Locus 2788

Sequence ID	X_DroMel_CAF1
Location	7,476,539 – 7,476,746
Length	207
Max. P	0.795309

overview

Window 9

Location	7,476,539 – 7,476,651
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.27
Mean single sequence MFE	-30.56
Consensus MFE	-26.84
Energy contribution	-26.52
Covariance contribution	-0.32
Combinations/Pair	1.08
Mean z-score	-1.21
Structure conservation index	0.88
SVM decision value	0.12
SVM RNA-class probability	0.595137
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7476539 112 - 22224390
AGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCAU-----AUCUGCC--UGACGAGCUCGUAAUAUAGCCAUAGAUAUAGCCGAGAUAUCAGUUAAUCGGUGGGCCAUAUAGUC
..(((.(((.((-(........((((......(((((....-----..)))))--))))((.((((...((((........))))..))))...))......))).))))))........ ( -30.50)
>DroSec_CAF1 9751 112 - 1
AGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCAU-----AUCUGCC--UGACGAGCUCGAAAUAUAGCCAUAGAUAUAGCCGAGAUAUCAGUUAAUCGGUGGGCCAUAUAGUC
..(((.(((.((-(........((((......(((((....-----..)))))--))))((.((((...((((........))))..))))...))......))).))))))........ ( -30.50)
>DroSim_CAF1 9301 112 - 1
AGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCAU-----AUCUGCC--UGACGAGCUCGAAAUAUAGCCAUAGAUAUAGCCGAGAUAUCAGUUAAUCGGUGGGCCAUAUAGUC
..(((.(((.((-(........((((......(((((....-----..)))))--))))((.((((...((((........))))..))))...))......))).))))))........ ( -30.50)
>DroEre_CAF1 10486 114 - 1
AGGGUGCCAGCA-AGAUAAGAAGUCAAAAAGUGGCAGUCAU-----AUCUGCCUCUGACGAGCUCGAAAUAUAGCCAUAGAUAUAGUCGAGAUAUCAGUUAAUCGGUGGGCCAUAUAGUC
..(((.(((.(.-.........((((....(.(((((....-----..))))).)))))((.(((((..((((........)))).)))))...))........).))))))........ ( -29.30)
>DroYak_CAF1 13802 118 - 1
AGGGUGCCAGCAAAGAUAAGAAGUCAAGAAGUGGCAGUCAUACAGUAUCUGCC--UGACGAGCUCGAAAUAUGGCCAUAGAUAUAGCCGAGAUAUCAGUUAAUCGGUGGACCAUAUACAC
.((((((((.....(((.....)))......)))).((((..(((...)))..--))))..))))...((((((((((.(((.((((.((....)).))))))).)))).)))))).... ( -32.00)
>consensus
AGGGUGCCAGCG_AGAUAAGAAGUCAAGAAGUGGCAGUCAU_____AUCUGCC__UGACGAGCUCGAAAUAUAGCCAUAGAUAUAGCCGAGAUAUCAGUUAAUCGGUGGGCCAUAUAGUC
..(((.(((.(...........((((......(((((...........)))))..))))((.((((...((((........))))..))))...))........).))))))........ (-26.84 = -26.52 +  -0.32)

