Locus 5862

Sequence ID	2L_DroMel_CAF1
Location	16,589,105 – 16,589,413
Length	308
Max. P	0.993591

overview

Window 7

Location	16,589,105 – 16,589,210
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-21.94
Consensus MFE	-20.38
Energy contribution	-20.76
Covariance contribution	0.38
Combinations/Pair	1.07
Mean z-score	-1.77
Structure conservation index	0.93
SVM decision value	1.99
SVM RNA-class probability	0.984976
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16589105 105 + 22407834
ACGAUUUUUCCUUCUAGCCAAAUUGCUCCAAUUGCUAAUAAGGCUCACUCGAAAGCCACAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUU
..((((((......((((..(((((...)))))))))....((((....(....)....))))))))))...(((....(((((....))))).....))).... ( -22.20)
>DroSec_CAF1 44405 105 + 1
CCGAUUUUUCCUUCUAGCCAAAUUGCUCCAAUUGCUAAUAAGGCUCACUCGAAAGCCACAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUU
..((((((......((((..(((((...)))))))))....((((....(....)....))))))))))...(((....(((((....))))).....))).... ( -22.20)
>DroSim_CAF1 43214 105 + 1
CCGAUUUUUCCUUCUAGCCAAAUUGCUCCAAUUGCUAAUAAGGCUCACUCGAAAGCCACAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUU
..((((((......((((..(((((...)))))))))....((((....(....)....))))))))))...(((....(((((....))))).....))).... ( -22.20)
>DroEre_CAF1 42812 105 + 1
CCGAUUUUUCCUUCUAGCCAAAUUGCUCCGAUUGCUAAUAAGGCUCACUCGAAAGCCACAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUU
..((((((......((((..(((((...)))))))))....((((....(....)....))))))))))...(((....(((((....))))).....))).... ( -21.90)
>DroYak_CAF1 43023 105 + 1
CCGAUUUUUCCUUCUAGCCAAAUUGCUCCAAUUGCUAAUAAGGCUCACUUGAGAGCCGCAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGAGAUCAGACACUU
..((((((..((.(((((..(((((...)))))))))....(((((......)))))).))..))))))...(((..(..((((....))))..)...))).... ( -21.20)
>consensus
CCGAUUUUUCCUUCUAGCCAAAUUGCUCCAAUUGCUAAUAAGGCUCACUCGAAAGCCACAGCCAAAAUCCAAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUU
..((((((......((((..(((((...)))))))))....((((....(....)....))))))))))...(((....(((((....))))).....))).... (-20.38 = -20.76 +   0.38)

alignment

secondary structure

dotplot

Window 8

Location	16,589,175 – 16,589,276
Length	101
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	97.23
Mean single sequence MFE	-24.20
Consensus MFE	-22.60
Energy contribution	-23.00
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.21
Structure conservation index	0.93
SVM decision value	0.26
SVM RNA-class probability	0.655471
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16589175 101 + 22407834
AAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUUUGGAACAAUCGGAAUCCCAGCCCGGAGUUGAAUCAGACGAUUUUCAUUUCGAUUUCCAUUACCAUU
..(((....(((((....))))).....)))....(((((..((((((((((......)))(..(((((....))))).).))))))))))))........ ( -23.00)
>DroSec_CAF1 44475 101 + 1
AAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUUCGGAACAAUCGGAAUCCGAGCCCGGAGUUGAAUCAGACGAUUUUCAUUUCGAUUUCCAUUACCAUU
..(((....(((((....))))).....))).....((((..(((((((((((....))))(..(((((....))))).).)))))))))))......... ( -25.40)
>DroSim_CAF1 43284 101 + 1
AAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUUCGGAACAAUCGGAAUCCGAGCCCGGAGUUGAAUCAGACGAUUUUCAUUUCGAUUUCCAUUACCAUU
..(((....(((((....))))).....))).....((((..(((((((((((....))))(..(((((....))))).).)))))))))))......... ( -25.40)
>DroEre_CAF1 42882 101 + 1
AAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUUCGGAACAAUCGGAAUCCGAGCCCGGAGUUGAAUCAGACGUUAUUCAUUUCGAUUUCCAUUACCAUU
..(((....(((((....))))).....))).....((((..(((((((((((....))))..(((((........))))))))))))))))......... ( -25.10)
>DroYak_CAF1 43093 101 + 1
AAGUCGUUAGCAAUGCCAAUUGAGAUCAGACACUUCGGAACAAUCGGAAUCCGAGCCCGGAGUUGAAUCAGACGAUUUUCAUUUCGAUUUCCAUUAUCAUU
((((((((..((((....)))).(((((...(((((((.....((((...))))..))))))))).))).)))))))).......(((.......)))... ( -22.10)
>consensus
AAGUCGUUAGCAAUGCCAAUUGCGCUCAGACACUUCGGAACAAUCGGAAUCCGAGCCCGGAGUUGAAUCAGACGAUUUUCAUUUCGAUUUCCAUUACCAUU
..(((....(((((....))))).....))).....((((..(((((((((((....))))(((......)))........)))))))))))......... (-22.60 = -23.00 +   0.40)

