Locus 4507

Sequence ID	3L_DroMel_CAF1
Location	13,001,226 – 13,001,412
Length	186
Max. P	0.996534

overview

Window 9

Location	13,001,226 – 13,001,342
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.30
Mean single sequence MFE	-28.33
Consensus MFE	-28.28
Energy contribution	-28.28
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.45
Structure conservation index	1.00
SVM decision value	1.26
SVM RNA-class probability	0.937248
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13001226 116 - 23771897
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
...(((...((((((.....(((....))).........)))))).....)))----.....(((((..((.((((...((((((.(((....))).))))))...))))))..))))). ( -28.14)
>DroSec_CAF1 8260 116 - 1
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCAACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
..............((..(((((....)))....((.....))...))..)).----.....(((((..((.((((...((((((.(((....))).))))))...))))))..))))). ( -29.00)
>DroSim_CAF1 10821 116 - 1
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
...(((...((((((.....(((....))).........)))))).....)))----.....(((((..((.((((...((((((.(((....))).))))))...))))))..))))). ( -28.14)
>DroEre_CAF1 8044 116 - 1
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
...(((...((((((.....(((....))).........)))))).....)))----.....(((((..((.((((...((((((.(((....))).))))))...))))))..))))). ( -28.14)
>DroYak_CAF1 8438 120 - 1
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCGUAUGUAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
((((((...((((((.....(((....))).........)))))).....))).))).....(((((..((.((((...((((((.(((....))).))))))...))))))..))))). ( -28.24)
>consensus
UAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG____UAACUUUUUCCCCAUCGGCCAAACGACAUUUGAAGUCAAUUGUCGUCGCGUCGUGCAGAAAAA
..............((..(((((....)))....((.....))...))..))..........(((((..((.((((...((((((.(((....))).))))))...))))))..))))). (-28.28 = -28.28 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,001,266 – 13,001,372
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.98
Mean single sequence MFE	-27.55
Consensus MFE	-23.07
Energy contribution	-23.67
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.84
SVM decision value	2.71
SVM RNA-class probability	0.996534
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13001266 106 - 23771897
GCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAA
(((((------.----...(((((..(((((((((((....)))))..))))))......(((....)))....)))))....)))))(((((----...............)))))... ( -27.96)
>DroSec_CAF1 8300 106 - 1
GCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCAACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAA
(((((------.----...(((((..(((((((((((....)))))..))))))......(((....)))....)))))....)))))(((((----...............)))))... ( -28.86)
>DroSim_CAF1 10861 106 - 1
GCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAA
(((((------.----...(((((..(((((((((((....)))))..))))))......(((....)))....)))))....)))))(((((----...............)))))... ( -27.96)
>DroEre_CAF1 8084 112 - 1
GCUAUGUAUAUA----UUCGUUACAAUUCGCUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG----UAACUUUUUCCCCAUCGGCCAAA
((((((......----((((((....((((.((((((....))))))...))))...)))(((....)))....))).....))))))(((((----...............)))))... ( -26.66)
>DroYak_CAF1 8478 120 - 1
GCCAUAUAUAUAUACAUACGUUUCAAUUCGCUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCGUAUGUAACUUUUUCCCCAUCGGCCAAA
(((((....)).(((((((((((...((((.((((((....))))))...))))..))))(((....)))....((.(((.....)))..)))))))))..............))).... ( -26.30)
>consensus
GCUAU______A____UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACUUUCAUAGUGGUCG____UAACUUUUUCCCCAUCGGCCAAA
...................(((((..(((((((((((....))))))..)))))......(((....)))....)))))........((((((...................)))))).. (-23.07 = -23.67 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	13,001,302 – 13,001,412
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.18
Mean single sequence MFE	-25.52
Consensus MFE	-23.90
Energy contribution	-24.54
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.72
Structure conservation index	0.94
SVM decision value	2.37
SVM RNA-class probability	0.992999
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13001302 110 - 23771897
UUAAAAGGCGCUUUUCAUUUUCUUUUGGGAAAGUUAUCAAGCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACU
.........((((...(((((((....)))))))....))))...------.----...(((((..(((((((((((....)))))..))))))......(((....)))....))))). ( -26.40)
>DroSec_CAF1 8336 110 - 1
UUAAAAGGCGCUUUUCAUUUUCUUUUGGGAAAGUUAUCAAGCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCAACAGAAACU
.........((((...(((((((....)))))))....))))...------.----...(((((..(((((((((((....)))))..))))))......(((....)))....))))). ( -27.30)
>DroSim_CAF1 10897 110 - 1
UUAAAAGGCGCUUUUCAUUUUCUUUUGGGAAAGUUAUCAAGCUAU------A----UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACU
.........((((...(((((((....)))))))....))))...------.----...(((((..(((((((((((....)))))..))))))......(((....)))....))))). ( -26.40)
>DroEre_CAF1 8120 116 - 1
UUAAAAGGCGCUUUUCAUUUUCUUUUGGGAAAGUUAUCAAGCUAUGUAUAUA----UUCGUUACAAUUCGCUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACU
.........((((...(((((((....)))))))....))))..........----((((((....((((.((((((....))))))...))))...)))(((....)))....)))... ( -22.20)
>DroYak_CAF1 8518 120 - 1
UUAAAAGGCGCUUUUCAUUUGCUUUUGGGAAAGUUAUCAAGCCAUAUAUAUAUACAUACGUUUCAAUUCGCUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACU
......((((((((((...........)))))))......)))................(((((..((((.((((((....))))))...))))......(((....)))....))))). ( -25.30)
>consensus
UUAAAAGGCGCUUUUCAUUUUCUUUUGGGAAAGUUAUCAAGCUAU______A____UUCGUUUCAAUUCGUUUCGGUUAUUAUCGAAAAAUGAAGAAAACGCCGAAAGGCCACAGAAACU
......(((.......(((((((....)))))))......)))................(((((..(((((((((((....))))))..)))))......(((....)))....))))). (-23.90 = -24.54 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:16 2006