Locus 5695

Sequence ID 3R_DroMel_CAF1
Location 14,926,755 – 14,926,976
Length 221
Max. P 0.999703
window9306 window9307 window9308 window9309

overview

Window 6

Location 14,926,755 – 14,926,872
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.58
Mean single sequence MFE -20.08
Consensus MFE -17.86
Energy contribution -18.06
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.89
SVM decision value 3.91
SVM RNA-class probability 0.999703
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14926755 117 + 27905053
---AAAAAUUAACGCCAAAAUAUAUAAAGCACAAACAGAGUUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGA
---..........((..............((((......(((.....))).((((......)))).((((((...)))))).)))).(((((((........)))))))))......... ( -19.30)
>DroSec_CAF1 56785 120 + 1
UAAAAAAAUUAAAUCCAAAAUAUAUAAAGCACAAGCAGAGUUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGA
...................((((((((..((((......(((.....))).((((......)))).((((((...)))))).)))).))))))))......................... ( -19.20)
>DroSim_CAF1 55418 120 + 1
UAAAAAAAUUAACGCCAAAAUAUAUAAAGCACAAGCAGAGUUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGA
........((((((..............((....))...((((........)))).....))))))((((((...)))))).(((..(((((((........))))))).....)))... ( -21.20)
>DroEre_CAF1 53331 113 + 1
-----AAAUUAACGCCAAAAUA--AGAAACACAAACAAAGGUGAAAAAACGCAACAAAUCUGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUGUACAAGA
-----.......((((......--...............))))........(((((....))))).((((((...)))))).((((.(((((((........)))))))....))))... ( -20.60)
>DroYak_CAF1 60151 113 + 1
-----AAAUUAACGCCAAAAUA--AAAAACACAAACAAAGGUGAAAAAACGCAACAAAUCUGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAUACAAGA
-----........((.......--.....((((..................(((((....))))).((((((...)))))).)))).(((((((........)))))))))......... ( -20.10)
>consensus
___AAAAAUUAACGCCAAAAUAUAUAAAGCACAAACAGAGUUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGA
.............((..............((((..................((((......)))).((((((...)))))).)))).(((((((........)))))))))......... (-17.86 = -18.06 +   0.20)

