Locus 499

Sequence ID 2L_DroMel_CAF1
Location 1,490,867 – 1,491,018
Length 151
Max. P 0.817715
window795 window796 window797 window798

overview

Window 5

Location 1,490,867 – 1,490,957
Length 90
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -17.44
Consensus MFE -11.31
Energy contribution -12.20
Covariance contribution 0.89
Combinations/Pair 1.15
Mean z-score -1.46
Structure conservation index 0.65
SVM decision value -0.02
SVM RNA-class probability 0.522560
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1490867 90 + 22407834
GAAUCGAACAGAGGGAA--------AACAAAAAAUAUAUCGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU--GAGCCAAGUUCAAUUCCAG
((((.((((....((..--------.((........(((((((....))))))).............(((....)))))--...))..)))).))))... ( -19.40)
>DroGri_CAF1 145876 80 + 1
GCA----A-------AU--------AAUGGCAAAUAUAUUG-AACACUGCGAUAAACAUAUGAAAAAUGCACAUGCGACUGGCGCCAAGUUCAAUUCCGC
((.----.-------..--------....))......((((-(((...(((.......((((.........)))).......)))...)))))))..... ( -10.54)
>DroSim_CAF1 111157 90 + 1
AAAUCGAACAGAGGGAA--------AACGGAAAAUAUAUCGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU--GAGCCAAGUUCAAUUCCAG
.................--------...((((....(((((((....)))))))......((((....((....))((.--...))...)))).)))).. ( -17.70)
>DroEre_CAF1 114764 90 + 1
GAAUCGAACUGAGGAAA--------AGCGGAAAAUGUAUCGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU--GAGCCAAGUUCAAUUCCAG
((((.(((((..((...--------.((.....((((((((((....))))))..))))........(((....)))))--...)).))))).))))... ( -21.40)
>DroYak_CAF1 111731 98 + 1
GAAUCGAACAGAGGGAAAAACGGCAAGCGGAAAAUAUAUCGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU--GAGCCAAGUUCAAUUCCAG
((((.((((....((....((.(((.(((....((((((((((....)))))))....)))......)))...))).))--...))..)))).))))... ( -22.80)
>DroAna_CAF1 111288 83 + 1
GAA----AGAAAGUAAA-----------AUAAAAUACAACGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU--GAGCCAAGUUCAAUUCCAG
...----.(((......-----------...........((((..((((((.....(....).....)))))))))).(--((((...))))).)))... ( -12.80)
>consensus
GAAUCGAACAGAGGGAA________AACGGAAAAUAUAUCGCAACUGUGCGAUAAACAUAUGAAAAAUGCACAUGCGGU__GAGCCAAGUUCAAUUCCAG
............((((....................(((((((....)))))))......((((....((....))(((....)))...)))).)))).. (-11.31 = -12.20 +   0.89) 

alignment

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secondary structure

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dotplot

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Window 6

Location 1,490,867 – 1,490,957
Length 90
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 81.30
Mean single sequence MFE -20.84
Consensus MFE -12.83
Energy contribution -14.75
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -2.36
Structure conservation index 0.62
SVM decision value 0.67
SVM RNA-class probability 0.817715
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1490867 90 - 22407834
CUGGAAUUGAACUUGGCUC--ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGAUAUAUUUUUUGUU--------UUCCCUCUGUUCGAUUC
...(((((((((..((...--...(((((((.......))))))).(((((((....)))))))...........--------...))...))))))))) ( -23.40)
>DroGri_CAF1 145876 80 - 1
GCGGAAUUGAACUUGGCGCCAGUCGCAUGUGCAUUUUUCAUAUGUUUAUCGCAGUGUU-CAAUAUAUUUGCCAUU--------AU-------U----UGC
((((((((((((...(((......(((((((.......)))))))....)))...)))-))))...)))))....--------..-------.----... ( -19.00)
>DroSim_CAF1 111157 90 - 1
CUGGAAUUGAACUUGGCUC--ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGAUAUAUUUUCCGUU--------UUCCCUCUGUUCGAUUU
...(((((((((..((...--...(((((((.......))))))).(((((((....)))))))...........--------...))...))))))))) ( -22.20)
>DroEre_CAF1 114764 90 - 1
CUGGAAUUGAACUUGGCUC--ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGAUACAUUUUCCGCU--------UUUCCUCAGUUCGAUUC
...((((((((((.((...--...(((((((.......))))))).(((((((....)))))))...........--------...))..)))))))))) ( -23.60)
>DroYak_CAF1 111731 98 - 1
CUGGAAUUGAACUUGGCUC--ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGAUAUAUUUUCCGCUUGCCGUUUUUCCCUCUGUUCGAUUC
...(((((((((.((((..--...(((((((.......))))))).(((((((....)))))))............))))...........))))))))) ( -24.60)
>DroAna_CAF1 111288 83 - 1
CUGGAAUUGAACUUGGCUC--ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGUUGUAUUUUAU-----------UUUACUUUCU----UUC
..((((.((((.......(--(.(((((((((..................)))))..)))).))........-----------)))).)))).----... ( -12.23)
>consensus
CUGGAAUUGAACUUGGCUC__ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAGUUGCGAUAUAUUUUCCGUU________UUCCCUCUGUUCGAUUC
...(((((((((..((......))(((((((.......))))))).(((((((....)))))))...........................))))))))) (-12.83 = -14.75 +   1.92) 