alignment

secondary structure

dotplot

Window 0

Location	7,476,612 – 7,476,727
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.74
Mean single sequence MFE	-22.86
Consensus MFE	-19.06
Energy contribution	-19.06
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.83
SVM decision value	0.60
SVM RNA-class probability	0.795309
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7476612 115 - 22224390
AGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAAGAAAUUACAACAA---AAAGCGAGACAAGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCA
..........(((((..(((...((......))...)-))(((...............))).....---...)))))....((.(((((.(.-.(((.....)))..)...))))).)). ( -23.26)
>DroSec_CAF1 9824 115 - 1
AGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAACAAAUUACAACAA---AAAGCGAGACAAGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCA
..........(((((..(((...((......))...)-))(((...............))).....---...)))))....((.(((((.(.-.(((.....)))..)...))))).)). ( -23.26)
>DroSim_CAF1 9374 115 - 1
AGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAACAAAUUACAACAA---AAAGCGAGACAAGGGUGCCAGCG-AGAUAAGAAGUCAAGAAGUGGCAGUCA
..........(((((..(((...((......))...)-))(((...............))).....---...)))))....((.(((((.(.-.(((.....)))..)...))))).)). ( -23.26)
>DroEre_CAF1 10561 119 - 1
GGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUACGCGUAUAAAUAAAAACAAAUUACAACAAAAAAAAGCGAGACGAGGGUGCCAGCA-AGAUAAGAAGUCAAAAAGUGGCAGUCA
(((((....(((((.((((((.(((............)))(((...............))).........)))).)).))))))))))....-.........((((.....))))..... ( -22.16)
>DroYak_CAF1 13880 117 - 1
AGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUACGCGUAUAAAUAAAAGCAAAUUACAACAA---AAAGCGAGACGAGGGUGCCAGCAAAGAUAAGAAGUCAAGAAGUGGCAGUCA
.......(((((((.((((((.(((............)))(((...............))).....---.)))).)).)))))))((((.....(((.....)))......))))..... ( -22.36)
>consensus
AGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA_GCGUAUAAAUAAAAACAAAUUACAACAA___AAAGCGAGACAAGGGUGCCAGCG_AGAUAAGAAGUCAAGAAGUGGCAGUCA
..........(((((..((....((......)).....))(((...............)))...........)))))....((.(((((.....(((.....)))......))))).)). (-19.06 = -19.06 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	7,476,651 – 7,476,746
Length	95
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.42
Mean single sequence MFE	-15.84
Consensus MFE	-11.53
Energy contribution	-11.13
Covariance contribution	-0.40
Combinations/Pair	1.10
Mean z-score	-1.67
Structure conservation index	0.73
SVM decision value	0.12
SVM RNA-class probability	0.592571
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7476651 95 - 22224390
-----CCGCAUAUAUAGUAUAUA----------------UAGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAAGAAAUUACAACAA---AAAGCGAGACA
-----....(((((((.((....----------------)).))))))).(((((..(((...((......))...)-))(((...............))).....---...)))))... ( -15.96)
>DroSec_CAF1 9863 95 - 1
-----CCGCGUAUAUAGUAUAUA----------------UAGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAACAAAUUACAACAA---AAAGCGAGACA
-----....(((((((.((....----------------)).))))))).(((((..(((...((......))...)-))(((...............))).....---...)))))... ( -16.26)
>DroSim_CAF1 9413 95 - 1
-----CCGCGUAUAUAGUAUAUA----------------UAGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA-GCGUAUAAAUAAAAACAAAUUACAACAA---AAAGCGAGACA
-----....(((((((.((....----------------)).))))))).(((((..(((...((......))...)-))(((...............))).....---...)))))... ( -16.26)
>DroEre_CAF1 10600 99 - 1
-----GCACAUAUAUAGUAUAAA----------------UGGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUACGCGUAUAAAUAAAAACAAAUUACAACAAAAAAAAGCGAGACG
-----....(((((((.((....----------------)).))))))).(((((..((....((......)).....))(((...............)))...........)))))... ( -12.66)
>DroYak_CAF1 13920 117 - 1
AAAACACACAUAUAUAGUAUAUAUAUAGUAGAUAUAGUAUAGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUACGCGUAUAAAUAAAAGCAAAUUACAACAA---AAAGCGAGACG
.........(((((((.(((((.((((.....))))))))).))))))).(((((..((....((......)).....))(((...............))).....---...)))))... ( -18.06)
>consensus
_____CCGCAUAUAUAGUAUAUA________________UAGUAUAUAUCCUCGCCUGCUUAGUGGACAAACAAAUA_GCGUAUAAAUAAAAACAAAUUACAACAA___AAAGCGAGACA
.........(((((((.((....................)).))))))).(((((..((....((......)).....))(((...............)))...........)))))... (-11.53 = -11.13 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:20 2006