alignment

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secondary structure

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Window 7

Location 14,926,792 – 14,926,912
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -24.92
Consensus MFE -23.00
Energy contribution -23.20
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.03
Structure conservation index 0.92
SVM decision value 2.62
SVM RNA-class probability 0.995858
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14926792 120 + 27905053
UUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGCU
..........((((..(((..((((.((((((...)))))).((((.(((((((........)))))))(((...((.(((...))))).)))........)))))))).)))..)))). ( -25.20)
>DroSec_CAF1 56825 120 + 1
UUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUU
............(((((....((((.((((((...))))))(((((.(((((((........)))))))(((...((.(((...))))).)))........)))))..))))...))))) ( -24.60)
>DroSim_CAF1 55458 120 + 1
UUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUU
............(((((....((((.((((((...))))))(((((.(((((((........)))))))(((...((.(((...))))).)))........)))))..))))...))))) ( -24.60)
>DroEre_CAF1 53364 120 + 1
GUGAAAAAACGCAACAAAUCUGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUGUACAAGACAUUGUCUGGGGCAUUAAAAAAGCAUAACAAUUAAUUGCU
..........((((..(((.(((((.((((((...)))))).(((..(((((((........)))))))(((.(((((....))))..).))).........)))))))))))..)))). ( -23.60)
>DroYak_CAF1 60184 120 + 1
GUGAAAAAACGCAACAAAUCUGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAUACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUU
(((......)))(((((....((((.((((((...))))))(((((.(((((((........)))))))(((...((.(((...))))).)))........)))))..))))...))))) ( -26.60)
>consensus
UUGAAAAAACGCAACAAAUCCGUUGAGUGUGCAAUGCACACAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUU
...........((((......)))).((((((...))))))(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).............. (-23.00 = -23.20 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,926,832 – 14,926,936
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.63
Mean single sequence MFE -19.26
Consensus MFE -15.19
Energy contribution -15.11
Covariance contribution -0.08
Combinations/Pair 1.07
Mean z-score -2.05
Structure conservation index 0.79
SVM decision value 1.12
SVM RNA-class probability 0.917724
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14926832 104 + 27905053
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGCUGGAAAA----------------AAACAAUCAGCGACAGCA
.(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).........(((((((....----------------......)))))))..... ( -18.60)
>DroSec_CAF1 56865 118 + 1
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUUGGAAAA--AAACAACAACAAAAAAACAAUCCGCGACAGCA
.(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).........((((((.....--...))))))..............((....)). ( -20.50)
>DroSim_CAF1 55498 120 + 1
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUUGGAAAAAGAAACAACAACAAAAAAACAAUCAGCGACAGCA
.(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).........((((((.............))))))...........((....)). ( -19.52)
>DroEre_CAF1 53404 102 + 1
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUGUACAAGACAUUGUCUGGGGCAUUAAAAAAGCAUAACAAUUAAUUGCUGA------------------AAAAACAAUCAGCGACAGCA
.......(((((((........)))))))(((((.......(((((.....((.........))...)))))....((((((------------------........))))))))))). ( -19.20)
>DroYak_CAF1 60224 102 + 1
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAUACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUUGA------------------AAAAACAAUCAGCGACAGCA
.(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).........(((((((------------------........)))))))..... ( -18.50)
>consensus
CAUGUGAUUAUAUAUCCAUACUUAUAUAAGCUAAACAAGACAUUGUCUGGGGCAUUAAAAACGCAUAACAAUUAAUUGUUGGAAAA______________AAAAACAAUCAGCGACAGCA
.(((((.(((((((........)))))))(((...((.(((...))))).)))........))))).........(((((((..........................)))))))..... (-15.19 = -15.11 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,926,872 – 14,926,976
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.54
Mean single sequence MFE -20.98
Consensus MFE -16.80
Energy contribution -17.30
Covariance contribution 0.50
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.709462
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14926872 104 - 27905053
AUCGCAAAUAUCCAAGAGUGUCAUCUACUUUUGAUUCAUUUGCUGUCGCUGAUUGUUU----------------UUUUCCAGCAAUUAAUUGUUAUGCGUUUUUAAUGCCCCAGACAAUG
...(((((((..((((((((.....))))))))..).))))))((((((((.......----------------.....)))).............((((.....))))....))))... ( -22.10)
>DroSim_CAF1 55538 120 - 1
AUCGCAAAUAUCCAAGAUUUUCAUCUACUUUUGAUUCAUUUGCUGUCGCUGAUUGUUUUUUUGUUGUUGUUUCUUUUUCCAACAAUUAAUUGUUAUGCGUUUUUAAUGCCCCAGACAAUG
...(((((((..(((((...........)))))..).))))))((((((((((.(((...((((((..(.......)..))))))..))).)))).))((.......))....))))... ( -17.30)
>DroEre_CAF1 53444 102 - 1
AUCGCAAAUAUCCAAGAGUGUCAUCUACUUUUGAUUCAUUUGCUGUCGCUGAUUGUUUUU------------------UCAGCAAUUAAUUGUUAUGCUUUUUUAAUGCCCCAGACAAUG
...(((((((..((((((((.....))))))))..).))))))(((((((((........------------------))))).............((.........))....))))... ( -23.30)
>DroYak_CAF1 60264 102 - 1
AUCGCAAAUAUCAAAGAGUGUCAUCUACUUUUGAUUCAUUUGCUGUCGCUGAUUGUUUUU------------------UCAACAAUUAAUUGUUAUGCGUUUUUAAUGCCCCAGACAAUG
...(((((((((((.(((((.....))))))))))..))))))((((..((((((((...------------------..))))))))........((((.....))))....))))... ( -21.20)
>consensus
AUCGCAAAUAUCCAAGAGUGUCAUCUACUUUUGAUUCAUUUGCUGUCGCUGAUUGUUUUU__________________CCAACAAUUAAUUGUUAUGCGUUUUUAAUGCCCCAGACAAUG
...(((((((((.(((((((.....))))))))))..))))))((((..((((((((.......................))))))))........((((.....))))....))))... (-16.80 = -17.30 +   0.50)

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 12:01:57 2006