Locus 2475

Sequence ID	3L_DroMel_CAF1
Location	6,975,641 – 6,975,761
Length	120
Max. P	0.894184

overview

Window 2

Location	6,975,641 – 6,975,761
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.17
Mean single sequence MFE	-35.58
Consensus MFE	-31.70
Energy contribution	-32.10
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.19
Structure conservation index	0.89
SVM decision value	0.08
SVM RNA-class probability	0.574925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975641 120 + 23771897
GUGACUCAGGCAUAAAAGUGAGUGAACAAUCGCCGAUGUGAUAACUGGAGGAACUUACGUCUCAAUUAGGUCACUUGUGAAUGGUAGUGCGCGAUUUUCGUUCGAUUCGCGCACUUGCAA
(((((((((.((((...((((........))))...))))....)))((((........)))).....)))))).........(((((((((((...((....)).)))))))).))).. ( -35.90)
>DroSec_CAF1 45537 120 + 1
GUGACUCAGGCAUACAAGUGAGUGAACAAUCGCCGCUGUGAUAACUGGAGGAACUUACGUCUCAAUUAGGUCACUUGUGAAUGGUAGUGCGCGAUUUUCGUUCGAUUCGCGCACUUGCGA
(((((((((..((...((((.((((....))))))))...))..)))((((........)))).....)))))).........(((((((((((...((....)).)))))))).))).. ( -39.70)
>DroSim_CAF1 45329 120 + 1
GUGACUCAGGCAUAAAAGUGAGUGAACAAUCGCCGCUGUGAUAACUGGAGGAACUUACGUCUCAAUUAGGUCACUUGUGAAUGGUAGUUCGCGAUUUUCCAUCGAUUCGCGCACUUGCAA
(((((((((..((...((((.((((....))))))))...))..)))((((........)))).....)))))).........(((((.(((((...((....)).))))).)).))).. ( -32.00)
>DroEre_CAF1 45441 120 + 1
GUGACUCAGGCAUAAAAGUGAGUGAAAAAUCGCGGCUGUGAUAACUGGAAGAACUUACGGCUCAAUUAGGUCACUUGUGAAUGGUAGUGCGCGAUUUUUGUUCGAUUCGCGCACUUGCGA
......((..((((..(((((((((....))))((((((((.............))))))))........)))))))))..))(((((((((((.((......)).)))))))).))).. ( -35.82)
>DroYak_CAF1 46815 120 + 1
GUGACUCAGGCAUAAAAGUGAGUGAACAAUCGCUGCAGUGAUAACUGGAAGAACUUACGUCUCAAUUAGGUCACUUGUGAAUGGUAGUGCGCGAUUUUAGUUCGAUUCGCGCACUUGCAA
(((((..((........((((((...(((((((....)))))...)).....)))))).......))..))))).........(((((((((((.((......)).)))))))).))).. ( -34.46)
>consensus
GUGACUCAGGCAUAAAAGUGAGUGAACAAUCGCCGCUGUGAUAACUGGAGGAACUUACGUCUCAAUUAGGUCACUUGUGAAUGGUAGUGCGCGAUUUUCGUUCGAUUCGCGCACUUGCAA
(((((..((........((((((...(((((((....)))))...)).....)))))).......))..))))).........(((((((((((.((......)).)))))))).))).. (-31.70 = -32.10 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	6,975,641 – 6,975,761
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.17
Mean single sequence MFE	-29.84
Consensus MFE	-28.28
Energy contribution	-28.44
Covariance contribution	0.16
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.95
SVM decision value	0.98
SVM RNA-class probability	0.894184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975641 120 - 23771897
UUGCAAGUGCGCGAAUCGAACGAAAAUCGCGCACUACCAUUCACAAGUGACCUAAUUGAGACGUAAGUUCCUCCAGUUAUCACAUCGGCGAUUGUUCACUCACUUUUAUGCCUGAGUCAC
((((.(((((((((.((....))...)))))))))...........((((..((((((((((....))..)).))))))))))....))))......(((((..........)))))... ( -30.60)
>DroSec_CAF1 45537 120 - 1
UCGCAAGUGCGCGAAUCGAACGAAAAUCGCGCACUACCAUUCACAAGUGACCUAAUUGAGACGUAAGUUCCUCCAGUUAUCACAGCGGCGAUUGUUCACUCACUUGUAUGCCUGAGUCAC
..((((((((((((.((....))...))))))))).......((((((((.......(..((....))..)..(((((..(.....)..))))).....)))))))).)))......... ( -34.00)
>DroSim_CAF1 45329 120 - 1
UUGCAAGUGCGCGAAUCGAUGGAAAAUCGCGAACUACCAUUCACAAGUGACCUAAUUGAGACGUAAGUUCCUCCAGUUAUCACAGCGGCGAUUGUUCACUCACUUUUAUGCCUGAGUCAC
.....((.(((..((..((((((.(((((((((......)))....((((..((((((((((....))..)).))))))))))....)))))).)))).))...))..)))))....... ( -25.30)
>DroEre_CAF1 45441 120 - 1
UCGCAAGUGCGCGAAUCGAACAAAAAUCGCGCACUACCAUUCACAAGUGACCUAAUUGAGCCGUAAGUUCUUCCAGUUAUCACAGCCGCGAUUUUUCACUCACUUUUAUGCCUGAGUCAC
((((.(((((((((............)))))))))...........((((..((((((((.(....)..))..))))))))))....))))......(((((..........)))))... ( -28.90)
>DroYak_CAF1 46815 120 - 1
UUGCAAGUGCGCGAAUCGAACUAAAAUCGCGCACUACCAUUCACAAGUGACCUAAUUGAGACGUAAGUUCUUCCAGUUAUCACUGCAGCGAUUGUUCACUCACUUUUAUGCCUGAGUCAC
((((.(((((((((............)))))))))..........(((((..((((((((((....).)))..)))))))))))...))))......(((((..........)))))... ( -30.40)
>consensus
UUGCAAGUGCGCGAAUCGAACGAAAAUCGCGCACUACCAUUCACAAGUGACCUAAUUGAGACGUAAGUUCCUCCAGUUAUCACAGCGGCGAUUGUUCACUCACUUUUAUGCCUGAGUCAC
((((.(((((((((............)))))))))...........((((..((((((.(((....)))....))))))))))....))))......(((((..........)))))... (-28.28 = -28.44 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:18 2006