Locus 2232

Sequence ID 2R_DroMel_CAF1
Location 8,249,993 – 8,250,125
Length 132
Max. P 0.978459
window3675 window3676 window3677

overview

Window 5

Location 8,249,993 – 8,250,097
Length 104
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -21.45
Consensus MFE -14.10
Energy contribution -14.77
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.66
SVM decision value 0.68
SVM RNA-class probability 0.821962
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8249993 104 + 20766785
UCA-UUUGAUUUUCCACUUUUUGGCCUGUGUCUGUG--UGUGUGUUUGCCCACUCGAAUGCCUCCGAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGC-UGCAAAUU
..(-((((((.((((((((...(((...((...(((--.((......)).))).))...)))...)))))).))....))))))).(((((((......-))))))). ( -25.20)
>DroPse_CAF1 36868 84 + 1
-GCUGGUGC---------UUUUGGCUG--------------GCGUUUGCCCACUCGAAUGCCUCCAAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGCUUGCAAAUU
-((((((((---------.(((((..(--------------(((((((......)))))))).)))))....(((((....)))))....)))).))))......... ( -23.40)
>DroGri_CAF1 59068 81 + 1
--------G---------CUGUGGCUUGU----------GUGCUGUUGCCCACUCGAAUGCCUUCAAGUGCCAAUUUUAUCAAAUUAUUUGCACUUAACUCGCAAAUU
--------(---------(...(((..((----------(.((....)).)))......)))...((((((.(((...........))).)))))).....))..... ( -16.90)
>DroSim_CAF1 39708 99 + 1
UCA-UUCGAUU-------UUUUGGCCUGUGUGUGUGUGUGUUUGUUUGCCCACUCGAAUGCCUCCGAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGC-UGCAAAUU
...-.......-------.....((..((..(((((...(((((.(((((.(((((........))))))))))......)))))....)))))...))-.))..... ( -22.90)
>DroEre_CAF1 37114 83 + 1
UGC-UUUGU---------UUUUGGCCU--------------GUGUUUGCCCACUCGAAUGCCUCCGAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGC-UGCAAAUU
.((-(....---------....)))..--------------....(((((.(((((........))))))))))............(((((((......-))))))). ( -19.90)
>DroYak_CAF1 38770 83 + 1
UGU-UUUGG---------UUUUGGCCU--------------GUGUUUGCCCACUCGAAUGCCUCCGAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGC-UGCAAAUU
...-...((---------(....))).--------------....(((((.(((((........))))))))))............(((((((......-))))))). ( -20.40)
>consensus
UGA_UUUGA_________UUUUGGCCU______________GUGUUUGCCCACUCGAAUGCCUCCGAGUGGCAAUUUUAUCGAAUUAUUUGCACUUAGC_UGCAAAUU
.............................................(((((.(((((........))))))))))............(((((((.......))))))). (-14.10 = -14.77 +   0.67)

alignment

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secondary structure

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Window 6

Location 8,249,993 – 8,250,097
Length 104
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.03
Mean single sequence MFE -22.77
Consensus MFE -19.63
Energy contribution -19.30
Covariance contribution -0.33
Combinations/Pair 1.16
Mean z-score -2.78
Structure conservation index 0.86
SVM decision value 1.81
SVM RNA-class probability 0.978459
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8249993 104 - 20766785
AAUUUGCA-GCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUUCGAGUGGGCAAACACACA--CACAGACACAGGCCAAAAAGUGGAAAAUCAAA-UGA
.(((((((-......))))))).....(((....((((((((((((....))))))).))))).......--............(((.....)))...)))...-... ( -24.60)
>DroPse_CAF1 36868 84 - 1
AAUUUGCAAGCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUUGGAGGCAUUCGAGUGGGCAAACGC--------------CAGCCAAAA---------GCACCAGC-
.........(((..((((.....((((((......((((.......)))).)))))).(((....))--------------)........---------)))).)))- ( -21.30)
>DroGri_CAF1 59068 81 - 1
AAUUUGCGAGUUAAGUGCAAAUAAUUUGAUAAAAUUGGCACUUGAAGGCAUUCGAGUGGGCAACAGCAC----------ACAAGCCACAG---------C--------
...(((.(.(((..((((...((((((....)))))).((((((((....))))))))(....).))))----------...)))).)))---------.-------- ( -19.10)
>DroSim_CAF1 39708 99 - 1
AAUUUGCA-GCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUUCGAGUGGGCAAACAAACACACACACACACAGGCCAAAA-------AAUCGAA-UGA
.(((((((-......))))))).(((((((....((((((((((((....))))))).))))).............(.....).......-------.))))))-).. ( -26.20)
>DroEre_CAF1 37114 83 - 1
AAUUUGCA-GCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUUCGAGUGGGCAAACAC--------------AGGCCAAAA---------ACAAA-GCA
.(((((((-......))))))).............(((((((((((....))))))))(((......--------------..)))....---------.....-))) ( -22.70)
>DroYak_CAF1 38770 83 - 1
AAUUUGCA-GCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUUCGAGUGGGCAAACAC--------------AGGCCAAAA---------CCAAA-ACA
.(((((((-......)))))))............((((((((((((....))))))).)))))....--------------.((......---------))...-... ( -22.70)
>consensus
AAUUUGCA_GCUAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUUCGAGUGGGCAAACAC______________AGGCCAAAA_________CCAAA_GCA
.(((((((.......)))))))............((((((((((((....))))))).)))))............................................. (-19.63 = -19.30 +  -0.33)

