Locus 2456

Sequence ID	2L_DroMel_CAF1
Location	6,723,313 – 6,723,492
Length	179
Max. P	0.961872

overview

Window 2

Location	6,723,313 – 6,723,413
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-25.26
Consensus MFE	-16.06
Energy contribution	-16.50
Covariance contribution	0.44
Combinations/Pair	1.18
Mean z-score	-2.78
Structure conservation index	0.64
SVM decision value	1.53
SVM RNA-class probability	0.961872
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6723313 100 + 22407834
AACCAAAAUCGAUGUUUGUAUGGUGCUAUCGAUGUUUUUACUGGCUCAACACCAUCGAUGAUUUAUUUAUUAGCUUCCAAGCAUCGAUAACACAUGAGCU
.......(((((((((((.((((((.....((.(((......)))))..)))))).(((((.....)))))......)))))))))))............ ( -21.10)
>DroSec_CAF1 35961 96 + 1
AACCAAAAUCGAUGUUUGUAUGGUGAUAUCGAUGUUUCUACUGGCUCAGCACCAUCGAUGAUUUAUUU----GCUUCCAAGCAUCGAUACCUCAUGGGCU
.......(((((((((((...((..(((((((((...((........))...))))))))......).----.))..))))))))))).((....))... ( -25.20)
>DroSim_CAF1 36137 96 + 1
AACCAAAAUCGAUCGUUGUAUGGUGCUAUCGAUGUUUCUACUGGCUCAGCACCAUCGAUGAUUUAUUU----GCUUCCAACCAUCGAUACCUCAUGGGCU
.....((((.((((((((.((((((((...((.(((......))))))))))))))))))))).))))----........((((.((....))))))... ( -26.00)
>DroEre_CAF1 42327 88 + 1
AACAAAAAUCGAUGUUUGUAUGAUGUUAUCGAUGUUUAUACUGGUUCAGACACAUCGAUGAUUUACAU----G----U----AUCGAUAACUCACGAGUU
.......(((((((..((((....(((((((((((.....(((...)))..))))))))))).)))).----.----)----))))))((((....)))) ( -24.10)
>DroYak_CAF1 37677 92 + 1
AACAAAAAUCGAUGUUUGUAUGAUGAUAUCGAUGUUUCUACUGGCUCAGCGACAUCGAUGAUUUACUU----G----CAAACAUCGAUAACUCAUGGAUU
.......(((((((((((((....((((((((((((.((........)).))))))))).)))....)----)----)))))))))))............ ( -29.90)
>consensus
AACCAAAAUCGAUGUUUGUAUGGUGAUAUCGAUGUUUCUACUGGCUCAGCACCAUCGAUGAUUUAUUU____GCUUCCAAGCAUCGAUAACUCAUGGGCU
.......(((((((((........))))))))).........((((((.....(((((((.....................)))))))......)))))) (-16.06 = -16.50 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	6,723,336 – 6,723,453
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	77.65
Mean single sequence MFE	-27.92
Consensus MFE	-15.62
Energy contribution	-16.62
Covariance contribution	1.00
Combinations/Pair	1.17
Mean z-score	-2.25
Structure conservation index	0.56
SVM decision value	1.43
SVM RNA-class probability	0.952881
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6723336 117 - 22407834
AGCGAUUAAAUUAUUCGAUAAGAAUCAUUGCUCUUAUACGAGCUCAUGUGUUAUCGAUGCUUGGAAGCUAAUAAAUAAAUCAUCGAUGGUGUUGAGCCAGUAAAAACAUCGAUAGCA
.((((((.......(((((((.(......((((......)))).....).))))))).(((....))).........))))(((((((...(((......)))...))))))).)). ( -27.70)
>DroSec_CAF1 35984 113 - 1
AACGAUUAAAUUAUUCGAUAAGAAUCGUUGCUCUUAUACGAGCCCAUGAGGUAUCGAUGCUUGGAAGC----AAAUAAAUCAUCGAUGGUGCUGAGCCAGUAGAAACAUCGAUAUCA
...((((.......((((((....((((.((((......))))..))))..))))))((((....)))----)....))))(((((((.(((((...)))))....))))))).... ( -30.10)
>DroSim_CAF1 36160 113 - 1
AACGAUUAAAUGAUUCGAUAAGAAUCGUUGCUCUUAUACGAGCCCAUGAGGUAUCGAUGGUUGGAAGC----AAAUAAAUCAUCGAUGGUGCUGAGCCAGUAGAAACAUCGAUAGCA
........((((((((.....))))))))((((......))))......(.((((((((.(((....)----))........((..((((.....))))...))..)))))))).). ( -31.30)
>DroEre_CAF1 42350 94 - 1
----------UUGUUCGAUAA-AUUCAUUGGUAUUAUGGGAACUCGUGAGUUAUCGAU----A----C----AUGUAAAUCAUCGAUGUGUCUGAACCAGUAUAAACAUCGAUAACA
----------.((((((((((-.(((((.(((.........))).)))))))))))).----)----)----)........((((((((..(((...))).....)))))))).... ( -23.10)
>DroYak_CAF1 37700 108 - 1
AGCGAUUAAAUUAUUCGAUUA-AUUAAUUGGCACUAUGGGAAUCCAUGAGUUAUCGAUGUUUG----C----AAGUAAAUCAUCGAUGUCGCUGAGCCAGUAGAAACAUCGAUAUCA
..............(((((..-.((.((((((..(((((....)))))(((((((((((((((----.----...)))).))))))))..)))..)))))).))...)))))..... ( -27.40)
>consensus
AACGAUUAAAUUAUUCGAUAAGAAUCAUUGCUCUUAUACGAGCCCAUGAGUUAUCGAUGCUUGGAAGC____AAAUAAAUCAUCGAUGGUGCUGAGCCAGUAGAAACAUCGAUAGCA
..............((((((....((((.((((......))))..))))..))))))........................(((((((...(((......)))...))))))).... (-15.62 = -16.62 +   1.00)

