Locus 5501

Sequence ID 2R_DroMel_CAF1
Location 17,654,008 – 17,654,327
Length 319
Max. P 0.999692
window8791 window8792 window8793 window8794 window8795 window8796

overview

Window 1

Location 17,654,008 – 17,654,128
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.75
Mean single sequence MFE -23.98
Consensus MFE -19.22
Energy contribution -19.10
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.45
Structure conservation index 0.80
SVM decision value 0.16
SVM RNA-class probability 0.613721
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654008 120 + 20766785
CCAUGAAAUGAAAACUUUUCCCUCAAAUAUUCAUUAGUUAGUUCCAAGCUCAUUUAAGCAUAGCUUGGGGAAAUAAAAUUUCCAGUUUUGUUAUUUAAAUAGCUGAAUACAUUUCGAAGA
...(((((((((((((...........................(((((((...........)))))))((((((...))))))))))))(((((....)))))......))))))).... ( -23.50)
>DroSec_CAF1 7645 120 + 1
CCAUGAAAUGAAAACUUUUCCCCCAAAUAUUCAUUAGUUAGUUCCAAGCUCAUUUGAGCAUAGCUUGGGGAAAUAAAAUUUCCAGUUUUGUUAUUUAAAUGGCUGAAUACAUUUCGAAGA
...(((((((......(((((((............(((((.......((((....)))).))))).)))))))...........((((.(((((....))))).)))).))))))).... ( -23.52)
>DroSim_CAF1 13556 116 + 1
CCAUGAAAUGAAAACUUUUCCCCCAAAUAUUCAUUA----GUUCCAAGCUCAUUUGAGCAUAGCUUGGGGAAAUAAAAUUUCCAGUUUUGUUAUUUAAAUAGCUGAAUACAUUUCGAAGA
...(((((((......(((((((............(----(((....((((....))))..)))).)))))))...........((((.(((((....))))).)))).))))))).... ( -23.82)
>DroEre_CAF1 7823 119 + 1
CGAUGAUAUGAAAAC-UUUUCCCCAAAUAUUCAUUAGUUAACUCCAAGCUCAUUUGGGCAUGCCUUAGGGAAAUAAAAUGUUCAGUUUUGUUAUUUAAAUAGCUGAAUACAUUUCGAAGA
...(((.(((.....-.((((((............((....))....((((....))))........)))))).....(((((((((.............)))))))))))).))).... ( -21.22)
>DroYak_CAF1 19229 120 + 1
CCAUGAAAUGAAAACCUUUUCCCCAAAUAUUCAUUAGUUAACUCCAGGCUCAUUUGGGUAUGCCUUGGGGAAAUAAAAUGAUCAGUUUUGUUAUUUAAAUAGCUGAAUACAUUUCGGAGA
...(((((((.......((((((((((((((((..((((.......))))....)))))))...)))))))))........((((((.............))))))...))))))).... ( -27.82)
>consensus
CCAUGAAAUGAAAACUUUUCCCCCAAAUAUUCAUUAGUUAGUUCCAAGCUCAUUUGAGCAUAGCUUGGGGAAAUAAAAUUUCCAGUUUUGUUAUUUAAAUAGCUGAAUACAUUUCGAAGA
...(((((((..........((((((.((.....))...........((((....)))).....))))))..............((((.(((((....))))).)))).))))))).... (-19.22 = -19.10 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,654,128 – 17,654,247
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.99
Mean single sequence MFE -21.40
Consensus MFE -17.98
Energy contribution -17.94
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.84
SVM decision value 1.42
SVM RNA-class probability 0.952716
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654128 119 + 20766785
ACUGAA-AGGCAGAAGCACAAAAACCAUUCGAAAAUCAUCAACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUUGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
((((.(-((((((.................((......)).(((......)))...................)))))))(((.((....)).))).............))))........ ( -21.50)
>DroSec_CAF1 7765 120 + 1
ACUGAACUGGCAGAAGCACAAAAACCAUUCGAAAAUCAUCAACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCAUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
..(((((((((((.................((......)).(((......)))...................))))...(((.((....)).))).............)))))))..... ( -20.60)