alignment

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secondary structure

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dotplot

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Window 7

Location 1,490,896 – 1,490,995
Length 99
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.17
Mean single sequence MFE -28.70
Consensus MFE -18.96
Energy contribution -19.94
Covariance contribution 0.97
Combinations/Pair 1.08
Mean z-score -1.63
Structure conservation index 0.66
SVM decision value 0.23
SVM RNA-class probability 0.646031
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1490896 99 - 22407834
UGCGUCAAGUUCCAUUAAGUGGCGUAAACU--UUUGGCCUCUGGAAUUGAACUUGGC--UC---ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACA--------GUUG----CGAU
((.(((((((((.(((.((.(((.......--....))).))..))).)))))))))--.)---)..(((((((.......)))))))..((((((..--------..))----)))) ( -30.20)
>DroVir_CAF1 167574 101 - 1
UGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUGCGGAAUCGAGCUUGGC--GCCCAGCCGCAUGUGCAUUUUUCAUAUGUUUAUCGCAGU--------GUU-----CAAU
.(((((((((((.(((..(((((.......--....))).))..))).)))))))))--))...((.(((((((.......))))))).....))...--------...-----.... ( -29.30)
>DroPse_CAF1 151325 109 - 1
UGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUCUGGAAUUGAACUUGGCUCUC---ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAUAGCGCGGGUCC----CGAU
...(((((((((.(((.((.(((.......--....))).))..))).)))))))))....---.((((((((((..................))))))...))))....----.... ( -31.67)
>DroSec_CAF1 108658 88 - 1
UGCGUCAAGUUC-AUUA-GU-GCGUAAACU--UUG---CUCUGCA--UGAGCU-AGC--UC---A-CGCAUGUGCAUUUUUCAUAUGUUUAUCGCACA--------G-UG----CGAU
.((....(((((-((((-(.-(((......--.))---).))).)--))))))-.))--..---.-(((((((((..................)))))--------.-))----)).. ( -24.37)
>DroWil_CAF1 161267 105 - 1
UGCGUCAAGUUCUAUUAAGUGGCGUAAAGUUUUUUGGCCUUCGGAAUUGAACUUGGG--CC---GCAGCAUGUGCAUUUUUCAUAUGUUUAUCGUAGA--------GUUUCGUUCGAU
((((((((((((.(((..(.(((.((((....)))))))..)..))).)))))))).--.)---)))(((((((.......)))))))..((((..(.--------....)...)))) ( -25.00)
>DroPer_CAF1 149470 109 - 1
UGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUCUGGAAUUGAACUUGGCUCUC---ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACAUAGCGCGGGUCU----CGAU
...(((((((((.(((.((.(((.......--....))).))..))).)))))))))....---.((((((((((..................))))))...))))....----.... ( -31.67)
>consensus
UGCGUCAAGUUCUAUUAAGUGGCGUAAACU__UUUGGCCUCUGGAAUUGAACUUGGC__UC___ACCGCAUGUGCAUUUUUCAUAUGUUUAUCGCACA________GUUG____CGAU
((((((((((((.(((....(((.............))).....))).)))))))))..........(((((((.......))))))).....)))...................... (-18.96 = -19.94 +   0.97) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,490,922 – 1,491,018
Length 96
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -30.60
Consensus MFE -20.22
Energy contribution -20.25
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.66
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.510160
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1490922 96 - 22407834
-----AGGA---GCCAUGU-----UGUAAUUGAAUUUGCGUCAAGUUCCAUUAAGUGGCGUAAACU--UUUGGCCUCUGGAAUUGAACUUGGCUC---ACCGCAUGUGCAUUUU
-----....---(((((((-----.((((......))))(((((((((.(((.((.(((.......--....))).))..))).)))))))))..---...))))).))..... ( -28.90)
>DroVir_CAF1 167599 101 - 1
-----UGGGGC-GCCACGU-----UGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUGCGGAAUCGAGCUUGGCGCCCAGCCGCAUGUGCAUUUU
-----((((((-(((((..-----..((((.(((((((...))))))).)))).))))))).....--....(((.((........))..))).))))...((....))..... ( -34.20)
>DroGri_CAF1 145919 98 - 1
-----GGGGG---CAACGU-----UGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUGCGGAAUUGAACUUGGCGC-CAGUCGCAUGUGCAUUUU
-----....(---((.(((-----.(..((((.....(((((((((((.(((..(((((.......--....))).))..))).)))))))))))-))))..)))))))..... ( -31.40)
>DroWil_CAF1 161297 99 - 1
-----UCUU--GCCAAUGU-----UGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAAGUUUUUUGGCCUUCGGAAUUGAACUUGGGCC---GCAGCAUGUGCAUUUU
-----...(--((..((((-----(((.......(((((((((..(......)..))))))))).......(((((..(........)..)))))---)))))))..))).... ( -29.50)
>DroMoj_CAF1 174505 106 - 1
-----GGGGGC-GUGGCCUGUGUCUGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUGCGGAAUUGAACUUGGCGCCCAGCCGCAUGUGCAUUUU
-----.(.(((-..(((........((((......))))(((((((((.(((..(((((.......--....))).))..))).))))))))))))..))).)........... ( -33.10)
>DroAna_CAF1 111336 104 - 1
UGGUAAGAGGUCGAAAUGU-----UGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAACU--UUUGGCCUCUGGAAUUGAACUUGGCUC---ACCGCAUGUGCAUUUU
........(((.((.....-----.((((......))))(((((((((.(((.((.(((.......--....))).))..))).)))))))))))---)))((....))..... ( -26.50)
>consensus
_____AGGGG__GCAACGU_____UGUAAUUGAAUUUGCGUCAAGUUCUAUUAAGUGGCGUAAACU__UUUGGCCUGCGGAAUUGAACUUGGCGC___GCCGCAUGUGCAUUUU
.........................((((......))))(((((((((.(((....(((.((((....))))))).....))).)))))))))........((....))..... (-20.22 = -20.25 +   0.03) 

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 09:37:38 2006