Locus 705

Sequence ID 2R_DroMel_CAF1
Location 3,458,897 – 3,459,076
Length 179
Max. P 0.999453
window1236 window1237 window1238 window1239 window1240

overview

Window 6

Location 3,458,897 – 3,459,007
Length 110
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 86.09
Mean single sequence MFE -32.11
Consensus MFE -24.27
Energy contribution -24.91
Covariance contribution 0.64
Combinations/Pair 1.10
Mean z-score -3.58
Structure conservation index 0.76
SVM decision value 2.80
SVM RNA-class probability 0.997098
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3458897 110 + 20766785
UUGGAAAAGAAGCAUUUUCUUUCUUUGGAUUCAUCAAUUAAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGCCAGGAAGUGAACACAGAGUUCAUUUCAGAUGAAUUC
..((((((......))))))......(((((((((......((((((((((((((((((.....(--------(.((....)).))...))))))))))))))))))..))))))))) ( -38.80)
>DroSec_CAF1 9977 109 + 1
UUGGAA-AUAAGCAUUUUCUUUGUUUGAAUUAACCAAUUGAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUGAACACAGAGUUCAUUUUAGAUGAAUUC
.(((..-.((((((.......))))))......)))(((.(((((((((((((((((((.(((..--------............))).))))))))))))))))))).)))...... ( -30.94)
>DroSim_CAF1 12788 109 + 1
UUGGAA-AUAAGCAUUUUCUUUGUUUGGAUUAACCAAUUGAAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUUAACACAGAGUUCAUUUUAGAUGAAUUC
.(((..-.((((((.......))))))......)))(((.(((((((((((((((((.((((..(--------(.((....)).)).))))))))))))))))))))).)))...... ( -29.80)
>DroEre_CAF1 9271 107 + 1
UAAGAA-AUUAGCAUUCUCUUUGUUUGGAUAAACCAAUUGAAAAUGAGCUCUGUGUUUAAUUC---------GUAGAAGUGACAGG-AGUGAACACAGAGUUCAUUUUAGAUGAAUUC
......-......(((((((....((((.....))))...(((((((((((((((((((.(((---------............))-).)))))))))))))))))))))).)))).. ( -31.40)
>DroYak_CAF1 9568 115 + 1
--AGAA-AUUAGCAUGUUCUUUGUUUGAAUGAACCAAUUGAGAAUGAGCUCUGUGUUGAAUUCGCAGAAUUCGCAGAAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAAAUGAAUUC
--....-.....((((((((((....))).))))......(((((((((((((((((.(.(((((.......)).((....))..))).).)))))))))))))))))..)))..... ( -29.60)
>consensus
UUGGAA_AUAAGCAUUUUCUUUGUUUGGAUUAACCAAUUGAAAAUGAGCUCUGUGUUUAAUUCGC________CAGGAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAGAUGAAUUC
..........................(((((.....(((.(((((((((((((((((((.(((......................))).))))))))))))))))))).))).))))) (-24.27 = -24.91 +   0.64)

alignment

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secondary structure

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Window 7

Location 3,458,897 – 3,459,007
Length 110
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 86.09
Mean single sequence MFE -25.80
Consensus MFE -17.81
Energy contribution -17.93
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -3.75
Structure conservation index 0.69
SVM decision value 2.22
SVM RNA-class probability 0.990555
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3458897 110 - 20766785
GAAUUCAUCUGAAAUGAACUCUGUGUUCACUUCCUGGCACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUUAAUUGAUGAAUCCAAAGAAAGAAAAUGCUUCUUUUCCAA
(.(((((((.(((((((.(((((((((.(.((((..(.....)..--------).))).).))))))))).))))))).....))))))).)...(((((((.....))))))).... ( -33.00)
>DroSec_CAF1 9977 109 - 1
GAAUUCAUCUAAAAUGAACUCUGUGUUCAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUCAAUUGGUUAAUUCAAACAAAGAAAAUGCUUAU-UUCCAA
(((((.(((.(((((((.(((((((((...(((((.........)--------).)))...))))))))).))))))).....))).)))))...................-...... ( -24.00)
>DroSim_CAF1 12788 109 - 1
GAAUUCAUCUAAAAUGAACUCUGUGUUAAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUUCAAUUGGUUAAUCCAAACAAAGAAAAUGCUUAU-UUCCAA
...(((....(((((((.((((((((((((((((.(......).)--------).))))).))))))))).)))))))...((((.....)))).....))).........-...... ( -25.50)
>DroEre_CAF1 9271 107 - 1
GAAUUCAUCUAAAAUGAACUCUGUGUUCACU-CCUGUCACUUCUAC---------GAAUUAAACACAGAGCUCAUUUUCAAUUGGUUUAUCCAAACAAAGAGAAUGCUAAU-UUCUUA
..((((.((((((((((.(((((((((....-....((........---------))....))))))))).)))))))...((((.....))))....)))))))......-...... ( -22.80)
>DroYak_CAF1 9568 115 - 1
GAAUUCAUUUAAAAUGAACUCUGUGUUCACUUCCUGACACUUCUGCGAAUUCUGCGAAUUCAACACAGAGCUCAUUCUCAAUUGGUUCAUUCAAACAAAGAACAUGCUAAU-UUCU--
............(((((.(((((((((((.....))).........((((((...)))))).)))))))).)))))...(((((((...(((.......)))...))))))-)...-- ( -23.70)
>consensus
GAAUUCAUCUAAAAUGAACUCUGUGUUCACUUCCUGACACUCCUG________GCGAAUUAAACACAGAGCUCAUUUUCAAUUGGUUAAUCCAAACAAAGAAAAUGCUUAU_UUCCAA
...(((....(((((((.(((((((((...(((......................)))...))))))))).)))))))...((((.....)))).....)))................ (-17.81 = -17.93 +   0.12)

