Locus 3578

Sequence ID 2L_DroMel_CAF1
Location 10,443,910 – 10,444,047
Length 137
Max. P 0.989750
window5655 window5656 window5657

overview

Window 5

Location 10,443,910 – 10,444,016
Length 106
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -33.58
Consensus MFE -29.40
Energy contribution -29.80
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -1.92
Structure conservation index 0.88
SVM decision value 2.18
SVM RNA-class probability 0.989750
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10443910 106 + 22407834
UUAGGAACUCGCAUACCCGCCAACUUGUACAC--UUCUAGGGUAUGCAAUUGCCGCUCCACGAAUGUGUGUCACUGGCGGCAGAGCACUUUGCUCUUUAUAAGGAAUC-
..........((((((((..............--.....))))))))...(((((((.((((....)))).....)))))))((((.....)))).............- ( -32.11)
>DroSec_CAF1 4294 106 + 1
UUAGGAACACGCAUACCCGCCAACUCGUACAC--UUCUAGGGUAUGCAAUUGCCGCUCCACGAAUGUGUGUCACUGGCGGCAUAGCACUUUGCUCUUUAUAAGGAGUC-
..........((((((((..............--.....))))))))...(((((((.((((....)))).....))))))).........((((((....)))))).- ( -30.61)
>DroSim_CAF1 4266 106 + 1
UUAGGAACACGCAUACCCGCCAACUCGUACAC--UUCUAGGGUAUGCAAUUGCCGCUCCACGAAUGUGUGUCACUGGCGGCAGAGCACUUUGCUCUUUAUAAGGAGUC-
..........((((((((..............--.....))))))))...(((((((.((((....)))).....)))))))((((.....)))).............- ( -32.11)
>DroEre_CAF1 4380 106 + 1
UUAGGAACUCGCAUACCCGCU-ACUCGUACAC--UUCUAGGGUAUGCAAUUGCCGCCCAAAGAAUGUGUGUCACUGGCGGCAGAGCACUUUGCUCUUCAUAAGGAGUCU
...(((.(((((((((((...-..........--.....))))))))...(((((((....((.......))...)))))))((((.....))))........)))))) ( -35.67)
>DroYak_CAF1 4353 108 + 1
UUAGGAACUCGUAUACCCGCU-ACUCACACACAGUUCUAGGGUAUGCAAUUGCCGCCCAACGAAUGUGUGUCACUGGCGGCAGAGCACUUUGCUCUUUAUAAGGAGUCU
...(((.(((.((((.(((((-(.(.(((((((.(((..((((..((....)).))))...)))))))))).).)))))).(((((.....))))).))))..)))))) ( -37.40)
>consensus
UUAGGAACUCGCAUACCCGCCAACUCGUACAC__UUCUAGGGUAUGCAAUUGCCGCUCCACGAAUGUGUGUCACUGGCGGCAGAGCACUUUGCUCUUUAUAAGGAGUC_
......((((((((((((.....................))))))))...(((((((....((.......))...)))))))((((.....))))........)))).. (-29.40 = -29.80 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,443,910 – 10,444,016
Length 106
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -34.15
Consensus MFE -28.12
Energy contribution -28.96
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -1.53
Structure conservation index 0.82
SVM decision value 0.54
SVM RNA-class probability 0.774703
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10443910 106 - 22407834
-GAUUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA--GUGUACAAGUUGGCGGGUAUGCGAGUUCCUAA
-............(((((.....)))))((((((..(((.......)))..).)))))..((((((((((..((.--.(....)..))...))))))))))........ ( -32.80)
>DroSec_CAF1 4294 106 - 1
-GACUCCUUAUAAAGAGCAAAGUGCUAUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA--GUGUACGAGUUGGCGGGUAUGCGUGUUCCUAA
-.............(((((........(((((((..(((.......)))..).))))))...((((((((..((.--.(....)..))...)))))))).))))).... ( -30.00)
>DroSim_CAF1 4266 106 - 1
-GACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA--GUGUACGAGUUGGCGGGUAUGCGUGUUCCUAA
-.............(((((..((((.((((((((.((..(((......)))..)))))..(((.((((.......--)))).)))...)))))))))...))))).... ( -31.80)
>DroEre_CAF1 4380 106 - 1
AGACUCCUUAUGAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCUUUGGGCGGCAAUUGCAUACCCUAGAA--GUGUACGAGU-AGCGGGUAUGCGAGUUCCUAA
.(((((.......(((((.....)))))((((((...((.......))....))))))....((((((((.....--..........-...)))))))))))))..... ( -36.67)
>DroYak_CAF1 4353 108 - 1
AGACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUUGGGCGGCAAUUGCAUACCCUAGAACUGUGUGUGAGU-AGCGGGUAUACGAGUUCCUAA
.(((((..((((.(((((.....))))).((((.(.(.((((((((((...(((..((....))...)))..))).))))))).).)-.)))).)))).)))))..... ( -39.50)
>consensus
_GACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA__GUGUACGAGUUGGCGGGUAUGCGAGUUCCUAA
.(((((.......(((((.....)))))((((((..(((.......)))..).)))))....((((((((.....................)))))))))))))..... (-28.12 = -28.96 +   0.84)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,443,942 – 10,444,047
Length 105
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 81.62
Mean single sequence MFE -29.04
Consensus MFE -17.16
Energy contribution -18.64
Covariance contribution 1.48
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.59
SVM decision value 0.30
SVM RNA-class probability 0.676400
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10443942 105 - 22407834
UAUGUACUAUGUUAUGUUGUUAGCAUUUCUG-----GAUUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA-
........((((((......))))))(((((-----(...........(((((.....)))))((((((..(((.......)))..).)))))...........))))))- ( -26.20)
>DroSec_CAF1 4326 94 - 1
-AUAUACUAUGUAAUGU----------UCUG-----GACUCCUUAUAAAGAGCAAAGUGCUAUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA-
-...............(----------((((-----(.(((........)))....((((..(((((((..(((.......)))..).))))))...))))...))))))- ( -22.70)
>DroSim_CAF1 4298 94 - 1
-AUAUACUAUGUAAUGU----------UCUG-----GACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA-
-......((((((((..----------....-----............(((((.....)))))((((((..(((.......)))..).))))).))))))))........- ( -24.10)
>DroEre_CAF1 4411 101 - 1
-AUAU---AUGGG-----GUUAGCAGUUCCAGAGGAGACUCCUUAUGAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCUUUGGGCGGCAAUUGCAUACCCUAGAA-
-....---.((((-----((..((((((...(((....))).......(((((.....)))))((((((...((.......))....))))))))))))..))))))...- ( -38.90)
>DroYak_CAF1 4385 102 - 1
-AUAU---AUGUA-----GUUAGCAGUUCCAGAGGAGACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUUGGGCGGCAAUUGCAUACCCUAGAAC
-...(---(((((-----(((..........(((....))).......(((((.....)))))((((((...(((........))).)))))))))))))))......... ( -33.30)
>consensus
_AUAUACUAUGUAAUGU_GUUAGCA_UUCUG_____GACUCCUUAUAAAGAGCAAAGUGCUCUGCCGCCAGUGACACACAUUCGUGGAGCGGCAAUUGCAUACCCUAGAA_
........(((((((.................................(((((.....)))))((((((..(((.......)))..).))))).))))))).......... (-17.16 = -18.64 +   1.48)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:06 2006