Locus 7018

Sequence ID 3L_DroMel_CAF1
Location 18,977,859 – 18,977,990
Length 131
Max. P 0.908748
window11381 window11382 window11383

overview

Window 1

Location 18,977,859 – 18,977,954
Length 95
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 79.42
Mean single sequence MFE -27.43
Consensus MFE -16.86
Energy contribution -16.36
Covariance contribution -0.50
Combinations/Pair 1.16
Mean z-score -1.89
Structure conservation index 0.61
SVM decision value 0.63
SVM RNA-class probability 0.805323
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18977859 95 + 23771897
CAUUUUUCAUUUGCGCGAGCCGCGUCCUUGCCAAG--GACCCCGCCCAUUUG-----------AGUAGAGCCCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
.....((((..((.(((.(..(.(((((.....))--)))))))).))..))-----------)).((((((........))))))...((((((((...)))))))) ( -24.30)
>DroPse_CAF1 118386 83 + 1
CAUUUCUCAUUUG--AGAGCUGCGUCCUUGCCGGGCAGGCCCCGCCCAG-----------------------CAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
..........(((--((((((..(((((.((.((((.(....))))).)-----------------------))))))..)))))))))((((((((...)))))))) ( -34.90)
>DroEre_CAF1 112966 88 + 1
-------CAUUUGUGCGAGCCGCGUCCUUGCCAAG--GACCCCGCCCAUUUG-----------AGUAGAGACCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
-------.........((((((.((((((((((((--(.......))..)))-----------.)))......))))).))))))....((((((((...)))))))) ( -22.00)
>DroYak_CAF1 128149 94 + 1
CAUUUUUCAUUUGUGCAAGCCGCGUCCUUGCCAAG--GACCCCGCCCAUUUG-----------AGUAGAG-CCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
.........((..(((((((.(.(((((.....))--))).).)).......-----------...((((-(((.....)))))))...)))))..)).......... ( -24.50)
>DroAna_CAF1 109752 106 + 1
CAUUUUUCAUUUGUGCGAGUCGCGUCCUUGCCAAG--GACCCCGCCCAUUUUCAGUGUUUUCCAGCUCAGCCGAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
................((((((.(((((((....(--((...(((.........)))...))).((...))))))))).))))))....((((((((...)))))))) ( -24.00)
>DroPer_CAF1 119699 83 + 1
CAUUUCUCAUUUG--AGAGCUGCGUCCUUGCCGGGCAGGCCCCGCCCAG-----------------------CAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
..........(((--((((((..(((((.((.((((.(....))))).)-----------------------))))))..)))))))))((((((((...)))))))) ( -34.90)
>consensus
CAUUUUUCAUUUGUGCGAGCCGCGUCCUUGCCAAG__GACCCCGCCCAUUUG___________AGUAGAG_CCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAA
................((((((.(((((.............................................))))).))))))....((((((((...)))))))) (-16.86 = -16.36 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,977,859 – 18,977,954
Length 95
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 79.42
Mean single sequence MFE -29.98
Consensus MFE -19.43
Energy contribution -19.48
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -2.13
Structure conservation index 0.65
SVM decision value 1.06
SVM RNA-class probability 0.908748
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18977859 95 - 23771897
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUGGGCUCUACU-----------CAAAUGGGCGGGGUC--CUUGGCAAGGACGCGGCUCGCGCAAAUGAAAAAUG
((((....(((....)))......((((.((((((((((((..((-----------(....)))..)))))--)......)))))).))))...)))).......... ( -30.90)
>DroPse_CAF1 118386 83 - 1
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUG-----------------------CUGGGCGGGGCCUGCCCGGCAAGGACGCAGCUCU--CAAAUGAGAAAUG
((((((.......))))))......((..(((((((-----------------------((((((((...))))))))).))))))..))(((--(....)))).... ( -35.10)
>DroEre_CAF1 112966 88 - 1
