21; HSPs: 3)
Name: chr4
Description:

Target: chr4; HSP #1
Raw Score: 52; E-Value: 3e-21
Query Start/End: Original strand, 1 - 136
Target Start/End: Original strand, 31599153 - 31599287
Alignment:
Q  1 agtatcagagacgacctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaacata 100  Q
    ||||| ||| ||||||| ||||| ||||||||| | ||||||||||||| |||||| ||||||||| |||||| ||||  | ||||||||||||||  ||    
T  31599153 agtattagacacgaccttcaattagtgcaacctcaaacatgtttaacttgacaaaactttatgaaatatcaaatactataataaaattaaatgaaatgta 31599252  T
Q  101 ataactaataaattgacggaaacatatacatatata 136  Q
    ||| | |||||||||||| ||||||  |||||||||    
T  31599253 atatc-aataaattgacgaaaacattgacatatata 31599287  T

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Target: chr4; HSP #2
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Original strand, 18579317 - 18579414
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaa--atcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    |||||| |||||||| |||||||||| |||| ||||||| |||| |||||  |||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  18579317 caatttttgcaacctcagacatgtttcacttgacaaaagctttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacgaataaat 18579414  T

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Target: chr4; HSP #3
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Complemental strand, 44050482 - 44050385
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaa--aatcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    ||||||||||||||| |||||||| | |||| ||||||| |||| ||||  ||||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  44050482 caatttgtgcaacctcagacatgtcttacttgacaaaagctttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacgaataaat 44050385  T

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Target: chr7 (Bit Score: 40; Significance: 0.00000000000005; HSPs: 1)
Name: chr7
Description:

Target: chr7; HSP #1
Raw Score: 40; E-Value: 0.00000000000005
Query Start/End: Original strand, 1 - 96
Target Start/End: Original strand, 5732562 - 5732657
Alignment:
Q  1 agtatcagagacgacctacaatttgtgcaaccttagacatgtttaactttacaaaagtttatgaaaaatcaaacactaggacaaaattaaatgaaa 96  Q
    ||||||| | ||||| | ||||||||||||||| | ||||||||||||| | |||||||||||||| ||||||||  |  | ||||||||||||||    
T  5732562 agtatcaaacacgacattcaatttgtgcaacctcatacatgtttaacttcaaaaaagtttatgaaatatcaaacataaaaataaaattaaatgaaa 5732657  T

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Target: scaffold0219 (Bit Score: 35; Significance: 0.00000000005; HSPs: 1)
Name: scaffold0219
Description:

Target: scaffold0219; HSP #1
Raw Score: 35; E-Value: 0.00000000005
Query Start/End: Original strand, 11 - 113
Target Start/End: Complemental strand, 19331 - 19226
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaa--atcaaacactaggacaaaattaaatgaaacataataacta 107  Q
    ||||||| |||||| |||||||| |||||||||| |||| ||||||| |||| |||||  |||| | | ||| ||||||||||||||||  ||||||| |    
T  19331 acgaccttcaatttttgcaacctcagacatgtttcacttgacaaaagctttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacga 19232  T
Q  108 ataaat 113  Q
    ||||||    
T  19231 ataaat 19226  T

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Target: chr6 (Bit Score: 35; Significance: 0.00000000005; HSPs: 2)
Name: chr6
Description:

Target: chr6; HSP #1
Raw Score: 35; E-Value: 0.00000000005
Query Start/End: Original strand, 19 - 113
Target Start/End: Original strand, 29286886 - 29286983
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaagttt-atgaaaa--atcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    ||||||||||||||| |||||||| | ||||||||||||||| | |||||  |||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  29286886 caatttgtgcaacctcagacatgtctcactttacaaaagttttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacgaataaat 29286983  T

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Target: chr6; HSP #2
Raw Score: 32; E-Value: 0.000000003
Query Start/End: Original strand, 14 - 113
Target Start/End: Original strand, 2259763 - 2259865
Alignment:
Q  14 acctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaaa--tcaaacactaggacaaaattaaatgaaacataataactaata 110  Q
    |||| |||||| |||||||| |||||||||| |||| ||||||| |||||||||||  |||  || |||||  |||||||||||||  ||||||| ||||    
T  2259763 accttcaatttttgcaacctcagacatgtttcacttcacaaaagctttatgaaaaaaatcacccattaggatgaaattaaatgaaatgtaataacgaata 2259862  T
Q  111 aat 113  Q
    |||    
T  2259863 aat 2259865  T

