Locus 2934

Sequence ID 3R_DroMel_CAF1
Location 7,863,870 – 7,864,011
Length 141
Max. P 0.992821
window4720 window4721 window4722 window4723

overview

Window 0

Location 7,863,870 – 7,863,976
Length 106
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 92.45
Mean single sequence MFE -38.24
Consensus MFE -35.70
Energy contribution -35.22
Covariance contribution -0.48
Combinations/Pair 1.09
Mean z-score -1.57
Structure conservation index 0.93
SVM decision value 1.81
SVM RNA-class probability 0.978138
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7863870 106 + 27905053
AUGCAUUUUCAGCUGCAUGUGACUGGGACGAUGGGUUGCCAAAA-UG------------GGCUGGUGGCUAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCA
........((((((.((((..(((.(.....).)))..)....)-))------------)))))).((((((.((.(((((((........)))))))))))))))((((....)))). ( -34.10)
>DroSec_CAF1 24706 106 + 1
AUGCAUUUUCAGCUGCAUGUGACUGGGACGAUGGGUUGCCAAAA-UG------------GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCA
........((((((.((((..(((.(.....).)))..)....)-))------------)))))).((((((.((.(((((((........)))))))))))))))((((....)))). ( -36.40)
>DroSim_CAF1 25005 106 + 1
AUGCAUUUUCAGCUGCAUGUGACUGGGACGAUGGGUUGCCAAAA-UG------------GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCA
........((((((.((((..(((.(.....).)))..)....)-))------------)))))).((((((.((.(((((((........)))))))))))))))((((....)))). ( -36.40)
>DroEre_CAF1 24868 106 + 1
AUGCAUUUUCAGCUGCAUGUGACUGGGACGAUGGGUGGCCAAAA-UG------------GGCUGGCGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCU
(((((........)))))......((((...(((....)))...-..------------((((..(((((((.((.(((((((........))))))))))))))))..)))).)))). ( -37.50)
>DroYak_CAF1 25226 119 + 1
GUGCAGUUUCAGCUGCAUGUGACUGGGACGAUGGGUGGCCAAAAAUGGUGGUGCCUGGUGGCUGGUGGCCAGUGGAUAUGAGGUCAACGACCCUUAUACCCUGGCUGAGAGCUAUCUCU
(((((((....)))))))..............(((((((((....))))..)))))(((((((..(((((((.((.(((((((........))))))))))))))))..)))))))... ( -46.80)
>consensus
AUGCAUUUUCAGCUGCAUGUGACUGGGACGAUGGGUUGCCAAAA_UG____________GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCA
(((((........)))))......((((...(((....)))..................((((..(((((((.((.(((((((........))))))))))))))))..)))).)))). (-35.70 = -35.22 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,863,870 – 7,863,976
Length 106
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.45
Mean single sequence MFE -28.78
Consensus MFE -25.64
Energy contribution -26.04
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.17
Structure conservation index 0.89
SVM decision value 0.08
SVM RNA-class probability 0.574845
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7863870 106 - 27905053
UGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUAGCCACCAGCC------------CA-UUUUGGCAACCCAUCGUCCCAGUCACAUGCAGCUGAAAAUGCAU
(((((....)))))((((((((((.(((........))).))))))....((.....)).------------..-...))))...................(((((........))))) ( -25.40)
>DroSec_CAF1 24706 106 - 1
UGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC------------CA-UUUUGGCAACCCAUCGUCCCAGUCACAUGCAGCUGAAAAUGCAU
(((((....)))))(((((((.....(((((...))))).....)).))))).....(((------------..-....)))...................(((((........))))) ( -28.50)
>DroSim_CAF1 25005 106 - 1
UGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC------------CA-UUUUGGCAACCCAUCGUCCCAGUCACAUGCAGCUGAAAAUGCAU
(((((....)))))(((((((.....(((((...))))).....)).))))).....(((------------..-....)))...................(((((........))))) ( -28.50)
>DroEre_CAF1 24868 106 - 1
AGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCGCCAGCC------------CA-UUUUGGCCACCCAUCGUCCCAGUCACAUGCAGCUGAAAAUGCAU
.((((....)))).(((((((.....(((((...))))).....)).))))).(((((..------------..-..)))))...................(((((........))))) ( -29.30)
>DroYak_CAF1 25226 119 - 1
AGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCGUUGACCUCAUAUCCACUGGCCACCAGCCACCAGGCACCACCAUUUUUGGCCACCCAUCGUCCCAGUCACAUGCAGCUGAAACUGCAC
.((((....)))).(((.((((((.(((........))).))))))..((((.....))))...)))....(((....))).....................(((((......))))). ( -32.20)
>consensus
UGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC____________CA_UUUUGGCAACCCAUCGUCCCAGUCACAUGCAGCUGAAAAUGCAU
