Locus 6855

Sequence ID 3L_DroMel_CAF1
Location 18,406,592 – 18,406,756
Length 164
Max. P 0.894682
window11115 window11116 window11117 window11118 window11119

overview

Window 5

Location 18,406,592 – 18,406,692
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.49
Mean single sequence MFE -21.28
Consensus MFE -14.86
Energy contribution -15.20
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.70
SVM decision value 0.21
SVM RNA-class probability 0.635088
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18406592 100 + 23771897
--------CAUUCU------------CAAAGGCAAAACAAAGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCG
--------......------------...(((((((((((.........))))))).))))...((((((((........))))))))((((((((..............))).))))). ( -19.04)
>DroPse_CAF1 45293 96 + 1
AG--GAGACAUUCU------------CAAAAGCAAAACAAAGAAGA-AAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAA---------
..--(((.((..(.------------...(((((((((((......-..))))))).))))...((((((((........)))))))))..)).)))..............--------- ( -18.30)
>DroEre_CAF1 50360 104 + 1
----AAGGC------------AAAGGCAAAGGCAAAACAAAGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACCAGUGCAGGCG
----...((------------....(((..((.........(((((......)))))(((....((((((((........))))))))....))).............))..)))..)). ( -21.80)
>DroWil_CAF1 463200 106 + 1
AGGCAAAAAAUUCU------------CAAAAGCAAAACAAAGAAGA-AAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGC-
((((..........------------...(((((((((((......-..))))))).))))...((((((((........)))))))))))).(((...(((.........)))..)))- ( -19.90)
>DroYak_CAF1 51339 116 + 1
----AAGGCAUUCUCCAGAGCAAAAGCAAGAGCAAAACAAAGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCG
----...((........((((..((((..(((((((((((.........))))))).))))...((((((((........)))))))))))).))))..(((.........)))...)). ( -27.50)
>DroAna_CAF1 39325 104 + 1
----AAGGGAUUCU------------CGAAAGCAAAAUAAAGAAAGGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACGAAUGCAGGCG
----...(.((((.------------.((((((((..............))))))))(((....((((((((........))))))))....)))..............)))).)..... ( -21.14)
>consensus
____AAGGCAUUCU____________CAAAAGCAAAACAAAGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCG
.............................(((((((((((.........))))))).))))...((((((((........))))))))(((((.....................))))). (-14.86 = -15.20 +   0.34)

alignment

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secondary structure

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Window 6

Location 18,406,592 – 18,406,692
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.49
Mean single sequence MFE -22.46
Consensus MFE -16.38
Energy contribution -16.55
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.73
SVM decision value 0.04
SVM RNA-class probability 0.554646
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18406592 100 - 23771897
CGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCUUUGUUUUGCCUUUG------------AGAAUG--------
.(((.((((.........)))).).))......((((((((......))))))))((((((((.(((((((.........)))))))))..)))------------)))...-------- ( -18.70)
>DroPse_CAF1 45293 96 - 1
---------UUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUU-UCUUCUUUGUUUUGCUUUUG------------AGAAUGUCUC--CU
---------...(((((((.(.....)))))))).............((((((((((..((((.(((((((..-......)))))))))))..)------------))))))).))--.. ( -21.90)
>DroEre_CAF1 50360 104 - 1
CGCCUGCACUGGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCUUUGUUUUGCCUUUGCCUUU------------GCCUU----
.....(((..(((((((((.(.....)))))))((((((((......))))))))......((.(((((((.........)))))))))....)))..)------------))...---- ( -23.00)
>DroWil_CAF1 463200 106 - 1
-GCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUU-UCUUCUUUGUUUUGCUUUUG------------AGAAUUUUUUGCCU
-(((.((((.........)))).).))...(((((((((((......)))))(((((..((((.(((((((..-......)))))))))))..)------------))))..)))))).. ( -25.00)
>DroYak_CAF1 51339 116 - 1
CGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCUUUGUUUUGCUCUUGCUUUUGCUCUGGAGAAUGCCUU----
..((.((((.........)))).((((.(((((((((((((......)))))))).....(((.(((((((.........))))))))))..)))))..)))).))..........---- ( -27.10)
>DroAna_CAF1 39325 104 - 1
CGCCUGCAUUCGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCCUUUCUUUAUUUUGCUUUCG------------AGAAUCCCUU----
.....(((((((.((...(((((..((...))..)))))...))..)))))))((((..((((((((................))))))))..)------------))).......---- ( -19.09)
>consensus
CGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCUUUGUUUUGCUUUUG____________AGAAUGCCUU____
.............((((((.(.....)))))))((((((((......))))))))......((.(((((((.........)))))))))............................... (-16.38 = -16.55 +   0.17)

