Locus 6208

Sequence ID	X_DroMel_CAF1
Location	15,808,366 – 15,808,555
Length	189
Max. P	0.807275

overview

Window 1

Location	15,808,366 – 15,808,486
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.58
Mean single sequence MFE	-34.07
Consensus MFE	-28.98
Energy contribution	-29.82
Covariance contribution	0.84
Combinations/Pair	1.06
Mean z-score	-1.34
Structure conservation index	0.85
SVM decision value	0.32
SVM RNA-class probability	0.686870
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15808366 120 + 22224390
CUAUUCGUAUCCCUACAAAGCACUUAGCUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUAUUGGCCAC
..(((((.........(((((.....))))).(((((((((((.....))....)))))))))...............)))))......(((((..(((((.....)))))..))))).. ( -34.60)
>DroSec_CAF1 10274 120 + 1
CUAUUCGUAUCCCUACAAGGCACUCAGCUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCAC
..(((((........((((((.....))....(((((((((((.....))....)))))))))..)))).........)))))......(((((..(((((.....)))))..))))).. ( -36.83)
>DroSim_CAF1 10156 120 + 1
CUAUUCGUAUCCCUACAAGGCACUCAGCUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAUGCCAUGGAGGAGCCAAUCCUUUUUGGCCAC
...........(((.((.((((....(((...(((((((((((.....))....))))))))).....))).......(((....))).)))).)).))).(((((......)))))... ( -33.20)
>DroEre_CAF1 8740 120 + 1
CUACUCGUAUCCCUACAAGGCGCUCAGUUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGCUCCUGGCCAGUAAGCGAAUCAUCGAGGCCAUGGAAGAGGCAAUCCUUUUUGGCCAC
....(((....((.....))(((((((((((.(((..(.....)..)))..)))))))).((((.....))))....)))......)))(((((...((((((....))))))))))).. ( -34.40)
>DroYak_CAF1 9594 120 + 1
CUAUUCAUAUCCCUACAAAGCACUCCGAUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCACUAUCGGAAUCAUCGAGGCCAUGGAAGAGUGACUCCUUUUUGGCCAC
.........(((.......(((((..((........)))))))...((((..(((((....)))).)..)))).....)))........(((((..((.(((...))).))..))))).. ( -31.30)
>consensus
CUAUUCGUAUCCCUACAAGGCACUCAGCUUUCCCAUUCAGUGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCAC
..(((((.........(((((.....))))).(((((((((((.....))....)))))))))...............)))))......(((((..(((((.....)))))..))))).. (-28.98 = -29.82 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	15,808,366 – 15,808,486
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.58
Mean single sequence MFE	-37.08
Consensus MFE	-30.32
Energy contribution	-31.04
Covariance contribution	0.72
Combinations/Pair	1.11
Mean z-score	-1.30
Structure conservation index	0.82
SVM decision value	-0.08
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15808366 120 - 22224390
GUGGCCAAUAAGGAUUGGCUCCUCCAUGGCCUCGAUGAUUCGGUUAAUGGCCAAGAACCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAGCUAAGUGCUUUGUAGGGAUACGAAUAG
(((.((.((((((.((((((..(((.(((((((((....)))).....))))).....((((((((....((.....))))))))))))).))))))...)))))).))..)))...... ( -38.50)
>DroSec_CAF1 10274 120 - 1
GUGGCCAAAAAGGAUUGGCUCCUCCAUGGCCUCGAUGAUUCGGUUAAUGGCCAAGAACCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAGCUGAGUGCCUUGUAGGGAUACGAAUAG
(((.((...((((.(..(((..(((.(((((((((....)))).....))))).....((((((((....((.....))))))))))))).)))..)...))))....)).)))...... ( -38.70)
>DroSim_CAF1 10156 120 - 1
GUGGCCAAAAAGGAUUGGCUCCUCCAUGGCAUCGAUGAUUCGGUUAAUGGCCAAGAACCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAGCUGAGUGCCUUGUAGGGAUACGAAUAG
(((.((...((((.(..(((..(((.(((((((((....))))).....)))).....((((((((....((.....))))))))))))).)))..)...))))....)).)))...... ( -36.80)
>DroEre_CAF1 8740 120 - 1
GUGGCCAAAAAGGAUUGCCUCUUCCAUGGCCUCGAUGAUUCGCUUACUGGCCAGGAGCCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAACUGAGCGCCUUGUAGGGAUACGAGUAG
(((.((...((((...((.((((((.(((((.(((....)))......)))))))))(((((((((....((.....))))))))))).......)))).))))....)).)))...... ( -36.70)
>DroYak_CAF1 9594 120 - 1
GUGGCCAAAAAGGAGUCACUCUUCCAUGGCCUCGAUGAUUCCGAUAGUGGCCAAGAACCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAUCGGAGUGCUUUGUAGGGAUAUGAAUAG
(((.((.....((((.((((((....((((((((.......)))....)))))....(((((((((....((.....)))))))))))......))))))))))....)).)))...... ( -34.70)
>consensus
GUGGCCAAAAAGGAUUGGCUCCUCCAUGGCCUCGAUGAUUCGGUUAAUGGCCAAGAACCAUUCAGUUUCAGCCAAACGCACUGAAUGGGAAAGCUGAGUGCCUUGUAGGGAUACGAAUAG
(((.((...((((.((((((......(((((((((....)))).....)))))....(((((((((....((.....)))))))))))...))))))...))))....)).)))...... (-30.32 = -31.04 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	15,808,406 – 15,808,526
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.50
Mean single sequence MFE	-42.28
Consensus MFE	-38.40
Energy contribution	-38.92
Covariance contribution	0.52
Combinations/Pair	1.08
Mean z-score	-1.28
Structure conservation index	0.91
SVM decision value	0.57
SVM RNA-class probability	0.784383
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15808406 120 + 22224390
UGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUAUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCUGUG
((((..((((........((((((.....)))))).((((.........(((((..(((((.....)))))..)))))..(((((((.....)))))))))))..)))).))))...... ( -43.80)
>DroSec_CAF1 10314 120 + 1
UGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCCGUG
((((..((((........((((((.....)))))).((((.........(((((..(((((.....)))))..)))))..(((((((.....)))))))))))..)))).))))...... ( -45.50)
>DroSim_CAF1 10196 120 + 1
UGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAUGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAACGUGUGGGCGUGGUACGUCAUUGCAUCCGUG
.(((..((((..(((((....)))).)..))))..............(((((((..(((((.....)))))..))(((((.((((((.....)))))))))))........)))))))). ( -43.00)
>DroEre_CAF1 8780 120 + 1
UGCGUUUGGCUGAAACUGAAUGGCUCCUGGCCAGUAAGCGAAUCAUCGAGGCCAUGGAAGAGGCAAUCCUUUUUGGCCACCGCCUACAUAGUGUGGGCGUGGUACGUUGUUGCAUCCGUG
((((..((((..(((..((.((.(((((((((......(((....))).))))).)))...).)).))..)))..))))((((((((.....))))))).).........))))...... ( -40.30)
>DroYak_CAF1 9634 120 + 1
UGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCACUAUCGGAAUCAUCGAGGCCAUGGAAGAGUGACUCCUUUUUGGCCACCGCCUACGUAAUGUGGGCGUGGUACGUCAUUGCAUCCGUU
......((((..(((((....)))).)..))))....((((..((..(((((((..((.(((...))).))..))))).((((((((.....))))))).).....))..))..)))).. ( -38.80)
>consensus
UGCGUUUGGCUGAAACUGAAUGGUUCUUGGCCAUUAACCGAAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCCGUG
((((..((((........((((((.....))))))....(.((((....(((((..(((((.....)))))..)))))..(((((((.....))))))))))).))))).))))...... (-38.40 = -38.92 +   0.52)