>DroSim_CAF1 13672 120 + 1
ACUGAACUGGCAGAAGCACAAAAACCAUUCGAAAAUCAUCAACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
..(((((((((((.................((......)).(((......)))...................)))))..(((.((....)).)))..............))))))..... ( -20.00)
>DroEre_CAF1 7942 117 + 1
ACUGAAC-GGCAGAAGC--AGAAACCAUUCGAAAAUCAUCAACGAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
((((...-(((((....--.((....(((((...........))))).....))....((((.....)))).)))))..(((.((....)).))).............))))........ ( -22.60)
>DroYak_CAF1 19349 117 + 1
ACUGAAC-GGCAGAAGC--AAAAACCAUUCGAAAAUCAUCAACGAAUAAAUGUCAAAAUAAUAACAAAUUAACUGCCUUGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
((((...-(((((....--.......(((((...........)))))...........((((.....)))).))))).((((.((....)).))))............))))........ ( -22.30)
>consensus
ACUGAAC_GGCAGAAGCACAAAAACCAUUCGAAAAUCAUCAACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAAC
((((....(((((.................((......)).(((......)))...................)))))..(((.((....)).))).............))))........ (-17.98 = -17.94 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,654,128 – 17,654,247
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.99
Mean single sequence MFE -29.88
Consensus MFE -24.48
Energy contribution -24.68
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.82
SVM decision value 1.04
SVM RNA-class probability 0.904954
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654128 119 - 20766785
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCAAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUUGAUGAUUUUCGAAUGGUUUUUGUGCUUCUGCCU-UUCAGU
(.((((...((((((((.....)))))))).....)))).)(((((((...(((((..((((((..((((......))))))))))...)))))(((......))).))))))-)..... ( -27.70)
>DroSec_CAF1 7765 120 - 1
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAUGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUUGAUGAUUUUCGAAUGGUUUUUGUGCUUCUGCCAGUUCAGU
.........((((((((.....))))))))....(((((..(.(((((...(((((..((((((..((((......))))))))))...))))).....))))))..)))))........ ( -27.90)
>DroSim_CAF1 13672 120 - 1
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUUGAUGAUUUUCGAAUGGUUUUUGUGCUUCUGCCAGUUCAGU
.........((((((((.....))))))))....(((((..(((((((...(((((..((((((..((((......))))))))))...))))).....)))).))))))))........ ( -28.50)
>DroEre_CAF1 7942 117 - 1
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUCGUUGAUGAUUUUCGAAUGGUUUCU--GCUUCUGCC-GUUCAGU
.........((((((((.....))))))))..((((((...(((((((...(((((..((((((..(((........)))))))))...))))).....))--)))))))))-))..... ( -33.70)
>DroYak_CAF1 19349 117 - 1
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCAAGGCAGUUAAUUUGUUAUUAUUUUGACAUUUAUUCGUUGAUGAUUUUCGAAUGGUUUUU--GCUUCUGCC-GUUCAGU
.........((((((((.....))))))))..(((((((...((((((((((..((....))..)))))..(((((((...........)))))))....)--)))))))))-))..... ( -31.60)
>consensus
GUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUUGAUGAUUUUCGAAUGGUUUUUGUGCUUCUGCC_GUUCAGU
.........((((((((.....))))))))....(((((...((((.(((((..((....))..))))).........((((......))))...........)))))))))........ (-24.48 = -24.68 +   0.20)