.((((....)))).((((((((((.(((........))).))))))...(((.....)))..................))))...................(((((........))))) (-25.64 = -26.04 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,863,910 – 7,864,011
Length 101
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -35.14
Consensus MFE -26.70
Energy contribution -26.38
Covariance contribution -0.32
Combinations/Pair 1.10
Mean z-score -2.81
Structure conservation index 0.76
SVM decision value 2.35
SVM RNA-class probability 0.992821
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7863910 101 + 27905053
AAAA-UG------------GGCUGGUGGCUAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCAAUUUGUUUUGGAGUGGCGAGUGUUUUCGUGUUUAU-----
....-..------------((((..(((((((.((.(((((((........))))))))))))))))..))))((..(((......)))..)).(((((....)))))......----- ( -30.00)
>DroSec_CAF1 24746 85 + 1
AAAA-UG------------GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCAAUUUGUUUUGA----------------GAACUUGU-----
....-..------------((((..(((((((.((.(((((((........))))))))))))))))..)))).((((((......))))----------------))......----- ( -32.90)
>DroSim_CAF1 25045 101 + 1
AAAA-UG------------GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCAAUUUGUUUUGGAGUGGUGAGUGUUUUCGUGUUUAU-----
...(-((------------(((....((((((.((.(((((((........)))))))))))))))((((((...((((((((......))))..)))).))))))..))))))----- ( -30.90)
>DroEre_CAF1 24908 106 + 1
AAAA-UG------------GGCUGGCGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCUACUUGUUUUGGAGUGGCGAGUGUUUUCGUGUUUAUAUACA
....-..------------((((..(((((((.((.(((((((........))))))))))))))))..)))).((.((((((......)))))).))........((((....)))). ( -37.60)
>DroYak_CAF1 25266 119 + 1
AAAAAUGGUGGUGCCUGGUGGCUGGUGGCCAGUGGAUAUGAGGUCAACGACCCUUAUACCCUGGCUGAGAGCUAUCUCUAUUUGUUUUGGAGUGGAGAGUGUUCUCGUGUUUAUAUACA
............(((....)))....((((((.((.(((((((........)))))))))))))))((((((..(((((((((......)))))))))..))))))((((....)))). ( -44.30)
>consensus
AAAA_UG____________GGCUGGUGGCCAGUGGAUAUGAGGUCAAAGACCCUUAUACCCUGGCUGAGAGCUAUCUCAAUUUGUUUUGGAGUGGCGAGUGUUUUCGUGUUUAU_____
...................((((..(((((((.((.(((((((........))))))))))))))))..)))).............................................. (-26.70 = -26.38 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,863,910 – 7,864,011
Length 101
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -22.26
Consensus MFE -18.60
Energy contribution -18.80
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.84
SVM decision value 1.25
SVM RNA-class probability 0.935658
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7863910 101 - 27905053
-----AUAAACACGAAAACACUCGCCACUCCAAAACAAAUUGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUAGCCACCAGCC------------CA-UUUU
-----..................((..............((((((....))))))...((((((.(((........))).))))))....))........------------..-.... ( -16.50)
>DroSec_CAF1 24746 85 - 1
-----ACAAGUUC----------------UCAAAACAAAUUGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC------------CA-UUUU
-----......((----------------((((......))))))..(((....(((((((.....(((((...))))).....)).)))))....))).------------..-.... ( -24.10)
>DroSim_CAF1 25045 101 - 1
-----AUAAACACGAAAACACUCACCACUCCAAAACAAAUUGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC------------CA-UUUU
-----...................................(((((....)))))(((((((.....(((((...))))).....)).)))))........------------..-.... ( -20.70)
>DroEre_CAF1 24908 106 - 1
UGUAUAUAAACACGAAAACACUCGCCACUCCAAAACAAGUAGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCGCCAGCC------------CA-UUUU
....................(((...(((........))).)))...(((..(.(((((((.....(((((...))))).....)).))))).)..))).------------..-.... ( -22.40)
>DroYak_CAF1 25266 119 - 1
UGUAUAUAAACACGAGAACACUCUCCACUCCAAAACAAAUAGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCGUUGACCUCAUAUCCACUGGCCACCAGCCACCAGGCACCACCAUUUUU
.............((((....))))................((((....)))).(((.((((((.(((........))).))))))..((((.....))))...)))............ ( -27.60)
>consensus
_____AUAAACACGAAAACACUCGCCACUCCAAAACAAAUUGAGAUAGCUCUCAGCCAGGGUAUAAGGGUCUUUGACCUCAUAUCCACUGGCCACCAGCC____________CA_UUUU
.........................................((((....)))).(((((((.....(((((...))))).....)).)))))........................... (-18.60 = -18.80 +   0.20)

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 10:48:08 2006