alignment

secondary structure

dotplot

Window 4

Location	15,808,446 – 15,808,555
Length	109
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	91.01
Mean single sequence MFE	-37.16
Consensus MFE	-29.68
Energy contribution	-30.20
Covariance contribution	0.52
Combinations/Pair	1.14
Mean z-score	-1.69
Structure conservation index	0.80
SVM decision value	0.64
SVM RNA-class probability	0.807275
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15808446 109 + 22224390
AAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUAUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCUGUGGGCAUAACAAUCAGCUAUCAGACGGCCUU
.......((((((((((((((.....)))))....(((((.((((((.....))))))))))).))).......((((..(((..........)))..)))).)))))) ( -38.70)
>DroSec_CAF1 10354 109 + 1
AAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCCGUGGCCAUAACAAUCAGCUAUCAGACGGCCUU
.......((((((..((((((.....)))))).(((((((.((((((.....))))))(..((.....))..)....)))))))...................)))))) ( -40.90)
>DroSim_CAF1 10236 109 + 1
AAUCAUCGAUGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAACGUGUGGGCGUGGUACGUCAUUGCAUCCGUGGGCAUAACAAUCAGCUAUCAGACGGCCUU
...(((.(((((((..(((((.....)))))..))(((((.((((((.....)))))))))))........))))).)))(((.....................))).. ( -36.10)
>DroEre_CAF1 8820 109 + 1
AAUCAUCGAGGCCAUGGAAGAGGCAAUCCUUUUUGGCCACCGCCUACAUAGUGUGGGCGUGGUACGUUGUUGCAUCCGUGGGCAUAACAAUCAGUUUCCAGACCACUUU
.........(.(((((((....(((((........(((((.((((((.....))))))))))).....))))).))))))).).......................... ( -35.12)
>DroYak_CAF1 9674 109 + 1
AAUCAUCGAGGCCAUGGAAGAGUGACUCCUUUUUGGCCACCGCCUACGUAAUGUGGGCGUGGUACGUCAUUGCAUCCGUUGGCAUAACAAUCAGUUACCAGACGGCAUU
..........((((((((.(((((((..(.....)(((((.((((((.....)))))))))))..)))))).).)))))(((..((((.....)))))))...)))... ( -35.00)
>consensus
AAUCAUCGAGGCCAUGGAGGAGCCAAUCCUUUUUGGCCACCGCCUACAUCGUGUGGGCGUGGUACGUCAUUGCAUCCGUGGGCAUAACAAUCAGCUAUCAGACGGCCUU
.........(((((..(((((.....)))))..)))))..(((((((.....))))))).(((.((((...((.....((.......))....)).....))))))).. (-29.68 = -30.20 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:16 2006