Locus 3496

Sequence ID	X_DroMel_CAF1
Location	9,390,586 – 9,390,938
Length	352
Max. P	0.981613

overview

Window 5

Location	9,390,586 – 9,390,701
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.74
Mean single sequence MFE	-34.60
Consensus MFE	-30.59
Energy contribution	-31.02
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-2.57
Structure conservation index	0.88
SVM decision value	1.89
SVM RNA-class probability	0.981613
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9390586 115 + 22224390
CAAUUACCAAAGUCAAUGUCAAAGUUAGCAAUCUGCCAAGUUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG-GUAAA----GU
...(((((.(((((...(((((..((.((.....)).)).))))))))))....((((((((((((((((......))))))))))))))))....))))).......-.....----.. ( -34.20)
>DroSec_CAF1 4610 114 + 1
CAAUUACCACAGUCAAUGUCA-AGUUAGCAAUCUGCCAAGUUGACGACUUAAUUUCAGGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG-GUAAA----GU
......((((((((...((((-(.((.((.....)).)).))))))))).....(((.((((((((((((......)))))))))))).)))............))))-.....----.. ( -35.60)
>DroSim_CAF1 8950 114 + 1
CAAUUACCAAAGUCAAUGUCA-AGUUAGCAAUCUGCCAAGUUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUCAUUGCGAUUCGACGUGACAGCGGUGAAAAGUGG-GUAAA----GU
...(((((.(((((...((((-(.((.((.....)).)).))))))))))....((((((((((((((((......))))))))))))))))....))))).......-.....----.. ( -39.40)
>DroYak_CAF1 8310 119 + 1
CAAUUACCAAAGUCAAAAUCA-AGUUAACAAUCUGUCAAGUUGACGACUUAAUUUCAUGUCGUAUUGCGGACCUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGGUGUAGAAGUGGU
.....((((...((...((((-..((.((...((((((.(((((((((..........)))))(((((((......))))))).)))).))))))..))..))..))))...))..)))) ( -29.20)
>consensus
CAAUUACCAAAGUCAAUGUCA_AGUUAGCAAUCUGCCAAGUUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG_GUAAA____GU
...(((((.(((((...((((.(.((.((.....)).)).))))))))))....((((((((((((((((......))))))))))))))))....)))))................... (-30.59 = -31.02 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	9,390,586 – 9,390,701
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.74
Mean single sequence MFE	-27.65
Consensus MFE	-22.69
Energy contribution	-22.38
Covariance contribution	-0.31
Combinations/Pair	1.08
Mean z-score	-2.03
Structure conservation index	0.82
SVM decision value	0.73
SVM RNA-class probability	0.834459
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9390586 115 - 22224390
AC----UUUAC-CCACUUUUCACCGCUGUCACAUCGAAUCGCAAUCAGUUCCGCAAUUCGACAUGAAAUUAAGUCGUCAACUUGGCAGAUUGCUAACUUUGACAUUGACUUUGGUAAUUG
..----.....-.........((((..((((..((((((.((..........)).))))))..............(((((.(((((.....)))))..)))))..))))..))))..... ( -25.10)
>DroSec_CAF1 4610 114 - 1
AC----UUUAC-CCACUUUUCACCGCUGUCACAUCGAAUCGCAAUCAGUUCCGCAAUUCGACCUGAAAUUAAGUCGUCAACUUGGCAGAUUGCUAACU-UGACAUUGACUGUGGUAAUUG
..----.....-.........(((((.((((..((((((.((..........)).))))))..............(((((.(((((.....))))).)-))))..)))).)))))..... ( -30.10)
>DroSim_CAF1 8950 114 - 1
AC----UUUAC-CCACUUUUCACCGCUGUCACGUCGAAUCGCAAUGAGUUCCGCAAUUCGACAUGAAAUUAAGUCGUCAACUUGGCAGAUUGCUAACU-UGACAUUGACUUUGGUAAUUG
..----.....-.........((((..((((.(((((((.((..........)).))))))).............(((((.(((((.....))))).)-))))..))))..))))..... ( -31.00)
>DroYak_CAF1 8310 119 - 1
ACCACUUCUACACCACUUUUCACCGCUGUCACAUCGAAUCGCAAUCAGGUCCGCAAUACGACAUGAAAUUAAGUCGUCAACUUGACAGAUUGUUAACU-UGAUUUUGACUUUGGUAAUUG
.....................((((..((((.(((((...((((((..(((......(((((..........)))))......))).))))))....)-))))..))))..))))..... ( -24.40)
>consensus
AC____UUUAC_CCACUUUUCACCGCUGUCACAUCGAAUCGCAAUCAGUUCCGCAAUUCGACAUGAAAUUAAGUCGUCAACUUGGCAGAUUGCUAACU_UGACAUUGACUUUGGUAAUUG
.....................((((..((((..((((((.((..........)).))))))..............((((..(((((.....)))))...))))..))))..))))..... (-22.69 = -22.38 +  -0.31)

