Locus 9549

Sequence ID	3R_DroMel_CAF1
Location	25,233,852 – 25,233,993
Length	141
Max. P	0.522190

overview

Window 2

Location	25,233,852 – 25,233,958
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	82.08
Mean single sequence MFE	-18.10
Consensus MFE	-11.88
Energy contribution	-11.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.66
SVM decision value	-0.05
SVM RNA-class probability	0.509104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25233852 106 - 27905053
GGCCAGCAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCAUCCAUCUAAGCCCCAAACUCUCGGCUUUUCAUCAGAGCUGCUACACUUG
(((..((((((((((((....))))))))))))((.........))....................))).........(((((((.....)))))))......... ( -21.50)
>DroSim_CAF1 92635 106 - 1
GGCCAGCAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCAAACUCUCGGCUUUUCAUCAGAGCUGCUACACUGA
(((..((((((((((((....))))))))))))((.........))....................))).........(((((((.....)))))))......... ( -21.50)
>DroEre_CAF1 93933 106 - 1
GGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCGCACUCUCUGCCUUUCAUUAGUGCUGCUACACUUG
(((....((((((((((....))))))))))(((.(((....))).))).................)))..(((((...((.....))..)))))........... ( -16.40)
>DroYak_CAF1 94968 106 - 1
GGCCAGCAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCACACUCCCUGCUUUUCAUCAGUGCUGCUACAUUUG
(((..((((((((((((....)))))))))))))))...((((((..(((((((..........((((............))))......)))).)))..)))))) ( -17.99)
>DroAna_CAF1 87936 104 - 1
GGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUUCAUCU--GCCCCGCACUUGCUCUUUGUCAAGAGUGUUUCCAAUUGUU
(((....((((((((((....))))))))))(((.(((....))).)))...............--))).(((.(((((.....).)))).)))............ ( -17.10)
>DroPer_CAF1 96840 97 - 1
GGCGAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCCACUCCCAUUGCCCCC---CCGC-UCUUUCCAUCAGUCUAUCUCG-----
(((((..((((((((((....))))))))))(((.(((....))).)))...............)))))...---....-.....................----- ( -14.10)
>consensus
GGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCACACUCUCUGCUUUUCAUCAGUGCUGCUACACUUG
(((....((((((((((....))))))))))(((.(((....))).))).................)))..................................... (-11.88 = -11.88 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	25,233,886 – 25,233,993
Length	107
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.70
Mean single sequence MFE	-27.14
Consensus MFE	-14.59
Energy contribution	-14.48
Covariance contribution	-0.11
Combinations/Pair	1.18
Mean z-score	-2.21
Structure conservation index	0.54
SVM decision value	-0.02
SVM RNA-class probability	0.522190
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25233886 107 - 27905053
UACAAUGCAAAAACAGGCG-GUGGAACGGU----UUGUCUGGCCAGCAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCAUCCAUCUAAGCCCCA-----
...............((((-(((((.((((----(((..((((..((((((((((((....))))))))))))))))..)))..)))).........))))))...)))...----- ( -27.30)
>DroPse_CAF1 95864 114 - 1
AACAAUGCGAAC--CUCCA-GUGGAACGGAGCCGUCUGCUGGCGAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCCACUCCCAUUGCCCCCCCCCC
....(((((...--...((-(..((.((....))))..)))(((..(((((((((((....))))))))))))))...........))))).......................... ( -27.50)
>DroEre_CAF1 93967 105 - 1
UACAAUGCAAA--AAGGCG-GUGGAACGGC----UUGUCUGGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCG-----
...........--..((((-(((((.((((----(((..((((...(((((((((((....))))))))))).))))..)))..)))).........))))))...)))...----- ( -25.40)
>DroYak_CAF1 95002 107 - 1
UACAAUGCAAGCGCAGGCG-GUGGAACGGC----UUGUCUGGCCAGCAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUCCAUCUAAGCCCCA-----
.....(((....)))((((-(((((..(((----(.....)))).((((((((((((....))))))))))))........................))))))...)))...----- ( -30.80)
>DroAna_CAF1 87970 105 - 1
-ACAAUGCAAACACAGGCGGGCGGAACGAG----UUGUCUGGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUUAUUCAUCU--GCCCCG-----
-.....((........))(((((((..(((----(......((...(((((((((((....))))))))))).((.........)).)).......)))).)))--))))..----- ( -24.32)
>DroPer_CAF1 96865 109 - 1
AACAAUGCGAAC--AUCCA-GUGGAACGGAGCCGUCUGCUGGCGAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCCACUCCCAUUGCCCCC-----
....(((((...--...((-(..((.((....))))..)))(((..(((((((((((....))))))))))))))...........))))).....................----- ( -27.50)
>consensus
UACAAUGCAAAC_CAGGCG_GUGGAACGGA____UUGUCUGGCCAACAAAAAUAUUUUCAUAGAUAUUUUUGCGCUAUUUAAAUGCCGCAUAUUUCAUCCAUCUAAGCCCCA_____
....................((((...(((......)))((((...(((((((((((....))))))))))).))))........))))............................ (-14.59 = -14.48 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:36:56 2006