Locus 4464

Sequence ID	2L_DroMel_CAF1
Location	12,807,661 – 12,807,816
Length	155
Max. P	0.987408

overview

Window 1

Location	12,807,661 – 12,807,776
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.91
Mean single sequence MFE	-43.34
Consensus MFE	-36.00
Energy contribution	-36.16
Covariance contribution	0.16
Combinations/Pair	1.12
Mean z-score	-1.55
Structure conservation index	0.83
SVM decision value	0.63
SVM RNA-class probability	0.805235
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807661 115 + 22407834
UUUUUUUACUUUCUGGUCUUUUAAGAGCCCAGUUGAGUGGCUCACCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGUUCUUGCCACCG-----CCGCUCAUCGUUAGCCA
.......((((.((((.(((....))).))))..))))((((.((..(((((((((((((((..........)))))))))(.((((....)))).))-----)).)))...)).)))). ( -40.60)
>DroSec_CAF1 73420 115 + 1
UUUUUUUACUUUCUGGUCUUUUAAGAGCCCAGUUGAGUGGCUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCA
............((((.(((....))).)))).((((((((..(((....)))(((((((((..........)))))))))(.((((....)))).))-----))))))).......... ( -43.50)
>DroSim_CAF1 76666 112 + 1
UUUUU---CUUUUUGGUCUUUUAAGAGCCCAGUUGAGUGGCUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCA
.....---.....(((.(((....))).)))(.((((((((..(((....)))(((((((((..........)))))))))(.((((....)))).))-----))))))).)........ ( -41.80)
>DroEre_CAF1 76777 111 + 1
----UUUACUUUCUGGUCCUUUAAGAGCCCGGUUGAGUGGCUCGCCCGGGGGCGCGAUGUUGUCGUGGGGCUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCA
----..........((..(.....)..))((((.(((((((..(((....)))(((((((((((....)))..))))))))(.((((....)))).))-----))))))))))....... ( -44.00)
>DroYak_CAF1 76953 116 + 1
----UUUACUUUCUGGUCUUUUAAGAGCCCAGUUGAGUGGCUUGCCCGGGGGCGCAAAGUUGUCGUAGGGCUUGACAUCGCGAUGGCUCUUCCCACCGCGGCGCCGCUCGUCGUUAGCCA
----...((((.((((.(((....))).))))..))))((((.((.(((((((((.....(((((.......))))).((((.(((......))).))))))))).))))..)).)))). ( -46.80)
>consensus
UUUUUUUACUUUCUGGUCUUUUAAGAGCCCAGUUGAGUGGCUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG_____CCGCUCAUCGUUAGCCA
............((((.(((....))).)))).(((((((......(((.((((.((.((..(((((((......).))))))..)))).)))).))).....))))))).......... (-36.00 = -36.16 +   0.16)

alignment

secondary structure

dotplot

Window 2

Location	12,807,661 – 12,807,776
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.91
Mean single sequence MFE	-41.33
Consensus MFE	-32.28
Energy contribution	-33.00
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.76
Structure conservation index	0.78
SVM decision value	2.08
SVM RNA-class probability	0.987408
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807661 115 - 22407834
UGGCUAACGAUGAGCGG-----CGGUGGCAAGAACCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGUGAGCCACUCAACUGGGCUCUUAAAAGACCAGAAAGUAAAAAAA
(((((..(((((....(-----((((((......)))))))..((((.........)))).)))))((((....))))))))).....((((.((......)).))))............ ( -38.10)
>DroSec_CAF1 73420 115 - 1
UGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAGCCACUCAACUGGGCUCUUAAAAGACCAGAAAGUAAAAAAA
(((((..(((((....(-----(((((((....))))))))..((((.........)))).)))))((((....))))))))).....((((.((......)).))))............ ( -43.60)
>DroSim_CAF1 76666 112 - 1
UGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAGCCACUCAACUGGGCUCUUAAAAGACCAAAAAG---AAAAA
(((((..(((((....(-----(((((((....))))))))..((((.........)))).))))).(((....)))(((((.(......)))))).....)).))).....---..... ( -41.10)
>DroEre_CAF1 76777 111 - 1
UGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAGCCCCACGACAACAUCGCGCCCCCGGGCGAGCCACUCAACCGGGCUCUUAAAGGACCAGAAAGUAAA----
(((((......((((((-----(((((((....))))))(((((((..............)))))))))).((((..(((...)))..)))))))).....)).))).........---- ( -42.34)
>DroYak_CAF1 76953 116 - 1
UGGCUAACGACGAGCGGCGCCGCGGUGGGAAGAGCCAUCGCGAUGUCAAGCCCUACGACAACUUUGCGCCCCCGGGCAAGCCACUCAACUGGGCUCUUAAAAGACCAGAAAGUAAA----
..(((......(((.(((((((((((((......)))))))).((((.........)))).....))(((....)))..))).)))..((((.((......)).))))..)))...---- ( -41.50)
>consensus
UGGCUAACGAUGAGCGG_____CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAGCCACUCAACUGGGCUCUUAAAAGACCAGAAAGUAAAAAAA
(((((..(((((..........(((((((....)))))))...((((.........)))).)))))((((....))))))))).....((((.((......)).))))............ (-32.28 = -33.00 +   0.72)

