Locus 5901

Sequence ID	2R_DroMel_CAF1
Location	18,626,881 – 18,627,019
Length	138
Max. P	0.839171

overview

Window 3

Location	18,626,881 – 18,626,983
Length	102
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	80.58
Mean single sequence MFE	-27.75
Consensus MFE	-17.96
Energy contribution	-18.68
Covariance contribution	0.73
Combinations/Pair	1.30
Mean z-score	-2.09
Structure conservation index	0.65
SVM decision value	0.74
SVM RNA-class probability	0.839171
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18626881 102 + 20766785
AUUUGCAACUUGGCCCAAUCAGUCGGACGUGAUGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACGUUCGCUUC
....(((((((((.(((((((((.(((((....(((((........)))))...))))).)))))))))...)))).....((((....---))))))).))... ( -32.10)
>DroSec_CAF1 37603 102 + 1
AUUUGCAACUUGGCCCAAUCAGUCGGACGUGAUGUAACGGCCAAAAGAUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACGAUCUCUCC
.........((((.(((((((((.(((((.(((((............)))))..))))).)))))))))...)))).....((((....---))))......... ( -25.50)
>DroSim_CAF1 32165 102 + 1
AUUUGCAACUUGGCCCAAUCAGUCGGACGUGAUGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACCUUAUCUCC
.........((((.(((((((((.(((((....(((((........)))))...))))).)))))))))...)))).(((.((((....---)))).)))..... ( -28.70)
>DroEre_CAF1 39805 102 + 1
AUUUGCAACUUGGCCCAAUCAGUCGGACGUGAUGUAACGGCCAAAAGUUAUUUUCGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GUGCCUUCUCUCU
...........((((((((((((.(((((....(((((........)))))...))))).)))))))))...............(....---).)))........ ( -25.70)
>DroYak_CAF1 36439 102 + 1
AUUUGCAACUUGGCCCAAUCAGACGGACGUGAUGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGGCUUUCUCUCU
.........((((.((((((((..(((((....(((((........)))))...)))))..))))))))...))))..(((((((....---)))))))...... ( -27.40)
>DroAna_CAF1 42763 96 + 1
AUUCGCAACUCGCCCCAAUCGGCUGAAUGUCACAUAAUGGG----GCCUGUCAGGGGCCUAUUGAUUGGUUGCCAUUUUGAGAUGUUUAUUUUUGCCUC-----C
....((((...(((......)))((((((((.((.((((((----(((.(((((.......))))).)))).))))).)).))))))))...))))...-----. ( -27.10)
>consensus
AUUUGCAACUUGGCCCAAUCAGUCGGACGUGAUGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG___GGACCUUCUCUCC
..............(((((((((.(((((....(((((........)))))...))))).)))))))))............((((.......))))......... (-17.96 = -18.68 +   0.73)

alignment

secondary structure

dotplot

Window 4

Location	18,626,913 – 18,627,019
Length	106
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	69.21
Mean single sequence MFE	-24.10
Consensus MFE	-12.19
Energy contribution	-12.98
Covariance contribution	0.79
Combinations/Pair	1.19
Mean z-score	-1.52
Structure conservation index	0.51
SVM decision value	0.26
SVM RNA-class probability	0.657431
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18626913 106 + 20766785
UGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACGUUCGCUUCACUCCCUUAAUGUG-CUAUAUGGCCAGU--UGUUUAUUU
..(((((((((.((((.............(((((((.....))))))).((((....---))))....))))(((.........)))-.....))))).))--))....... ( -24.70)
>DroSec_CAF1 37635 106 + 1
UGUAACGGCCAAAAGAUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACGAUCUCUCCACUCCCUUAAUACG-CUACAAGGCCAGU--UGUUUAUUU
..((((((((...................(((((((.....))))))).((((....---)))).......................-......)))).))--))....... ( -22.80)
>DroSim_CAF1 32197 106 + 1
UGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGACCUUAUCUCCACUCCCUUAAUGCG-CUAUAUGGCCAGU--UGUUUAUUU
..(((((((((..(((.............(((((((.....))))))).((((....---))))......................)-))...))))).))--))....... ( -22.90)
>DroEre_CAF1 39837 91 + 1
UGUAACGGCCAAAAGUUAUUUUCGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GUGCCUUCUCUCU------------------UAUGGCCGGCCUGGCCUGUUU
......(((((............(..((.(((((((.....)))))))))..)...(---(((((........------------------...)))..))))))))..... ( -19.80)
>DroYak_CAF1 36471 106 + 1
UGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG---GGGCUUUCUCUCU-CUUAUUUCCUUCG-CUAUAUGGCCAGUCUGGCAUGUU-
(((.(((((((..(((.............(((((((.....)))))))(((((....---)))))........-............)-))...))))).))...)))....- ( -22.80)
>DroAna_CAF1 42795 98 + 1
CAUAAUGGG----GCCUGUCAGGGGCCUAUUGAUUGGUUGCCAUUUUGAGAUGUUUAUUUUUGCCUC-----CGGGCACUAAAGGUGGCUA---GGCCACG--GGCUUACUU
.......((----((((((....((((((..........((((((((.((...........((((..-----..)))))).))))))))))---)))))))--))))).... ( -31.60)
>consensus
UGUAACGGCCAAAAGUUAUUUUUGUUCUAUUGAUUGGUUUUCAAUUAAAGUCCUUCG___GGACCUUCUCUCCACUCCCUUAAUGCG_CUAUAUGGCCAGU__GGCUUAUUU
......(((((..................(((((((.....))))))).((((.......)))).............................))))).............. (-12.19 = -12.98 +   0.79)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:41 2006