Locus 5906

Sequence ID 2L_DroMel_CAF1
Location 16,690,041 – 16,690,226
Length 185
Max. P 0.992259
window9375 window9376 window9377 window9378 window9379

overview

Window 5

Location 16,690,041 – 16,690,136
Length 95
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 73.76
Mean single sequence MFE -30.85
Consensus MFE -17.86
Energy contribution -18.37
Covariance contribution 0.51
Combinations/Pair 1.43
Mean z-score -2.33
Structure conservation index 0.58
SVM decision value 2.14
SVM RNA-class probability 0.988831
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16690041 95 + 22407834
AGCGGUCUAGCGCCUG--UUGGGUUUGGCAACAAAACAUCCUUUUCCCAGCCACGAUGGGAAAUUGGUAAGGGAAGGGG---UGGGGUGGUCGUGGAAUA
.(((..(....((((.--.....((((....)))).(((((((((((..((((...........))))..)))))))))---)))))))..)))...... ( -32.40)
>DroSec_CAF1 144791 89 + 1
AGCGGUCUAGCGCCUG--UUG-GUUGGGCAACAAAAUAUCCUUUUCCCAGCCAGGAUAUUAAAUUGGCAAGGGAAGAGG--------UGUUCGUGGAAGA
.((((((((((.....--...-))))))).....((((.(((((((((.(((((.........)))))..)))))))))--------)))))))...... ( -30.40)
>DroSim_CAF1 144702 89 + 1
AGCGGUCUAGCGCCUG--UUG-GUUGGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAUUAAAUUGGUAAGGGAAGAGG--------UGGUAGUGGAAGA
.((......))(((((--...-..)))))..((..((..(((((((((.(((((.........)))))..)))))))))--------..))..))..... ( -28.80)
>DroEre_CAF1 145203 91 + 1
AGCGGUCUAGCGCCUGUGUUG-GUUGGGCAACAAAGCAUCCUUUUCCCAGCCAGGAUGGCAAGUUGGCAGGGGAAGAGG--------AGCUCGUGGGAGA
.((((((((..(((......)-))))))).....(((.((((((((((.(((((.........)))))..)))))))))--------)))))))...... ( -34.60)
>DroWil_CAF1 245856 83 + 1
----GCCUGGCGCCUG--UUG-GGUAUGCAGCAAAAAAAAUCUCUCUAAGCUGC---------UUGGAAAAGGAGGUUAGGUUGGGUUGGUUGUGUUGU-
----(((..((....)--)..-)))..((((((.((..(((((.(((((.((.(---------((....))).)).)))))..)))))..)).))))))- ( -28.10)
>DroYak_CAF1 144516 89 + 1
AGCGGUCUAGCGCCUG--UUG-GUUUGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAGGAAAUUGGUAAGGGAAGAGG--------AGCUCGUGGGAGA
.((......)).((..--(.(-(((((....)))....((((((((((.(((((.........)))))..)))))))))--------)))).)..))... ( -30.80)
>consensus
AGCGGUCUAGCGCCUG__UUG_GUUGGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAGGAAAUUGGUAAGGGAAGAGG________UGGUCGUGGAAGA
....(((((((...........)))))))..........(((((((((.(((((.........)))))..)))))))))..................... (-17.86 = -18.37 +   0.51)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,690,041 – 16,690,136
Length 95
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 73.76
Mean single sequence MFE -20.22
Consensus MFE -11.24
Energy contribution -12.18
Covariance contribution 0.95
Combinations/Pair 1.16
Mean z-score -1.56
Structure conservation index 0.56
SVM decision value 0.31
SVM RNA-class probability 0.683039
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16690041 95 - 22407834
UAUUCCACGACCACCCCA---CCCCUUCCCUUACCAAUUUCCCAUCGUGGCUGGGAAAAGGAUGUUUUGUUGCCAAACCCAA--CAGGCGCUAGACCGCU
.......((.((......---((..(((((...(((...........)))..)))))..))......(((((.......)))--)))))).......... ( -16.60)
>DroSec_CAF1 144791 89 - 1
UCUUCCACGAACA--------CCUCUUCCCUUGCCAAUUUAAUAUCCUGGCUGGGAAAAGGAUAUUUUGUUGCCCAAC-CAA--CAGGCGCUAGACCGCU
.............--------(((.(((((..((((...........)))).))))).)))......(((((......-)))--))((((......)))) ( -22.80)
