Locus 3361

Sequence ID	3R_DroMel_CAF1
Location	9,077,408 – 9,077,512
Length	104
Max. P	0.764469

overview

Window 9

Location	9,077,408 – 9,077,512
Length	104
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	81.58
Mean single sequence MFE	-25.83
Consensus MFE	-16.03
Energy contribution	-16.72
Covariance contribution	0.68
Combinations/Pair	1.24
Mean z-score	-2.12
Structure conservation index	0.62
SVM decision value	0.41
SVM RNA-class probability	0.727009
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9077408 104 + 27905053
CCGAAAUAAA-AAAUCAAUAAUCGGGG-AAUGGCAAGUCAACAGCCAACAG----CAGCUCAGCUGAACUCAGGCGAAGCCGCCAUUUCUGACUGUUCCUGCCUCCGACA------
..........-..........((((((-...((..(((((........(((----(......))))......((((....)))).....)))))...))...))))))..------ ( -28.90)
>DroSec_CAF1 191710 105 + 1
CCGAAAUAAAAAAAUCAAUAAUCGGGG-AAUGACAAGUCAACAGCCAACAG----CAACUCAGCUGAACUUAGGCGAAGCCGCCAUUUCUGACUGUUCCUGCCUCCGACA------
.....................((((((-...((((.((((........(((----(......))))......((((....)))).....))))))))....)).))))..------ ( -27.50)
>DroEre_CAF1 198165 104 + 1
CCGAAAUAAA-AAAUCAAUAAUCGGGG-AAUGACAAGUCAACAGUCAACAG----CAGCUCAGCUGAACGCAGGCGAAGCCGCCAUUUCUGACUGUUCCUGCCUCCGACA------
..........-..........((((((-..(((....)))(((((((.(((----(......))))......((((....)))).....)))))))......))))))..------ ( -30.80)
>DroWil_CAF1 197995 87 + 1
CCAAA-CAA--AAAUCAAUAAUCGAGAAAAUGACAAGUCAAAUGCCAACAG----CAGCUAAGCUGA----------------CAUUUCUGGCUGCUCCUGCUCCUGUUC------
.....-...--............(((....(((....))).....((..((----((((((......----------------......))))))))..)))))......------ ( -13.50)
>DroYak_CAF1 207015 104 + 1
CCGAAAUAAA-AAAUCAAUAAUCGGGG-AAUGACAAGUCAACAGUCAACAG----CAGCUCAGCUGAACGCAGGCGAAGCCGCCAUUUCUGACUGUUCCUGCCUCCGACA------
..........-..........((((((-..(((....)))(((((((.(((----(......))))......((((....)))).....)))))))......))))))..------ ( -30.80)
>DroAna_CAF1 203369 114 + 1
CCAAAAUAA--AAAUCAAUAAUCGGGAAAAUGACAAGUCAACAGCCAAAAGCAAGCAGCUGAGCUGAACUCAAGCGAAGUCGCCAUUUCUGACGGCUCCUGCCUCCAAAAAUUCAG
.........--.............(((.........((((.((((....(((.....)))..)))).......(((....)))......))))(((....)))))).......... ( -23.50)
>consensus
CCGAAAUAAA_AAAUCAAUAAUCGGGG_AAUGACAAGUCAACAGCCAACAG____CAGCUCAGCUGAACUCAGGCGAAGCCGCCAUUUCUGACUGUUCCUGCCUCCGACA______
.....................((((((....((..(((((...............((((...))))......((((....)))).....)))))..))....))))))........ (-16.03 = -16.72 +   0.68)

alignment

secondary structure

dotplot

Window 0

Location	9,077,408 – 9,077,512
Length	104
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	81.58
Mean single sequence MFE	-33.12
Consensus MFE	-23.23
Energy contribution	-22.72
Covariance contribution	-0.51
Combinations/Pair	1.30
Mean z-score	-1.87
Structure conservation index	0.70
SVM decision value	0.51
SVM RNA-class probability	0.764469
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9077408 104 - 27905053
------UGUCGGAGGCAGGAACAGUCAGAAAUGGCGGCUUCGCCUGAGUUCAGCUGAGCUG----CUGUUGGCUGUUGACUUGCCAUU-CCCCGAUUAUUGAUUU-UUUAUUUCGG
------....((((((((((((((((((....((((((((.((.((....)))).))))))----)).)))))))))..))))))..)-))((((....(((...-.)))..)))) ( -40.30)
>DroSec_CAF1 191710 105 - 1
------UGUCGGAGGCAGGAACAGUCAGAAAUGGCGGCUUCGCCUAAGUUCAGCUGAGUUG----CUGUUGGCUGUUGACUUGUCAUU-CCCCGAUUAUUGAUUUUUUUAUUUCGG
------....((((((((((((((((((....((((....))))......((((......)----))))))))))))..))))))..)-))((((....(((.....)))..)))) ( -32.90)
>DroEre_CAF1 198165 104 - 1
------UGUCGGAGGCAGGAACAGUCAGAAAUGGCGGCUUCGCCUGCGUUCAGCUGAGCUG----CUGUUGACUGUUGACUUGUCAUU-CCCCGAUUAUUGAUUU-UUUAUUUCGG
------....((((((((((((((((((....((((((((.((.((....)))).))))))----)).)))))))))..))))))..)-))((((....(((...-.)))..)))) ( -36.60)
>DroWil_CAF1 197995 87 - 1
------GAACAGGAGCAGGAGCAGCCAGAAAUG----------------UCAGCUUAGCUG----CUGUUGGCAUUUGACUUGUCAUUUUCUCGAUUAUUGAUUU--UUG-UUUGG
------((((((((((((.((((((((....))----------------...)))..))).----))))(((((.......))))).................))--)))-))).. ( -20.40)
>DroYak_CAF1 207015 104 - 1
------UGUCGGAGGCAGGAACAGUCAGAAAUGGCGGCUUCGCCUGCGUUCAGCUGAGCUG----CUGUUGACUGUUGACUUGUCAUU-CCCCGAUUAUUGAUUU-UUUAUUUCGG
------....((((((((((((((((((....((((((((.((.((....)))).))))))----)).)))))))))..))))))..)-))((((....(((...-.)))..)))) ( -36.60)
>DroAna_CAF1 203369 114 - 1
CUGAAUUUUUGGAGGCAGGAGCCGUCAGAAAUGGCGACUUCGCUUGAGUUCAGCUCAGCUGCUUGCUUUUGGCUGUUGACUUGUCAUUUUCCCGAUUAUUGAUUU--UUAUUUUGG
...(((..((((((((.((((.(((((....))))).))))))))((((((((((.(((.....)))...)))))..))))).........))))..))).....--......... ( -31.90)
>consensus
______UGUCGGAGGCAGGAACAGUCAGAAAUGGCGGCUUCGCCUGAGUUCAGCUGAGCUG____CUGUUGGCUGUUGACUUGUCAUU_CCCCGAUUAUUGAUUU_UUUAUUUCGG
.............(((((((((((((((....((((....))))......((((...)))).......)))))))))..))))))......((((....(((.....)))..)))) (-23.23 = -22.72 +  -0.51)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:15 2006