Locus 3833

Sequence ID X_DroMel_CAF1
Location 10,173,361 – 10,173,508
Length 147
Max. P 0.962922
window6305 window6306 window6307

overview

Window 5

Location 10,173,361 – 10,173,468
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.25
Mean single sequence MFE -22.62
Consensus MFE -16.87
Energy contribution -16.75
Covariance contribution -0.12
Combinations/Pair 1.21
Mean z-score -1.47
Structure conservation index 0.75
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10173361 107 + 22224390
------UAUA-------UUCUGUGGUUUGGCCAACUGUGUGUUCUAGUUUUCCACUAAUGCCCUUUAUAUUAAAUAAUAAGAACAUUAUCAAUUUAAUGAGGGCAUGCAUUAUCAGCUUA
------....-------.....(((.....))).(((.((((..((((.....))))((((((((...(((((((.((((.....))))..)))))))))))))))))))...))).... ( -21.60)
>DroSec_CAF1 1517 107 + 1
------UAUA-------CUCUGUGGUUUGGCCAACUCUGUGUUCCAGUUUUCCGCUAAUGCCCUUUAUAUUAAAUAAUAAGAACAUUAUCAAUUUAAUGAGGGCAUGCAUUAUCAGCUAA
------....-------....((((.((((..(((.....)))))))....))))..((((((((...(((((((.((((.....))))..)))))))))))))))((.......))... ( -22.50)
>DroSim_CAF1 5193 107 + 1
------UAUA-------UUCUGUGGUUUGGCCAACUCUGUGUUCUAGUUUUCCGCUAAUGCCCUUUAUAUUAAAUAAUAAGAACAUUAUCAAUUUAAUGAGGGCAUGCAUUAUCAGCUAA
------.(((-------(....(((.....))).....))))..(((((........((((((((...(((((((.((((.....))))..)))))))))))))))........))))). ( -20.49)
>DroEre_CAF1 7687 116 + 1
CUUAGUUAUAUUUAUGCUUCUGCGG-UUGGACUUCUAUGUGCUUUAGUUUUCUGCCAAUGCCCUUUAUAUUAAAUAAUA---ACACUAUCUUUUUAAUGAGGGCAUGCAUUAUCAGCUUA
...............(((..(((((-(.(((...(((.......)))..))).))).((((((((...((((((..(((---....)))...))))))))))))))))).....)))... ( -22.30)
>DroYak_CAF1 4841 114 + 1
CUUCGUUAUAUUUUU------GCGGUUUGGACUUCUAUGUGUUCUAGUUUUCUGCCAAUGCCCUUUGUAUUAGAUAAUAAGAACACUAUCUAUUUAAUGAGGGCAUGCAUUAUCAGCAUA
....((((((....(------(((((..(((((............)))))...))).((((((((.....((((((..........))))))......))))))))))).))).)))... ( -26.20)
>consensus
______UAUA_______UUCUGUGGUUUGGCCAACUAUGUGUUCUAGUUUUCCGCUAAUGCCCUUUAUAUUAAAUAAUAAGAACAUUAUCAAUUUAAUGAGGGCAUGCAUUAUCAGCUUA
.....................((((.((((..(((.....)))))))....))))..((((((((...(((((((................)))))))))))))))((.......))... (-16.87 = -16.75 +  -0.12)

