Locus 6924

Sequence ID	3L_DroMel_CAF1
Location	18,688,794 – 18,688,980
Length	186
Max. P	0.962828

overview

Window 5

Location	18,688,794 – 18,688,914
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.24
Mean single sequence MFE	-31.82
Consensus MFE	-14.56
Energy contribution	-16.80
Covariance contribution	2.24
Combinations/Pair	1.05
Mean z-score	-2.02
Structure conservation index	0.46
SVM decision value	0.19
SVM RNA-class probability	0.626589
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18688794 120 + 23771897
AUAUAUUGAGCUCUUUAAGAUCUGAAAGAUAAUUACGCAUUCAGAUUCUGGGAACCCCUAUGGAUAAUCUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCGUGUUCUGCUUGCUA
.......((((....((..(((((((.(.........).)))))))..))(((((....((((((..((((..(((((((......)))))))...)))).))))))))))))))).... ( -28.20)
>DroSec_CAF1 18155 119 + 1
AGAUAUUGAGCUCUUUAAGAUCUGGAAGAUAAUUAUGCAUGCAGAUUCUGGGAAC-CCUAUGGACAAUAUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCCAGUUCUGCUUGCUA
........(((......(((.((((((.....(((.(((.((((.(((.((....-))...))).......((((((....)))))))))).))))))....)))))).)))....))). ( -32.50)
>DroSim_CAF1 18151 120 + 1
AGAUAUUGAGCUCUUUAAGAUCUGGAAGAUAAUUACGCAUGCAGAUUCUGGGAACCCCUAUGGACACUAUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCCAAUUCUGCAUGCUA
...........(((((........))))).......(((((((((...((((....))))((((.....((..(((((((......)))))))...)).....))))..))))))))).. ( -32.30)
>DroEre_CAF1 18173 107 + 1
AGAUAGCGAGCACUUCAAGAACGGUAAGCUGAUUGCGCAUGCAGAUUCUG----------UGCACAAUCUCUAAAGCAGUGGC---ACUGCUUGCUAAGGCACUCGAGUGCUGCUUGCUA
...((((((((...........(((((((.(((((.((((.........)----------))).)))))......((....))---...)))))))..(((((....))))))))))))) ( -37.80)
>DroYak_CAF1 18701 107 + 1
AGGUAAUAAGCACUUAAAGAUCUGAAAGAUGAUUUCGCAUGCAGAUUCUU----------UGCAGAAUCUGUUAAGCAUUCGC---ACUGCUUGCUAAGGCACUCGAGCACUGCUUGCUG
........((((......((...((((.....))))((..(((((((((.----------...)))))))))...))..))((---(.(((((((....)))....)))).))).)))). ( -28.30)
>consensus
AGAUAUUGAGCUCUUUAAGAUCUGAAAGAUAAUUACGCAUGCAGAUUCUGGGAAC_CCUAUGGACAAUCUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCGAGUUCUGCUUGCUA
....................................(((.((((...((((((....................(((((((......)))))))(......).))))))..)))).))).. (-14.56 = -16.80 +   2.24)