alignment

secondary structure

dotplot

Window 9

Location	16,589,210 – 16,589,316
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	97.74
Mean single sequence MFE	-28.86
Consensus MFE	-27.84
Energy contribution	-27.88
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.57
Structure conservation index	0.96
SVM decision value	1.64
SVM RNA-class probability	0.969046
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16589210 106 - 22407834
CGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGGUAAUGGAAAUCGAAAUGAAAAUCGUCUGAUUCAACUCCGGGCUGGGAUUCCGAUUGUUCCA
.(((((((((((.(.((..((((..(((((......))))).......((((...(((........))).....))))..))))..)).)..)))).))))))).. ( -26.40)
>DroSec_CAF1 44510 106 - 1
CGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGGUAAUGGAAAUCGAAAUGAAAAUCGUCUGAUUCAACUCCGGGCUCGGAUUCCGAUUGUUCCG
((((((((((((.((((..((((..(((((......))))).......((((...(((........))).....))))..))))..))))..)))).)))).)))) ( -29.70)
>DroSim_CAF1 43319 106 - 1
CGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGGUAAUGGAAAUCGAAAUGAAAAUCGUCUGAUUCAACUCCGGGCUCGGAUUCCGAUUGUUCCG
((((((((((((.((((..((((..(((((......))))).......((((...(((........))).....))))..))))..))))..)))).)))).)))) ( -29.70)
>DroEre_CAF1 42917 106 - 1
CGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGGUAAUGGAAAUCGAAAUGAAUAACGUCUGAUUCAACUCCGGGCUCGGAUUCCGAUUGUUCCG
((((((((((((.((((..((((..(((((......)))))...................(((((........)))))..))))..))))..)))).)))).)))) ( -30.10)
>DroYak_CAF1 43128 106 - 1
CGGACAAUGGAAAUGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGAUAAUGGAAAUCGAAAUGAAAAUCGUCUGAUUCAACUCCGGGCUCGGAUUCCGAUUGUUCCG
((((((((((((.((((..((((..(((((......))))).(((...((((...(((........)))))))..)))..))))..))))..)))).)))).)))) ( -28.40)
>consensus
CGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCUAAUGGUAAUGGAAAUCGAAAUGAAAAUCGUCUGAUUCAACUCCGGGCUCGGAUUCCGAUUGUUCCG
.(((((((((((.((((..((((..(((((......))))).........(((.(((..(((.....))).))))))...))))..))))..)))).))))))).. (-27.84 = -27.88 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	16,589,276 – 16,589,388
Length	112
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	95.21
Mean single sequence MFE	-35.44
Consensus MFE	-32.44
Energy contribution	-32.24
Covariance contribution	-0.20
Combinations/Pair	1.06
Mean z-score	-1.51
Structure conservation index	0.92
SVM decision value	1.40
SVM RNA-class probability	0.950392
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16589276 112 - 22407834
UUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCU
..((-------(..((((.((((.(((((.((((((((....))).(.((((.((((((....)))))))))).)...............))))).))))).)))))))).....))). ( -34.30)
>DroSec_CAF1 44576 112 - 1
UUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCU
..((-------(..((((.((((.(((((.((((((((....))).(.((((.((((((....)))))))))).)...............))))).))))).)))))))).....))). ( -34.30)
>DroSim_CAF1 43385 112 - 1
UUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCU
