Locus 8963

Sequence ID 3R_DroMel_CAF1
Location 24,047,620 – 24,047,782
Length 162
Max. P 0.965958
window14366 window14367 window14368 window14369

overview

Window 6

Location 24,047,620 – 24,047,711
Length 91
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.41
Mean single sequence MFE -20.35
Consensus MFE -17.63
Energy contribution -18.13
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.87
SVM decision value 0.08
SVM RNA-class probability 0.571899
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24047620 91 + 27905053
----------------------------GUCGGGUCCCAUGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCU-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
----------------------------.((((.(((..((..(((((((.(((..(((.....)))..))).))))))).-.))....))).))))((((((((......)))))))). ( -20.90)
>DroVir_CAF1 265365 89 + 1
-----------------------------U-GUGUCCCACGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCU-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
-----------------------------.-(((...)))...(((((((.(((..(((.....)))..))).)))))))(-((.....)))....(((((((((......))))))))) ( -18.40)
>DroPse_CAF1 261204 91 + 1
-----------------------------GGGGGUCCCAUGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCUACCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
-----------------------------(((...))).....(((((((.(((..(((.....)))..))).)))))))..((.....)).....(((((((((......))))))))) ( -19.50)
>DroWil_CAF1 294303 119 + 1
UAUACUUCUUCUGGUUGUCCUCUUUUUUUUCUGGUCCCAGGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCU-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
.........(((((..(.((............)).))))))..(((((((.(((..(((.....)))..))).)))))))(-((.....)))....(((((((((......))))))))) ( -23.90)
>DroAna_CAF1 252211 89 + 1
------------------------------UGGGUCCCCUGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCU-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
------------------------------.((....))....(((((((.(((..(((.....)))..))).)))))))(-((.....)))....(((((((((......))))))))) ( -19.90)
>DroPer_CAF1 262608 91 + 1
-----------------------------GGGGGUCCCAUGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCUACCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
-----------------------------(((...))).....(((((((.(((..(((.....)))..))).)))))))..((.....)).....(((((((((......))))))))) ( -19.50)
>consensus
_____________________________UCGGGUCCCAUGUUGAUAAUUCGAAAUUUGUAUUCCAAUCUUCAAAUUGUCU_CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAU
....................................((((...(((((((.(((..(((.....)))..))).))))))).......)))).....(((((((((......))))))))) (-17.63 = -18.13 +   0.50)

alignment

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secondary structure

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Window 7

Location 24,047,620 – 24,047,711
Length 91
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.41
Mean single sequence MFE -20.97
Consensus MFE -18.18
Energy contribution -18.40
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -2.63
Structure conservation index 0.87
SVM decision value 1.59
SVM RNA-class probability 0.965958
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24047620 91 - 27905053
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACAUGGGACCCGAC----------------------------
((((.((((......)))).))))...((((((.((((-....(((((((((.(((.....))).))))))))).)))).))))))......---------------------------- ( -19.30)
>DroVir_CAF1 265365 89 - 1
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACGUGGGACAC-A-----------------------------
((((.((((......)))).))))...((((((.((((-....(((((((((.(((.....))).))))))))).)))).))))))...-.----------------------------- ( -19.60)
>DroPse_CAF1 261204 91 - 1
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGGUAGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACAUGGGACCCCC-----------------------------
((((.((((......)))).))))...((((((.((((((....((((((((.(((.....))).)))))))))))))).)))))).....----------------------------- ( -21.20)
>DroWil_CAF1 294303 119 - 1
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACCUGGGACCAGAAAAAAAAGAGGACAACCAGAAGAAGUAUA
(((((((((......)))).............((((((-.((.(((((((((.(((.....))).))))))))).))...(((....)))................)))))))))))... ( -25.40)
>DroAna_CAF1 252211 89 - 1
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACAGGGGACCCA------------------------------
((((.((((......)))).))))....(((.....))-)((.(((((((((.(((.....))).))))))))).))....((....)).------------------------------ ( -19.10)
>DroPer_CAF1 262608 91 - 1
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGGUAGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACAUGGGACCCCC-----------------------------
((((.((((......)))).))))...((((((.((((((....((((((((.(((.....))).)))))))))))))).)))))).....----------------------------- ( -21.20)
>consensus
AUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG_AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAACAUGGGACCCCA_____________________________
((((.((((......)))).))))...((((((.((((.....(((((((((.(((.....))).))))))))).)))).)))))).................................. (-18.18 = -18.40 +   0.22)