alignment

secondary structure

dotplot

Window 6

Location	18,688,794 – 18,688,914
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.24
Mean single sequence MFE	-30.88
Consensus MFE	-15.94
Energy contribution	-16.50
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.04
Structure conservation index	0.52
SVM decision value	0.44
SVM RNA-class probability	0.739192
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18688794 120 - 23771897
UAGCAAGCAGAACACGAAUGUCUUAGCAAGCAGUAAAGCGACUGCUUUAAAGAUUAUCCAUAGGGGUUCCCAGAAUCUGAAUGCGUAAUUAUCUUUCAGAUCUUAAAGAGCUCAAUAUAU
..(((..((((....((..(((((...(((((((......)))))))..)))))..))....(((...)))....))))..))).......(((((........)))))........... ( -25.10)
>DroSec_CAF1 18155 119 - 1
UAGCAAGCAGAACUGGAAUGUCUUAGCAAGCAGUAAAGCGACUGCUUUAAAUAUUGUCCAUAGG-GUUCCCAGAAUCUGCAUGCAUAAUUAUCUUCCAGAUCUUAAAGAGCUCAAUAUCU
..(((.(((((..((((..........(((((((......))))))).........))))..((-....))....))))).)))..............((.(((...))).))....... ( -27.21)
>DroSim_CAF1 18151 120 - 1
UAGCAUGCAGAAUUGGAAUGUCUUAGCAAGCAGUAAAGCGACUGCUUUAAAUAGUGUCCAUAGGGGUUCCCAGAAUCUGCAUGCGUAAUUAUCUUCCAGAUCUUAAAGAGCUCAAUAUCU
..(((((((((.(((((((.(((..(((.....((((((....)))))).....)))....))).)))))..)).)))))))))..............((.(((...))).))....... ( -32.60)
>DroEre_CAF1 18173 107 - 1
UAGCAAGCAGCACUCGAGUGCCUUAGCAAGCAGU---GCCACUGCUUUAGAGAUUGUGCA----------CAGAAUCUGCAUGCGCAAUCAGCUUACCGUUCUUGAAGUGCUCGCUAUCU
.....(((((((((((((.((...(((((((((.---....))))))....(((((((((----------(((...)))..))))))))).)))....)).)))).)))))).))).... ( -40.90)
>DroYak_CAF1 18701 107 - 1
CAGCAAGCAGUGCUCGAGUGCCUUAGCAAGCAGU---GCGAAUGCUUAACAGAUUCUGCA----------AAGAAUCUGCAUGCGAAAUCAUCUUUCAGAUCUUUAAGUGCUUAUUACCU
.(((..(((.((((....(((....))))))).)---))....((((((((((((((...----------.)))))))).....((((.....))))......)))))))))........ ( -28.60)
>consensus
UAGCAAGCAGAACUCGAAUGUCUUAGCAAGCAGUAAAGCGACUGCUUUAAAGAUUGUCCAUAGG_GUUCCCAGAAUCUGCAUGCGUAAUUAUCUUCCAGAUCUUAAAGAGCUCAAUAUCU
..(((.(((((........((....))(((((((......)))))))............................))))).))).................................... (-15.94 = -16.50 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	18,688,834 – 18,688,949
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.24
Mean single sequence MFE	-32.12
Consensus MFE	-15.96
Energy contribution	-15.92
Covariance contribution	-0.04
Combinations/Pair	1.12
Mean z-score	-2.68
Structure conservation index	0.50
SVM decision value	1.54
SVM RNA-class probability	0.962828
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18688834 115 + 23771897
UCAGAUUCUGGGAACCCCUAUGGAUAAUCUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCGUGUUCUGCUUGCUACAGCA-----UUUGCUUCGAUUAAGCAGAAUUAUGUACUU
....((((((((....)))).))))...(((..(((((((......)))))))...)))((((....((((((((((.(..(((.-----...)))...).)))))))))).)))).... ( -31.20)
>DroSec_CAF1 18195 118 + 1
GCAGAUUCUGGGAAC-CCUAUGGACAAUAUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCCAGUUCUGCUUGCUACGGCACUUUCUUUGCUUCCAUU-AGCAGAAUUAUGAACUU
(((((..((((((.(-(....))..........(((((((......))))))).........)))))).))))).(((....))).....((((((......-))))))........... ( -33.20)
>DroSim_CAF1 18191 119 + 1
