Locus 1283

Sequence ID	3R_DroMel_CAF1
Location	3,794,979 – 3,795,173
Length	194
Max. P	0.881594

overview

Window 7

Location	3,794,979 – 3,795,093
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.61
Mean single sequence MFE	-32.86
Consensus MFE	-18.18
Energy contribution	-19.70
Covariance contribution	1.52
Combinations/Pair	1.18
Mean z-score	-2.13
Structure conservation index	0.55
SVM decision value	0.92
SVM RNA-class probability	0.881594
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3794979 114 - 27905053
UGCGUCGGUUGUGGUGAGUGUGGAGUUGUUAAAAAUAAAACACACUGA----ACGCUGAUGAUCGAUGCGGGGGUCGCAAAGGUCCUACAAGG--AAAAAAGAGUAUCUGUCAGAUGCAG
.((((((((..(((((((((((...((((.....))))..))))))..----.)))).)..)))))))).(((..(.....)..)))......--........(((((.....))))).. ( -37.20)
>DroSec_CAF1 24323 115 - 1
UGCGUCGUUUGUGGUGAGUGUGGAGUUGUUAAAAAUAAAACACACUGA----UCGCUGGUGAUCGAUGCGGGGGUCGCAAAUGUCCAACGAGAA-AAAAAAGAGUAUCUGUCAGAUGCAG
((((((....(((((.((((((...((((.....))))..)))))).)----))))...((((.((((((((.((.....)).)))..(.....-......).))))).)))))))))). ( -34.60)
>DroSim_CAF1 28802 116 - 1
UGCGUCGUUUGUGGUGAGUGUGGAGUUGUUAAAAAUAAAACACACUGA----ACGCUGGUGAUCGAUGCGGGGGUCGCCAAUGUCCUACGAGAAGAAAAAAGAGUAUCUGUCAGAUGCAG
((((((.((((((((.((((((...((((.....))))..)))))).)----(((.((((((((........)))))))).))).)))))))..((....((.....)).)).)))))). ( -35.30)
>DroEre_CAF1 15485 97 - 1
UGCGUCGGUUGCGGUGGAGGUGUAGUUGUUAAAAAUAAAACACUCUGAAUAAAUGCUGAUGACCAAUGCGGG--------------------G---GAAAAGAGUAUCUGCCAUAUUGAG
.((((.((((((((((...((.(((.((((........))))..))).))...))))).))))).))))((.--------------------(---((........))).))........ ( -22.80)
>DroYak_CAF1 26584 117 - 1
UGCGUCGGUUGUGGUGGAUGUAGGGUUUUUAAAAAUAAAACACUCUGAAUAAACGCGGAUGACCAAUGCGGGGGUCGCAAAGGUCCUAUGAGG---GAAAAGAGUAUCGCCCAGAUGCAG
(((((((((..(.(((.((.(((((((((((....))))).)))))).))...)))..)..))).....(((.(..((.....((((....))---)).....))..).))).)))))). ( -34.40)
>consensus
UGCGUCGGUUGUGGUGAGUGUGGAGUUGUUAAAAAUAAAACACACUGA____ACGCUGAUGAUCGAUGCGGGGGUCGCAAAGGUCCUACGAGG__AAAAAAGAGUAUCUGUCAGAUGCAG
.((((((((((((.(.((((((...((((.....))))..)))))).).....)))....)))))))))..................................(((((.....))))).. (-18.18 = -19.70 +   1.52)

alignment

secondary structure

dotplot

Window 8

Location	3,795,053 – 3,795,173
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-22.02
Consensus MFE	-20.82
Energy contribution	-21.26
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.27
Structure conservation index	0.95
SVM decision value	0.86
SVM RNA-class probability	0.869136
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3795053 120 + 27905053
UUUUAUUUUUAACAACUCCACACUCACCACAACCGACGCAUCGGUGGCAAUUGCAAACAUUUAUACAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACCAAAGAUACA
.....................................((...((((((((((((..(((.(((.((........)).))).))).)))))))))))).(....)..))............ ( -24.50)
>DroSec_CAF1 24398 120 + 1
UUUUAUUUUUAACAACUCCACACUCACCACAAACGACGCAUCGGUGGCAAUUGCAAACAUUUAUAUAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACCAAAGAUACA
.....................................((...((((((((((((....((((....)))).((((......)))))))))))))))).(....)..))............ ( -24.20)
>DroSim_CAF1 28878 120 + 1
UUUUAUUUUUAACAACUCCACACUCACCACAAACGACGCAUCGGUGGCAAUUGCAAACAUUUAUACAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACCAAAGAUACA
.....................................((...((((((((((((..(((.(((.((........)).))).))).)))))))))))).(....)..))............ ( -24.50)
>DroEre_CAF1 15542 120 + 1
UUUUAUUUUUAACAACUACACCUCCACCGCAACCGACGCAUCAGUAGCAAUUGCAAACAUUUAUACAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACUAAAGAUUCA
....(((((((................((....))..((....((..(((((((..(((.(((.((........)).))).))).)))))))..))..(....)..))..)))))))... ( -16.20)
>DroYak_CAF1 26661 120 + 1
UUUUAUUUUUAAAAACCCUACAUCCACCACAACCGACGCAUCAGUGGCAAUUGCAAACAUUUAUACAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACCAAAGAUACA
.....................................((....(((((((((((..(((.(((.((........)).))).))).)))))))))))..(....)..))............ ( -20.70)
>consensus
UUUUAUUUUUAACAACUCCACACUCACCACAACCGACGCAUCGGUGGCAAUUGCAAACAUUUAUACAAAUUGACGUUUAGCUGUCGCAGUUGUCACCUCGAAAGCCGCACCAAAGAUACA
.....................................((...((((((((((((..(((.(((.((........)).))).))).)))))))))))).(....)..))............ (-20.82 = -21.26 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:39 2006