..((-------(..((((.((((.(((((.((((((((....))).(.((((.((((((....)))))))))).)...............))))).))))).)))))))).....))). ( -34.30)
>DroEre_CAF1 42983 119 - 1
UUGCACAUUGCACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGCUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCU
..(((..((((.((((...((((.(((((((((.((((....))))(.((((.((((((....)))))))))).)....))).))))(....))).))))..)))))))).....))). ( -37.40)
>DroYak_CAF1 43194 119 - 1
UUGCACAUUGCACAUUGCACAUUGCUCUUGCUGUUGCACUUUUGCAUGGGUGUGCUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAAUGGGAAUGGAAAUGGCAGGGAAAUGCU
((((.((((...((((.(.((((.((.((((((.((((....))))(.((((.((((((....)))))))))).)....))).))).)).))))).))))..))))))))......... ( -36.90)
>consensus
UUGC_______ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAUCGGACAAUGGAAACGGGAAUGGAAAUGGCAGGGAAAUGCU
..............((((.((((.(((((.((((((((....))).(.((((.((((((....)))))))))).)...............))))).))))).))))))))......... (-32.44 = -32.24 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	16,589,316 – 16,589,413
Length	97
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	91.02
Mean single sequence MFE	-37.78
Consensus MFE	-28.90
Energy contribution	-28.34
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-3.53
Structure conservation index	0.76
SVM decision value	2.41
SVM RNA-class probability	0.993591
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16589316 97 - 22407834
GCAAAUUGCUGUUGCGAGUU-------GCAGGUUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAU
(((((.(((....((((...-------((((..(((-------.....)))..))))..))))....)))..))))).(.((((.((((((....)))))))))).).... ( -33.90)
>DroSec_CAF1 44616 97 - 1
GCAAAUUGCUGUUGCGAGUU-------GCAGGUUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAU
(((((.(((....((((...-------((((..(((-------.....)))..))))..))))....)))..))))).(.((((.((((((....)))))))))).).... ( -33.90)
>DroSim_CAF1 43425 97 - 1
GCAAAUUGCUGUUGCGAGUU-------GCAGGUUGC-------ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAU
(((((.(((....((((...-------((((..(((-------.....)))..))))..))))....)))..))))).(.((((.((((((....)))))))))).).... ( -33.90)
>DroEre_CAF1 43023 111 - 1
GCAAAUUGCAGUUGCAAGUUGCAAGUUGCAAGUUGCACAUUGCACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGCUGACAUGCGUCAGCCACUGAAAAU
(((((.(((((..((((...((((..(((((..(((.....)))..)))))..))))..))))..)))))..))))).(.((((.((((((....)))))))))).).... ( -46.20)
>DroYak_CAF1 43234 104 - 1
GCAAAUUGCAGUUGCGAGUU-------GCAGGUUGCACAUUGCACAUUGCACAUUGCUCUUGCUGUUGCACUUUUGCAUGGGUGUGCUGACAUGCGUCAGCCACUGAAAAU
(((((.(((((..(((((..-------((((..((((..........))))..)))).)))))..)))))..))))).(.((((.((((((....)))))))))).).... ( -41.00)
>consensus
GCAAAUUGCUGUUGCGAGUU_______GCAGGUUGC_______ACAUUGCACAUUGCUAUUGCUGUUGCACUUUUGCAUGGGUGUGUUGACAUGCGUCAGCCACUGAAAAU
(((((.(((....((((..........((((..(((............)))..))))..))))....)))..))))).(.((((.((((((....)))))))))).).... (-28.90 = -28.34 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:59 2006