Locus 4563

Sequence ID X_DroMel_CAF1
Location 11,989,701 – 11,989,878
Length 177
Max. P 0.997853
window7503 window7504 window7505

overview

Window 3

Location 11,989,701 – 11,989,810
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.53
Mean single sequence MFE -20.45
Consensus MFE -15.15
Energy contribution -15.93
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -1.11
Structure conservation index 0.74
SVM decision value 0.27
SVM RNA-class probability 0.660686
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11989701 109 - 22224390
GCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCCAAAUGCAAAUGGGCUGUCAUAAUUAGCCCGCCCACACGAGUAC---CGCUUAUCAUUU--C------GACCCCCCAGC
......(((((.(((((((((......)))))))))..(((.(((((.....((((((.......))))))........(((...---..)))..)))))--.------)))..))))). ( -27.00)
>DroPse_CAF1 126694 105 - 1
GCAUAAUUAGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCAACAUGCAAAUGGCCUGUCAUAAUUAGCCAUCCC-------------CGCUU--CAUCCGCCAUCCUCCAUCCGCCAUC
((......(((((......(((((.....((((.....))))..))))).(((((..((....))..)))))...-------------.....--........)))))......)).... ( -15.90)
>DroSim_CAF1 30245 98 - 1
GCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCCAAAUGCAAAUGGGCUGUCAUAAUUAGCCCGCCCACACGAGUAC---CGCUUAUCAUUU--C-----------------
((((..(((((.(((((((((......)))))))))...)))))))))....((((((.......))))))........(((...---..))).......--.----------------- ( -24.20)
>DroEre_CAF1 27977 100 - 1
GCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCCAAAUGCAAAUGUGCUGUCAUAAUUAGCCCGCCCACUCGAGUACCGCCGCUUAUCAUUC--------------------
((......(((.((((((((((((....)))....((((..((........))..))))))))))))))))((..((....))...)).)).........-------------------- ( -18.50)
>DroYak_CAF1 29153 103 - 1
GCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCCAAAUGCAAAUGUGCUGUCAUAAUUAGCCCGCCCACACGAGCAC---CGCUUAUCAUUC--C------AUUCU------
((......(((.((((((((((((....)))....((((..((........))..))))))))))))))))((.(....).))..---.)).........--.------.....------ ( -19.70)
>DroPer_CAF1 131520 91 - 1
GCAUAAUUAGGAUUAAUUAUGCAUAAUUGUGAUUAACAGUCAACAUGCAAAUGGCCUGUCAUAAUUAGCCAUCCC-------------CGCUU--CAUCCGCC--------------AUC
(((((((((....))))))))).((((((((((.....((((.........))))..))))))))))........-------------.....--........--------------... ( -17.40)
>consensus
GCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGUCCAAAUGCAAAUGGGCUGUCAUAAUUAGCCCGCCCACACGAGUAC___CGCUUAUCAUUC__C_________________
(((((((((....))))))))).......((((((((((((((........))))))))..))))))..................................................... (-15.15 = -15.93 +   0.78)

alignment

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secondary structure

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Window 4

Location 11,989,770 – 11,989,878
Length 108
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 95.85
Mean single sequence MFE -20.52
Consensus MFE -17.57
Energy contribution -18.37
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.86
SVM decision value 2.72
SVM RNA-class probability 0.996599
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11989770 108 + 22224390
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCGCAUCAAUUAAGCCGGUAGCCUG-------UA
.((((((((........(((((((((......))))))))).........))))))))(((.....(((.....)))(((..(((.........).))..))).))-------). ( -21.93)
>DroSec_CAF1 29085 108 + 1
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCACAUCAAUUAAGCCGCUAGCCUG-------UA
.((((((((........(((((((((......))))))))).........))))))))........((((....((.(((.............))).)).....))-------)) ( -18.75)
>DroSim_CAF1 30303 108 + 1
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCGCAUCAAUUAAGCCGCUCGCCUG-------UA
.((((((((........(((((((((......))))))))).........))))))))........((((....((.(((.............))).)).....))-------)) ( -18.75)
>DroEre_CAF1 28037 115 + 1
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCGCAUCAAUUAAGCCGGUAGCCUAUUGCCCAUA
.((((((((........(((((((((......))))))))).........))))))))........(((.....)))(((..(((.........).))..)))............ ( -21.23)
>DroYak_CAF1 29216 108 + 1
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCGCAUCAAUUAAGCCGGUAGCCUG-------UA
.((((((((........(((((((((......))))))))).........))))))))(((.....(((.....)))(((..(((.........).))..))).))-------). ( -21.93)
>consensus
ACUGUUAAUCACGAUUAUGCAUAAUUAAUCCCAAUUAUGCACAAACACAAAUUAAUAGACAAAAUAUGCACAUUGCAGCUGUCGCAUCAAUUAAGCCGGUAGCCUG_______UA
.((((((((........(((((((((......))))))))).........))))))))........(((.....)))((((((((.........).)))))))............ (-17.57 = -18.37 +   0.80)

alignment

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secondary structure

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Window 5

Location 11,989,770 – 11,989,878
Length 108
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 95.85
Mean single sequence MFE -27.64
Consensus MFE -26.44
Energy contribution -26.44
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.88
Structure conservation index 0.96
SVM decision value 2.95
SVM RNA-class probability 0.997853
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11989770 108 - 22224390
UA-------CAGGCUACCGGCUUAAUUGAUGCGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
..-------.((((.....)))).(((((((.(((((.(((.....)))....))))))))))))(..((.(((((((((((((....))))))))))))).))..)........ ( -26.50)
>DroSec_CAF1 29085 108 - 1
UA-------CAGGCUAGCGGCUUAAUUGAUGUGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
..-------.((((.....)))).(((((((.(((((.(((.....)))....))))))))))))(..((.(((((((((((((....))))))))))))).))..)........ ( -26.50)
>DroSim_CAF1 30303 108 - 1
UA-------CAGGCGAGCGGCUUAAUUGAUGCGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
..-------...((((((((((.............))))))..((((((((.((.((((......((((((....))))))...)))).)).)))))))).)))).......... ( -28.02)
>DroEre_CAF1 28037 115 - 1
UAUGGGCAAUAGGCUACCGGCUUAAUUGAUGCGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
.(((((((((((((.....)))))....((((.(((.......)))))))...))))))))....(..((.(((((((((((((....))))))))))))).))..)........ ( -30.70)
>DroYak_CAF1 29216 108 - 1
UA-------CAGGCUACCGGCUUAAUUGAUGCGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
..-------.((((.....)))).(((((((.(((((.(((.....)))....))))))))))))(..((.(((((((((((((....))))))))))))).))..)........ ( -26.50)
>consensus
UA_______CAGGCUACCGGCUUAAUUGAUGCGACAGCUGCAAUGUGCAUAUUUUGUCUAUUAAUUUGUGUUUGUGCAUAAUUGGGAUUAAUUAUGCAUAAUCGUGAUUAACAGU
..........((((.....)))).(((((((.(((((.(((.....)))....))))))))))))(..((.(((((((((((((....))))))))))))).))..)........ (-26.44 = -26.44 +  -0.00)

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 11:28:15 2006