Locus 8324

Sequence ID	3R_DroMel_CAF1
Location	22,225,362 – 22,225,544
Length	182
Max. P	0.993676

overview

Window 9

Location	22,225,362 – 22,225,475
Length	113
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-35.55
Consensus MFE	-31.92
Energy contribution	-32.93
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.70
Structure conservation index	0.90
SVM decision value	2.42
SVM RNA-class probability	0.993676
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22225362 113 - 27905053
GCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCUGACAGCCACACUCA-CACUAUGACGCACACACACACACAC
((.((((((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))............(((-.....))).)).............. ( -37.80)
>DroSec_CAF1 68175 111 - 1
GCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCUGACAGCCACACUCA-CACUAUGACACACAC--ACACACAC
(((((((((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))....)))........-...............--........ ( -37.70)
>DroSim_CAF1 59699 113 - 1
GCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCUGACAGCCACACUCA-CACUAUGACACACACACACACACAC
(((((((((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))....)))........-......................... ( -37.70)
>DroAna_CAF1 93688 95 - 1
GCUGCCGGCAUGUGGUCGGUUGACCGGGCCAA--AACCAGAAUUGC---CGGGAACUUAAAUCAUUCGCCGGCUGACAGCCACACACAGCACU--GAUAUAC------------
((((((((((...((((....))))((.....--..)).....)))---)))..................(((.....))).....))))...--.......------------ ( -29.00)
>consensus
GCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCUGACAGCCACACUCA_CACUAUGACACACAC__ACACACAC
(((((((((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))....))).................................. (-31.92 = -32.93 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	22,225,401 – 22,225,515
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	95.18
Mean single sequence MFE	-40.20
Consensus MFE	-34.35
Energy contribution	-35.10
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.61
Structure conservation index	0.85
SVM decision value	1.19
SVM RNA-class probability	0.928491
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22225401 114 + 27905053
AGCCGGCGAAUGAUUUAAGUUGCCGGGCGCAAUUCUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAA
((((((((..(((..((.((((((((((.(((..........)))))))((((....)))).......)))))).))..)))...)).))))))......((......)).... ( -40.60)
>DroSec_CAF1 68212 114 + 1
AGCCGGCGAAUGAUUUAAGUUGCCGGGCGCAAUUCUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCAUGGGAAAACGCAAA
((((((((..(((..((.((((((((((.(((..........)))))))((((....)))).......)))))).))..)))...)).)))))).................... ( -40.30)
>DroSim_CAF1 59738 114 + 1
AGCCGGCGAAUGAUUUAAGUUGCCGGGCGCAAUUCUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAA
((((((((..(((..((.((((((((((.(((..........)))))))((((....)))).......)))))).))..)))...)).))))))......((......)).... ( -40.60)
>DroAna_CAF1 93714 109 + 1
AGCCGGCGAAUGAUUUAAGUUCCCG---GCAAUUCUGGUU--UUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCCAAAUCACAGGCGAACGCAAA
.(((((.((((.......)))))))---))....(((..(--((((((.((((....)))).......(((((...........))))).)))))))...)))((....))... ( -39.30)
>consensus
AGCCGGCGAAUGAUUUAAGUUGCCGGGCGCAAUUCUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAA
((((((((..(((..((.((((((((..........((((....)))).((((....)))).....)))))))).))..)))...)).)))))).................... (-34.35 = -35.10 +   0.75)

alignment

secondary structure

dotplot

Window 1

Location	22,225,401 – 22,225,515
Length	114
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	95.18
Mean single sequence MFE	-41.00
Consensus MFE	-35.67
Energy contribution	-36.30
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.87
SVM decision value	0.97
SVM RNA-class probability	0.892040
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22225401 114 - 27905053
UUUGCGUUUUCCCGUGAUUUAGCCGGACAGUUUGAAAUAUGCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCU
.(..((......))..)...((((((.((((.........))))))(((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))) ( -42.50)
>DroSec_CAF1 68212 114 - 1
UUUGCGUUUUCCCAUGAUUUAGCCGGACAGUUUGAAAUAUGCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCU
...(((.......(((((((((((((.((((.........)))))))))........(((((.(((((((((..........))).))))))))))))))))))).)))..... ( -40.80)
>DroSim_CAF1 59738 114 - 1
UUUGCGUUUUCCCGUGAUUUAGCCGGACAGUUUGAAAUAUGCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCU
.(..((......))..)...((((((.((((.........))))))(((..(((((.(((((.(((((((((..........))).)))))))))))...)))))..))))))) ( -42.50)
>DroAna_CAF1 93714 109 - 1
UUUGCGUUCGCCUGUGAUUUGGCCGGACAGUUUGAAAUAUGCUGCCGGCAUGUGGUCGGUUGACCGGGCCAA--AACCAGAAUUGC---CGGGAACUUAAAUCAUUCGCCGGCU
((((.(((.((((........(((((.((((.........)))))))))....((((....))))))))...--)))))))...((---((((((.........))).))))). ( -38.20)
>consensus
UUUGCGUUUUCCCGUGAUUUAGCCGGACAGUUUGAAAUAUGCUGCCGGCAUGUGGUCGGUUGACCGGGCCAAAAAACCAGAAUUGCGCCCGGCAACUUAAAUCAUUCGCCGGCU
...(((.......(((((((((((((.((((.........)))))))))........(((((.(((((((((..........))).))))))))))))))))))).)))..... (-35.67 = -36.30 +   0.63)

alignment

secondary structure

dotplot

Window 2

Location	22,225,435 – 22,225,544
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.37
Mean single sequence MFE	-33.38
Consensus MFE	-24.01
Energy contribution	-24.82
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-1.65
Structure conservation index	0.72
SVM decision value	0.08
SVM RNA-class probability	0.571860
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22225435 109 + 27905053
CUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAAAAUAAAAUCACAAAAGC----GUCCGGGAGGCG-------
...((((((((((((((((....))))....((((((((...........))).)))))........)))...((((..................))----))))))))))).------- ( -33.47)
>DroSec_CAF1 68246 109 + 1
CUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCAUGGGAAAACGCAAAAAUAAAAUCACAAAAGC----GACCGGGAGGCG-------
...((((((((((((((((....))))....((((((((...........))).)))))........)))....(((..................))----).))))))))).------- ( -33.07)
>DroSim_CAF1 59772 109 + 1
CUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAAAAUAAAAUCACAAAAGC----GACCGGGAGGCG-------
...((((((((((((((((....))))....((((((((...........))).)))))........)))....(((..................))----).))))))))).------- ( -33.37)
>DroAna_CAF1 93745 118 + 1
CUGGUU--UUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCCAAAUCACAGGCGAACGCAAAAAUAAAAUCACAUAAGAAGGAGUCGAGGUGGCGGGGUGGC
......--...((((.((((.(((((..(..((((((((...........))).)))))..........((....)).....................)..)))).).)))).))))... ( -33.60)
>consensus
CUGGUUUUUUGGCCCGGUCAACCGACCACAUGCCGGCAGCAUAUUUCAAACUGUCCGGCUAAAUCACGGGAAAACGCAAAAAUAAAAUCACAAAAGC____GACCGGGAGGCG_______
...((((((((((((((((....))))....((((((((...........))).)))))........)))....................(....).......)))))))))........ (-24.01 = -24.82 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:53 2006