Locus 1473

Sequence ID	X_DroMel_CAF1
Location	4,408,260 – 4,408,408
Length	148
Max. P	0.903465

overview

Window 9

Location	4,408,260 – 4,408,376
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	98.26
Mean single sequence MFE	-29.02
Consensus MFE	-25.78
Energy contribution	-25.66
Covariance contribution	-0.12
Combinations/Pair	1.04
Mean z-score	-1.39
Structure conservation index	0.89
SVM decision value	0.15
SVM RNA-class probability	0.605460
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4408260 116 - 22224390
CAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGAAAGGGGCACGUGCCGCUCAAUGUGCAAGGAUCAAGGAUCUCCCCCUUUGGCAAUUCUAUCUGCAACUGCA
......(((((....(((((.....((((......))))...((....)).((((((........))))))...)))))(((.......))).))))).........((....)). ( -29.60)
>DroSec_CAF1 10762 114 - 1
CAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAAGGAUCUCCCCCUUUGGCAAUUCUAUCUGCAACUGCA
......(((((....((((((((..((((......)))).....((--(.(((....))).)))....)))...)))))(((.......))).))))).........((....)). ( -29.50)
>DroSim_CAF1 10860 114 - 1
CAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAAGGAUCUCCCCCUUUGGCAAUUCUAUCUGCAACUGCA
......(((((....((((((((..((((......)))).....((--(.(((....))).)))....)))...)))))(((.......))).))))).........((....)). ( -29.50)
>DroEre_CAF1 11610 114 - 1
CAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAAGGAUCUCCCCCUUUGGCAAUUCUAUCUGCAACUGCA
......(((((....((((((((..((((......)))).....((--(.(((....))).)))....)))...)))))(((.......))).))))).........((....)). ( -29.50)
>DroYak_CAF1 10943 114 - 1
CAUCCCUGGCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGAAUCAAGGAUCUCCCCCUUUGUCAAUUCUAUCUGCAACUGCA
........(((((............((((......)))).....((--(.(((....))).)))..))))).((((((((((........)))))...)))))....((....)). ( -27.00)
>consensus
CAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA__GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAAGGAUCUCCCCCUUUGGCAAUUCUAUCUGCAACUGCA
......(((((.......(((....((((......))))....)))..(((((((((........))))))..(((((...)))))..)))..))))).........((....)). (-25.78 = -25.66 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	4,408,296 – 4,408,408
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.07
Mean single sequence MFE	-39.00
Consensus MFE	-35.18
Energy contribution	-35.42
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.90
SVM decision value	1.03
SVM RNA-class probability	0.903465
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4408296 112 + 22224390
UUGAUCCUUGCACAUUGAGCGGCACGUGCCCCUUUCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGGCAGGGAUGCAGCGCGUGCGAGGAUCCUCCGCUUCUCA--------AUU
..(((((((((((...(((.(((....))).)))(((...(((((......)))))...)))....((((.(((....))).)))))))))))))))............--------... ( -39.20)
>DroSec_CAF1 10798 110 + 1
UUGAUCCUUGCACAUUGAGCGGCACGUGCCCC--UCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGGCAGGGAUGCAGCGCGUGCGAGGAUCCUCCGCUCCUCG--------AUU
..(((((((((((((((((.(((....))).)--)))))..((((......))))(((((.(((.((.....))..))))))))..)))))))))))............--------... ( -42.30)
>DroSim_CAF1 10896 118 + 1
UUGAUCCUUGCACAUUGAGCGGCACGUGCCCC--UCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGGCAGGGAUGCAGCGCGUGCGAGUAUCCUCCGCUCCUCGAUUCCUCGAUU
................((((((((((((((((--(......((((......))))((..((......))..)))))).....))))))))(((....)))))))).((((....)))).. ( -37.80)
>DroEre_CAF1 11646 110 + 1
UUGAUCCUUGCACAUUGAGCGGCACGUGCCCC--UCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGGCAGGGAUGCAGCGCGUGCAACGAUCCUCUGCUCCUCA--------AUU
..((((.((((((((((((.(((....))).)--)))))..((((......))))(((((.(((.((.....))..))))))))..)))))).))))............--------... ( -36.10)
>DroYak_CAF1 10979 110 + 1
UUGAUUCUUGCACAUUGAGCGGCACGUGCCCC--UCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGCCAGGGAUGCAGCGCGUGCAAGGAUCCUCGGCUCCUCG--------AUU
..(((((((((((((((((.(((....))).)--)))))..((((......))))(((((.(((.((.....))..))))))))..))))))))))).((((....)))--------).. ( -39.60)
>consensus
UUGAUCCUUGCACAUUGAGCGGCACGUGCCCC__UCGGUUUUCGUUUAUUUACGAGUUGCGAUCAUGUGUGGCAGGGAUGCAGCGCGUGCGAGGAUCCUCCGCUCCUCG________AUU
..(((((((((((.....(((((....(((......)))..((((......)))))))))......((((.(((....))).)))))))))))))))....................... (-35.18 = -35.42 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	4,408,296 – 4,408,408
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.07
Mean single sequence MFE	-34.74
Consensus MFE	-26.96
Energy contribution	-27.76
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.56
Structure conservation index	0.78
SVM decision value	0.03
SVM RNA-class probability	0.549754
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4408296 112 - 22224390
AAU--------UGAGAAGCGGAGGAUCCUCGCACGCGCUGCAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGAAAGGGGCACGUGCCGCUCAAUGUGCAAGGAUCAA
...--------............((((((.(((((.((.((((...((((...............((((......))))...((....)))))).)))).))....))))).)))))).. ( -35.90)
>DroSec_CAF1 10798 110 - 1
AAU--------CGAGGAGCGGAGGAUCCUCGCACGCGCUGCAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAA
..(--------((.....)))..((((((.(((((((...(((...........)))..)))...((((......)))).....((--(.(((....))).)))...)))).)))))).. ( -33.40)
>DroSim_CAF1 10896 118 - 1
AAUCGAGGAAUCGAGGAGCGGAGGAUACUCGCACGCGCUGCAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAA
..((((....))))(..((((.((((.(.((....))..).))))))))..)...((((((((..((((......)))).....((--(.(((....))).)))....)))...))))). ( -36.10)
>DroEre_CAF1 11646 110 - 1
AAU--------UGAGGAGCAGAGGAUCGUUGCACGCGCUGCAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAA
...--------((.(..((((.((((.((.((....)).))))))))))..).))((((((((..((((......)))).....((--(.(((....))).)))....)))...))))). ( -36.00)
>DroYak_CAF1 10979 110 - 1
AAU--------CGAGGAGCCGAGGAUCCUUGCACGCGCUGCAUCCCUGGCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA--GGGGCACGUGCCGCUCAAUGUGCAAGAAUCAA
..(--------((......))).(((.((((((((...((((((..((.....)).))).)))..((((......)))).....((--(.(((....))).)))..)))))))).))).. ( -32.30)
>consensus
AAU________CGAGGAGCGGAGGAUCCUCGCACGCGCUGCAUCCCUGCCACACAUGAUCGCAACUCGUAAAUAAACGAAAACCGA__GGGGCACGUGCCGCUCAAUGUGCAAGGAUCAA
.......................((((((.(((((.((.((((...((((...............((((......))))...((....)))))).)))).))....))))).)))))).. (-26.96 = -27.76 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:17 2006