Locus 6340

Sequence ID 3R_DroMel_CAF1
Location 16,592,816 – 16,592,963
Length 147
Max. P 0.986140
window10341 window10342 window10343

overview

Window 1

Location 16,592,816 – 16,592,925
Length 109
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 79.53
Mean single sequence MFE -27.99
Consensus MFE -17.46
Energy contribution -18.63
Covariance contribution 1.17
Combinations/Pair 1.21
Mean z-score -1.77
Structure conservation index 0.62
SVM decision value 0.50
SVM RNA-class probability 0.762066
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592816 109 - 27905053
GUCCUAGAGUCUAA----UAUAAAAGUAGGUAUUAUUUUUGUAGCCAUGUAAGGCUAGAAAAAUGUUGCCACUUAGUCCUCUGCGGCAGGUA-ACGUGAAAACUGUUUGCCAAC
(((.(((((.(((.----......(((.((((.(((((((.(((((......))))).))))))).))))))))))..))))).))).((((-((((....)).).)))))... ( -34.41)
>DroSec_CAF1 149077 109 - 1
GUCCUACAAUCUAA----AAUAAAAGUAGGUAAUAUUUUUGUAGCCAUGUAAGGCUAGGAAAAUGUUGCCACUUAGUCCGCUGCGGCAGGUA-ACGUGAAAACUGUUUGCCAAC
..............----.....((((.((((((((((((.(((((......))))).))))))))))))))))..........((((..((-..((....))))..))))... ( -34.90)
>DroSim_CAF1 154075 109 - 1
GUGCAAGAAUCUAA----UAUAAAAGUAGGUAUUAAUUUUGUAGCCAUGUAAGGCUAGGAAAAUGUUGCCACUUAGUCCUCUGCGGCAGGUA-ACGUGAAAACUGUUUGCCAAC
..(((.((..(((.----......(((.((((.((.((((.(((((......))))).)))).)).))))))))))...)))))((((..((-..((....))))..))))... ( -29.21)
>DroEre_CAF1 152919 104 - 1
AUUCUAGAUCCUAA------UAAAUGGGUGUCUUAU-UUUGUAGCCAUG-CAGGCUAGGAAAAUGUUGCCACUUAGUCCUCUGCGGCAGGU--ACGUGAAAACUGUUUGCCAAC
.....((((((((.------....)))).))))..(-(((.(((((...-..))))).))))......................((((..(--(.((....))))..))))... ( -25.30)
>DroYak_CAF1 148561 107 - 1
GUCCUAGAUCCUUA----UAUAAAAGGAAGUGUUAU-UUUGUAGCCAUG-AAGGCUAGGAAAAUAUUGCCACUUAGUCCUCUGCGGCAGGUA-ACGUGAAAACUGUUUGCCAAC
(((.(((((((((.----.....)))))((((.(((-(((.(((((...-..))))).))))....)).))))......)))).))).((((-((((....)).).)))))... ( -27.30)
>DroAna_CAF1 145627 105 - 1
CUUCCCGAU-UUAAGGACAACAAAAUCGUGUACCAUUUUU--CCCAAUG------UAGAAAAAUGUUUCUAGUUUGGAUUAAGCCCCAGCUAAACGUGAAAACUGUUUGCCAAC
.........-....((..((((...((((((..(((((((--(......------..))))))))....(((((.((.......)).))))).))))))....))))..))... ( -16.80)
>consensus
GUCCUAGAUUCUAA____UAUAAAAGUAGGUAUUAUUUUUGUAGCCAUG_AAGGCUAGGAAAAUGUUGCCACUUAGUCCUCUGCGGCAGGUA_ACGUGAAAACUGUUUGCCAAC
.......................(((...(((.(((((((.(((((......))))).))))))).)))..))).(((......))).((((.((((....)).)).))))... (-17.46 = -18.63 +   1.17)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,592,855 – 16,592,963
Length 108
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 76.66
Mean single sequence MFE -14.82
Consensus MFE -9.84
Energy contribution -9.68
Covariance contribution -0.16
Combinations/Pair 1.10
Mean z-score -1.45
Structure conservation index 0.66
SVM decision value 0.07
SVM RNA-class probability 0.569726
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592855 108 + 27905053
AAGUGGCAACAUUUUUCUAGCCUUACAUGGCUACAAAAAUAAUACCUACUUUUAUAUUAGACUCUAGGACCAAAUUAUUAAUUUAAUUCUCAAA-AAAAAAAUUCAAUC-
((((((....((((((.(((((......))))).)))))).....))))))...........................................-..............- ( -14.00)
>DroSec_CAF1 149116 106 + 1
AAGUGGCAACAUUUUCCUAGCCUUACAUGGCUACAAAAAUAUUACCUACUUUUAUUUUAGAUUGUAGGACAAAAUUAUAAAUUUAAUUCUCAAA-AA--AAAUUGAAUC-