>DroSim_CAF1 144702 89 - 1
UCUUCCACUACCA--------CCUCUUCCCUUACCAAUUUAAUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCCAAC-CAA--CAGGCGCUAGACCGCU
.............--------(((.(((((...(((...........)))..))))).)))......(((((......-)))--))((((......)))) ( -19.00)
>DroEre_CAF1 145203 91 - 1
UCUCCCACGAGCU--------CCUCUUCCCCUGCCAACUUGCCAUCCUGGCUGGGAAAAGGAUGCUUUGUUGCCCAAC-CAACACAGGCGCUAGACCGCU
........(((((--------(((.(((((..((((...........)))).))))).)))).))))(((((......-)))))..((((......)))) ( -28.20)
>DroWil_CAF1 245856 83 - 1
-ACAACACAACCAACCCAACCUAACCUCCUUUUCCAA---------GCAGCUUAGAGAGAUUUUUUUUGCUGCAUACC-CAA--CAGGCGCCAGGC----
-..................(((...............---------(((((..(((((...)))))..)))))....(-(..--..))....))).---- ( -12.30)
>DroYak_CAF1 144516 89 - 1
UCUCCCACGAGCU--------CCUCUUCCCUUACCAAUUUCCUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCAAAC-CAA--CAGGCGCUAGACCGCU
........(((((--------(((.(((((...(((...........)))..))))).)))).))))(((((......-)))--))((((......)))) ( -22.40)
>consensus
UCUUCCACGACCA________CCUCUUCCCUUACCAAUUUACUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCCAAC_CAA__CAGGCGCUAGACCGCU
.....................(((.(((((...(((...........)))..))))).)))....((((.((((............)))).))))..... (-11.24 = -12.18 +   0.95)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,690,066 – 16,690,161
Length 95
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 74.27
Mean single sequence MFE -26.20
Consensus MFE -17.27
Energy contribution -17.15
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -2.20
Structure conservation index 0.66
SVM decision value 2.32
SVM RNA-class probability 0.992259
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16690066 95 + 22407834
GCAACAAAACAUCCUUUUCCCAGCCACGAUGGGAAAUUGGUAAGGGAAGGGGUGGGGUGGUCGUGGAAUAGGCGGAGGGACAGA--GGGGAGCCGAG
....((...(((((((((((..((((...........))))..)))))))))))...))(((........)))...........--((....))... ( -25.80)
>DroSim_CAF1 144726 83 + 1
GCAACAAAACAUCCUUUUCCCAGCCAGGAUAUUAAAUUGGUAAGGGAAGAGG-----UGGUAGUGGAAGAUGGAGAG---------GGGGGGCCGAG
....((..((..(((((((((.(((((.........)))))..)))))))))-----..))..))...........(---------(.....))... ( -21.70)
>DroEre_CAF1 145229 79 + 1
GCAACAAAGCAUCCUUUUCCCAGCCAGGAUGGCAAGUUGGCAGGGGAAGAGG-----AGCUCGUGGGAGAG-------------AGUGGGUGGCGAG
((.((...((.((((((((((.(((((.........)))))..)))))))))-----).(((......)))-------------.))..)).))... ( -29.70)
>DroYak_CAF1 144540 85 + 1
GCAACAAAACAUCCUUUUCCCAGCCAGGAUAGGAAAUUGGUAAGGGAAGAGG-----AGCUCGUGGGAGAGCG------UUAG-AGGGGGAGUCGAG
.......(((.((((((((((.(((((.........)))))..)))))))))-----)((((......)))))------))..-............. ( -27.60)
>consensus
GCAACAAAACAUCCUUUUCCCAGCCAGGAUAGGAAAUUGGUAAGGGAAGAGG_____AGCUCGUGGAAGAGGG_____________GGGGAGCCGAG
............(((((((((.(((((.........)))))..)))))))))............................................. (-17.27 = -17.15 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,690,066 – 16,690,161
Length 95
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 74.27
Mean single sequence MFE -17.87
Consensus MFE -11.52
Energy contribution -11.78
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value 1.43
SVM RNA-class probability 0.953496
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16690066 95 - 22407834
