Locus 627

Sequence ID	2L_DroMel_CAF1
Location	1,845,813 – 1,845,968
Length	155
Max. P	0.996698

overview

Window 3

Location	1,845,813 – 1,845,916
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	69.97
Mean single sequence MFE	-21.85
Consensus MFE	-9.16
Energy contribution	-8.88
Covariance contribution	-0.28
Combinations/Pair	1.39
Mean z-score	-1.80
Structure conservation index	0.42
SVM decision value	0.44
SVM RNA-class probability	0.735793
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1845813 103 + 22407834
-----------------UCCAUUUGAACUUUUGAAAAAAGCAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGA
-----------------....................((((........((((........((((((.....))))))...))))..((((((....))))))..........))))... ( -16.80)
>DroSec_CAF1 13960 103 + 1
-----------------UCCAUUUGAAUUUCUUAAAAAAUCAGUUGUAGCAGAUUUAAAAUCCAUUAAUAAUUUGUGGCCCUCUGAAAACCACAAAUGUGGUUAUUAAUUUAAGCUUAGA
-----------------.............((((((...((((..((.(((((((..............))))))).))...)))).((((((....)))))).....))))))...... ( -18.84)
>DroSim_CAF1 14072 103 + 1
-----------------UCCAUUUGAACUUCUUAAAAAAUCAGUUGUAGCUGAUUUAAAAUCCAUUAAUAAUUUGUGGCCUUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGA
-----------------..........((.((((((((((((((....)))))))).....(((((.....(((((((...........)))))))))))).......))))))...)). ( -19.70)
>DroEre_CAF1 14103 120 + 1
GAACUUAAUGUUUCUUUUGAAGUUUAAUUUUUAUAAUAAGCAAUAACGGGAGAUGCAAAAUGUAUAAAUAAUUUGCGGUCCUUUAAUAGCCACAGGAGUGGUUAUUUAAUUAAGUUUAGA
(((((((((((((.((.(((((......))))).)).))))......((((..((((((.(((....))).)))))).))))..(((((((((....)))))))))..)))))))))... ( -28.70)
>DroYak_CAF1 14354 120 + 1
GAGCUUAAUAUUUUGUUUAAAGCUUAAUUUGAUUAAUAAAAAAUAACAGGAGUUGUAAAGCGCUUAAAUUAUUUGUGGUCUUAUGAUAACCGCGAAAGUGGUAAUUAAUUUAAGUUUAGA
..((((....(((((((((((......)))))...)))))).(((((....))))).))))((((((((((......(((....))).(((((....)))))...))))))))))..... ( -25.20)
>consensus
_________________UCCAUUUGAAUUUCUUAAAAAAGCAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGA
.............................................((.(((((((..............))))))).))....(((.((((((....)))))).)))............. ( -9.16 =  -8.88 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	1,845,836 – 1,845,956
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.50
Mean single sequence MFE	-22.98
Consensus MFE	-13.98
Energy contribution	-14.14
Covariance contribution	0.16
Combinations/Pair	1.24
Mean z-score	-1.96
Structure conservation index	0.61
SVM decision value	0.11
SVM RNA-class probability	0.589740
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1845836 120 + 22407834
CAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUU
..(((((((((((........((((((.....))))))...))))..((((((....)))))).........((((((............))))))..)))))))............... ( -22.90)
>DroSec_CAF1 13983 119 + 1
CAGUUGUAGCAGAUUUAAAAUCCAUUAAUAAUUUGUGGCCCUCUGAAAACCACAAAUGUGGUUAUUAAUUUAAGCUUAGAAAA-AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUU
..(((((((((((((......((((.....((((((((...........)))))))))))).....))))).((((((.....-......))))))).)))))))............... ( -21.80)
>DroSim_CAF1 14095 119 + 1
CAGUUGUAGCUGAUUUAAAAUCCAUUAAUAAUUUGUGGCCUUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAA-AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUU
..(((((((.(((.((((...(((((.....(((((((...........))))))))))))...)))).)))((((((.....-......))))))..)))))))............... ( -21.80)
>DroEre_CAF1 14143 119 + 1
CAAUAACGGGAGAUGCAAAAUGUAUAAAUAAUUUGCGGUCCUUUAAUAGCCACAGGAGUGGUUAUUUAAUUAAGUUUAGAAAA-AAAGCACAAGCUGAUUAUAACCUAUUAACCAUUAUU
.(((((.((..((((((((.(((....))).)))))(((.(((.(((((((((....))))))))).....))).........-..(((....))).......))).)))..)).))))) ( -22.90)
>DroYak_CAF1 14394 119 + 1
AAAUAACAGGAGUUGUAAAGCGCUUAAAUUAUUUGUGGUCUUAUGAUAACCGCGAAAGUGGUAAUUAAUUUAAGUUUAGAAAA-AAAGCAUAAGCUGAUUAUAACCUAAUGCCCAUUAUU
........((.(((((((...((((((((((......(((....))).(((((....)))))...))))))))))........-..(((....)))..)))))))))............. ( -25.50)
>consensus
CAGUUGUAGCAGAUUUAAAAUCCAUAAAUAAUUUGUGGCCCUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAA_AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUU
...............................(((((((...........)))))))((((((((........((((((............)))))).............))))))))... (-13.98 = -14.14 +   0.16)