alignment

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secondary structure

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Window 7

Location 8,250,024 – 8,250,125
Length 101
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.03
Mean single sequence MFE -24.85
Consensus MFE -14.50
Energy contribution -14.12
Covariance contribution -0.39
Combinations/Pair 1.25
Mean z-score -2.29
Structure conservation index 0.58
SVM decision value 1.32
SVM RNA-class probability 0.941691
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8250024 101 - 20766785
-------ACGAAAAGUC-GCUCGUUAUU-UC---CAAUUGAAUUUGCA-GC-UAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUU---CGAGUGGGCAAACACACACACA
-------((((......-..))))....-..---..((((((((((((-..-....))))...))))))))....((((((((((((....))---))))).)))))........... ( -25.30)
>DroVir_CAF1 52719 96 - 1
---GGCAACAACAAUUU-GCUCGUUAUU-UC---AAAUUGAAUUUGUGAGU-UAAGUGCAAAUAAUUUGAUAAAAUUGGCACUCGGAGGCAUU---CGAGUGGGCAAU----------
---(....)......((-((((((((..-((---(((((..((((((....-.....)))))))))))))......))))(((((((....))---))))))))))).---------- ( -24.30)
>DroGri_CAF1 59080 104 - 1
ACA-GCAACAACAAUUU-GCUCGUUAUUUUC---AAAUUGAAUUUGCGAGU-UAAGUGCAAAUAAUUUGAUAAAAUUGGCACUUGAAGGCAUU---CGAGUGGGCAACAGCAC-----
...-.............-((((((....(((---.....)))...))))))-...((((...((((((....)))))).((((((((....))---))))))(....).))))----- ( -24.90)
>DroWil_CAF1 50335 104 - 1
----CAAAAG-AAAAUA-CCUCGUUAUU-UGCCCAAAUUGAAUUUGCA-ACUUAAGUGCAAAUAAUUUGAUAAAAUUGCCACUUGCAGGCAUUUCUUAAGUGGGCAAAAACA------
----......-......-....(((.((-((((((....(((..(((.-...((((((....((((((....)))))).))))))...))).))).....))))))))))).------ ( -25.10)
>DroAna_CAF1 39808 94 - 1
-------ACGAAAAGUC-GCUCGUUAUU-UC---CAAUUGAAUUUGCA-GC-UAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCAGUGGCAUA---CGAGUGGGCCAAAAA-------
-------........((-((((((....-..---..((((((((((((-..-....))))...)))))))).....((((((...)))))).)---)))))))........------- ( -25.70)
>DroPer_CAF1 36616 99 - 1
----CAAACGAAAAUUCGGCUCGUUAUU-UC---CAAUUGAAUUUGCAAGC-UAAGUGCAAAUAAUUCGAUAAAAUUGCCACUUGGAGGCAUU---CGAGUGGGCAAACGC-------
----..(((((.........)))))...-..---..((((((((((((...-....))))...))))))))....((((((((((((....))---))))).)))))....------- ( -23.80)
>consensus
______AACGAAAAUUC_GCUCGUUAUU_UC___AAAUUGAAUUUGCA_GC_UAAGUGCAAAUAAUUCGAUAAAAUUGCCACUCGGAGGCAUU___CGAGUGGGCAAAAAC_______
..................((((...................(((((((........))))))).(((((.......((((.......)))).....)))))))))............. (-14.50 = -14.12 +  -0.39)

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 10:24:28 2006