alignment

secondary structure

dotplot

Window 4

Location	6,723,373 – 6,723,492
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	75.92
Mean single sequence MFE	-22.98
Consensus MFE	-12.59
Energy contribution	-13.93
Covariance contribution	1.34
Combinations/Pair	1.13
Mean z-score	-2.50
Structure conservation index	0.55
SVM decision value	1.42
SVM RNA-class probability	0.952165
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6723373 119 + 22407834
AUUUAUUUAUUAGCUUCCAAGCAUCGAUAACACAUGAGCUCGUAUAAGAGCAAUGAUUCUUAUCGAAUAAUUUAAUCGCUGUAAAGCGAAUUGCAAAUUAAUUAAGAUAAAUAAAUACU
(((((((((((.(((....))).(((((((..(((..((((......)))).)))....))))))).........(((((....)))))................)))))))))))... ( -28.80)
>DroSim_CAF1 36197 115 + 1
AUUUAUUU----GCUUCCAACCAUCGAUACCUCAUGGGCUCGUAUAAGAGCAACGAUUCUUAUCGAAUCAUUUAAUCGUUUUAAAGCGAAUUGCAAAUUAAUUCAGAUAAAUUUAUAAU
((((((((----((((........((((.((....))((((......))))...(((((.....))))).....)))).....))))((((((.....))))))))))))))....... ( -23.32)
>DroYak_CAF1 37737 110 + 1
AUUUACUU----G----CAAACAUCGAUAACUCAUGGAUUCCCAUAGUGCCAAUUAAU-UAAUCGAAUAAUUUAAUCGCUCUAAGGCGAAUUGCGUAUUAAUAUAUUUAAAUAUACUAU
........----(----(((...(((((.(((.((((....)))))))..........-..))))).........(((((....))))).))))((((...((....))...))))... ( -16.82)
>consensus
AUUUAUUU____GCUUCCAAACAUCGAUAACUCAUGGGCUCGUAUAAGAGCAAUGAUUCUUAUCGAAUAAUUUAAUCGCUCUAAAGCGAAUUGCAAAUUAAUUAAGAUAAAUAUAUAAU
((((((((...............((((((........((((......)))).........)))))).........(((((....)))))...............))))))))....... (-12.59 = -13.93 +   1.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:25 2006