Locus 9330

Sequence ID	3R_DroMel_CAF1
Location	24,793,739 – 24,793,846
Length	107
Max. P	0.879240

overview

Window 8

Location	24,793,739 – 24,793,846
Length	107
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	86.19
Mean single sequence MFE	-47.86
Consensus MFE	-33.64
Energy contribution	-34.24
Covariance contribution	0.60
Combinations/Pair	1.18
Mean z-score	-2.37
Structure conservation index	0.70
SVM decision value	0.91
SVM RNA-class probability	0.879240
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24793739 107 + 27905053
A-AGGGGCCGGAGGCCUCAGGUCCUGAGUCCUGGAUCCUG-------AAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUUUGGCCUCCAUUCUCUACGUCC-CUGCUCCUCCU-
.-((((((.(((((((..(((((((..(((..((((((..-------...((........))...))))))..)))))))))).))))))).........))))-)).........- ( -45.00)
>DroSec_CAF1 10035 114 + 1
A-CGGGGCCGGAGGCCUCAGGUCCUGAGUCCUGGAUCCUGAAUCCUGAAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUUUGGCCCCCAUCCUCCACGCCC-CUGCUGCGCCA-
.-.(((((.(((((.(((((((((((.((((.((((.(........).)))).)))).....)).)))))))))..(((.........)))..)))))..))))-)..........- ( -48.50)
>DroSim_CAF1 10078 114 + 1
A-CGGGGCCGGAGGCCUCAGGUCCUGAGUCCUGGAUCCUGAAUCCUGAAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUUUGGCCCCCAUCCUCCACGCCC-CUGCUCCGCCA-
.-((((((.((.((((((((((((((.((((.((((.(........).)))).)))).....)).)))))))))...(((...(((...)))...)))..))))-).))))))...- ( -48.80)
>DroEre_CAF1 4778 114 + 1
A-AGGGGCCGGAGGCCUCAGGUCCUGAGUCCUGAGUCCGGAAUCCUGGAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUUAUG-CCCCAUCCUCCACUUCCUCUGCUCCUCCA-
.-((((((.(((((.(((((((((((.((((.(..(((((....)))))..).)))).....)).)))))))))..(((.(....)-.)))...........)))))))))))...- ( -49.10)
>DroYak_CAF1 4942 113 + 1
AAAGGGGCCGGAGGCCUCAGAUCCUGAAUCCAGAAUCCAGAGUCCUGGAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUU--U-CCCCAUCCCCGACUUCC-CUGCACCACCAG
..(((((.(((.((.(((((((((.....((((.((((((....)))))).))))((....))..)))))))))..(((....--.-.)))..)))))...)))-)).......... ( -47.90)
>consensus
A_AGGGGCCGGAGGCCUCAGGUCCUGAGUCCUGGAUCCUGAAUCCUGAAUCCUGGGCAUUGGCAUGGAUCUGAGACGGGACUUUGGCCCCCAUCCUCCACGUCC_CUGCUCCGCCA_
...(((((.(((((.(((((((((((.((((.((((.(........).)))).)))).....)).)))))))))..(((.........)))..)))))..)))).)........... (-33.64 = -34.24 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	24,793,739 – 24,793,846
Length	107
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	86.19
Mean single sequence MFE	-50.42
Consensus MFE	-34.30
Energy contribution	-34.86
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.45
Structure conservation index	0.68
SVM decision value	0.80
SVM RNA-class probability	0.854823
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24793739 107 - 27905053
-AGGAGGAGCAG-GGACGUAGAGAAUGGAGGCCAAAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUU-------CAGGAUCCAGGACUCAGGACCUGAGGCCUCCGGCCCCU-U
-..((((.((..-...(.....)..((((((((..(((((.((((..(((((...((........))...-------..)))))..))))...))).))..)))))))))).)))-) ( -38.70)
>DroSec_CAF1 10035 114 - 1
-UGGCGCAGCAG-GGGCGUGGAGGAUGGGGGCCAAAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUUCAGGAUUCAGGAUCCAGGACUCAGGACCUGAGGCCUCCGGCCCCG-U
-..........(-((((.(((((....(((((....)))))(((((((.(((..((....))((.((((((........)))))).)).....))).))))))))))))))))).-. ( -51.60)
>DroSim_CAF1 10078 114 - 1
-UGGCGGAGCAG-GGGCGUGGAGGAUGGGGGCCAAAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUUCAGGAUUCAGGAUCCAGGACUCAGGACCUGAGGCCUCCGGCCCCG-U
-.(((((.(((.-.((((((((((((((((.......))))))))....))))))))..))))).(((....((.((((((.(((........))))))))).))))).)))...-. ( -53.80)
>DroEre_CAF1 4778 114 - 1
-UGGAGGAGCAGAGGAAGUGGAGGAUGGGG-CAUAAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUCCAGGAUUCCGGACUCAGGACUCAGGACCUGAGGCCUCCGGCCCCU-U
-..((((.((...(((.(((((((((((((-(....)))))))))....)))))......(((((((.(((..((.(((.......))).)).))))))).))).))).)).)))-) ( -49.30)
>DroYak_CAF1 4942 113 - 1
CUGGUGGUGCAG-GGAAGUCGGGGAUGGGG-A--AAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUCCAGGACUCUGGAUUCUGGAUUCAGGAUCUGAGGCCUCCGGCCCCUUU
..........((-((..(((((((...(((-.--....)))(((((((((((..((....))(((((((((((....))))))))))).....)))))))))))))))))))))).. ( -58.70)
>consensus
_UGGAGGAGCAG_GGACGUGGAGGAUGGGGGCCAAAGUCCCGUCUCAGAUCCAUGCCAAUGCCCAGGAUUCAGGAUUCAGGAUCCAGGACUCAGGACCUGAGGCCUCCGGCCCCU_U
....(((.((...(((...........(((((....)))))(((((((.(((..((....))((.((((((........)))))).)).....))).))))))).))).)).))).. (-34.30 = -34.86 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:55 2006