alignment

secondary structure

dotplot

Window 3

Location	12,807,701 – 12,807,816
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.36
Mean single sequence MFE	-47.44
Consensus MFE	-39.81
Energy contribution	-39.85
Covariance contribution	0.04
Combinations/Pair	1.09
Mean z-score	-1.39
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.659870
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807701 115 + 22407834
CUCACCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGUUCUUGCCACCG-----CCGCUCAUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCUUUCCAC
....(((((((((((((((..((.(((((((..(((((....)))..))..))).)))-----).)).))))))..))).......(((((.........)))))))))))......... ( -45.80)
>DroSec_CAF1 73460 115 + 1
CUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCAUUCCAC
...((((.(((((((((((.(((((.......)))))..(((.((((....)))).))-----)....))))))..)))......((((((.........)))))))).))))....... ( -48.30)
>DroSim_CAF1 76703 115 + 1
CUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCAUUCCAC
...((((.(((((((((((.(((((.......)))))..(((.((((....)))).))-----)....))))))..)))......((((((.........)))))))).))))....... ( -48.30)
>DroEre_CAF1 76813 115 + 1
CUCGCCCGGGGGCGCGAUGUUGUCGUGGGGCUUGACAUCGCGAUGGCUCUUGCCACCG-----CCGCUCAUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCCUUCCAC
...((((.(((((((((((..((.(((((((..(((((....)))..))..))).)))-----).)).))))))..)))......((((((.........)))))))).))))....... ( -48.60)
>DroYak_CAF1 76989 120 + 1
CUUGCCCGGGGGCGCAAAGUUGUCGUAGGGCUUGACAUCGCGAUGGCUCUUCCCACCGCGGCGCCGCUCGUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCUUUCCAC
......(((((((((.....(((((.......))))).((((.(((......))).))))))))).))))..(..((((.((...((((((.........))))))..))))))..)... ( -46.20)
>consensus
CUCGCCCGGGGGCGCGAUGUUGUCGUGGGGUUUGACAUCGCGAUGGCUCUUGCCACCG_____CCGCUCAUCGUUAGCCACCUUAGUGUCCAAUAUGCCAGGACACCCGGGGCAUUCCAC
...((((.((((((((((((((((....)))..))))))))((((((..................)).))))....)))......((((((.........)))))))).))))....... (-39.81 = -39.85 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	12,807,701 – 12,807,816
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.36
Mean single sequence MFE	-48.94
Consensus MFE	-41.86
Energy contribution	-42.14
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.56
Structure conservation index	0.86
SVM decision value	0.92
SVM RNA-class probability	0.881842
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12807701 115 - 22407834
GUGGAAAGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGAUGAGCGG-----CGGUGGCAAGAACCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGUGAG
......((((((.(((((((.........)))))))..)).))))..(((((....(-----((((((......)))))))..((((.........)))).)))))((((....)))).. ( -45.10)
>DroSec_CAF1 73460 115 - 1
GUGGAAUGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAG
......(((((..(((((((.........)))))))..((.(((...(((((....(-----(((((((....))))))))..((((.........)))).))))).))).))))))).. ( -50.20)
>DroSim_CAF1 76703 115 - 1
GUGGAAUGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAG
......(((((..(((((((.........)))))))..((.(((...(((((....(-----(((((((....))))))))..((((.........)))).))))).))).))))))).. ( -50.20)
>DroEre_CAF1 76813 115 - 1
GUGGAAGGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGAUGAGCGG-----CGGUGGCAAGAGCCAUCGCGAUGUCAAGCCCCACGACAACAUCGCGCCCCCGGGCGAG
......((((((.(((((((.........)))))))..)).))))..(((((....(-----(((((((....))))))))..((((.........)))).)))))((((....)))).. ( -50.60)
>DroYak_CAF1 76989 120 - 1
GUGGAAAGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGACGAGCGGCGCCGCGGUGGGAAGAGCCAUCGCGAUGUCAAGCCCUACGACAACUUUGCGCCCCCGGGCAAG
.......((((..(((((((.........)))))))..((.((((.......)))(((((((((((((......)))))))).((((.........)))).....))))))))))))... ( -48.60)
>consensus
GUGGAAAGCCCCGGGUGUCCUGGCAUAUUGGACACUAAGGUGGCUAACGAUGAGCGG_____CGGUGGCAAGAGCCAUCGCGAUGUCAAACCCCACGACAACAUCGCGCCCCCGGGCGAG
.......((((..(((((((.........)))))))..((.(((...................((((((....))))))(((((((..............)))))))))).))))))... (-41.86 = -42.14 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:26 2006