Locus 1324

Sequence ID 2R_DroMel_CAF1
Location 5,133,025 – 5,133,165
Length 140
Max. P 0.999987
window2294 window2295 window2296 window2297

overview

Window 4

Location 5,133,025 – 5,133,141
Length 116
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 82.88
Mean single sequence MFE -31.56
Consensus MFE -28.99
Energy contribution -28.74
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.92
SVM decision value 1.30
SVM RNA-class probability 0.939313
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5133025 116 + 20766785
AUGUAUUUC-ACUGGUGCCAGUUAGUUUCGUGGAUACUCUGUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCA
.........-((((....))))((((.....((((.....)))).))))..((((((((((...((.(((((((............-......))))))).))...)))))))))).. ( -33.97)
>DroVir_CAF1 12232 111 + 1
--UAAUGC--UCAAUUGC--GUUGGCUUAGUGGAUACUCUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAAAUCG-AACUAACAUCACACCCAGGUUGAGUGAGUCA
--((((((--......))--))))...(((((((((...))))).))))..((((((((((...((.(((((((............-......))))))).))...)))))))))).. ( -36.17)
>DroGri_CAF1 10453 112 + 1
--UUAUCG--CCUGUCGCCUGUUU-UCUUGUGGAUAUUCUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAAAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCA
--......--..............-....(((((((...))))).))....((((((((((...((.(((((((............-......))))))).))...)))))))))).. ( -28.67)
>DroEre_CAF1 7957 99 + 1
------------------UAGUUAGUUUCGUGGAUACUCUGUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCA
------------------..(.((((.....((((.....)))).)))).)((((((((((...((.(((((((............-......))))))).))...)))))))))).. ( -30.97)
>DroWil_CAF1 11228 110 + 1
--AUAA---AUC---UUUCAUUGAACUUUGUGGAUAUUCUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUUAUAAAUAACAUCACACCCAGGUUGAGUGAGUCA
--....---...---..............(((((((...))))).))....((((((((((...((.(((((((...................))))))).))...)))))))))).. ( -28.61)
>DroAna_CAF1 31521 114 + 1
GAUUAUUUA-AC--AUUCUAGUUAGUCUUGUGGAUACUCUGUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCA
(((((.(((-..--....))).)))))..((((((.....)))).))....((((((((((...((.(((((((............-......))))))).))...)))))))))).. ( -30.97)
>consensus
__UUAU____AC___UGCCAGUUAGUUUUGUGGAUACUCUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG_AAAUAACAUCACACCCAGGUUGAGUGAGUCA
.............................(((((((...))))).))....((((((((((...((.(((((((...................))))))).))...)))))))))).. (-28.99 = -28.74 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,133,025 – 5,133,141
Length 116
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 82.88
Mean single sequence MFE -29.95
Consensus MFE -27.12
Energy contribution -27.28
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.91
SVM decision value 0.97
SVM RNA-class probability 0.891821
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5133025 116 - 20766785
UGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAGAGUAUCCACGAAACUAACUGGCACCAGU-GAAAUACAU
.(.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))).......(((.......))).........((((....))))-......... ( -31.40)
>DroVir_CAF1 12232 111 - 1
UGACUCACUCAACCUGGGUGUGAUGUUAGUU-CGAUUUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAGAGUAUCCACUAAGCCAAC--GCAAUUGA--GCAUUA--
.(.(((((((((...((.(((((((......-.(((.....)))))))))).))...))))))))))....((.(((((...))))).....((....--))......--))....-- ( -30.91)
>DroGri_CAF1 10453 112 - 1
UGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUUUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAGAAUAUCCACAAGA-AAACAGGCGACAGG--CGAUAA--
.(.(((((((((...((.(((((((.((((.-......))))..))))))).))...))))))))))....((.(((((...)))))......-.....(....)..)--).....-- ( -31.80)
>DroEre_CAF1 7957 99 - 1
UGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAGAGUAUCCACGAAACUAACUA------------------
.(.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))).......(((.......))).............------------------ ( -27.20)
>DroWil_CAF1 11228 110 - 1
UGACUCACUCAACCUGGGUGUGAUGUUAUUUAUAAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAGAAUAUCCACAAAGUUCAAUGAAA---GAU---UUAU--
.(.(((((((((...((.(((((((.((((........))))..))))))).))...)))))))))).......(((((...)))))................---...---....-- ( -29.50)
>DroAna_CAF1 31521 114 - 1
UGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAGAGUAUCCACAAGACUAACUAGAAU--GU-UAAAUAAUC
.(.(((((((((...((.(((((((.((((.-......))))..))))))).))...))))))))))..((((((((.......)))......((....))..)--))-))....... ( -28.90)
>consensus
UGACUCACUCAACCUGGGUGUGAUGUUAUUU_CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAGAGUAUCCACAAAACUAACUGGCA___GA____AUAA__
