Locus 3321

Sequence ID	X_DroMel_CAF1
Location	8,878,105 – 8,878,346
Length	241
Max. P	0.999749

overview

Window 1

Location	8,878,105 – 8,878,215
Length	110
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	79.41
Mean single sequence MFE	-30.03
Consensus MFE	-12.04
Energy contribution	-13.20
Covariance contribution	1.16
Combinations/Pair	1.06
Mean z-score	-2.18
Structure conservation index	0.40
SVM decision value	0.45
SVM RNA-class probability	0.740930
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878105 110 - 22224390
GACAUGUGGAUGUGGAUGUGGAUGUGA--AUA--UGGUUGUGGUUGUGUAUAUCGAUAUGGUUGUG--AAUCCAUGGCCAAUGCCUUCACGACAAUCUGCCGUAAUUGAACUUGAA
.((((.((.((....)).)).))))..--.((--((((.(..((((((..........((((..((--....))..)))).......))))))...).))))))............ ( -24.63)
>DroSec_CAF1 8448 90 - 1
GAC--------------GUGGAUUCGG--AUA--UGGUUGUGGUUGUG------GCUAUGGAUGUG--AAUCCAUGGCCAAUGCCUUCACGACAAUCUGAAGUAAUUGAACUUGAA
...--------------.....(((((--((.--..(((((((...((------(((((((((...--.)))))))))))......))))))).)))))))............... ( -33.50)
>DroSim_CAF1 8754 90 - 1
GAC--------------GUGGAUUCGG--AUA--UGGUUGUGGUUGUG------GCUAUGGAUGUG--AAUCCAUGGCCAAUGCCUUCACGACAAUCUGAAGUAAUUGAACUUGAA
...--------------.....(((((--((.--..(((((((...((------(((((((((...--.)))))))))))......))))))).)))))))............... ( -33.50)
>DroEre_CAF1 7914 94 - 1
GAC--------------GUGGAAGUGGGGAUACAAGCAUAUGGAUGUG------GAUGUGUUUGUG--GAUCCAUGGCCAAUGCCUUCACGACAAUCUGCCGUAAUUGAACUUGAA
..(--------------(((((.(((((..(((((((((((.......------.)))))))))))--..)))))(((....))))))))).((((........))))........ ( -28.80)
>DroYak_CAF1 8788 94 - 1
GUC--------------UUGGAUGUGGCCAUU--UGGUUGUGGUUGUG------GAUGUGGACGUGGAGAUCCAUGGCCAAUGCCUUCACGACAAUCUGGCGUAAUUGAACUUGAA
...--------------((.(((...((((..--..(((((((....(------(...(((.(((((....))))).)))...)).)))))))....))))...))).))...... ( -29.70)
>consensus
GAC______________GUGGAUGUGG__AUA__UGGUUGUGGUUGUG______GAUAUGGAUGUG__AAUCCAUGGCCAAUGCCUUCACGACAAUCUGACGUAAUUGAACUUGAA
....................................(((((((..............((((((......))))))(((....))).)))))))....................... (-12.04 = -13.20 +   1.16)