alignment

secondary structure

dotplot

Window 7

Location	9,390,626 – 9,390,741
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.77
Mean single sequence MFE	-34.70
Consensus MFE	-30.37
Energy contribution	-31.43
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.88
SVM decision value	0.95
SVM RNA-class probability	0.888219
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9390626 115 + 22224390
UUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG-GUAAA----GUGUGGAAACUCUGGCAAAUACAAGCACAAGCCGCAUUCGAU
....(((.......((((((((((((((((......))))))))))))))))..(((((.....((..-(((..----.((((....)....)))..)))..))....)))))..))).. ( -35.50)
>DroSec_CAF1 4649 115 + 1
UUGACGACUUAAUUUCAGGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG-GUAAA----GUGUGGAAACUCUGGCAAAUACAAGCACAAGCCGCAUUCGAU
....(((.......(((.((((((((((((......)))))))))))).)))..(((((.....((..-(((..----.((((....)....)))..)))..))....)))))..))).. ( -34.80)
>DroSim_CAF1 8989 115 + 1
UUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUCAUUGCGAUUCGACGUGACAGCGGUGAAAAGUGG-GUAAA----GUGUGGAAACUCUGGCAAAUACAAGCACAAGCCGCAUUCGAU
....(((.......((((((((((((((((......))))))))))))))))..(((((.....((..-(((..----.((((....)....)))..)))..))....)))))..))).. ( -38.00)
>DroYak_CAF1 8349 114 + 1
UUGACGACUUAAUUUCAUGUCGUAUUGCGGACCUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGGUGUAGAAGUGGUGUGGAAACUCUGGCAAAUACA------AGCCGCAUUCGAU
....(((.......((((((((.(((((((......))))))).))))))))..(((((.........((((...((.(.(.(....).)).))...))))------.)))))..))).. ( -30.50)
>consensus
UUGACGACUUAAUUUCAUGUCGAAUUGCGGAACUGAUUGCGAUUCGAUGUGACAGCGGUGAAAAGUGG_GUAAA____GUGUGGAAACUCUGGCAAAUACAAGCACAAGCCGCAUUCGAU
....(((.......((((((((((((((((......))))))))))))))))..(((((.....(((..(((........(.(....).).......)))...)))..)))))..))).. (-30.37 = -31.43 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	9,390,741 – 9,390,860
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	83.00
Mean single sequence MFE	-34.10
Consensus MFE	-24.96
Energy contribution	-25.97
Covariance contribution	1.01
Combinations/Pair	1.08
Mean z-score	-2.12
Structure conservation index	0.73
SVM decision value	0.70
SVM RNA-class probability	0.827894
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9390741 119 - 22224390
CGAUUGCGAUUGCUAUUGCGAGUCUAGCACAUUUGCAUGGAUGAGUGUUUGAGUGUUUGAGUAUUGCCAGAAUGGCAGAUAUACA-UAGUUCACUCACUUAUUCAUGCCCGUUCAUUUGC
.(((((((((....))))).))))..........(((((((((((((..(((((...((.((((((((.....)))).)))).))-..)))))..)))))))))))))............ ( -36.70)
>DroSec_CAF1 4764 100 - 1
CGAUUGCGAU------UGCGAGUCUAGCUCAUCUGCAUGGGUGAGUGUUUGAGUGUUUAAGUGUUGCC---------GAUA-----UAGUUCACUCACUUAUUCAUGCCCGUUCAUUUGC
.....((((.------.(((((.....)))....(((((((((((((..(((((((....(.....).---------...)-----)).))))..)))))))))))))..))....)))) ( -26.30)
>DroSim_CAF1 9104 110 - 1
CGAUUGCGAU------UGCGAGUCUAGCUCAUCUGCAUGGGUGAGU----GAGUGUUUAAGUGUUGCCAGGAUGGCAGAUAUAUAGUAGUUCACUCACUUAUUCAUGCCCGUUCAUUUGC
.....((((.------.(((((.....)))....((((((((((((----(((((.(((.((((((((.....)))).)))).))).....)))))))))))))))))..))....)))) ( -39.30)
>consensus
CGAUUGCGAU______UGCGAGUCUAGCUCAUCUGCAUGGGUGAGUGUUUGAGUGUUUAAGUGUUGCCAG_AUGGCAGAUAUA_A_UAGUUCACUCACUUAUUCAUGCCCGUUCAUUUGC
.((..(((...........(((.....)))....((((((((((((....(((((.(((.((((((((.....))).)))))....)))..))))))))))))))))).)))))...... (-24.96 = -25.97 +   1.01)