alignment

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secondary structure

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Window 4

Location 17,654,167 – 17,654,287
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -25.64
Consensus MFE -24.60
Energy contribution -25.00
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.96
SVM decision value 3.90
SVM RNA-class probability 0.999692
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654167 120 + 20766785
AACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUUGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
......(((((((.....((((.....))))..((((...(((((.((((..((..(((....).))(((.(((((.....)))))...))))).)))).)))))))))....))))))) ( -26.40)
>DroSec_CAF1 7805 120 + 1
AACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCAUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
......(((((((.....((((.....))))..(((....(((((.((((..((..(((....).))(((.(((((.....)))))...))))).)))).))))).)))....))))))) ( -24.10)
>DroSim_CAF1 13712 120 + 1
AACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
......(((((((.....((((.....))))..((((...(((((.((((..((..(((....).))(((.(((((.....)))))...))))).)))).)))))))))....))))))) ( -26.40)
>DroEre_CAF1 7979 120 + 1
AACGAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
......(((((((.....((((.....))))..((((...(((((.((((..((..(((....).))(((.(((((.....)))))...))))).)))).)))))))))....))))))) ( -26.40)
>DroYak_CAF1 19386 120 + 1
AACGAAUAAAUGUCAAAAUAAUAACAAAUUAACUGCCUUGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
........(((((.....((((.....))))..((((...(((((.((((..((..(((....).))(((.(((((.....)))))...))))).)))).)))))))))....))))).. ( -24.90)
>consensus
AACAAAUUAAUGUCAAAAUAAUAACAAAUUAACUGCCUCGGCUGCCGUGGCUGCCACAAGAAAUAUGACAGUUUACAAACGGUAAAAAAUGUGCCCCACAGCAGCGGCAAUAAACAUUAA
......(((((((.....((((.....))))..((((...(((((.((((..((..((.......))(((.(((((.....)))))...))))).)))).)))))))))....))))))) (-24.60 = -25.00 +   0.40)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,654,167 – 17,654,287
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -39.32
Consensus MFE -38.57
Energy contribution -38.97
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -4.69
Structure conservation index 0.98
SVM decision value 3.74
SVM RNA-class probability 0.999572
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654167 120 - 20766785
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCAAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUU
((((((((.((((((((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))...)))))).................))))))))...... ( -40.17)
>DroSec_CAF1 7805 120 - 1
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAUGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUU
((((((((.(((((.((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))....))))).................))))))))...... ( -36.77)
>DroSim_CAF1 13712 120 - 1
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUU
((((((((.((((((((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))...)))))).................))))))))...... ( -40.17)
>DroEre_CAF1 7979 120 - 1
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUCGUU
((((((((.((((((((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))...)))))).................))))))))...... ( -40.17)
>DroYak_CAF1 19386 120 - 1
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCAAGGCAGUUAAUUUGUUAUUAUUUUGACAUUUAUUCGUU
.....(((.((((((((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))...)))))).))).(((((......))))).......... ( -39.30)
>consensus
UUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGCCGAGGCAGUUAAUUUGUUAUUAUUUUGACAUUAAUUUGUU
((((((((.((((((((((((((((.........(((((.....)))))((((((((.....))))))))))))))))))...)))))).................))))))))...... (-38.57 = -38.97 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,654,207 – 17,654,327
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.67
Mean single sequence MFE -37.70
Consensus MFE -36.90
Energy contribution -37.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.98
SVM decision value 2.95
SVM RNA-class probability 0.997857
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17654207 120 - 20766785
AGUUGACGCCUUGAAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
((.(((((..((((......))))))))).)).......................((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) ( -36.50)
>DroSec_CAF1 7845 120 - 1
AGUUGACGCCUUGGAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
.((((((..((((((...((....))...))))))....))))))..........((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) ( -38.00)
>DroSim_CAF1 13752 120 - 1
AGUUGACGCCUUGGAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
.((((((..((((((...((....))...))))))....))))))..........((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) ( -38.00)
>DroEre_CAF1 8019 120 - 1
AGUUGACGCCUUGGAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
.((((((..((((((...((....))...))))))....))))))..........((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) ( -38.00)
>DroYak_CAF1 19426 120 - 1
AGUUGACGCCUUGGAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
.((((((..((((((...((....))...))))))....))))))..........((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) ( -38.00)
>consensus
AGUUGACGCCUUGGAAAUUGUCAACGUCAUCUAAGCCAAGUUAAUGUUUAUUGCCGCUGCUGUGGGGCACAUUUUUUACCGUUUGUAAACUGUCAUAUUUCUUGUGGCAGCCACGGCAGC
.((((((..((((((...((....))...))))))....))))))..........((((((((((.........(((((.....)))))((((((((.....)))))))))))))))))) (-36.90 = -37.10 +   0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:46 2006