alignment

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secondary structure

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Window 8

Location 3,458,937 – 3,459,047
Length 110
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 87.49
Mean single sequence MFE -33.21
Consensus MFE -26.77
Energy contribution -28.13
Covariance contribution 1.36
Combinations/Pair 1.08
Mean z-score -4.33
Structure conservation index 0.81
SVM decision value 3.58
SVM RNA-class probability 0.999413
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3458937 110 + 20766785
AAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGCCAGGAAGUGAACACAGAGUUCAUUUCAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUAAAAAUUCACCUAUG
.((((((((((((((((((.....(--------(.((....)).))...)))))))))))))))))).((.((((((...((((((((....))))))))......)))))).))... ( -36.40)
>DroSec_CAF1 10016 110 + 1
AAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUGAACACAGAGUUCAUUUUAGAUGAAUUCAUGGAAAUUAAAGCUUAUUUCUAUUACAAAUUCACCUAUG
(((((((((((((((((((.(((..--------............))).)))))))))))))))))))((.((((((.((((((((........))))))))....)))))).))... ( -35.14)
>DroSim_CAF1 12827 110 + 1
AAAAUGAGCUCUGUGUUUAAUUCGC--------CAGGAGUGUCAGGAAAUUAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAAUACAAAUUUACCUAUG
(((((((((((((((((.((((..(--------(.((....)).)).)))))))))))))))))))))((.((((((...((((((((....))))))))......)))))).))... ( -30.00)
>DroEre_CAF1 9310 108 + 1
AAAAUGAGCUCUGUGUUUAAUUC---------GUAGAAGUGACAGG-AGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAACGCUUAUUUCUAUUAUAAUUUCACCUAUG
(((((((((((((((((((.(((---------............))-).)))))))))))))))))))((.((((.....((((((((....))))))))........)))).))... ( -33.02)
>DroYak_CAF1 9605 118 + 1
AGAAUGAGCUCUGUGUUGAAUUCGCAGAAUUCGCAGAAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAAAUGAAUUCAAGGAAAUUAACGCUUUUUUGUAUUACAAUUUCACUUAUA
(((((((((((((((((.(.(((((.......)).((....))..))).).)))))))))))))))))..........(((((((((((..(......)..)))..))))).)))... ( -31.50)
>consensus
AAAAUGAGCUCUGUGUUUAAUUCGC________CAGGAGUGUCAGGAAGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUACAAAUUCACCUAUG
(((((((((((((((((((.(((......................))).)))))))))))))))))))((.((((((...((((((((....))))))))......)))))).))... (-26.77 = -28.13 +   1.36)