(((((....)))))...(((((......)))))...........(((((..((......))..)))))............((((((((......-..--.)))))))).- ( -18.40)
>DroSim_CAF1 154114 106 + 1
AAGUGGCAACAUUUUCCUAGCCUUACAUGGCUACAAAAUUAAUACCUACUUUUAUAUUAGAUUCUUGCACAAAAUUAUAAAUUUUAUUCUCAAA-AA--AAAUUGAAUC-
((((((......(((..(((((......)))))..))).......))))))........(((((..............................-..--.....)))))- ( -12.21)
>DroEre_CAF1 152957 97 + 1
AAGUGGCAACAUUUUCCUAGCCUG-CAUGGCUACAAA-AUAAGACACCCAUUUA--UUAGGAUCUAGAAUCUG---GUUUAUUUAAUUCUCACA-AC-----UUGCAUUU
(((((....)))))...(((((..-...)))))..((-(((((....((.....--...))..((((...)))---))))))))..........-..-----........ ( -13.40)
>DroYak_CAF1 148600 97 + 1
AAGUGGCAAUAUUUUCCUAGCCUU-CAUGGCUACAAA-AUAACACUUCCUUUUAUAUAAGGAUCUAGGACAAA------AAUUCGUAUCUCAUAUAC-----UUUCAUUU
((((((........((((((((..-...)))......-........(((((......)))))..)))))....------.....((((.....))))-----..)))))) ( -16.10)
>consensus
AAGUGGCAACAUUUUCCUAGCCUUACAUGGCUACAAAAAUAAUACCUACUUUUAUAUUAGAAUCUAGGACAAAAUUAUAAAUUUAAUUCUCAAA_AA__AAAUUGAAUC_
(((((....)))))...(((((......)))))............................................................................. ( -9.84 =  -9.68 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,592,855 – 16,592,963
Length 108
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 76.66
Mean single sequence MFE -23.24
Consensus MFE -15.06
Energy contribution -15.82
Covariance contribution 0.76
Combinations/Pair 1.19
Mean z-score -2.29
Structure conservation index 0.65
SVM decision value 2.03
SVM RNA-class probability 0.986140
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16592855 108 - 27905053
-GAUUGAAUUUUUUU-UUUGAGAAUUAAAUUAAUAAUUUGGUCCUAGAGUCUAAUAUAAAAGUAGGUAUUAUUUUUGUAGCCAUGUAAGGCUAGAAAAAUGUUGCCACUU
-(((..((((.((..-(((((...)))))..)).))))..)))................((((.((((.(((((((.(((((......))))).))))))).)))))))) ( -27.60)
>DroSec_CAF1 149116 106 - 1
-GAUUCAAUUU--UU-UUUGAGAAUUAAAUUUAUAAUUUUGUCCUACAAUCUAAAAUAAAAGUAGGUAAUAUUUUUGUAGCCAUGUAAGGCUAGGAAAAUGUUGCCACUU
-(((((((...--..-.)))(((((((......))))))).......))))........((((.((((((((((((.(((((......))))).)))))))))))))))) ( -27.50)
>DroSim_CAF1 154114 106 - 1
-GAUUCAAUUU--UU-UUUGAGAAUAAAAUUUAUAAUUUUGUGCAAGAAUCUAAUAUAAAAGUAGGUAUUAAUUUUGUAGCCAUGUAAGGCUAGGAAAAUGUUGCCACUU
-..........--((-((((...(((((((.....))))))).))))))..........((((.((((.((.((((.(((((......))))).)))).)).)))))))) ( -23.20)
>DroEre_CAF1 152957 97 - 1
AAAUGCAA-----GU-UGUGAGAAUUAAAUAAAC---CAGAUUCUAGAUCCUAA--UAAAUGGGUGUCUUAU-UUUGUAGCCAUG-CAGGCUAGGAAAAUGUUGCCACUU
....((((-----..-....((((((........---..))))))((((((((.--....)))).))))..(-(((.(((((...-..))))).))))...))))..... ( -19.70)
>DroYak_CAF1 148600 97 - 1
AAAUGAAA-----GUAUAUGAGAUACGAAUU------UUUGUCCUAGAUCCUUAUAUAAAAGGAAGUGUUAU-UUUGUAGCCAUG-AAGGCUAGGAAAAUAUUGCCACUU
........-----.((((((((((((((...------.)))).....)).))))))))...((.((((((..-(((.(((((...-..))))).))))))))).)).... ( -18.20)
>consensus
_GAUUCAAUUU__UU_UUUGAGAAUUAAAUUAAUAAUUUUGUCCUAGAAUCUAAUAUAAAAGUAGGUAUUAUUUUUGUAGCCAUGUAAGGCUAGGAAAAUGUUGCCACUU
................................................................((((.(((((((.(((((......))))).))))))).)))).... (-15.06 = -15.82 +   0.76)

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 12:19:09 2006