Locus 5550

Sequence ID 3R_DroMel_CAF1
Location 14,667,913 – 14,668,030
Length 117
Max. P 0.957301
window9047 window9048 window9049 window9050

overview

Window 7

Location 14,667,913 – 14,668,004
Length 91
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 78.89
Mean single sequence MFE -28.68
Consensus MFE -17.27
Energy contribution -17.05
Covariance contribution -0.22
Combinations/Pair 1.14
Mean z-score -2.54
Structure conservation index 0.60
SVM decision value 1.48
SVM RNA-class probability 0.957301
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14667913 91 + 27905053
UGGGAGAAAA-----AAAAAAAAAAAACGGUGGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGACUAUGCUACGCAUAA
..........-----.............(((....)))((((.((((((....)))))).)))).....((((.....))))(((((...))))). ( -20.10)
>DroPse_CAF1 80640 77 + 1
UGU-----GGCUGG--------------GGCAGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAA
.((-----(((.((--------------.(((.((((((.....)))))).))).))(((.((..(((((....))))))).))))))))...... ( -30.30)
>DroSim_CAF1 90281 96 + 1
UGCGAGGGAGCUGGUGAAUAAAAAAAGCGUUGGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCUACGCAUAA
((((....(((.((..((((......(((.....))).((((.((((((....)))))).))))..........))))..))...))).))))... ( -30.70)
>DroEre_CAF1 81937 88 + 1
--CGAGGGAGCUGG------GAAAAAAUGGUGGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCUCCGCAUAA
--....((((((((------(...(((((...((((..((((.((((((....)))))).))))....))))..))))).)))).)))))...... ( -31.50)
>DroAna_CAF1 79441 85 + 1
------GGCACUGGG-----GAAAGAAUGGCGGGCGCCAGUUAGUGGUGCGUGCCCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAA
------((((.((((-----.(((....((((.((((((.....)))))).)))).(((........)))......))).))))))))........ ( -29.20)
>DroPer_CAF1 82552 77 + 1
UGU-----GGCUGG--------------GGCAGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAA
.((-----(((.((--------------.(((.((((((.....)))))).))).))(((.((..(((((....))))))).))))))))...... ( -30.30)
>consensus
UGC___GGAGCUGG_______AAAAAA_GGCGGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAA
............................(((((((...((((.((((((....)))))).)))).(((((....)))))))))..)))........ (-17.27 = -17.05 +  -0.22)

alignment

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secondary structure

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Window 8

Location 14,667,913 – 14,668,004
Length 91
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 78.89
Mean single sequence MFE -21.98
Consensus MFE -15.05
Energy contribution -15.55
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.68
SVM decision value 0.89
SVM RNA-class probability 0.875428
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14667913 91 - 27905053
UUAUGCGUAGCAUAGUCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCCACCGUUUUUUUUUUUU-----UUUUCUCCCA
...(((((.((...((((.....))))......((.....)))))))))(((.....))).....................-----.......... ( -15.20)
>DroPse_CAF1 80640 77 - 1
UUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCUGCC--------------CCAGCC-----ACA
......((((((((((((((.........))).))))))((.(((.((.(((.....))).)).))).--------------)).)))-----)). ( -26.80)
>DroSim_CAF1 90281 96 - 1
UUAUGCGUAGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCCAACGCUUUUUUUAUUCACCAGCUCCCUCGCA
...((((.((((((((((((.........))).))))))((((...((.(((.....))).))....))))..............)))....)))) ( -19.80)
>DroEre_CAF1 81937 88 - 1
UUAUGCGGAGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCCACCAUUUUUUC------CCAGCUCCCUCG--
......((((((((((((((.........))).))))))(((((.((..........)))))))............------...)))))....-- ( -21.30)
>DroAna_CAF1 79441 85 - 1
UUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGGGCACGCACCACUAACUGGCGCCCGCCAUUCUUUC-----CCCAGUGCC------
....((((((((((((((((.........))).))))))).(((..((.(((.....))).))..)))........-----.))).))).------ ( -22.00)
>DroPer_CAF1 82552 77 - 1
UUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCUGCC--------------CCAGCC-----ACA
......((((((((((((((.........))).))))))((.(((.((.(((.....))).)).))).--------------)).)))-----)). ( -26.80)
>consensus
UUAUGCGUAGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCCACC_UUUUUU_______CCAGCUCC___ACA
...(((((..((((((((((.........))).)))))))))))).((.(((.....))).))................................. (-15.05 = -15.55 +   0.50)

