Locus 3033

Sequence ID	3R_DroMel_CAF1
Location	8,082,761 – 8,082,896
Length	135
Max. P	0.999759

overview

Window 8

Location	8,082,761 – 8,082,879
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	97.63
Mean single sequence MFE	-35.37
Consensus MFE	-34.58
Energy contribution	-34.50
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-2.42
Structure conservation index	0.98
SVM decision value	4.02
SVM RNA-class probability	0.999759
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8082761 118 + 27905053
CGUGGUAUUGAUACCCUUUUGCAUGUGACUCACACCGUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUU
.(.((((....)))))....(((((((((.......))))))............((((((((((.(((...(((((.....))))).))).))))))))))))).............. ( -38.00)
>DroSec_CAF1 7674 118 + 1
CGUGGUAUUAAUAUCCUUUUGCAUGUGACUCACACCAUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUU
.((((((.........(((((((((((.....)).))).)))))).......(.((((((((((.(((...(((((.....))))).))).)))))))))).).....)))))).... ( -36.60)
>DroSim_CAF1 6129 118 + 1
CGUGGUAUUAAUAUCCUUUUGCAUGUGACUCACACCGUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCUCCAUCCCAUUGUGCUAUUUAUCAUAAUU
.((((((.............(((((((((.......))))))............((((((((((..((...(((((.....))))).))..)))))))))))))....)))))).... ( -35.93)
>DroEre_CAF1 9399 118 + 1
CGUGGUAUUAAUAUCCUUUUGCAUGUGACUCACACCGUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAAGCCAUUGUGCUAUUUAUCAUAAUU
.(((((....(((((((.(((..((((...)))).((((.....))))......))).)))))))(((...(((((.....)))))...)))..)))))................... ( -29.50)
>DroYak_CAF1 2758 118 + 1
CAUGGUAUUAAUAUCCUUUUGCAUGUGACUCACACCGUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUU
.((((((.............(((((((((.......))))))............((((((((((.(((...(((((.....))))).))).)))))))))))))....)))))).... ( -36.83)
>consensus
CGUGGUAUUAAUAUCCUUUUGCAUGUGACUCACACCGUCGCGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUU
.((((((.........(((((((((((.....)).))).)))))).......(.((((((((((.(((...(((((.....))))).))).)))))))))).).....)))))).... (-34.58 = -34.50 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	8,082,761 – 8,082,879
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	97.63
Mean single sequence MFE	-29.16
Consensus MFE	-27.48
Energy contribution	-27.92
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.94
SVM decision value	0.98
SVM RNA-class probability	0.894730
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8082761 118 - 27905053
AAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGACGGUGUGAGUCACAUGCAAAAGGGUAUCAAUACCACG
..............((.((.((((((((((...((((.....))))....))).))))))).))......((((.....))))(((((...))))))).....((((....))))... ( -34.00)
>DroSec_CAF1 7674 118 - 1
AAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGAUGGUGUGAGUCACAUGCAAAAGGAUAUUAAUACCACG
..............((.((.((((((((((...((((.....))))....))).))))))).)).(((......)))))(.((((((..(((.(........))))....))))))). ( -30.50)
>DroSim_CAF1 6129 118 - 1
AAUUAUGAUAAAUAGCACAAUGGGAUGGAGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGACGGUGUGAGUCACAUGCAAAAGGAUAUUAAUACCACG
..............((.((.(((((((..((..((((.....))))....))..))))))).))......((((.....))))(((((...))))))).................... ( -27.30)
>DroEre_CAF1 9399 118 - 1
AAUUAUGAUAAAUAGCACAAUGGCUUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGACGGUGUGAGUCACAUGCAAAAGGAUAUUAAUACCACG
..............((.((.(((..(((((...((((.....))))....))).))..))).))......((((.....))))(((((...))))))).................... ( -23.20)
>DroYak_CAF1 2758 118 - 1
AAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGACGGUGUGAGUCACAUGCAAAAGGAUAUUAAUACCAUG
..............((.((.((((((((((...((((.....))))....))).))))))).))......((((.....))))(((((...))))))).................... ( -30.80)
