Locus 3623

Sequence ID	X_DroMel_CAF1
Location	9,698,425 – 9,698,612
Length	187
Max. P	0.988480

overview

Window 0

Location	9,698,425 – 9,698,541
Length	116
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.63
Mean single sequence MFE	-21.27
Consensus MFE	-15.00
Energy contribution	-15.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.71
SVM decision value	0.17
SVM RNA-class probability	0.615509
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9698425 116 + 22224390
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAGCAUCAACAUUGACCCAACGACAGCAACA--U--
.....(((..(((((((((((......)))))))....(((.......)))........))))...(((((((.((((.......))))..)))).))).........)))....--.-- ( -21.60)
>DroPse_CAF1 38774 87 + 1
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAG---------------------------------
...(((((...((.(((((((......))))))).)).(((.......)))........))))).......................--------------------------------- ( -15.00)
>DroGri_CAF1 15884 117 + 1
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAGCAUCAACAUUGACC-AGAGACGGCAGCACAA--
.....(((.((((((((((((......)))))))............((((..........))))..(((((((.((((.......))))..)))).)))..-...))))).)))....-- ( -28.50)
>DroWil_CAF1 19608 112 + 1
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAGCAUUAACAUUGCCAUAG----AGCAAGA--G--
.(((.(((...((.(((((((......))))))).)).(((.......)))........(((((.....((((.((((.......))))..)))))))))....----))).)))--.-- ( -24.60)
>DroAna_CAF1 15788 118 + 1
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCCCAUGUUUUGCUACUUAUCAGCAUCAACAUUGACCGACCGACAGCAGCC--ACU
.....(((.(.(((.((((.......((((((.....))))))...((((..........))))..(.(((((.((((.......))))..))))).)..)))).))).).))).--... ( -22.90)
>DroPer_CAF1 42620 87 + 1
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAG---------------------------------
...(((((...((.(((((((......))))))).)).(((.......)))........))))).......................--------------------------------- ( -15.00)
>consensus
AUCUCGCUACCGUCAGUUGCACACAAUUGCAAUUAACUUGCAACACUCGCAUAAUUACAGGCGACCUCAUGUUUUGCUACUUAUCAGCAUCAACAUUGACC_A_____AGCA_CA_____
...(((((...((.(((((((......))))))).)).(((.......)))........)))))........................................................ (-15.00 = -15.00 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	9,698,425 – 9,698,541
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.63
Mean single sequence MFE	-32.25
Consensus MFE	-20.33
Energy contribution	-21.00
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.10
Structure conservation index	0.63
SVM decision value	0.16
SVM RNA-class probability	0.613449
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9698425 116 - 22224390
--A--UGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
--.--(((((((((((((((..(.(((((..(((((.....))))).)))))..)..)............(((...(((((((.....)))))))..))).)))).)))))))))).... ( -37.20)
>DroPse_CAF1 38774 87 - 1
---------------------------------CUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
---------------------------------.......................((((((((.....((((...(((((((.....)))))))....))))....))))..))))... ( -19.30)
>DroGri_CAF1 15884 117 - 1
--UUGUGCUGCCGUCUCU-GGUCAAUGUUGAUGCUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
--...((((((((((...-(..(.(((((..(((((.....))))).)))))..)..)...........((((...(((((((.....)))))))....))))...)))))))))).... ( -40.40)
>DroWil_CAF1 19608 112 - 1
--C--UCUUGCU----CUAUGGCAAUGUUAAUGCUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
--.--(((((((----....(((.(((((..(((((.....))))).)))))...)))(((.((.....((((...(((((((.....)))))))....))))....)))))))))))). ( -33.10)
>DroAna_CAF1 15788 118 - 1
AGU--GGCUGCUGUCGGUCGGUCAAUGUUGAUGCUGAUAAGUAGCAAAACAUGGGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
...--.((((((((((((((..(.(((((..(((((.....))))).)))))..)..))..........((((...(((((((.....)))))))....))))))))))))))))..... ( -44.20)
>DroPer_CAF1 42620 87 - 1
---------------------------------CUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
---------------------------------.......................((((((((.....((((...(((((((.....)))))))....))))....))))..))))... ( -19.30)
>consensus
_____UG_UGCU_____U_GGUCAAUGUUGAUGCUGAUAAGUAGCAAAACAUGAGGUCGCCUGUAAUUAUGCGAGUGUUGCAAGUUAAUUGCAAUUGUGUGCAACUGACGGUAGCGAGAU
...............................(((((.....)))))..........((((((((.....((((...(((((((.....)))))))....))))....))))..))))... (-20.33 = -21.00 +   0.67)

alignment

secondary structure

dotplot

Window 2

Location	9,698,505 – 9,698,612
Length	107
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	82.17
Mean single sequence MFE	-37.63
Consensus MFE	-26.52
Energy contribution	-26.28
Covariance contribution	-0.24
Combinations/Pair	1.14
Mean z-score	-2.81
Structure conservation index	0.70
SVM decision value	2.12
SVM RNA-class probability	0.988480
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9698505 107 - 22224390
ACUGUAGCUACUCCGCUUACUA----CUACAGGGUAUCAGCGACUA-CCAUCACAAUUGCCAGCGAUUGCAGCUGGAUGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
.((((((...............----))))))(((((((((((...-...))...((((((((((((.(((((.....))))).))))))))..)))))))))))))..... ( -37.26)
>DroSec_CAF1 39996 107 - 1
ACUUUGGCUGCACCGGUUACUU----GUAUAGGGUAUCAGUGACUG-CCAUCACAAUUGCCAGCGAUAGCAGCUGGAUGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
...(..((.....((((((((.----((((...)))).))))))))-..((((..((((((((((((((((((.....))))))))))))))..))))..))))))..)... ( -40.80)
>DroSim_CAF1 14567 105 - 1
--UUAUGGUGCACCGGUUACUU----GUACAGGGUAUCAGUGACUG-CCAUCACAAUUGCCAGCGAUUGCAGCUGGAUGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
--...........((((((((.----((((...)))).))))))))-.(((((..((((((((((((.(((((.....))))).))))))))..))))..)))))....... ( -36.40)
>DroEre_CAF1 17702 94 - 1
-----------------UACUAUCAUGUACAGGGUAUGUAUGACUG-CCAUCACGAUGGCCGGCGAUUGCAGGUGGAUGCUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
-----------------...(((((.((((((.((.....((((((-((((....)))))(((((((.((((.......)))).)))))))))))))).))).)))))))). ( -32.30)
>DroYak_CAF1 16130 108 - 1
UUAUUAGCUGCUGCGGUUACUA----GUACAGGGUAUCAUGGACUGGCCAUCGCAAUUGCCAGCGAUUGCAGCUGGAUGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
.(((((((...((((((..(((----((.((........)).)))))..))))))....((((((((.(((((.....))))).))))))))((((....))))))))))). ( -41.40)
>consensus
__UUUAGCUGCACCGGUUACUA____GUACAGGGUAUCAGUGACUG_CCAUCACAAUUGCCAGCGAUUGCAGCUGGAUGUUGCUGUCGUUGGGUCAAUGUUGAUGCUGAUAA
.............................((((((.......)))...(((((..((((((((((((.(((((.....))))).))))))))..))))..)))))))).... (-26.52 = -26.28 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:02 2006