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Target: chr5 (Bit Score: 35; Significance: 0.00000000005; HSPs: 1)
Name: chr5
Description:

Target: chr5; HSP #1
Raw Score: 35; E-Value: 0.00000000005
Query Start/End: Original strand, 11 - 113
Target Start/End: Complemental strand, 33994546 - 33994441
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaa--atcaaacactaggacaaaattaaatgaaacataataacta 107  Q
    ||||||| |||||| |||||||| |||||||||| |||| ||||||| |||| |||||  |||| | | ||| ||||||||||||||||  ||||||| |    
T  33994546 acgaccttcaatttttgcaacctcagacatgtttcacttgacaaaagctttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacga 33994447  T
Q  108 ataaat 113  Q
    ||||||    
T  33994446 ataaat 33994441  T

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Target: chr1 (Bit Score: 33; Significance: 0.0000000007; HSPs: 3)
Name: chr1
Description:

Target: chr1; HSP #1
Raw Score: 33; E-Value: 0.0000000007
Query Start/End: Original strand, 11 - 113
Target Start/End: Original strand, 19495729 - 19495835
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaaa---tcaaacactaggacaaaattaaatgaaacataataact 106  Q
    ||||||| |||||| |||||||| |||||||||| |||| ||||||  |||||||||||   ||| ||| |||||  |||||||||||||  |||||||     
T  19495729 acgaccttcaatttttgcaacctcagacatgtttcacttcacaaaaactttatgaaaaaaaatcatacattaggatgaaattaaatgaaatgtaataacg 19495828  T
Q  107 aataaat 113  Q
    |||||||    
T  19495829 aataaat 19495835  T

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

Target: chr1; HSP #2
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Original strand, 7966672 - 7966769
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaa--aatcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    |||||| |||||||| |||||||||| |||| ||||||| |||| ||||  ||||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  7966672 caatttttgcaacctcagacatgtttcacttgacaaaagctttaagaaatgaatcatatattagaacaaaattaaatgaaatgtaataacgaataaat 7966769  T

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Target: chr1; HSP #3
Raw Score: 28; E-Value: 0.0000007
Query Start/End: Original strand, 38 - 73
Target Start/End: Complemental strand, 10165213 - 10165178
Alignment:
Q  38 catgtttaactttacaaaagtttatgaaaaatcaaa 73  Q
    |||||||||||| |||||||||||||||| ||||||    
T  10165213 catgtttaacttcacaaaagtttatgaaatatcaaa 10165178  T

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Target: scaffold0169 (Bit Score: 31; Significance: 0.00000001; HSPs: 1)
Name: scaffold0169
Description:

Target: scaffold0169; HSP #1
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 19 - 113
Target Start/End: Complemental strand, 10653 - 10556
Alignment:
Q  19 caatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaa--aatcaaacactaggacaaaattaaatgaaacataataactaataaat 113  Q
    ||||||||||||||| |||||||| | |||| ||||||| |||| ||||  ||||| | | ||| ||||||||||||||||  ||||||| |||||||    
T  10653 caatttgtgcaacctcagacatgtctcacttgacaaaagctttaagaaaagaatcatagattagaacaaaattaaatgaaatgtaataacgaataaat 10556  T

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Target: chr8 (Bit Score: 31; Significance: 0.00000001; HSPs: 1)
Name: chr8
Description:

Target: chr8; HSP #1
Raw Score: 31; E-Value: 0.00000001
Query Start/End: Original strand, 11 - 68
Target Start/End: Original strand, 31281486 - 31281544
Alignment:
Q  11 acgacctacaatttgtgcaaccttagacatgtttaactttacaaaag-tttatgaaaaa 68  Q
    ||||||| |||||| |||||||| | ||||||||||||| ||||||| |||||||||||    
T  31281486 acgaccttcaatttttgcaacctcatacatgtttaacttcacaaaagctttatgaaaaa 31281544  T

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