Locus 1060

Sequence ID	2R_DroMel_CAF1
Location	4,327,516 – 4,327,648
Length	132
Max. P	0.998989

overview

Window 0

Location	4,327,516 – 4,327,636
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.00
Mean single sequence MFE	-26.30
Consensus MFE	-25.26
Energy contribution	-25.10
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.23
Structure conservation index	0.96
SVM decision value	0.05
SVM RNA-class probability	0.559940
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4327516 120 - 20766785
UUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGUUCUUUGCUUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
.................(((((.((((((((((.((((.....)))).))))))......(((((((((....))))))))).))))..))))).......................... ( -26.20)
>DroSec_CAF1 6761 120 - 1
UUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGUUCUUUGCUUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
.................(((((.((((((((((.((((.....)))).))))))......(((((((((....))))))))).))))..))))).......................... ( -26.20)
>DroSim_CAF1 8743 120 - 1
UUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGUUCUUUGCUUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
.................(((((.((((((((((.((((.....)))).))))))......(((((((((....))))))))).))))..))))).......................... ( -26.20)
>DroEre_CAF1 6028 120 - 1
UUUGUACUCCAAAUUAAUGGCAUGCGAACAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCGAAAGUUCUUUGCAUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
.................(((((((((((((..((((.((.....)).))))..)).....(((((((((....))))))))))))))).))))).......................... ( -26.70)
>DroYak_CAF1 6902 120 - 1
UUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGUUCUUUGCUUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
.................(((((.((((((((((.((((.....)))).))))))......(((((((((....))))))))).))))..))))).......................... ( -26.20)
>consensus
UUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGUUCUUUGCUUUGCCAAACUUAUAAUCUAAUUGCGCCCUCAC
((((((..(((......)))..))))))......(((((...............(((...(((((((((....)))))))))..)))...(((((.............))).))))))). (-25.26 = -25.10 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	4,327,556 – 4,327,648
Length	92
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	96.54
Mean single sequence MFE	-20.50
Consensus MFE	-17.12
Energy contribution	-17.48
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-2.97
Structure conservation index	0.84
SVM decision value	2.61
SVM RNA-class probability	0.995779
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4327556 92 + 20766785
ACUUUUGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUUUUCGCAUGCCAUUAAUUUGGAGUACAAAAAGUGGAGCAAA-
.((((((....))))))((((((((.((((((.(((.......))).)))))).)))...(((......)))..........))))).....- ( -22.50)
>DroSec_CAF1 6801 92 + 1
ACUUUUGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUUUUCGCAUGCCAUUAAUUUGGAGUACAAAAAGUGGAGCAAA-
.((((((....))))))((((((((.((((((.(((.......))).)))))).)))...(((......)))..........))))).....- ( -22.50)
>DroSim_CAF1 8783 93 + 1
ACUUUUGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUUUUCGCAUGCCAUUAAUUUGGAGUACAAAAAGUGGAGCAAAA
.((((((....))))))((((((((.((((((.(((.......))).)))))).)))...(((......)))..........)))))...... ( -22.50)
>DroEre_CAF1 6068 91 + 1
ACUUUCGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUGUUCGCAUGCCAUUAAUUUGGAGUACAAAAAAUG-AACAAA-
................((.(((((((..((((.(((.......))).))))....)))))(((......)))...........))-.))...- ( -12.00)
>DroYak_CAF1 6942 92 + 1
ACUUUUGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUUUUCGCAUGCCAUUAAUUUGGAGUACAAAAAAUGGCACAAA-
(((((((....)))))))....(((.((((((.(((.......))).)))))).))).(((((((..((((.....)))).)))))))....- ( -23.00)
>consensus
ACUUUUGCACACAAAAGUCCACGUGCAAAUUUAUGGAAAUUCCCCAAAAAUUUUCGCAUGCCAUUAAUUUGGAGUACAAAAAGUGGAGCAAA_
(((((((....)))))))...(((((((((((.(((.......))).))))))..)))))(((((..((((.....)))).)))))....... (-17.12 = -17.48 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	4,327,556 – 4,327,648
Length	92
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	96.54
Mean single sequence MFE	-23.06
Consensus MFE	-21.52
Energy contribution	-21.72
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-2.18
Structure conservation index	0.93
SVM decision value	3.31
SVM RNA-class probability	0.998989
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4327556 92 - 20766785
-UUUGCUCCACUUUUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGU
-....(((((.((((((((..(((......)))..))))))))....)))))............((((((((..(....)..))))))))... ( -23.90)
>DroSec_CAF1 6801 92 - 1
-UUUGCUCCACUUUUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGU
-....(((((.((((((((..(((......)))..))))))))....)))))............((((((((..(....)..))))))))... ( -23.90)
>DroSim_CAF1 8783 93 - 1
UUUUGCUCCACUUUUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGU
.....(((((.((((((((..(((......)))..))))))))....)))))............((((((((..(....)..))))))))... ( -23.90)
>DroEre_CAF1 6068 91 - 1
-UUUGUU-CAUUUUUUGUACUCCAAAUUAAUGGCAUGCGAACAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCGAAAGU
-......-...........(((((((..((((.........)))))))))))............((((((((..(....)..))))))))... ( -19.20)
>DroYak_CAF1 6942 92 - 1
-UUUGUGCCAUUUUUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGU
-...((((((((.((((.....))))..))))))))(((.((((((.((((.....)))).))))))...)))..(((((((....))))))) ( -24.40)
>consensus
_UUUGCUCCACUUUUUGUACUCCAAAUUAAUGGCAUGCGAAAAUUUUUGGGGAAUUUCCAUAAAUUUGCACGUGGACUUUUGUGUGCAAAAGU
.....(((((.((((((((..(((......)))..))))))))....)))))............((((((((..(....)..))))))))... (-21.52 = -21.72 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:23 2006