>consensus
AAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCGCGACGGUGUGAGUCACAUGCAAAAGGAUAUUAAUACCACG
..............((.((.((((((((((...((((.....))))....))).))))))).))......((((.....))))(((((...)))))))....((.........))... (-27.48 = -27.92 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	8,082,801 – 8,082,896
Length	95
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	98.32
Mean single sequence MFE	-26.08
Consensus MFE	-25.24
Energy contribution	-25.48
Covariance contribution	0.24
Combinations/Pair	1.05
Mean z-score	-2.52
Structure conservation index	0.97
SVM decision value	3.81
SVM RNA-class probability	0.999629
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8082801 95 + 27905053
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUUUUUCAAUUUAACACUGC
.(((((.(....).((((((((((.(((...(((((.....))))).))).))))))))))................)))))............. ( -27.30)
>DroSec_CAF1 7714 95 + 1
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUUUUUCAAUUUAACACUGC
.(((((.(....).((((((((((.(((...(((((.....))))).))).))))))))))................)))))............. ( -27.30)
>DroSim_CAF1 6169 94 + 1
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCUCCAUCCCAUUGUGCUAUUUAUCAUAAUU-UUCAAUUUAACACUGC
.(((((.(....).((((((((((..((...(((((.....))))).))..))))))))))...............))-)))............. ( -26.20)
>DroEre_CAF1 9439 95 + 1
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAAGCCAUUGUGCUAUUUAUCAUAAUUUUUCAAUUUAACACUGC
..............(((((((...((((...(((((.....)))))...))))..))((((((........))))))............))))). ( -22.30)
>DroYak_CAF1 2798 95 + 1
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUUUUUCAAUUUAACACUGC
.(((((.(....).((((((((((.(((...(((((.....))))).))).))))))))))................)))))............. ( -27.30)
>consensus
CGAAGACGUUCUCUCAGUGGGAUGUGGGUUUGGUUGUUGUGCAACUUCCCCCAUCCCAUUGUGCUAUUUAUCAUAAUUUUUCAAUUUAACACUGC
............(.((((((((((.(((...(((((.....))))).))).)))))))))).)................................ (-25.24 = -25.48 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	8,082,801 – 8,082,896
Length	95
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	98.32
Mean single sequence MFE	-23.32
Consensus MFE	-22.14
Energy contribution	-22.74
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.95
SVM decision value	2.83
SVM RNA-class probability	0.997261
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8082801 95 - 27905053
GCAGUGUUAAAUUGAAAAAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
((..(((((((((....)))).)))))....)).((.((((((((((...((((.....))))....))).))))))).)).............. ( -26.00)
>DroSec_CAF1 7714 95 - 1
GCAGUGUUAAAUUGAAAAAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
((..(((((((((....)))).)))))....)).((.((((((((((...((((.....))))....))).))))))).)).............. ( -26.00)
>DroSim_CAF1 6169 94 - 1
GCAGUGUUAAAUUGAA-AAUUAUGAUAAAUAGCACAAUGGGAUGGAGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
...((((((.......-............))))))..(((((((..((..((((.....))))....))..)))))))..((((.....)))).. ( -20.21)
>DroEre_CAF1 9439 95 - 1
GCAGUGUUAAAUUGAAAAAUUAUGAUAAAUAGCACAAUGGCUUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
((..(((((((((....)))).)))))....)).((.(((..(((((...((((.....))))....))).))..))).)).............. ( -18.40)
>DroYak_CAF1 2798 95 - 1
GCAGUGUUAAAUUGAAAAAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
((..(((((((((....)))).)))))....)).((.((((((((((...((((.....))))....))).))))))).)).............. ( -26.00)
>consensus
GCAGUGUUAAAUUGAAAAAUUAUGAUAAAUAGCACAAUGGGAUGGGGGAAGUUGCACAACAACCAAACCCACAUCCCACUGAGAGAACGUCUUCG
((..(((((((((....)))).)))))....)).((.((((((((((...((((.....))))....))).))))))).)).............. (-22.14 = -22.74 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:41 2006