Locus 2184

Sequence ID	3R_DroMel_CAF1
Location	6,245,991 – 6,246,114
Length	123
Max. P	0.725114

overview

Window 3

Location	6,245,991 – 6,246,082
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.56
Mean single sequence MFE	-33.68
Consensus MFE	-23.45
Energy contribution	-24.15
Covariance contribution	0.70
Combinations/Pair	1.11
Mean z-score	-1.85
Structure conservation index	0.70
SVM decision value	0.26
SVM RNA-class probability	0.659390
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6245991 91 - 27905053
ACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGCGGCGGGUGAUAAAACACGUUUUAAUAUCAG-----------------------------
....(((((.....)))))..((..(......)..)).(((.((((((.((((......)))))))))).(((((....)))))...))).----------------------------- ( -27.00)
>DroVir_CAF1 9177 108 - 1
ACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACUCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGUUUUAAUAUCGA----GGCUCA---CUCCGG-CUCCA----
.((((((((.....)))))...)))(((......(((.(((...(((((((((......)))))(((((......)))))........)))----)..)))---.)))))-)....---- ( -36.30)
>DroPse_CAF1 6878 101 - 1
ACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGACUGAAUACCCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGUUUUAAUAUCUG----AGCCCC---C--AG------A----
....(((((.....)))))..(((((..((..(..((...........(((((......)))))(((((......))))).......))..----)))..)---)--))------)---- ( -31.80)
>DroGri_CAF1 14828 116 - 1
ACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUCGGAAUGAAUACUCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGUUUUAAUAUCAG----GGCUCAGGACUCUGGACUCUGGACU
.((((((((.....)))))...)))(((((..((((..(((....)))..).)))....)))))(((((......))))).......((((----((..(((....)))..))))))... ( -37.30)
>DroWil_CAF1 12357 105 - 1
ACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGUAUGAAUGCCCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGUUUUAAUAUCCAGCCAGGCCUC---A--CA------A----
....(((((.....))))).....((((....(((((((.........(((((......)))))(((((......)))))....))).))))...))))..---.--..------.---- ( -33.30)
>DroMoj_CAF1 16248 109 - 1
ACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGUGGCGCGUGAUAAAACACGUUUUAAUAUCGG----GGCUCA---CUCUGA-CUCCGG---
.((((((((.....)))))...))).(((...(..((.(((...(((((((((......)))))(((((......)))))........)))----)..)))---.))..)-...)))--- ( -36.40)
>consensus
ACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGUUUUAAUAUCAG____GGCUCA___C__CG______A____
....(((((.....))))).....((((....................(((((......)))))(((((......)))))...............))))..................... (-23.45 = -24.15 +   0.70)

alignment

secondary structure

dotplot

Window 4

Location	6,246,002 – 6,246,114
Length	112
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.50
Mean single sequence MFE	-34.07
Consensus MFE	-21.58
Energy contribution	-21.63
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-2.03
Structure conservation index	0.63
SVM decision value	0.41
SVM RNA-class probability	0.725114
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6246002 112 - 27905053
CCGCCCUCUUGC-----C--GCACACACGCAGUGCAUUAACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGCGGCGGGUGAUAAAACACGU
.(((((....((-----(--((.((..(((.(((......)))(((((.....))))).....(((((.....((........))))))))))...))))))))))))........... ( -39.50)
>DroVir_CAF1 9205 99 - 1
-----------------C--AAG-UGGCCAAGUGCAUUAACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACUCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGU
-----------------.--..(-((((((..((((((..(((....)))...))))))...)))))))..................(((((......)))))(((((......))))) ( -35.20)
>DroGri_CAF1 14864 98 - 1
--------------------ACG-UGUAAAAGUGCAUUAACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUCGGAAUGAAUACUCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGU
--------------------.((-.(((.((((((........))))))........((.(((((......))))).))..))).))(((((......)))))(((((......))))) ( -29.90)
>DroWil_CAF1 12382 119 - 1
UCUCUCUCUCACACUCACACAAACACACGCAGUGCAUUAACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGUAUGAAUGCCCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGU
.........................(((((.(.(((((.....(((((.....)))))......((((....))))...))))).).(((((......))))))))))........... ( -33.30)
>DroMoj_CAF1 16277 104 - 1
--------CAGC-----C--GUGCGGGCCAAAUGCAUUAACAGGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGUGGCGCGUGAUAAAACACGU
--------...(-----(--.(((((.(((..((((((..(((....)))...))))))...))))))))...))............(((((......)))))(((((......))))) ( -32.80)
>DroAna_CAF1 18902 104 - 1
-CGC-------C-----C--ACACACAUUGUGUGCAUUAACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGCGGCGGGUGAUAAAACACGU
-.((-------(-----(--((((.....))))).........(((((.....))))).....)))...............((((((.((((......))))))))))........... ( -33.70)
>consensus
___________C_____C__ACACACACCAAGUGCAUUAACACGCACUUGAAAAGUGCAAUCUGGCCGCAAUUGGAAUGAAUACCCGGCCGCGAAAUGGCGGCGCGUGAUAAAACACGU
...........................................(((((.....)))))..((...(((....)))...)).......(((((......)))))(((((......))))) (-21.58 = -21.63 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:22 2006