alignment

secondary structure

dotplot

Window 5

Location	1,845,876 – 1,845,968
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	86.98
Mean single sequence MFE	-20.24
Consensus MFE	-15.90
Energy contribution	-15.82
Covariance contribution	-0.08
Combinations/Pair	1.23
Mean z-score	-3.18
Structure conservation index	0.79
SVM decision value	2.73
SVM RNA-class probability	0.996698
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1845876 92 + 22407834
CUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAAAAAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUUUGCGGUUACUAU
.......((((.((((((((((((.(((((..((((((............)))))))))))........)))))))).)))).))))..... ( -19.00)
>DroSec_CAF1 14023 91 + 1
CUCUGAAAACCACAAAUGUGGUUAUUAAUUUAAGCUUAGAAAA-AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUUUGCGGUUACUAU
.......((((.((((((((((((.(((((..((((((.....-......)))))))))))........)))))).)))))).))))..... ( -19.70)
>DroSim_CAF1 14135 91 + 1
UUCUAAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAA-AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUUUGCGGUUACUAC
.......((((.((((((((((((.(((((..((((((.....-......)))))))))))........)))))))).)))).))))..... ( -19.10)
>DroEre_CAF1 14183 91 + 1
CUUUAAUAGCCACAGGAGUGGUUAUUUAAUUAAGUUUAGAAAA-AAAGCACAAGCUGAUUAUAACCUAUUAACCAUUAUUUGCGGUUAUUUA
....(((((((.(((((((((((((((((......)))))...-..(((....))).............)))))))).)))).))))))).. ( -20.40)
>DroYak_CAF1 14434 91 + 1
UUAUGAUAACCGCGAAAGUGGUAAUUAAUUUAAGUUUAGAAAA-AAAGCAUAAGCUGAUUAUAACCUAAUGCCCAUUAUUUGCGGUUAUUUA
....(((((((((((((((((..((((..(((((((((.....-......)))))).....)))..))))..))))).)))))))))))).. ( -23.00)
>consensus
CUCUGAAAACCACAAAAGUGGUUAUUAAUUUAAGCUUAGAAAA_AAAGAAUAAGCUGAUUACAACCUAUUAACCAUUAUUUGCGGUUACUAA
.......((((.((((((((((((........((((((............)))))).............)))))))).)))).))))..... (-15.90 = -15.82 +  -0.08)

alignment

secondary structure

dotplot

Window 6

Location	1,845,876 – 1,845,968
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	86.98
Mean single sequence MFE	-19.60
Consensus MFE	-14.95
Energy contribution	-16.43
Covariance contribution	1.48
Combinations/Pair	1.09
Mean z-score	-2.51
Structure conservation index	0.76
SVM decision value	1.61
SVM RNA-class probability	0.967363
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1845876 92 - 22407834
AUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUUUUUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUCAGAG
...(.(((((((((...((((((((((((((....)))))))).(((........)))..........))))))..)))))))))..).... ( -21.70)
>DroSec_CAF1 14023 91 - 1
AUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUU-UUUUCUAAGCUUAAAUUAAUAACCACAUUUGUGGUUUUCAGAG
...(.((((((((((..((((((((((((((....)))))))).(((.-......)))..........)))))).))))))))))..).... ( -21.70)
>DroSim_CAF1 14135 91 - 1
GUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUU-UUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUUAGAA
.(((.(((((((((...((((((((((((((....)))))))).(((.-......)))..........))))))..))))))))).)))... ( -22.20)
>DroEre_CAF1 14183 91 - 1
UAAAUAACCGCAAAUAAUGGUUAAUAGGUUAUAAUCAGCUUGUGCUUU-UUUUCUAAACUUAAUUAAAUAACCACUCCUGUGGCUAUUAAAG
..((((.(((((.....((((((.((((((..((..(((....)))..-)).....))))))......))))))....))))).)))).... ( -15.20)
>DroYak_CAF1 14434 91 - 1
UAAAUAACCGCAAAUAAUGGGCAUUAGGUUAUAAUCAGCUUAUGCUUU-UUUUCUAAACUUAAAUUAAUUACCACUUUCGCGGUUAUCAUAA
...((((((((.((...(((((((.(((((......)))))))))(((-......))).............)))..)).))))))))..... ( -17.20)
>consensus
AUAGUAACCGCAAAUAAUGGUUAAUAGGUUGUAAUCAGCUUAUUCUUU_UUUUCUAAGCUUAAAUUAAUAACCACUUUUGUGGUUUUCAGAG
.....(((((((((...((((((((((((((....)))))))).........................))))))..)))))))))....... (-14.95 = -16.43 +   1.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:21 2006