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUGGUCUCUACU-----------CAAAUGGGCGGGGUC--CUUGGCAAGGACGCGGCUCGCACAAAUG-------
((((((.......)))))).....((((.((((((((.(((..((-----------(....)))..))).)--)......)))))).))))..........------- ( -27.20)
>DroYak_CAF1 128149 94 - 1
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUGG-CUCUACU-----------CAAAUGGGCGGGGUC--CUUGGCAAGGACGCGGCUUGCACAAAUGAAAAAUG
((((((.......))))))....(((((.((((((((-(((..((-----------(....)))..)))))--.......)))))).)))))................ ( -28.51)
>DroAna_CAF1 109752 106 - 1
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUCGGCUGAGCUGGAAAACACUGAAAAUGGGCGGGGUC--CUUGGCAAGGACGCGACUCGCACAAAUGAAAAAUG
((((((.......))))))......((((.(.(((((.(((((.((.....)))).....))).))))).)--..))))......(((...))).............. ( -23.10)
>DroPer_CAF1 119699 83 - 1
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUG-----------------------CUGGGCGGGGCCUGCCCGGCAAGGACGCAGCUCU--CAAAUGAGAAAUG
((((((.......))))))......((..(((((((-----------------------((((((((...))))))))).))))))..))(((--(....)))).... ( -35.10)
>consensus
UUGCAUAAUGUUCAUGCAAUUAAAAGCCAUGUCCUGG_CUCUACU___________CAAAUGGGCGGGGUC__CUUGGCAAGGACGCGGCUCGCACAAAUGAAAAAUG
((((((.......)))))).....((((.((((((............................((.(((....))).)).)))))).))))................. (-19.43 = -19.48 +   0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,977,897 – 18,977,990
Length 93
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -20.68
Consensus MFE -17.23
Energy contribution -17.40
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.83
SVM decision value -0.01
SVM RNA-class probability 0.528363
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18977897 93 + 23771897
CCCGCCCAUUUG-----------AGUAGAGCCCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUCUACAUUUUGUAUACUUUG----
............-----------.(((((.(...((((...(((((...((((((((...))))))))..))))).))))...))))))...............---- ( -23.00)
>DroPse_CAF1 118424 85 + 1
CCCGCCCAG-----------------------CAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUUUCCAUUUUGUGUAAUUUUCCCU
........(-----------------------((((((...(((((...((((((((...))))))))..))))).))))((((.......))))))).......... ( -18.40)
>DroSim_CAF1 116730 93 + 1
CCCGCCCAUUUA-----------UGCAGAGCCCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUCUACAUUUUGUAUACUUUG----
..........((-----------(((((((....((((...(((((...((((((((...))))))))..))))).))))...(....).))))))))).....---- ( -22.30)
>DroEre_CAF1 112997 93 + 1
CCCGCCCAUUUG-----------AGUAGAGACCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCACAGCAGUCCCAAGUCUACAUUUUGUAUACUUUG----
...........(-----------((((.((((..((((...(((.....((((((((...))))))))....))).))))...))))((.....)).)))))..---- ( -20.80)
>DroAna_CAF1 109790 104 + 1
CCCGCCCAUUUUCAGUGUUUUCCAGCUCAGCCGAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUCUCCGUUUUGUAUACUUUG----
.............(((((.....(((..((.(..((((...(((((...((((((((...))))))))..))))).))))...).))..)))....)))))...---- ( -21.20)
>DroPer_CAF1 119737 85 + 1
CCCGCCCAG-----------------------CAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUUUCCAUUUUGUGUAAUUUUCCCU
........(-----------------------((((((...(((((...((((((((...))))))))..))))).))))((((.......))))))).......... ( -18.40)
>consensus
CCCGCCCAUUU____________AG_AGAGCCCAGGACAUGGCUUUUAAUUGCAUGAACAUUAUGCAAGCAAAGCAGUCCCAAGUCUACAUUUUGUAUACUUUG____
..................................((((...(((((...((((((((...))))))))..))))).))))............................ (-17.23 = -17.40 +   0.17)

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 12:35:39 2006