alignment

secondary structure

dotplot

Window 2

Location	8,878,141 – 8,878,255
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.38
Mean single sequence MFE	-16.75
Consensus MFE	-10.72
Energy contribution	-11.16
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-1.63
Structure conservation index	0.64
SVM decision value	-0.00
SVM RNA-class probability	0.532327
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878141 114 + 22224390
UGGCCAUGGAUU--CACAACCAUAUCGAUAUACACAACCACAACCA--UAU--UCACAUCCACAUCCACAUCCACAUGUCCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCUAAAUGA
(((((((((...--.....)))).......................--...--......((((((..((((....))))..))).)))......................)))))..... ( -14.80)
>DroSec_CAF1 8484 94 + 1
UGGCCAUGGAUU--CACAUCCAUAGC------CACAACCACAACCA--UAU--CCGAAUCCAC--------------GUCCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCAAAAUGA
((((.((((((.--...)))))).))------))............--...--.........(--------------((...(((((((..................)))))))..))). ( -17.87)
>DroSim_CAF1 8790 94 + 1
UGGCCAUGGAUU--CACAUCCAUAGC------CACAACCACAACCA--UAU--CCGAAUCCAC--------------GUCCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCAAGCUGA
((((.((((((.--...)))))).))------))............--...--..........--------------(.((.....)).).(((((...................))))) ( -18.51)
>DroEre_CAF1 7950 98 + 1
UGGCCAUGGAUC--CACAAACACAUC------CACAUCCAUAUGCUUGUAUCCCCACUUCCAC--------------GUCCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCAAAAUGA
..(((((((((.--............------...)))))).((((.(....((.((......--------------......)).))....))))).............)))....... ( -13.99)
>DroYak_CAF1 8824 98 + 1
UGGCCAUGGAUCUCCACGUCCACAUC------CACAACCACAACCA--AAUGGCCACAUCCAA--------------GACCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCAAAAUGA
..(((.(((((......)))))....------..............--.((((((((((....--------------....))).)))))))..................)))....... ( -18.60)
>consensus
UGGCCAUGGAUU__CACAUCCAUAUC______CACAACCACAACCA__UAU__CCACAUCCAC______________GUCCAUGUUGGUCAUCAGCAACUUUCACUCACCGGCAAAAUGA
..(((.(((((......)))))............................................................(((((.....))))).............)))....... (-10.72 = -11.16 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	8,878,255 – 8,878,346
Length	91
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	92.70
Mean single sequence MFE	-27.86
Consensus MFE	-23.62
Energy contribution	-24.42
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-3.81
Structure conservation index	0.85
SVM decision value	4.00
SVM RNA-class probability	0.999749
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878255 91 + 22224390
CGAUGACGAUGUGUGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAA----AGAAAAAAAGAC
(((((((((.((((((.....)))))).)))))))))((((((..((((((.....)))))).(((.....))).....----.))))))..... ( -30.50)
>DroSec_CAF1 8578 94 + 1
CGAUGACGAUGUGUGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAAA-AAAGAAAAAAAGAC
(((((((((.((((((.....)))))).)))))))))((((((..((((((.....)))))).(((.....)))......-...))))))..... ( -30.50)
>DroSim_CAF1 8884 95 + 1
CGAUGACGAUGUGUGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAAAAAAAGAAAAAAAUAC
(((((((((.((((((.....)))))).)))))))))((((((..((((((.....)))))).(((.....)))..........))))))..... ( -30.50)
>DroEre_CAF1 8048 84 + 1
CGAUGACGAUG--UGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAAA---------AAAGAC
.((((((((((--(((.....)))))))..))))))((((((...((((((.....)))))).(((.....)))......---------)))))) ( -23.90)
>DroYak_CAF1 8922 86 + 1
CGAUGACGAUG--UGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAAA-------AAAAAGAC
.((((((((((--(((.....)))))))..))))))((((((...((((((.....)))))).(((.....)))......-------..)))))) ( -23.90)
>consensus
CGAUGACGAUGUGUGCCUCCUGCACAUUUUGUCAUCGUUUUUCAUGUGGGAAAAUCUCUCGCCUCUGCAAAAGAUCCAAA___AGAAAAAAAGAC
(((((((((.((((((.....)))))).)))))))))........((((((.....)))))).(((.....)))..................... (-23.62 = -24.42 +   0.80)

alignment

secondary structure

dotplot

Window 4

Location	8,878,255 – 8,878,346
Length	91
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	92.70
Mean single sequence MFE	-29.50
Consensus MFE	-24.10
Energy contribution	-24.90
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-3.22
Structure conservation index	0.82
SVM decision value	3.11
SVM RNA-class probability	0.998477
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8878255 91 - 22224390
GUCUUUUUUUCU----UUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCACACAUCGUCAUCG
.....((((((.----.((((((((((((....)))))))))....)))...))))))(((((((....(((((.....)))))....))))))) ( -30.30)
>DroSec_CAF1 8578 94 - 1
GUCUUUUUUUCUUU-UUUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCACACAUCGUCAUCG
.....((((((...-...(((((((((((....)))))))))))........))))))(((((((....(((((.....)))))....))))))) ( -29.94)
>DroSim_CAF1 8884 95 - 1
GUAUUUUUUUCUUUUUUUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCACACAUCGUCAUCG
.....((((((.......(((((((((((....)))))))))))........))))))(((((((....(((((.....)))))....))))))) ( -30.36)
>DroEre_CAF1 8048 84 - 1
GUCUUU---------UUUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCA--CAUCGUCAUCG
((.(((---------(.((((((((((((....)))))))))....)))...)))).))((((((...((((((.....)))--))).)))))). ( -28.10)
>DroYak_CAF1 8922 86 - 1
GUCUUUUU-------UUUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCA--CAUCGUCAUCG
((.((((.-------..((((((((((((....)))))))))....)))...)))).))((((((...((((((.....)))--))).)))))). ( -28.80)
>consensus
GUCUUUUUUUCU___UUUGGAUCUUUUGCAGAGGCGAGAGAUUUUCCCACAUGAAAAACGAUGACAAAAUGUGCAGGAGGCACACAUCGUCAUCG
..................(((((((((((....)))))))))))..............(((((((....(((((.....)))))....))))))) (-24.10 = -24.90 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:23 2006