CUCGGCUCCCC--UCUGUCCCUCCGCCUAUUCCACGACCACCCCACCCCUUCCCUUACCAAUUUCCCAUCGUGGCUGGGAAAAGGAUGUUUUGUUGC
...(((.....--...........))).......((((.....((((..(((((...(((...........)))..)))))..)).))....)))). ( -14.89)
>DroSim_CAF1 144726 83 - 1
CUCGGCCCCCC---------CUCUCCAUCUUCCACUACCA-----CCUCUUCCCUUACCAAUUUAAUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGC
...........---------....................-----(((.(((((...(((...........)))..))))).)))............ ( -12.90)
>DroEre_CAF1 145229 79 - 1
CUCGCCACCCACU-------------CUCUCCCACGAGCU-----CCUCUUCCCCUGCCAACUUGCCAUCCUGGCUGGGAAAAGGAUGCUUUGUUGC
.............-------------.........(((((-----(((.(((((..((((...........)))).))))).)))).))))...... ( -22.40)
>DroYak_CAF1 144540 85 - 1
CUCGACUCCCCCU-CUAA------CGCUCUCCCACGAGCU-----CCUCUUCCCUUACCAAUUUCCUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGC
..((((.......-....------.((((......))))(-----(((.(((((...(((...........)))..))))).))))......)))). ( -21.30)
>consensus
CUCGGCUCCCC_____________CCCUCUCCCACGACCA_____CCUCUUCCCUUACCAAUUUCCCAUCCUGGCUGGGAAAAGGAUGUUUUGUUGC
.............................................(((.(((((...(((...........)))..))))).)))............ (-11.52 = -11.78 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,690,136 – 16,690,226
Length 90
Sequences 6
Columns 93
Reading direction reverse
Mean pairwise identity 79.46
Mean single sequence MFE -14.58
Consensus MFE -14.01
Energy contribution -13.57
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.96
SVM decision value 1.01
SVM RNA-class probability 0.899708
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16690136 90 - 22407834
CAUGUGUGCAUCUCCAUUAUGUUUCAUUUGCAUAUUGAACCUAUUUAUGGCAG-CCAUUCAUUGCACUCGGCUCCCC--UCUGUCCCUCCGCC
...(.(((((....((.(((((.......))))).)).........((((...-))))....))))).)(((.....--...)))........ ( -13.80)
>DroPse_CAF1 161195 75 - 1
UGUGUGUGCCUUUCCAUUAUGUUCCAUUUGCAUAUUGAACCUAUUUAUGGCAACCCAUUCAUGGCACUCCAUGCC------------------
.(((.(((((....((.(((((.......))))).)).........((((....))))....)))))..)))...------------------ ( -15.40)
>DroSim_CAF1 144791 83 - 1
CAUGUGUGCAUCUCCAUUAUGUUUCAUUUGCAUAUUGAACCUAUUUAUGGCAG-CCAUUCAUUGCACUCGGCCCCCC---------CUCUCCA
..((.(((((....((.(((((.......))))).)).........((((...-))))....))))).)).......---------....... ( -12.60)
>DroEre_CAF1 145294 79 - 1
CAAGUGUGCAUCUCCAUUAUGUUGCAUUUGCAUAUUGAACCUAUUUAUGGCAG-CCAUUCAUUGCACUCGCCACCCACU-------------C
..((((((((....((......))....))))))))...........((((((-.((.....))..)).))))......-------------. ( -12.90)
>DroYak_CAF1 144605 85 - 1
CAUGUGUGCAUUUCCAUUAUGUUUCAUUUGCAUAUUGGACCUAUUUAUGGCAG-CCAUUCAUUGCACUCGACUCCCCCU-CUAA------CGC
..((.(((((..((((.(((((.......))))).)))).......((((...-))))....))))).)).........-....------... ( -17.10)
>DroPer_CAF1 163098 75 - 1
UAUGUGUGCCUUUCCAUUAUGUUCCAUUUGCAUAUUGAACCUAUUUAUGGCAACCCAUUCAUGGCACUCCAUGCC------------------
((((.(((((....((.(((((.......))))).)).........((((....))))....)))))..))))..------------------ ( -15.70)
>consensus
CAUGUGUGCAUCUCCAUUAUGUUUCAUUUGCAUAUUGAACCUAUUUAUGGCAG_CCAUUCAUUGCACUCGACGCCCC_______________C
...(.(((((....((.(((((.......))))).)).........((((....))))....))))).)........................ (-14.01 = -13.57 +  -0.44)

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 11:56:05 2006