Locus 1450

Sequence ID	3L_DroMel_CAF1
Location	4,192,263 – 4,192,403
Length	140
Max. P	0.836112

overview

Window 0

Location	4,192,263 – 4,192,383
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.25
Mean single sequence MFE	-27.70
Consensus MFE	-21.36
Energy contribution	-21.44
Covariance contribution	0.08
Combinations/Pair	1.11
Mean z-score	-1.91
Structure conservation index	0.77
SVM decision value	0.39
SVM RNA-class probability	0.718663
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4192263 120 - 23771897
AAGCAAUGCCAAUUCAGAAAUCUGCAUUCGAAUUUUAUUGCUUUAUUGAGCAACUGGUAUGCAAAUUUUGAUUUUGCCAGACAUUUUUAUGAAGUGUUUAUGGAAGCUUAGAACUAUUAA
((((((((..(((((.(((.......)))))))).))))))))..((((((..((((((..((.....))....))))))(((((((...)))))))........))))))......... ( -25.10)
>DroSec_CAF1 42164 120 - 1
AAGCAAUGCCAAUUCAGAAAUCUGCAUUCGAAUUUUAUUGCUUUAUUAAGCAACUGGUAUGCAAAUUUUGAUUUUGCCAGACAUUUUUAUGAAGUGUUUAUGGAAGCUAAGAACUAUUAA
.(((.((((((...(((....))).............((((((....)))))).))))))(((((.......))))).(((((((((...)))))))))......)))............ ( -23.30)
>DroSim_CAF1 42360 120 - 1
AAGCAAUGCCAAUUCAGAAAUCUGCAUUCGAAUUUUAUUGCUUUAUUAAGCAACUGGUAUGCAAAUUUUGAUUUUGCCAGACAUUUUUAUGAAGUGUUUAUGGAAGCUAAGAACUAUUAA
.(((.((((((...(((....))).............((((((....)))))).))))))(((((.......))))).(((((((((...)))))))))......)))............ ( -23.30)
>DroEre_CAF1 38572 119 - 1
AAGCAAUGGCAAUUCCGAAAUCUGCAUCUGAAUUUUAUUGCU-UAUUGAGCAACCGGUAUGCAAAUUUUGAUUUUGCGAGACAUUUUUAUGAAGUGUUUAUGGAAGCUUAGAACUAUUAA
(((((((((.(((((.((........)).)))))))))))))-).((((((..(((...((((((.......))))))(((((((((...))))))))).)))..))))))......... ( -30.20)
>DroYak_CAF1 44165 120 - 1
AAGCAAUGCCAAUUCAGAAAACUGCAUCAGCAUUUUAUUGCUUUAUUGAGCAACUGGUAUGCAAAUUCUGAGUUUGCCAGACACUUUUAUGAGGUGUUUAUGGAAGCUUAGAACUAUUAA
..(((.(((((.......(((.(((....))).))).((((((....)))))).))))))))...((((((((((.(((((((((((...))))))))..)))))))))))))....... ( -36.60)
>consensus
AAGCAAUGCCAAUUCAGAAAUCUGCAUUCGAAUUUUAUUGCUUUAUUGAGCAACUGGUAUGCAAAUUUUGAUUUUGCCAGACAUUUUUAUGAAGUGUUUAUGGAAGCUUAGAACUAUUAA
((((((((..(((((.((........)).))))).))))))))..((((((..((.....(((((.......))))).(((((((((...)))))))))..))..))))))......... (-21.36 = -21.44 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	4,192,303 – 4,192,403
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.66
Mean single sequence MFE	-25.07
Consensus MFE	-18.00
Energy contribution	-18.36
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-2.08
Structure conservation index	0.72
SVM decision value	0.73
SVM RNA-class probability	0.836112
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4192303 100 + 23771897
CUGGCAAAAUCAAAAUUUGCAUACCAGUUGCUCAAUAAAGCAAUAAAAUUCGAAUGCAGAUUUCUGAAUUGGCAUUGCUUUUUAUGAGGUGACUAAUA--------------------AC
...(((((.......))))).....(((..((((..((((((((..((((((((.......))).)))))...))))))))...))).)..)))....--------------------.. ( -23.10)
>DroSec_CAF1 42204 100 + 1
CUGGCAAAAUCAAAAUUUGCAUACCAGUUGCUUAAUAAAGCAAUAAAAUUCGAAUGCAGAUUUCUGAAUUGGCAUUGCUUUUUAUGAGGUGACUAAUA--------------------AC
...(((((.......))))).....(((..(((...((((((((..((((((((.......))).)))))...)))))))).....)))..)))....--------------------.. ( -23.10)
>DroSim_CAF1 42400 102 + 1
CUGGCAAAAUCAAAAUUUGCAUACCAGUUGCUUAAUAAAGCAAUAAAAUUCGAAUGCAGAUUUCUGAAUUGGCAUUGCUUUUUAUGAGGUGACUAAUA----A--------------AAC
.((.(((..(((((((((((((....(((((((....))))))).........)))))))))).))).))).)).....((((((.((....)).)))----)--------------)). ( -23.12)
>DroEre_CAF1 38612 105 + 1
CUCGCAAAAUCAAAAUUUGCAUACCGGUUGCUCAAUA-AGCAAUAAAAUUCAGAUGCAGAUUUCGGAAUUGCCAUUGCUUUUUAUGAGGUGUCUAAUGGGCUA--------------UAC
...((....((.((((((((((....((((((.....-)))))).........)))))))))).)).....((((((((((....)))))....)))))))..--------------... ( -22.52)
>DroYak_CAF1 44205 120 + 1
CUGGCAAACUCAGAAUUUGCAUACCAGUUGCUCAAUAAAGCAAUAAAAUGCUGAUGCAGUUUUCUGAAUUGGCAUUGCUUUUUAUGAGGUGACUAAGUGACUAAGGUGACUAUGCAGUGC
((((.....))))...((((((...(((..((((..((((((.....((((..((.(((....))).))..))))))))))...))).)..))).(((.((....)).)))))))))... ( -33.50)
>consensus
CUGGCAAAAUCAAAAUUUGCAUACCAGUUGCUCAAUAAAGCAAUAAAAUUCGAAUGCAGAUUUCUGAAUUGGCAUUGCUUUUUAUGAGGUGACUAAUA____A_______________AC
...(((((.......))))).....(((((((((..((((((((..((((((((.......))).)))))...))))))))...))).)))))).......................... (-18.00 = -18.36 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:03 2006