Locus 2779

Sequence ID	3L_DroMel_CAF1
Location	7,871,108 – 7,871,217
Length	109
Max. P	0.894816

overview

Window 8

Location	7,871,108 – 7,871,217
Length	109
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.83
Mean single sequence MFE	-27.58
Consensus MFE	-15.93
Energy contribution	-16.82
Covariance contribution	0.89
Combinations/Pair	1.17
Mean z-score	-2.41
Structure conservation index	0.58
SVM decision value	0.98
SVM RNA-class probability	0.894816
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7871108 109 + 23771897
AGCGUGCUGACAUUCACAUCACUUAUGUCCACCUCCAGUUCCUGGGAGGUGCGACAAAUCAAAAGUUUGUCCUGCAAAACAAGAAUAAGAACAUGAAUUUCAGAACAUA-
...((.((((.(((((.....(((((((((((((((........))))))).))).........((((........))))....)))))....))))).)))).))...- ( -30.90)
>DroVir_CAF1 38094 104 + 1
AACGUGCUGACAUUUACAUCGCUGAUGUCCACCUCGAGUUCCAGUGAAGUGCGACUCAGCAUCAUUUUGUCCUGCAAUCAAA--AU--GUACAUCAGU--CAGUCUAUAC
.....((((((.........(((((.((((((.(((........))).))).))))))))..(((((((.........))))--))--).......))--))))...... ( -28.30)
>DroSim_CAF1 24360 109 + 1
AGCGUGCUGACAUUCACAUCGCUUAUGUCCACCUCCAGUUCCUGGGAGGUACGACAAAUCAAAAGUUUGUCCUGCACAACAAUAAUAAAAACAUAAAUUCCAGAAUAUU-
...((((.(((((...........))))).((((((........))))))..(((((((.....)))))))..))))................................- ( -23.90)
>DroEre_CAF1 27560 109 + 1
AGCGUGCUGACGUUCACAUCGCUUAUGUCCACCUCCAGUUCCUGGGAGGUGCGGCAAAUCAAGAGUUUGUCCUGCAAUACAAGAAUAAGAACAUGAAUUCCAGAAUAUU-
......(((..(((((.....(((((((((((((((........))))))).))).........(((((.....))).))....)))))....)))))..)))......- ( -26.50)
>DroYak_CAF1 17219 104 + 1
AGCGUGCUGACAUUCACAUCGCUUAUGUCCACCUCCAGUUCCUGUGAGGUACGACAAAUCAAAAGUUUGUCCUGCA-----AGAAAAGGAACAUUAAUACCAGAAUAAU-
((((((.((.....)))).)))).((((((((((((((...))).)))))..(((((((.....))))))).....-----......)).))))...............- ( -23.50)
>DroMoj_CAF1 35977 105 + 1
AAUGUGCUGACAUUUACAUCGCUGAUGUCCACCUCCAAUUCCAGUGAAGUGCGACUCAGCAGCAUUUUGUCCUGCAAAGGAU--AUUAGAACAUUAGU--CAGCUUAUA-
.(((.((((((.........(((((.((((((.(((.......).)).))).)))))))).......((((((....)))))--)...........))--)))).))).- ( -32.40)
>consensus
AGCGUGCUGACAUUCACAUCGCUUAUGUCCACCUCCAGUUCCUGGGAGGUGCGACAAAUCAAAAGUUUGUCCUGCAAAACAAGAAUAAGAACAUGAAUUCCAGAAUAUA_
....(((.((((.............(((((((((((........))))))).))))...........))))..))).................................. (-15.93 = -16.82 +   0.89)

alignment

secondary structure

dotplot

Window 9

Location	7,871,108 – 7,871,217
Length	109
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.83
Mean single sequence MFE	-30.70
Consensus MFE	-16.65
Energy contribution	-16.24
Covariance contribution	-0.41
Combinations/Pair	1.24
Mean z-score	-1.90
Structure conservation index	0.54
SVM decision value	0.07
SVM RNA-class probability	0.567118
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7871108 109 - 23771897
-UAUGUUCUGAAAUUCAUGUUCUUAUUCUUGUUUUGCAGGACAAACUUUUGAUUUGUCGCACCUCCCAGGAACUGGAGGUGGACAUAAGUGAUGUGAAUGUCAGCACGCU
-...((.((((.(((((((((((((.(((((.....))))).............((((.(((((((........))))))))))))))).))))))))).)))).))... ( -36.90)
>DroVir_CAF1 38094 104 - 1
GUAUAGACUG--ACUGAUGUAC--AU--UUUGAUUGCAGGACAAAAUGAUGCUGAGUCGCACUUCACUGGAACUCGAGGUGGACAUCAGCGAUGUAAAUGUCAGCACGUU
.....(((((--.(((((((.(--((--((((.........))))))).(((((((((.((((((..........))))))))).))))))......))))))))).))) ( -31.40)
>DroSim_CAF1 24360 109 - 1
-AAUAUUCUGGAAUUUAUGUUUUUAUUAUUGUUGUGCAGGACAAACUUUUGAUUUGUCGUACCUCCCAGGAACUGGAGGUGGACAUAAGCGAUGUGAAUGUCAGCACGCU
-((((....(((((....)))))...))))...((((..((((.((..(((...((((.(((((((........)))))))))))....))).))...)))).))))... ( -27.40)
>DroEre_CAF1 27560 109 - 1
-AAUAUUCUGGAAUUCAUGUUCUUAUUCUUGUAUUGCAGGACAAACUCUUGAUUUGCCGCACCUCCCAGGAACUGGAGGUGGACAUAAGCGAUGUGAACGUCAGCACGCU
-......((((..(((((((((((((((..(((...(((((.....)))))...)))..(((((((........))))))))).))))).))))))))..))))...... ( -30.60)
>DroYak_CAF1 17219 104 - 1
-AUUAUUCUGGUAUUAAUGUUCCUUUUCU-----UGCAGGACAAACUUUUGAUUUGUCGUACCUCACAGGAACUGGAGGUGGACAUAAGCGAUGUGAAUGUCAGCACGCU
-...............((((((.......-----.....(((((((....).))))))..(((((.(((...)))))))))))))).((((.(((........))))))) ( -24.20)
>DroMoj_CAF1 35977 105 - 1
-UAUAAGCUG--ACUAAUGUUCUAAU--AUCCUUUGCAGGACAAAAUGCUGCUGAGUCGCACUUCACUGGAAUUGGAGGUGGACAUCAGCGAUGUAAAUGUCAGCACAUU
-.....((((--((...((((((...--.........))))))..((..(((((((((.((((((.(.......)))))))))).))))))..))....))))))..... ( -33.70)
>consensus
_AAUAUUCUGGAAUUAAUGUUCUUAUUCUUGUUUUGCAGGACAAACUUUUGAUUUGUCGCACCUCACAGGAACUGGAGGUGGACAUAAGCGAUGUGAAUGUCAGCACGCU
.................(((((................)))))............(((.((((((..........)))))))))...((((.(((........))))))) (-16.65 = -16.24 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:28 2006