Locus 3112

Sequence ID 3L_DroMel_CAF1
Location 9,019,878 – 9,020,043
Length 165
Max. P 0.989982
window4849 window4850 window4851 window4852

overview

Window 9

Location 9,019,878 – 9,019,983
Length 105
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.91
Mean single sequence MFE -27.07
Consensus MFE -12.96
Energy contribution -16.14
Covariance contribution 3.18
Combinations/Pair 1.04
Mean z-score -2.64
Structure conservation index 0.48
SVM decision value 0.35
SVM RNA-class probability 0.700555
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9019878 105 + 23771897
--UUGCGGAUAGUUCAAAGGGG----CAACGAAUCGAUUUGGCUUCCAUUCAUAGAAAUCGAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACC
--(((((....((((....)))----)........((((((((((.((((....(....).(((((((...))))))))))).))))))))))..)))))........... ( -29.10)
>DroSec_CAF1 58764 105 + 1
--UUGCGGAUAGUUCAAAGGGG----AAUCGAAUCGGUUUGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACC
--((((((((.((((......)----)))...)))((((((((((.((((.((((....))))(((((...)))))..)))).))))))))))..)))))........... ( -28.50)
>DroSim_CAF1 59907 105 + 1
--UUGCGGAUAGUUCAAAGGGC----CAUCGAAUCGGUUUGGCUUCCAUUCAUAGAAACCGAUGCAUAAAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACC
--((((((((.(((.....)))----.))).....((((((((((.((((...........(((((((...))))))))))).))))))))))..)))))........... ( -29.30)
>DroEre_CAF1 62239 100 + 1
GAAGGCGGUUAGUUCAAAGGGC----CAACCAAUUGGUUUGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAU-------GUAAGCCAAAUCAGCGCGAAAUAAUUCACC
....((((((.(((.....)))----.))))..((((((((((((.(((.(((((....)))))........))-------).)))))))))))).))............. ( -27.60)
>DroYak_CAF1 61449 107 + 1
AAAAGCGGAUAGUUCAAAGGGC----CAGCGAAUUGGUUUGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACC
......((((.(((.....)))----..(((...(((((((((((.((((.((((....))))(((((...)))))..)))).))))))))))).)))......))))... ( -28.40)
>DroPer_CAF1 58802 96 + 1
CAAGGCGGCUGGUUCAAAGGUUUUCAAAACGAAU----------CCCAUUCAUAGAAAACUUUGCAUAGAUUAUUAAUAAUC-----AAUCCCAGCGCGAAAUAAUUCACU
....(((.((((....(((((((((.....((((----------...))))...))))))))).....(((((....)))))-----....)))))))............. ( -19.50)
>consensus
__AUGCGGAUAGUUCAAAGGGC____CAACGAAUCGGUUUGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACC
....(((....((((...............)))).((((((((((.((((...........(((((((...))))))))))).))))))))))..)))............. (-12.96 = -16.14 +   3.18)

