Locus 1068

Sequence ID	X_DroMel_CAF1
Location	3,127,197 – 3,127,349
Length	152
Max. P	0.999143

overview

Window 6

Location	3,127,197 – 3,127,317
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.59
Mean single sequence MFE	-32.80
Consensus MFE	-28.16
Energy contribution	-29.40
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-2.70
Structure conservation index	0.86
SVM decision value	3.40
SVM RNA-class probability	0.999143
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3127197 120 + 22224390
AUAAACUGUGAUGACGGUAUUUUUAUAUAAGAUGAACAAGAGAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGU
....(((((....)))))...((((((.(((.(((.((((((.(((....))).)))))))))...(((((((....)))))))(((((.....)))))...........))))))))). ( -31.60)
>DroSec_CAF1 85527 116 + 1
AUAAACUGUGAUGGCGGUAUUUAUAUAUAAGAUGAACAA--GAUGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAU--
.((((.((((.((((...............(.(((.(((--(((((....)))..)))))))).).(((((((....))))))))))).))))))))...((((.........)))).-- ( -29.00)
>DroSim_CAF1 86771 116 + 1
AUAAACUGUGAUGGCGGUAUUUAUAUAUAAGAUGAACAA--GAUGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAU--
.((((.((((.((((...............(.(((.(((--(((((....)))..)))))))).).(((((((....))))))))))).))))))))...((((.........)))).-- ( -29.00)
>DroEre_CAF1 90098 118 + 1
AUAAGUUGUGCUGGCGGUAUUUAUAUAUGGGAUGAACAA--GAUGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGU
.(((((.((((((((.................(((.(((--(((((....)))..))))))))...(((((((....))))))))))))))))))))(((((((.........))))))) ( -40.50)
>DroYak_CAF1 92360 118 + 1
AUAAAUUGUGAUGGCGGUGUUUAUAUAUAAAAUGAACAA--GAUGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGU
.(((((.(((.((((.................(((.(((--(((((....)))..))))))))...(((((((....))))))))))).))))))))(((((((.........))))))) ( -33.90)
>consensus
AUAAACUGUGAUGGCGGUAUUUAUAUAUAAGAUGAACAA__GAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGU
.((((.((((.((((.................(((.(((....(((....)))....))))))...(((((((....))))))))))).))))))))(((((((.........))))))) (-28.16 = -29.40 +   1.24)

alignment

secondary structure

dotplot

Window 7

Location	3,127,197 – 3,127,317
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.59
Mean single sequence MFE	-26.22
Consensus MFE	-24.10
Energy contribution	-23.94
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.84
Structure conservation index	0.92
SVM decision value	2.55
SVM RNA-class probability	0.995205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3127197 120 - 22224390
ACUUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCAUCUCUUGUUCAUCUUAUAUAAAAAUACCGUCAUCACAGUUUAU
.........((((((((((((((((.......))))((.((((....)))).))....(((((....(((....)))....)))))....)))))))))...)))............... ( -23.70)
>DroSec_CAF1 85527 116 - 1
--AUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCAUC--UUGUUCAUCUUAUAUAUAAAUACCGCCAUCACAGUUUAU
--.......(((((.....))))).....((.((((((.((((((.((.....)).))))))......(((((.....)--))))..................)))))).))........ ( -26.20)
>DroSim_CAF1 86771 116 - 1
--AUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGGAGCAUC--UUGUUCAUCUUAUAUAUAAAUACCGCCAUCACAGUUUAU
--.......(((((.....))))).....((.((((((.((((((.((.....)).))))))......(((((.....)--))))..................)))))).))........ ( -26.20)
>DroEre_CAF1 90098 118 - 1
ACUUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCAUC--UUGUUCAUCCCAUAUAUAAAUACCGCCAGCACAACUUAU
.........(((((.....))))).....(((((((((.((((((.((.....)).)))))).....(((....)))..--......................)))))))))........ ( -30.80)
>DroYak_CAF1 92360 118 - 1
ACUUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAACUGCAGAAGCAUC--UUGUUCAUUUUAUAUAUAAACACCGCCAUCACAAUUUAU
.........(((((.....))))).....((.((((((.((((((.((.....)).)))))).....(((....)))..--......................)))))).))........ ( -24.20)
>consensus
ACUUACAAAGGUUUUAUGUAAGCCAAAUAUGCUGGCGGCUGUCAGAAGACAACCUGUUGACAAAAAUUGCAGAAGCAUC__UUGUUCAUCUUAUAUAUAAAUACCGCCAUCACAGUUUAU
.........(((((.....))))).....((.((((((.((((....)))).......(((((....(((....)))....))))).................)))))).))........ (-24.10 = -23.94 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	3,127,237 – 3,127,349
Length	112
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	92.08
Mean single sequence MFE	-32.54
Consensus MFE	-26.80
Energy contribution	-27.00
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.82
SVM decision value	2.53
SVM RNA-class probability	0.994982
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3127237 112 + 22224390
AGAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGUUGGCAUAAAGACGGUGGUA-AACAUGUCCACAG
...(((....))).(((.(((((((.(((((((....)))))))(((((.....)))))(((((.........)))))))))))).)))....((((..-.......)))).. ( -34.50)
>DroSec_CAF1 85566 104 + 1
-GAUGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAU-------AAAAGACGGUGGUA-AACAUGUCCACAG
-..(((....))).....((((....(((((((....)))))))(((((.....))))).((((.........)))).-------....))))((((..-.......)))).. ( -27.80)
>DroSim_CAF1 86810 104 + 1
-GAUGCUCCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAU-------AAAAGACGGUGGUA-AACAUGUCCACAG
-..(((....))).....((((....(((((((....)))))))(((((.....))))).((((.........)))).-------....))))((((..-.......)))).. ( -27.80)
>DroEre_CAF1 90137 112 + 1
-GAUGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGUUGGCAUAAAGAGGGUGGUAAAACACGUCCACAG
-....(((((........(((((((.(((((((....)))))))(((((.....)))))(((((.........))))))))))))...)))))((((..........)))).. ( -35.00)
>DroYak_CAF1 92399 111 + 1
-GAUGCUUCUGCAGUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGUUGGCAUAAAGACGGUGGUA-AACACGUCCACUG
-..(((....)))((((((((((((.(((((((....)))))))(((((.....)))))(((((.........))))))))))))..)))))(((((..-.......))))). ( -37.60)
>consensus
_GAUGCUUCUGCAAUUUUUGUCAACAGGUUGUCUUCUGACAGCCGCCAGCAUAUUUGGCUUACAUAAAACCUUUGUAAGUUGGCAUAAAGACGGUGGUA_AACAUGUCCACAG
...(((....))).....((((....(((((((....)))))))(((((.....))))).((((.........))))............))))((((..........)))).. (-26.80 = -27.00 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:52 2006