Locus 5740

Sequence ID	3L_DroMel_CAF1
Location	15,611,739 – 15,611,899
Length	160
Max. P	0.999770

overview

Window 0

Location	15,611,739 – 15,611,859
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.17
Mean single sequence MFE	-35.92
Consensus MFE	-28.70
Energy contribution	-31.10
Covariance contribution	2.40
Combinations/Pair	1.00
Mean z-score	-3.24
Structure conservation index	0.80
SVM decision value	2.67
SVM RNA-class probability	0.996270
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611739 120 + 23771897
CCCGACUGGCAUAUUUGUGUGUGAAUGUUUGCGUAGAAGCAUUCAUUUCUGUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
.(((..(((((.(((((.(((((....((((.((.(((((.(((((....))))).)))))......(((((.....)))))......))))))...)))))))))).)))))....))) ( -37.00)
>DroSec_CAF1 34812 120 + 1
CCCGACUGGCAUAUUUGUGUGUGAAUGUUUGUGUAGAAGCAUUCAUUUCUGUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
.(((..(((((.(((((.(((((....((((.((.(((((.(((((....))))).)))))......(((((.....)))))......))))))...)))))))))).)))))....))) ( -37.00)
>DroSim_CAF1 34851 120 + 1
CCCGACUGGCAUAUUUGCGUGUGAAUGUUUGUGUAGAAGCAUUCAUUUCUGUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
.(((..(((((.(((((((((((....((((.((.(((((.(((((....))))).)))))......(((((.....)))))......)))))).)))))).))))).)))))....))) ( -38.50)
>DroEre_CAF1 34906 120 + 1
CCCGUCUGGCAUAUUUGUGUGUGCAUGUUUGUGUAGAAGCAUUCAUUUCUCUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
.((((.(((((.(((((.((((((...((((.((.(((((.((((......)))).)))))......(((((.....)))))......))))))..))))))))))).)))))...)))) ( -39.80)
>DroYak_CAF1 37268 106 + 1
CCAGUCUGGCAUAUUU--------------GUGUAGAAGCAUUCAUUUCUCUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
......(((((.((((--------------(.((((((((.((((......)))).)))))(((...(((((..((((....))))..))))))))...)))))))).)))))....... ( -27.30)
>consensus
CCCGACUGGCAUAUUUGUGUGUGAAUGUUUGUGUAGAAGCAUUCAUUUCUGUGAACGUUUCGUUAACUUGGCCAAAAGCCAAUUUUCAGCCAAAACGCAUGCCAAAUUUGCCAAAAACGG
.(((..(((((.(((((.(((((....((((.((.(((((.(((((....))))).)))))......(((((.....)))))......))))))...)))))))))).)))))....))) (-28.70 = -31.10 +   2.40)

alignment

secondary structure

dotplot

Window 1

Location	15,611,739 – 15,611,859
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.17
Mean single sequence MFE	-36.88
Consensus MFE	-31.96
Energy contribution	-32.36
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-3.11
Structure conservation index	0.87
SVM decision value	4.04
SVM RNA-class probability	0.999770
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611739 120 - 23771897
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAUGCUUCUACGCAAACAUUCACACACAAAUAUGCCAGUCGGG
(((...((((((.(((((....((((((((..(((...(((((.....))))).))).)))))))).....(((.((..(((......)))..))))).....))))).)))))).))). ( -37.30)
>DroSec_CAF1 34812 120 - 1
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAUGCUUCUACACAAACAUUCACACACAAAUAUGCCAGUCGGG
(((...((((((.(((((....((((((((..(((...(((((.....))))).))).)))))))).........((((((.((......)).))))))....))))).)))))).))). ( -36.70)
>DroSim_CAF1 34851 120 - 1
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAUGCUUCUACACAAACAUUCACACGCAAAUAUGCCAGUCGGG
(((...((((((.(((((.(..((((((((..(((...(((((.....))))).))).)))))))).........((((((.((......)).))))))...)))))).)))))).))). ( -36.50)
>DroEre_CAF1 34906 120 - 1
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCAGAGAAAUGAAUGCUUCUACACAAACAUGCACACACAAAUAUGCCAGACGGG
(((((..(((((.((((((..(((((((((((..(((......)))..)))))).....(((.((((((......)))))).))).........)))))..).))))).)))))))))). ( -41.00)
>DroYak_CAF1 37268 106 - 1
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCAGAGAAAUGAAUGCUUCUACAC--------------AAAUAUGCCAGACUGG
(((..(((((((.(((((........((((((..(((......)))..)))))).....(((.((((((......)))))).)))....)--------------)))).))))))).))) ( -32.90)
>consensus
CCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAUGCUUCUACACAAACAUUCACACACAAAUAUGCCAGUCGGG
(((...((((((.(((((........((((((..(((......)))..)))))).....(((.((((((......)))))).)))..................))))).)))))).))). (-31.96 = -32.36 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	15,611,779 – 15,611,899
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.50
Mean single sequence MFE	-27.40
Consensus MFE	-26.00
Energy contribution	-25.84
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.26
Structure conservation index	0.95
SVM decision value	0.24
SVM RNA-class probability	0.650959
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611779 120 - 23771897
AUCAUAAAAUAUUUAGCUAUUUCUCUUAUUUCGCUUCGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAU
.........................((((((((((.....(((....))).......)))..((((((((..(((...(((((.....))))).))).)))))))).....))))))).. ( -25.60)
>DroSec_CAF1 34852 120 - 1
AUCAUAAAAUAUUUAGCUAUUUCUCUUAUUUCGCUACGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAU
.........................(((((((((((....(((....)))......))))..((((((((..(((...(((((.....))))).))).)))))))).....))))))).. ( -26.10)
>DroSim_CAF1 34891 120 - 1
AUCAUAAAAUAUUUAGCUAUGUCUCUUAUUUCGCUUCGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAU
.........................((((((((((.....(((....))).......)))..((((((((..(((...(((((.....))))).))).)))))))).....))))))).. ( -25.60)
>DroEre_CAF1 34946 120 - 1
AUCAUAAAAUAUUUAGCUAUUUCUCUUAUUUCGCCUCGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCAGAGAAAUGAAU
.................(((((((((......(((.....(((....))).......)))..((((((((..(((...(((((.....))))).))).))))))))..)))))))))... ( -30.80)
>DroYak_CAF1 37294 120 - 1
AUCAUAAAAUAUUUAGCUAUUUCUCUUAUUUCGCUUCGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCAGAGAAAUGAAU
.................(((((((((......(((.....(((....))).......)))..((((((((..(((...(((((.....))))).))).))))))))..)))))))))... ( -28.90)
>consensus
AUCAUAAAAUAUUUAGCUAUUUCUCUUAUUUCGCUUCGCUCCGUUUUUGGCAAAUUUGGCAUGCGUUUUGGCUGAAAAUUGGCUUUUGGCCAAGUUAACGAAACGUUCACAGAAAUGAAU
.........................((((((((((.....(((....))).......)))..((((((((..(((...(((((.....))))).))).)))))))).....))))))).. (-26.00 = -25.84 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:25 2006