alignment

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secondary structure

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Window 0

Location 9,019,911 – 9,020,004
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 92.47
Mean single sequence MFE -19.96
Consensus MFE -14.18
Energy contribution -16.02
Covariance contribution 1.84
Combinations/Pair 1.04
Mean z-score -2.17
Structure conservation index 0.71
SVM decision value -0.03
SVM RNA-class probability 0.517114
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9019911 93 + 23771897
UGGCUUCCAUUCAUAGAAAUCGAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGCCGCGUUUC
((((((.((((....(....).(((((((...))))))))))).))))))....((((((((....)))....((........)).))))).. ( -20.20)
>DroSec_CAF1 58797 93 + 1
UGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGCCGCGUUUC
((((((.((((.((((....))))(((((...)))))..)))).))))))....((((((((....)))....((........)).))))).. ( -20.60)
>DroSim_CAF1 59940 93 + 1
UGGCUUCCAUUCAUAGAAACCGAUGCAUAAAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGCAGCGUUUC
((((((.((((...........(((((((...))))))))))).))))))....((((((((....)))....((........)).))))).. ( -20.80)
>DroEre_CAF1 62274 86 + 1
UGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAU-------GUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGUCGCGUUUC
((((((.(((.(((((....)))))........))-------).))))))....(((((((.....(((...........))).))))))).. ( -19.90)
>DroYak_CAF1 61484 89 + 1
UGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGCCGCU----
.((((((..............((((((((...)))))))).(((..(((......).))(((....))).......))).))))))...---- ( -18.30)
>consensus
UGGCUUCCAUUCAUAGAAACCUAUGCAUAUAUUAUGCAUAAUGUAAGCCAAAUCAGCGCGAAAUAAUUCACCAGCCACACGAAGCCGCGUUUC
((((((.((((...........(((((((...))))))))))).))))))....((((((((....)))....((........)).))))).. (-14.18 = -16.02 +   1.84)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,019,911 – 9,020,004
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 92.47
Mean single sequence MFE -26.30
Consensus MFE -21.38
Energy contribution -22.22
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.95
Structure conservation index 0.81
SVM decision value 1.32
SVM RNA-class probability 0.941755
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9019911 93 - 23771897
GAAACGCGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCAUAAUAUAUGCAUCGAUUUCUAUGAAUGGAAGCCA
.......((((((((((((...(((((....)))))(((.....))))))))).(((((((...)))))))...............)))))). ( -25.00)
>DroSec_CAF1 58797 93 - 1
GAAACGCGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCAUAAUAUAUGCAUAGGUUUCUAUGAAUGGAAGCCA
......(((((......)))))(((((....)))))(((.....)))......((((((((...))))))))((((((((....)))))))). ( -28.50)
>DroSim_CAF1 59940 93 - 1
GAAACGCUGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCAUAAUUUAUGCAUCGGUUUCUAUGAAUGGAAGCCA
.....((..(.....)..))..(((((....)))))(((.....))).......(((((((...))))))).((((((((....)))))))). ( -26.40)
>DroEre_CAF1 62274 86 - 1
GAAACGCGACUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUAC-------AUAAUAUAUGCAUAGGUUUCUAUGAAUGGAAGCCA
...(((((....))))).((..(((((....)))))(((.....)))....-------.........))...((((((((....)))))))). ( -23.10)
>DroYak_CAF1 61484 89 - 1
----AGCGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCAUAAUAUAUGCAUAGGUUUCUAUGAAUGGAAGCCA
----..(((((......)))))(((((....)))))(((.....)))......((((((((...))))))))((((((((....)))))))). ( -28.50)
>consensus
GAAACGCGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCAUAAUAUAUGCAUAGGUUUCUAUGAAUGGAAGCCA
.....((.((.....)).))..(((((....)))))(((.....))).......(((((((...))))))).((((((((....)))))))). (-21.38 = -22.22 +   0.84)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,019,945 – 9,020,043
Length 98
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 77.82
Mean single sequence MFE -29.32
Consensus MFE -16.97
Energy contribution -18.58
Covariance contribution 1.61
Combinations/Pair 1.12
Mean z-score -3.04
Structure conservation index 0.58
SVM decision value 2.19
SVM RNA-class probability 0.989982
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9019945 98 - 23771897
UAAUACAAAACUAAGCCCAAAUUAGUCAAAA-AGCCGCUUGAAACG------------------CGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCA
...........((((((.((((((((((..(-((((((.......)------------------))))))..))......(((((....)))))))))))))))))))......... ( -31.60)
>DroSec_CAF1 58831 98 - 1
UAAUACAAAACUAAGCCCAAAUUAGUCAAAA-AGCCGCUUGAAACG------------------CGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCA
...........((((((.((((((((((..(-((((((.......)------------------))))))..))......(((((....)))))))))))))))))))......... ( -31.60)
>DroSim_CAF1 59974 98 - 1
UAAUACAAAACUAAGCCCAAAUUAGUCAAAA-AGCCGCUUGAAACG------------------CUGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCA
...........((((((.((((((((.....-((((((.((((...------------------....)))).)))))).(((((....)))))))))))))))))))......... ( -30.30)
>DroEre_CAF1 62308 92 - 1
UAAUACGAAACUAAGCCGAAAUUAGUCAAAAAAGCAGCUUGAAACG------------------CGACUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUAC-------A
...........((((((.((((((((........(((((....(((------------------((....))))))))))(((((....))))))))))))))))))).-------. ( -30.50)
>DroYak_CAF1 61518 88 - 1
UAAUACAAAACUAAGCGCAAAUUAGUCAAAAAA-----------AG------------------CGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCA
...........(((((.(((((((((.......-----------((------------------(.((.....)).))).(((((....)))))))))))))))))))......... ( -24.80)
>DroPer_CAF1 58865 109 - 1
UAAAAUAAAACUAACUUCAAAUUAGUCAA---AGCAACUUUGAACUCGGAGUCGGAAUGGGAUUCGGUUUCGUGUGGCCAGUGAAUUAUUUCGCGCUGGGAUU-----GAUUAUUAA
...................((((((((..---(((........((.((((..((((......))))..)))).)).....(((((....))))))))..))))-----))))..... ( -27.10)
>consensus
UAAUACAAAACUAAGCCCAAAUUAGUCAAAA_AGCCGCUUGAAACG__________________CGGCUUCGUGUGGCUGGUGAAUUAUUUCGCGCUGAUUUGGCUUACAUUAUGCA
...........((((((.((((((((......................................(((((......)))))(((((....)))))))))))))))))))......... (-16.97 = -18.58 +   1.61)

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 10:49:49 2006