alignment

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secondary structure

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Window 6

Location 10,173,361 – 10,173,468
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.25
Mean single sequence MFE -22.00
Consensus MFE -15.88
Energy contribution -15.08
Covariance contribution -0.80
Combinations/Pair 1.22
Mean z-score -1.79
Structure conservation index 0.72
SVM decision value 0.44
SVM RNA-class probability 0.738507
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10173361 107 - 22224390
UAAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGUGGAAAACUAGAACACACAGUUGGCCAAACCACAGAA-------UAUA------
....(((.......(((((((..(((.((((((((((....))))).))))).))))))))))...(((..((((.(......)))))..))).....)))..-------....------ ( -21.20)
>DroSec_CAF1 1517 107 - 1
UUAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUGGAACACAGAGUUGGCCAAACCACAGAG-------UAUA------
...((..((..((((((((((..(((.((((((((((....))))).))))).))))))))))..))).....(((.....))).))..))............-------....------ ( -23.30)
>DroSim_CAF1 5193 107 - 1
UUAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUAGAACACAGAGUUGGCCAAACCACAGAA-------UAUA------
....(((.....(((((((((..(((.((((((((((....))))).))))).))))))))))..))((..((((.........))))..))......)))..-------....------ ( -22.70)
>DroEre_CAF1 7687 116 - 1
UAAGCUGAUAAUGCAUGCCCUCAUUAAAAAGAUAGUGU---UAUUAUUUAAUAUAAAGGGCAUUGGCAGAAAACUAAAGCACAUAGAAGUCCAA-CCGCAGAAGCAUAAAUAUAACUAAG
...(((.....(((((((((((((((......))))).---..((((.....))))))))))).((..((...(((.......)))...))...-)))))..)))............... ( -19.30)
>DroYak_CAF1 4841 114 - 1
UAUGCUGAUAAUGCAUGCCCUCAUUAAAUAGAUAGUGUUCUUAUUAUCUAAUACAAAGGGCAUUGGCAGAAAACUAGAACACAUAGAAGUCCAAACCGC------AAAAAUAUAACGAAG
..(((......((((((((((.......(((((((((....)))))))))......)))))))..)))((...(((.......)))...))......))------).............. ( -23.52)
>consensus
UAAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUAGAACACAGAGUUGGCCAAACCACAGAA_______UAUA______
...(((((.......((((((.........(((((((....)))))))........)))))))))))..................................................... (-15.88 = -15.08 +  -0.80)

alignment

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secondary structure

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Window 7

Location 10,173,388 – 10,173,508
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -22.70
Consensus MFE -18.83
Energy contribution -19.31
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.97
Structure conservation index 0.83
SVM decision value 1.55
SVM RNA-class probability 0.962922
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10173388 120 - 22224390
UAUCUUUAUAAUUGCACUUAACACAAUUAUAAACACUUACUAAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGUGGAAAACUAGAAC
....((((((((((.........))))))))))...(((((((((.......)).((((((..(((.((((((((((....))))).))))).))))))))))))))))........... ( -23.80)
>DroSec_CAF1 1544 120 - 1
UAUCUUUAUAAUUGCACUUAACACAAUUAUAAACACUGACUUAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUGGAAC
....((((((((((.........))))))))))..(((.((..((.......))(((((((..(((.((((((((((....))))).))))).)))))))))).)))))........... ( -22.00)
>DroSim_CAF1 5220 120 - 1
UAUCUUUAUAAUUGCACUUAACACAAUUAUAAACACUGACUUAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUAGAAC
....((((((((((.........))))))))))..(((.((..((.......))(((((((..(((.((((((((((....))))).))))).)))))))))).)))))........... ( -22.00)
>DroEre_CAF1 7726 117 - 1
UAUCAUGCUAAUUGCACUUAACACGAAUAUAACCACUGACUAAGCUGAUAAUGCAUGCCCUCAUUAAAAAGAUAGUGU---UAUUAUUUAAUAUAAAGGGCAUUGGCAGAAAACUAAAGC
.....(((.....)))...................(((.((((((.......)).(((((((((((......))))).---..((((.....)))))))))))))))))........... ( -19.00)
>DroYak_CAF1 4875 120 - 1
CAUCAUUCUAAUUGCACUUAACACGAGUAUAAACACUGACUAUGCUGAUAAUGCAUGCCCUCAUUAAAUAGAUAGUGUUCUUAUUAUCUAAUACAAAGGGCAUUGGCAGAAAACUAGAAC
.....(((((.(((.((((.....)))).)))...(((.((((((.......)))((((((.......(((((((((....)))))))))......)))))).)))))).....))))). ( -26.72)
>consensus
UAUCUUUAUAAUUGCACUUAACACAAUUAUAAACACUGACUAAGCUGAUAAUGCAUGCCCUCAUUAAAUUGAUAAUGUUCUUAUUAUUUAAUAUAAAGGGCAUUAGCGGAAAACUAGAAC
.....(((((((((.........)))))))))...(((.(((.((.......))(((((((.........(((((((....)))))))........)))))))))))))........... (-18.83 = -19.31 +   0.48)

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 11:09:51 2006