alignment

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secondary structure

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Window 9

Location 14,667,929 – 14,668,030
Length 101
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.73
Mean single sequence MFE -33.00
Consensus MFE -23.09
Energy contribution -23.48
Covariance contribution 0.39
Combinations/Pair 1.17
Mean z-score -2.07
Structure conservation index 0.70
SVM decision value 1.30
SVM RNA-class probability 0.939859
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14667929 101 + 27905053
AAAAAACGGUGGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGACUAUGCUACGCAUAAAA--UGCCAAGGCAUAUGCCUUGUGGUG---------
........(((.((((((.....)))))).)))(((((((((......((((.....))))((((((..((((...)--)))...)))))).).)))))))).--------- ( -32.40)
>DroVir_CAF1 96580 112 + 1
CCAAAACGGGAAGCGUCAGUUAGUGGCGCGUGCUCCAUAAGCCCAAAUGUCAAUAUUUGCCUAUGCCAGGCAUUAAACGCGCCAAAGCAUGUGCCUCAUAGUAUGUGUUUGG
((((((((.((.(((.(((((..(((((((((((.....)))...............(((((.....)))))....)))))))).))).))))).))......))).))))) ( -31.80)
>DroPse_CAF1 80649 96 + 1
-------GGCAGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAAAA--UGCCAAGGCAUAUGCCUUCUCGGAGG-------
-------(((((((...((((.((((((....)))))).)))).(((((....))))))))((((((..((((...)--)))...))))))))))..........------- ( -31.30)
>DroWil_CAF1 98302 94 + 1
UGUAGGCAGUUGGCGCCAGUUAGUGGUGCGUGCGGCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAAAA--UGCCAUAGCAUAUGCCG----------------
....((((....((((((.....))))))(((.((((((.((..(((((....))))))).)))))).))).....(--(((....)))).)))).---------------- ( -32.90)
>DroAna_CAF1 79451 100 + 1
AAAGAAUGGCGGGCGCCAGUUAGUGGUGCGUGCCCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAAAG--UGCCAAGGCAUAUGCCUUGUGGU----------
.......((((.((((((.....)))))).))))(((((((...(((((....)))))((.((((((..((((...)--)))...)))))).))))))))).---------- ( -36.80)
>DroPer_CAF1 82561 97 + 1
-------GGCAGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAAAA--UGCCAAGGCAUAUGCCUUCUCGGAGGC------
-------((((((((..((((.((((((....)))))).))))....))))......))))((((((..((((...)--)))...)))))).(((((....)))))------ ( -32.80)
>consensus
__AAAACGGCAGGCGCCAGUUAGUGGUGCGUGCGCCAUAAGCUAAAAUGUCAAUAUUUGCCUAUGCCACGCAUAAAA__UGCCAAGGCAUAUGCCUUCUCGUA_________
.......(((..((((((.....))))))(((((.((((.((..(((((....))))))).))))...))))).......)))(((((....)))))............... (-23.09 = -23.48 +   0.39)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,667,929 – 14,668,030
Length 101
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.73
Mean single sequence MFE -29.90
Consensus MFE -22.31
Energy contribution -22.70
Covariance contribution 0.39
Combinations/Pair 1.14
Mean z-score -1.80
Structure conservation index 0.75
SVM decision value 1.14
SVM RNA-class probability 0.920806
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14667929 101 - 27905053
---------CACCACAAGGCAUAUGCCUUGGCA--UUUUAUGCGUAGCAUAGUCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCCACCGUUUUUU
---------.....((((((....))))))((.--.....(((((.((...((((.....))))......((.....)))))))))(((.....))).))............ ( -26.60)
>DroVir_CAF1 96580 112 - 1
CCAAACACAUACUAUGAGGCACAUGCUUUGGCGCGUUUAAUGCCUGGCAUAGGCAAAUAUUGACAUUUGGGCUUAUGGAGCACGCGCCACUAACUGACGCUUCCCGUUUUGG
(((((.((.......(((((....)))))(((((((....((((((...))))))...............((((...))))))))))).................))))))) ( -30.60)
>DroPse_CAF1 80649 96 - 1
-------CCUCCGAGAAGGCAUAUGCCUUGGCA--UUUUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCUGCC-------
-------........(((((....)))))(((.--.....(((((((((((((((((.........))).)))))).)).))))))(((.....))).)))....------- ( -29.70)
>DroWil_CAF1 98302 94 - 1
----------------CGGCAUAUGCUAUGGCA--UUUUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGCCGCACGCACCACUAACUGGCGCCAACUGCCUACA
----------------.((((.((((....)))--).....(.((((((((((((((.........))).))))))))))).)((.(((.....))).))....)))).... ( -31.10)
>DroAna_CAF1 79451 100 - 1
----------ACCACAAGGCAUAUGCCUUGGCA--CUUUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGGGCACGCACCACUAACUGGCGCCCGCCAUUCUUU
----------.(((((((((....))))).(((--.....)))))))((((((((((.........))).))))))).(((..((.(((.....))).))..)))....... ( -31.30)
>DroPer_CAF1 82561 97 - 1
------GCCUCCGAGAAGGCAUAUGCCUUGGCA--UUUUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCUGCC-------
------((.......(((((....)))))(((.--.....(((((((((((((((((.........))).)))))).)).))))))(((.....))).))).)).------- ( -30.10)
>consensus
_________UACCACAAGGCAUAUGCCUUGGCA__UUUUAUGCGUGGCAUAGGCAAAUAUUGACAUUUUAGCUUAUGGCGCACGCACCACUAACUGGCGCCUGCCGUUUU__
...............(((((....)))))(((........((((((.(((((((((((......))))..)))))))...))))))(((.....))).)))........... (-22.31 = -22.70 +   0.39)

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 11:57:52 2006