alignment

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secondary structure

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Window 8

Location 24,047,632 – 24,047,751
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -21.27
Consensus MFE -18.63
Energy contribution -18.13
Covariance contribution -0.50
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.88
SVM decision value 1.27
SVM RNA-class probability 0.938948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24047632 119 - 27905053
ACAUUUAUUUACACCAGCAUGCAAAACUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
.............((((.(((.....(((.....)))...((((.((((......)))).))))......))).))))-.((.(((((((((.(((.....))).))))))))).))... ( -21.30)
>DroVir_CAF1 265375 119 - 1
GCAUUUAUUUACUCUAACAUGGUAAAUUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
...........((((((.((((.......(((.((((.((......))))))..)))............)))).))))-))..(((((((((.(((.....))).)))))))))...... ( -23.51)
>DroPse_CAF1 261215 120 - 1
ACAUUUAUUUACACUAACAUGCAAAACUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGGUAGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
............(((((.(((.....(((.....)))...((((.((((......)))).))))......))).))))).((.(((((((((.(((.....))).))))))))).))... ( -20.40)
>DroGri_CAF1 222658 119 - 1
GCAUUUAUUUACACUAACAUGGUAAAUUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
......((((((.(......)))))))..(((.((((.((......))))))..)))...........(((.....))-)((.(((((((((.(((.....))).))))))))).))... ( -22.40)
>DroWil_CAF1 294343 119 - 1
ACAUUUAUUUACACUAACAUGCAAAACUCGCUUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG-AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
.............................((..((((.((......))))))...))...........(((.....))-)((.(((((((((.(((.....))).))))))))).))... ( -19.60)
>DroPer_CAF1 262619 120 - 1
ACAUUUAUUUACACUAACAUGCAAAACUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGGUAGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
............(((((.(((.....(((.....)))...((((.((((......)))).))))......))).))))).((.(((((((((.(((.....))).))))))))).))... ( -20.40)
>consensus
ACAUUUAUUUACACUAACAUGCAAAACUCGCAUUGAGACAAUUUCAUGCUCAUCUGCAUAAAAUCAAUUCCAUUUUGG_AGACAAUUUGAAGAUUGGAAUACAAAUUUCGAAUUAUCAAC
.............((((.(((.....(((.....)))...((((.((((......)))).))))......))).))))..((.(((((((((.(((.....))).))))))))).))... (-18.63 = -18.13 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 24,047,672 – 24,047,782
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.70
Mean single sequence MFE -26.48
Consensus MFE -14.04
Energy contribution -14.65
Covariance contribution 0.61
Combinations/Pair 1.04
Mean z-score -1.64
Structure conservation index 0.53
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24047672 110 + 27905053
U-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAGUUUUGCAUGCUGGUGUAAAUAAAUGUAAAGAUGUCCUGGC---------CGAGGGAACAAGGACAA
(-((.....)))...((((((((((......))))))))))((((...((((...(((((((....)))))))....)))).))))(((((..(---------(...))....))))).. ( -26.80)
>DroVir_CAF1 265415 97 + 1
U-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAAUUUACCAUGUUAGAGUAAAUAAAUGCUGCACAGUC---------------G--G-----UGAACUA
(-((.....)))(((((((...(((((.((((((......)).))))......(((((((......).)))))).....))))).))))---------------)--)-----)...... ( -19.80)
>DroPse_CAF1 261255 120 + 1
UACCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAGUUUUGCAUGUUAGUGUAAAUAAAUGUCACGAUGCGAUGGCGUCACGAGGCACAGGGGCAAGGACGA
..((...........((((((((((......))))))))))(((((..(((....(((((((....)))))))..........(((((....))))).....)))..)))))..)).... ( -32.80)
>DroGri_CAF1 222698 99 + 1
U-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAAUUUACCAUGUUAGUGUAAAUAAAUGCUGCACAGUC---------------GAGG-----CGAACUA
(-((.....)))...((((((((((......))))))))))(((((.(((.(......))))....(((((.........)))))....---------------))))-----)...... ( -22.10)
>DroWil_CAF1 294383 99 + 1
U-CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAAGCGAGUUUUGCAUGUUAGUGUAAAUAAAUGUAACGACGG----UU---------CAAGAG-ACAA------
(-((.....)))...((((((((((......))))))))))(((((.........(((((((....)))))))....((.(((....)----))---------)).)))-))..------ ( -24.60)
>DroPer_CAF1 262659 120 + 1
UACCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAGUUUUGCAUGUUAGUGUAAAUAAAUGUCACGAUGCGAUGGCGUCACGAGGCACAGGGGCAAGGACGA
..((...........((((((((((......))))))))))(((((..(((....(((((((....)))))))..........(((((....))))).....)))..)))))..)).... ( -32.80)
>consensus
U_CCAAAAUGGAAUUGAUUUUAUGCAGAUGAGCAUGAAAUUGUCUCAAUGCGAGUUUUGCAUGUUAGUGUAAAUAAAUGUAACGAUGUC___GC_________CAAGGG__CAAGGACGA
..........((..(((((((((((......)))))))))))..))...(((...(((((((....)))))))....)))........................................ (-14.04 = -14.65 +   0.61)

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 13:23:43 2006