alignment

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secondary structure

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Window 9

Location 3,458,937 – 3,459,047
Length 110
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 87.49
Mean single sequence MFE -27.94
Consensus MFE -22.79
Energy contribution -23.79
Covariance contribution 1.00
Combinations/Pair 1.09
Mean z-score -3.86
Structure conservation index 0.82
SVM decision value 3.62
SVM RNA-class probability 0.999453
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3458937 110 - 20766785
CAUAGGUGAAUUUUUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUGAAAUGAACUCUGUGUUCACUUCCUGGCACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUU
..(((((((((((......(((((........)))))...)))))))))))((((((.(((((((((.(.((((..(.....)..--------).))).).))))))))).)))))). ( -32.50)
>DroSec_CAF1 10016 110 - 1
CAUAGGUGAAUUUGUAAUAGAAAUAAGCUUUAAUUUCCAUGAAUUCAUCUAAAAUGAACUCUGUGUUCAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUU
..((((((((((..(....(((((........))))).)..))))))))))((((((.(((((((((...(((((.........)--------).)))...))))))))).)))))). ( -31.80)
>DroSim_CAF1 12827 110 - 1
CAUAGGUAAAUUUGUAUUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUAAUUUCCUGACACUCCUG--------GCGAAUUAAACACAGAGCUCAUUUU
..(((((.((((((.....(((((........)))))..)))))).)))))((((((.((((((((((((((((.(......).)--------).))))).))))))))).)))))). ( -26.10)
>DroEre_CAF1 9310 108 - 1
CAUAGGUGAAAUUAUAAUAGAAAUAAGCGUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCACU-CCUGUCACUUCUAC---------GAAUUAAACACAGAGCUCAUUUU
..((((((((.(((.....(((((........)))))..))).))))))))((((((.(((((((((....-....((........---------))....))))))))).)))))). ( -24.80)
>DroYak_CAF1 9605 118 - 1
UAUAAGUGAAAUUGUAAUACAAAAAAGCGUUAAUUUCCUUGAAUUCAUUUAAAAUGAACUCUGUGUUCACUUCCUGACACUUCUGCGAAUUCUGCGAAUUCAACACAGAGCUCAUUCU
..((((.(((((((................)))))))))))...........(((((.(((((((((((.....))).........((((((...)))))).)))))))).))))).. ( -24.49)
>consensus
CAUAGGUGAAUUUGUAAUAGAAAUAAGCUUUCAUUUCCUUGAAUUCAUCUAAAAUGAACUCUGUGUUCACUUCCUGACACUCCUG________GCGAAUUAAACACAGAGCUCAUUUU
..((((((((((((.....(((((........)))))..))))))))))))((((((.(((((((((...(((......................)))...))))))))).)))))). (-22.79 = -23.79 +   1.00)

alignment

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secondary structure

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Window 0

Location 3,458,969 – 3,459,076
Length 107
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 78.35
Mean single sequence MFE -20.13
Consensus MFE -12.52
Energy contribution -13.00
Covariance contribution 0.48
Combinations/Pair 1.10
Mean z-score -1.62
Structure conservation index 0.62
SVM decision value 0.03
SVM RNA-class probability 0.547746
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3458969 107 + 20766785
GCCAGGAAGUGAACACAGAGUUCAUUUCAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUAAAAAUUCACCUAUGC-UUGGUA-------AGCAUUAUAUGUAAUAACCAGC
((((((..(((((....(((((((((...)))))))))..((((((((....))))))))........))))).....)-))))).-------...................... ( -24.50)
>DroSec_CAF1 10048 104 + 1
GUCAGGAAAUGAACACAGAGUUCAUUUUAGAUGAAUUCAUGGAAAUUAAAGCUUAUUUCUAUUACAAAUUCACCUAUGCCUUGGUA-------AGCAUUAU----AAUCACCAGC
...(((((((((((.....))))))))(((.((((((.((((((((........))))))))....)))))).)))..)))((((.-------........----....)))).. ( -20.02)
>DroSim_CAF1 12859 111 + 1
GUCAGGAAAUUAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAAUACAAAUUUACCUAUGCCUUGGUUUUACCUUGCCAUUAU----AAUCACCAGC
...((((((((......(((((((((...)))))))))..((((((((....))))))))......))))).)))......((((........))))....----.......... ( -20.60)
>DroEre_CAF1 9341 81 + 1
GACAGG-AGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAACGCUUAUUUCUAUUAUAAUUUCACCUAUG---------------------------------CAAC
....((-.(((((....(((((((((...)))))))))..((((((((....))))))))........)))))))...---------------------------------.... ( -18.30)
>DroYak_CAF1 9645 103 + 1
GUCAGGAAGUGAACACAGAGUUCAUUUUAAAUGAAUUCAAGGAAAUUAACGCUUUUUUGUAUUACAAUUUCACUUAUAC-UUGGUA-------AACAUUAU----AAUCACCAGC
.(((.(((((((((.....)))))))))...)))....(((((((((((..(......)..)))..))))).)))....-(((((.-------........----....))))). ( -17.22)
>consensus
GUCAGGAAGUGAACACAGAGUUCAUUUUAGAUGAAUUCAAGGAAAUGAAAGCUUAUUUCUAUUACAAAUUCACCUAUGC_UUGGUA_______AGCAUUAU____AAUCACCAGC
...(((...........(((((((((...)))))))))..((((((((....))))))))............)))........................................ (-12.52 = -13.00 +   0.48)

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 09:45:06 2006