alignment

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secondary structure

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Window 7

Location 18,406,612 – 18,406,732
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 88.19
Mean single sequence MFE -23.08
Consensus MFE -20.43
Energy contribution -21.10
Covariance contribution 0.67
Combinations/Pair 1.16
Mean z-score -1.76
Structure conservation index 0.89
SVM decision value 0.79
SVM RNA-class probability 0.851190
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18406612 120 + 23771897
AGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCGCACACACAAACUGCAUUUAUUUAGUUAGCAAACAAAAUAG
.........((((((.((((....((((((((........))))))))....)))..............((((((((.............)))))))).........).))))))..... ( -23.92)
>DroVir_CAF1 122606 115 + 1
AGAAGA-AAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGC----AAACAAACUGCAUUUAUUUAGUUAACAAAAAAAAAAA
......-..(((((..((((....((((((((........))))))))....)))..............((((((((..----.......)))))))).....)..)))))......... ( -24.20)
>DroPse_CAF1 45319 101 + 1
AGAAGA-AAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAA------------------GCUGCAUUUAUUUGGUUAGCAAACAAAAAAU
......-..((((((..(((....((((((((........))))))))....)))................------------------((((.(((.....)))))))))))))..... ( -17.30)
>DroEre_CAF1 50384 120 + 1
AGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACCAGUGCAGGCGCACACACAAACUGCAUUUAUUUGGUUAGCAGGAAAAAUGG
............((((((((....((((((((........))))))))....)))...........(((((((((((.............)))))).....))))).....))))).... ( -24.82)
>DroYak_CAF1 51375 119 + 1
AGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCGCACACACAAACUGCAUUUAUUUAGUUAGCAAGCAAAAUG-
.........((((((.((((....((((((((........))))))))....)))..............((((((((.............)))))))).........).))))))....- ( -23.92)
>DroAna_CAF1 39349 120 + 1
AGAAAGGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACGAAUGCAGGCGCGCACACAAACUGCAUUUAUUUAGUUAGCAAACAAAAAGG
.........((((((.((((....((((((((........))))))))....)))..............((((((((.............)))))))).........).))))))..... ( -24.32)
>consensus
AGAAAAGAAUUGUUUUCGCUUAAAAGAACAUUCAAAUGGAAAUGUUCUGCUUGGCUCAACACAAACAACAAGUGCAGGCGCACACACAAACUGCAUUUAUUUAGUUAGCAAACAAAAAAG
.........(((((..((((....((((((((........))))))))....)))..............((((((((.............)))))))).....)..)))))......... (-20.43 = -21.10 +   0.67)