.(.(((((((((...((.(((((((.((((........))))..))))))).))...)))))))))).......(((.......)))............................... (-27.12 = -27.28 +   0.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,133,062 – 5,133,165
Length 103
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 91.85
Mean single sequence MFE -32.91
Consensus MFE -31.26
Energy contribution -31.13
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -3.46
Structure conservation index 0.95
SVM decision value 4.80
SVM RNA-class probability 0.999951
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5133062 103 + 20766785
CUGUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAA-AUGCU--G--CUAACU
.((((.((((.(.((((((((((...((.(((((((............-......))))))).))...)))))))))).).)))).))))..-.....--.--...... ( -35.77)
>DroVir_CAF1 12264 105 + 1
CUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAAAUCG-AACUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAA-AUGUUCGG--UUUAUU
...((.((((.(.((((((((((...((.(((((((............-......))))))).))...)))))))))).).)))).))....-........--...... ( -31.37)
>DroPse_CAF1 7400 105 + 1
CUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAA-AUGCG--ACCCGAACU
...((.((((.(.((((((((((...((.(((((((............-......))))))).))...)))))))))).).)))).))....-.....--......... ( -31.37)
>DroWil_CAF1 11258 103 + 1
CUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUUAUAAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGGCAAA-AUG-U--G--UUAAGU
....((((((.(.((((((((((...((.(((((((...................))))))).))...)))))))))).).))).)))....-...-.--.--...... ( -31.81)
>DroAna_CAF1 31556 104 + 1
CUGUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAAAAGGCU--G--CUAACU
.((((.((((.(.((((((((((...((.(((((((............-......))))))).))...)))))))))).).)))).))))........--.--...... ( -35.77)
>DroPer_CAF1 7072 105 + 1
CUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG-AAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAA-AUGCG--ACCCGAACU
...((.((((.(.((((((((((...((.(((((((............-......))))))).))...)))))))))).).)))).))....-.....--......... ( -31.37)
>consensus
CUAUCCUGCUAUCGCUCACUCAAGGAGGUUGUGAUGGAUACCAUAUCG_AAAUAACAUCACACCCAGGUUGAGUGAGUCAAAGCAAGACAAA_AUGCU__G__CUAACU
...((.((((.(.((((((((((...((.(((((((...................))))))).))...)))))))))).).)))).))..................... (-31.26 = -31.13 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,133,062 – 5,133,165
Length 103
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 91.85
Mean single sequence MFE -38.88
Consensus MFE -38.97
Energy contribution -39.08
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -4.43
Structure conservation index 1.00
SVM decision value 5.43
SVM RNA-class probability 0.999987
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5133062 103 - 20766785
AGUUAG--C--AGCAU-UUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAG
......--.--.....-..((((((((((((.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))))).))))))))). ( -41.00)
>DroVir_CAF1 12264 105 - 1
AAUAAA--CCGAACAU-UUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAGUU-CGAUUUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAG
......--........-..((((((((((((.(((((((((...((.(((((((......-.(((.....)))))))))).))...)))))))))))).))))))))). ( -37.61)
>DroPse_CAF1 7400 105 - 1
AGUUCGGGU--CGCAU-UUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAG
.........--.....-..((((((((((((.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))))).))))))))). ( -39.10)
>DroWil_CAF1 11258 103 - 1
ACUUAA--C--A-CAU-UUUGCCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUUAUAAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAG
......--.--.-...-.....(((((((((.(((((((((...((.(((((((.((((........))))..))))))).))...)))))))))))).)))))).... ( -35.50)
>DroAna_CAF1 31556 104 - 1
AGUUAG--C--AGCCUUUUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGACAG
......--.--........((((((((((((.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))))).))))))))). ( -41.00)
>DroPer_CAF1 7072 105 - 1
AGUUCGGGU--CGCAU-UUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUU-CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAG
.........--.....-..((((((((((((.(((((((((...((.(((((((.((((.-......))))..))))))).))...)))))))))))).))))))))). ( -39.10)
>consensus
AGUUAG__C__AGCAU_UUUGUCUUGCUUUGACUCACUCAACCUGGGUGUGAUGUUAUUU_CGAUAUGGUAUCCAUCACAACCUCCUUGAGUGAGCGAUAGCAGGAUAG
...................((((((((((((.(((((((((...((.(((((((.((((........))))..))))))).))...)))))))))))).))))))))). (-38.97 = -39.08 +   0.11)

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 10:02:15 2006