GCAGAUUCUGGGAACCCCUAUGGACACUAUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCCAAUUCUGCAUGCUACGGCACUUUCUUUGCUUCCAUU-AGCAGAAUUAUGAACUU
(((((...((((....))))((((.....((..(((((((......)))))))...)).....))))..))))).(((....))).....((((((......-))))))........... ( -31.70)
>DroEre_CAF1 18213 106 + 1
GCAGAUUCUG----------UGCACAAUCUCUAAAGCAGUGGC---ACUGCUUGCUAAGGCACUCGAGUGCUGCUUGCUACAGCACUAGCUUUGCUUCCAUU-UGCAGAAUUAUGUACUU
((((((((((----------(............((((((....---.))))))((.(((((.....(((((((.......))))))).))))))).......-.)))))))).))).... ( -32.70)
>DroYak_CAF1 18741 106 + 1
GCAGAUUCUU----------UGCAGAAUCUGUUAAGCAUUCGC---ACUGCUUGCUAAGGCACUCGAGCACUGCUUGCUGCAGCACAUGCUUUGCUUUCAUU-UGCAGAAUUAUGUACUU
(((((((((.----------...)))))))))...((((....---.((((..(..((((((...(((((((((.....))))....)))))))))))..).-.))))....)))).... ( -31.80)
>consensus
GCAGAUUCUGGGAAC_CCUAUGGACAAUCUUUAAAGCAGUCGCUUUACUGCUUGCUAAGACAUUCGAGUUCUGCUUGCUACAGCACUUGCUUUGCUUCCAUU_AGCAGAAUUAUGUACUU
...(((((((.......................(((((((......)))))))((..((((......)).))....))...((((.......)))).........)))))))........ (-15.96 = -15.92 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	18,688,874 – 18,688,980
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.86
Mean single sequence MFE	-26.72
Consensus MFE	-11.35
Energy contribution	-13.31
Covariance contribution	1.96
Combinations/Pair	1.15
Mean z-score	-1.92
Structure conservation index	0.42
SVM decision value	0.28
SVM RNA-class probability	0.665766
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18688874 106 + 23771897
CGCUUUACUGCUUGCUAAGACAUUCGUGUUCUGCUUGCUACAGCA-----UUUGCUUCGAUUAAGCAGAAUUAUGUACUUUGUAUGUAUUAGUAGCGUCUUUUGUUUAUCA---------
(((((((.(((.(((.(((((((....((((((((((.(..(((.-----...)))...).)))))))))).)))).))).))).))).))).))))..............--------- ( -28.40)
>DroSec_CAF1 18234 110 + 1
CGCUUUACUGCUUGCUAAGACAUUCCAGUUCUGCUUGCUACGGCACUUUCUUUGCUUCCAUU-AGCAGAAUUAUGAACUUUGAAUGUGUUUGUAGCGUCUUUUGUUUAUCA---------
.........(((.((.((.((((((.(((((....(((....))).....((((((......-)))))).....)))))..)))))).)).)))))...............--------- ( -26.70)
>DroSim_CAF1 18231 110 + 1
CGCUUUACUGCUUGCUAAGACAUUCCAAUUCUGCAUGCUACGGCACUUUCUUUGCUUCCAUU-AGCAGAAUUAUGAACUUUGUAUGUGUUAGUAGCGUCUGUUGUUUAUCA---------
.........(((.(((((.((((..(((.....(((((....))......((((((......-))))))...)))....))).)))).))))))))...............--------- ( -23.80)
>DroEre_CAF1 18243 107 + 1
GGC---ACUGCUUGCUAAGGCACUCGAGUGCUGCUUGCUACAGCACUAGCUUUGCUUCCAUU-UGCAGAAUUAUGUACUUGGUA----UUAGCAGCGUAUUUUGUUUAUCCCUAA-----
.((---.(((((((((((((((....(((((((.......)))))))...(((((.......-.)))))....))).)))))))----..))))).)).................----- ( -31.00)
>DroYak_CAF1 18771 112 + 1
CGC---ACUGCUUGCUAAGGCACUCGAGCACUGCUUGCUGCAGCACAUGCUUUGCUUUCAUU-UGCAGAAUUAUGUACUUUGUA----AAUAAGUUGUAUUUUGUUGAUCCUUGUUGAUC
.((---(.(((((((....)))....)))).)))......(((((.((((...((((..(((-((((((.........))))))----))))))).))))..)))))............. ( -23.70)
>consensus
CGCUUUACUGCUUGCUAAGACAUUCGAGUUCUGCUUGCUACAGCACUUGCUUUGCUUCCAUU_AGCAGAAUUAUGUACUUUGUAUGU_UUAGUAGCGUCUUUUGUUUAUCA_________
((((........(((.(((((((...((((((((.......((((.......))))........)))))))))))).))).))).........))))....................... (-11.35 = -13.31 +   1.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:13 2006