alignment

secondary structure

dotplot

Window 9

Location	9,390,820 – 9,390,938
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.06
Mean single sequence MFE	-30.70
Consensus MFE	-17.85
Energy contribution	-20.41
Covariance contribution	2.56
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.58
SVM decision value	0.02
SVM RNA-class probability	0.545250
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9390820 118 + 22224390
CCAUGCAAAUGUGCUAGACUCGCAAUAGCAAUCGCAAUCGCACGGCUACUGCUAUUUUUCCCGCCAUUCAGGGAUAUAUCUCAUCUGCAUCAAGUGCGUUGCGCAACAACAAAGGACA--
((..(((..(((((.(((...(((.((((....((....))...)))).)))......((((........)))).........)))))).))..)))((((.....))))...))...-- ( -30.30)
>DroSec_CAF1 4830 112 + 1
CCAUGCAGAUGAGCUAGACUCGCA------AUCGCAAUCGCAUGGCUACUGAUAUUUUUCCCGCCAUUCAGCGAUAUAUCUCAUCUGCAUCAAGUGCGUUGCGCAACAACAAAGGACG--
(((((((((((((.((...((((.------...((....))(((((....((......))..)))))...))))..)).)))))))))))...((((...)))).........))...-- ( -35.30)
>DroSim_CAF1 9180 112 + 1
CCAUGCAGAUGAGCUAGACUCGCA------AUCGCAAUCGCAUGGCUACUGCUAUUUUUCCCGCCAUUCAGCGAUAUAUCUCAUCUGCAUCAAGUGCGUUGCGCAACAACAAAGGACG--
(((((((((((((.((...((((.------...((....))(((((................)))))...))))..)).)))))))))))...((((...)))).........))...-- ( -34.59)
>DroYak_CAF1 8528 102 + 1
CCAUGCAGAUGAGCUAGACCCA------------------CACAGAUACUGCCAUUUUUCCCGCCAUUCACGGAUAUAUCUCAUCUGCAUCAAGUGCGUUACGCAACAACAAAGUACGGC
(((((((((((((.((......------------------..(((...))).........(((.......)))...)).)))))))))))...((((................)))))). ( -22.59)
>consensus
CCAUGCAGAUGAGCUAGACUCGCA______AUCGCAAUCGCACGGCUACUGCUAUUUUUCCCGCCAUUCAGCGAUAUAUCUCAUCUGCAUCAAGUGCGUUGCGCAACAACAAAGGACG__
(((((((((((((.((...((((..........((....))..(((................))).....))))..)).)))))))))))....((((...))))........))..... (-17.85 = -20.41 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:47 2006