Locus 5668

Sequence ID	3L_DroMel_CAF1
Location	15,556,509 – 15,556,655
Length	146
Max. P	0.999341

overview

Window 0

Location	15,556,509 – 15,556,615
Length	106
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-28.66
Consensus MFE	-25.34
Energy contribution	-25.70
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.71
Structure conservation index	0.88
SVM decision value	3.52
SVM RNA-class probability	0.999341
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15556509 106 + 23771897
-----UUGUUCCACGGCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUU
-----(((((....(((((..(((.((((....)))).)))................(((((.(((((((....))))))).)))))..))))).)))))........... ( -27.40)
>DroSec_CAF1 19182 106 + 1
-----UUGUUCCUCGGCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUU
-----..((((((.(((((..(((.((((....)))).)))................(((((.(((((((....))))))).)))))..)))))))).))).......... ( -29.70)
>DroSim_CAF1 19669 106 + 1
-----UUGUUCCUCGGCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUU
-----..((((((.(((((..(((.((((....)))).)))................(((((.(((((((....))))))).)))))..)))))))).))).......... ( -29.70)
>DroEre_CAF1 19286 106 + 1
-----UUGUUUCUCGCCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUAUGCCAGGCAAUUUGCAUAAUU
-----.(((.....(((....(((.((((....)))).)))................(((((.(((((((....))))))).)))))........))).....)))..... ( -24.10)
>DroYak_CAF1 39450 111 + 1
GUUUGUUGUUUCUCGGCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUU
((..(((((((...(((((..(((.((((....)))).)))................(((((.(((((((....))))))).)))))..))))))))))))..))...... ( -32.40)
>consensus
_____UUGUUCCUCGGCACUUGUUGACACAUUUGUGUGGAUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUU
..........(((.(((((..(((.((((....)))).)))................(((((.(((((((....))))))).)))))..)))))))).............. (-25.34 = -25.70 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	15,556,509 – 15,556,615
Length	106
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-27.84
Consensus MFE	-24.18
Energy contribution	-24.02
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.71
Structure conservation index	0.87
SVM decision value	3.21
SVM RNA-class probability	0.998737
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15556509 106 - 23771897
AAUUAUGUAAAUUGCCUGGCACAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGCCGUGGAACAA-----
..............((((((((.....((.(((((((....))))))).))....(((..(((.(((......)))...)))...)))....)))))).)).....----- ( -28.20)
>DroSec_CAF1 19182 106 - 1
AAUUAUGUAAAUUGCCUGGCACAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGCCGAGGAACAA-----
..............((((((((.....((.(((((((....))))))).))....(((..(((.(((......)))...)))...)))....))))).))).....----- ( -28.90)
>DroSim_CAF1 19669 106 - 1
AAUUAUGUAAAUUGCCUGGCACAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGCCGAGGAACAA-----
..............((((((((.....((.(((((((....))))))).))....(((..(((.(((......)))...)))...)))....))))).))).....----- ( -28.90)
>DroEre_CAF1 19286 106 - 1
AAUUAUGCAAAUUGCCUGGCAUAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGGCGAGAAACAA-----
.....(((...(((..((((((((...((.(((((((....))))))).))..........((((((......))).))))))))))).)))...)))........----- ( -26.80)
>DroYak_CAF1 39450 111 - 1
AAUUAUGUAAAUUGCCUGGCACAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGCCGAGAAACAACAAAC
.....(((......(.((((((.....((.(((((((....))))))).))....(((..(((.(((......)))...)))...)))....)))))).).....)))... ( -26.40)
>consensus
AAUUAUGUAAAUUGCCUGGCACAUCUAAGGGUUAAGCGAACGCUUAACGCUCAAGUGAAAAUUGGUGAAAAUCCACACAAAUGUGUCAACAAGUGCCGAGGAACAA_____
...........(((..((((((((...((.(((((((....))))))).))..........((((((......))).))))))))))).)))................... (-24.18 = -24.02 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	15,556,543 – 15,556,655
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	93.46
Mean single sequence MFE	-27.48
Consensus MFE	-22.82
Energy contribution	-22.82
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.83
SVM decision value	0.41
SVM RNA-class probability	0.724438
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15556543 112 + 23771897
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAGUGGAUGUGUUUGGU
......(((((..((((((((((.(((((((....))))))).))))..((((((..((((..........))))..)))).))............)))))).....))))) ( -29.00)
>DroSec_CAF1 19216 103 + 1
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAUCGGAU---------
.......((..........((((.(((((((....))))))).))))((((((((..((((..........))))..)))....(......)..)))))))..--------- ( -24.20)
>DroSim_CAF1 19703 103 + 1
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAUCGGAU---------
.......((..........((((.(((((((....))))))).))))((((((((..((((..........))))..)))....(......)..)))))))..--------- ( -24.20)
>DroEre_CAF1 19320 110 + 1
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUAUGCCAGGCAAUUUGCAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAGUGGAUG--UUUGGU
......(((((..((((((((((.(((((((....))))))).)))))...(((...((.....))....(((.(((....))).)))......))))))))..--.))))) ( -30.70)
>DroYak_CAF1 39489 110 + 1
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAGUGGAUG--UUUGGC
.......((((..((((((((((.(((((((....))))))).))))..((((((..((((..........))))..)))).))............))))))..--.)))). ( -29.30)
>consensus
AUUUUCACCAAUUUUCACUUGAGCGUUAAGCGUUCGCUUAACCCUUAGAUGUGCCAGGCAAUUUACAUAAUUUGUGCGGCAGCAGAAAAAACAAGCAGUGGAUG__UUUGG_
...........(((((..(((((.(((((((....))))))).)))))...((((..((((..........))))..))))...)))))....................... (-22.82 = -22.82 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:07 2006