Locus 2641

Sequence ID 2R_DroMel_CAF1
Location 9,329,875 – 9,330,048
Length 173
Max. P 0.948841
window4350 window4351

overview

Window 0

Location 9,329,875 – 9,329,973
Length 98
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 77.99
Mean single sequence MFE -24.86
Consensus MFE -14.99
Energy contribution -15.02
Covariance contribution 0.03
Combinations/Pair 1.07
Mean z-score -2.27
Structure conservation index 0.60
SVM decision value 1.39
SVM RNA-class probability 0.948841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9329875 98 - 20766785
-AAGC----CAUGUAUGACACAAAA---------GAUCCACAGAUUUUGAAGGCAUUUAACUUACAAUUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
-..((----(.(((.....))).((---------((((....))))))...))).....(((..((.(..(((....)))..).))....)))...((((((....)))))) ( -23.80)
>DroVir_CAF1 172 110 - 1
AAAGGUAUACAUAUAGUGUUGAAAA-GUGUAAAUAUUUCUGGUAUUUUGUUG-UCUAGUACUUACAAUUGGACGAAAAUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
......((((.....))))......-(((((......((..(.((((..(((-((((((.......))))))))))))))..))........)))))(((((....))))). ( -20.04)
>DroSec_CAF1 174 99 - 1
-AAGA----CAAGGAUUAUUUAAAA----U---AAUUCCUACUAUUUCGAUGGCAUUC-ACUUACAAUUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
-....----...(((((((.....)----)---))))).(((((((((((......))-........(..(((....)))..)..)))))))))..((((((....)))))) ( -25.30)
>DroSim_CAF1 196 98 - 1
-AAGC----CAUGUAUUACCCAAAA---------GUUCCAAAGAUUUUGAAGGCAUUUAACUUACAAUUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
-....----.(((((((........---------((((((......((((((........))).)))(..(((....)))..).)))))))))))))(((((....))))). ( -24.00)
>DroEre_CAF1 178 105 - 1
AAAGC----CAAGAAUUAUUCCAAGCCUUU---UAUGCCAAGCAUUUCGAAGGGAUGUCACUUACAAUUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
.....----...(.(((((((((..(((((---.((((...))))...)))))..............(..(((....)))..).))))))))).).((((((....)))))) ( -29.90)
>DroYak_CAF1 2883 104 - 1
AAAGA----AAUGGAUUAUUGAAAACGUUU---UAUGCCUAGGAUUUCGA-GACAUUUCACUUACAACUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
...((----((((.....(((((...((((---((....)))))))))))-..))))))(((..((.(..(((....)))..).))....)))...((((((....)))))) ( -26.10)
>consensus
_AAGC____CAUGUAUUAUUCAAAA____U___UAUUCCAAGGAUUUCGAAGGCAUUUAACUUACAAUUGGACGAAAGUCUGGAUGGAAUAGUACAUAACCAUUGUUGGUUA
...........................................................(((..((.(..(((....)))..).))....)))...((((((....)))))) (-14.99 = -15.02 +   0.03)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,329,951 – 9,330,048
Length 97
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.65
Mean single sequence MFE -22.85
Consensus MFE -17.61
Energy contribution -17.33
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -1.41
Structure conservation index 0.77
SVM decision value 0.22
SVM RNA-class probability 0.637756
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9329951 97 + 20766785
UC---------UUUUGUGUCAUACAUG----GCUU-UAAAUUCCAGUUCCAAGGCUACAUAUUAAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
..---------...(((((......((----((((-(((.....(((......))).....))))))))))))))(((((((.(((((.........)))))))))))).. ( -26.00)
>DroVir_CAF1 247 110 + 1
AUAUUUACAC-UUUUCAACACUAUAUGUAUACCUUUUGCUGAGCAGUUCCAAGGUUAUAUACUAAAGCCAGCUUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
..........-............((((((.(((((..(((....)))...)))))))))))...(((....))).(((((((.(((((.........)))))))))))).. ( -22.90)
>DroSec_CAF1 249 99 + 1
AUU---A----UUUUAAAUAAUCCUUG----UCUU-UGAAUUUCAGUUCCAAGGCUACAUAUUGAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
...---.----...............(----((((-.((((....)))).)))))....................(((((((.(((((.........)))))))))))).. ( -20.20)
>DroSim_CAF1 272 97 + 1
AC---------UUUUGGGUAAUACAUG----GCUU-UAAAUUCCAGUUCCAAGGCUACAUAUUAAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUUGAGCUAUUGGA
..---------..............((----((((-(((.....(((......))).....))))))))).....(((((((.(..((.........))..)))))))).. ( -22.60)
>DroEre_CAF1 254 104 + 1
AUA---AAAGGCUUGGAAUAAUUCUUG----GCUUUUCAAUUCCAGUUCCAAGGCUACAUAUUAAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
...---....(((((((((.....(((----(....)))).....)))))))((((.........)))).))...(((((((.(((((.........)))))))))))).. ( -26.70)
>DroYak_CAF1 2958 104 + 1
AUA---AAACGUUUUCAAUAAUCCAUU----UCUUUUCGAGUACAGUUCCAAGGCUACAUAUUAAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
...---.......(((((((.((.(((----((...(((.((.(((......((((.........)))).((........)).))))).)))..))))).))..))))))) ( -18.70)
>consensus
AUA___A____UUUUGAAUAAUACAUG____GCUU_UAAAUUCCAGUUCCAAGGCUACAUAUUAAAGCCAGCAUACAAUAGCGUUGACAUGAUUGAAGUCGAGCUAUUGGA
....................................................((((.........))))......(((((((.(((((.........)))))))))))).. (-17.61 = -17.33 +  -0.28)

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 10:35:12 2006