alignment

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secondary structure

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Window 8

Location 18,406,612 – 18,406,732
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.19
Mean single sequence MFE -25.95
Consensus MFE -21.79
Energy contribution -22.83
Covariance contribution 1.04
Combinations/Pair 1.08
Mean z-score -1.71
Structure conservation index 0.84
SVM decision value 0.13
SVM RNA-class probability 0.599792
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18406612 120 - 23771897
CUAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCU
...(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).))).....(((((((((......)))))))))...))))))))............. ( -27.10)
>DroVir_CAF1 122606 115 - 1
UUUUUUUUUUUGUUAACUAAAUAAAUGCAGUUUGUUU----GCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUU-UCUUCU
......((((((((.....(((((.(((((.......----..))))).)))))(((((.(.....))))))(((((((((......)))))))))....)))))))).....-...... ( -22.90)
>DroPse_CAF1 45319 101 - 1
AUUUUUUGUUUGCUAACCAAAUAAAUGCAGC------------------UUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUU-UCUUCU
....((((((((.....)))))))).((.((------------------(((..((((.....)))))))))(((((((((......))))))))).....))((((....))-)).... ( -20.90)
>DroEre_CAF1 50384 120 - 1
CCAUUUUUCCUGCUAACCAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUGGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCU
....((((((((((((((((((((.(((((...(((....))))))))....))))))).))).))).....(((((((((......)))))))))....)).)))))............ ( -27.30)
>DroYak_CAF1 51375 119 - 1
-CAUUUUGCUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCU
-..(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).))).....(((((((((......)))))))))...))))))))............. ( -29.50)
>DroAna_CAF1 39349 120 - 1
CCUUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGCGCGCCUGCAUUCGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCCUUUCU
..((((((((((((((((((((((((((((...(((....)))))))))...))))))).))).))).....(((((((((......)))))))))...)))))))))............ ( -28.00)
>consensus
CCAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUUUCCAUUUGAAUGUUCUUUUAAGCGAAAACAAUUCUUUUCU
...(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).))).....(((((((((......)))))))))...))))))))............. (-21.79 = -22.83 +   1.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,406,652 – 18,406,756
Length 104
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 86.78
Mean single sequence MFE -22.18
Consensus MFE -21.18
Energy contribution -21.15
Covariance contribution -0.03
Combinations/Pair 1.07
Mean z-score -1.51
Structure conservation index 0.95
SVM decision value 0.98
SVM RNA-class probability 0.894682
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18406652 104 - 23771897
-UUUGCUCCUUUUCACUU-------UUUUUUU---CUAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUU
-.................-------.......---...(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).)).))))))))).... ( -21.40)
>DroSec_CAF1 42897 110 - 1
-UUUGCUCCUUUGCUCCUU-UCCCGUUUUUUU---CUAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUU
-...((......)).....-............---...(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).)).))))))))).... ( -22.60)
>DroSim_CAF1 42051 111 - 1
-UUUGCUCCUUUGCUCCUUUUCCCUUUUUUUU---CUAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUU
-...((......))..................---...(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).)).))))))))).... ( -22.60)
>DroEre_CAF1 50424 103 - 1
-UUUGCUGCUUU--------UCCCUUUUUUCC---CCAUUUUUCCUGCUAACCAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUGGUUGUUUGUGUUGAGCCAAGCAGAACAUU
-....((((((.--------............---...........(((((((((((((.(((((...(((....))))))))....))))))).))).))).))))))...... ( -20.91)
>DroYak_CAF1 51415 101 - 1
-UUUGCUCCUUU--------UCCCUUUUUUC-----CAUUUUGCUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUU
-...........--------...........-----..(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).)).))))))))).... ( -23.80)
>DroAna_CAF1 39389 109 - 1
UUUUGCUCCUUUUUA------UCCUUUUUUUGCUCCCUUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGCGCGCCUGCAUUCGUUGUUUGUGUUGAGCCAAGCAGAACAUU
...............------.................(((((((((((((((((((((((((((...(((....)))))))))...))))))).))).)).))))))))).... ( -21.80)
>consensus
_UUUGCUCCUUU_C______UCCCUUUUUUUU___CCAUUUUGUUUGCUAACUAAAUAAAUGCAGUUUGUGUGUGCGCCUGCACUUGUUGUUUGUGUUGAGCCAAGCAGAACAUU
......................................(((((((((((((((((((((.(((((...(((....))))))))....))))))).))).)).))))))))).... (-21.18 = -21.15 +  -0.03)

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 12:31:26 2006