Locus 6738

Sequence ID	3L_DroMel_CAF1
Location	18,053,454 – 18,053,602
Length	148
Max. P	0.997672

overview

Window 6

Location	18,053,454 – 18,053,564
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.50
Mean single sequence MFE	-34.13
Consensus MFE	-13.72
Energy contribution	-15.64
Covariance contribution	1.92
Combinations/Pair	1.33
Mean z-score	-2.59
Structure conservation index	0.40
SVM decision value	2.91
SVM RNA-class probability	0.997672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18053454 110 + 23771897
-------UUGCGUGAAGAUGUUAACUGCUUUAUUCGCACGAAGCUCAUGU---GCAUACUGCUUGUUGCACGAAAAACGCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUUAGUA
-------.(((.......(((((((((........(((((.......)))---))..((((((((.(((.........)))...)))))))).......)))))..)))).......))) ( -23.54)
>DroSec_CAF1 168120 117 + 1
CAACUGCUUGCAUGAAGUCGUUUACUGCUUUGUUGGUGCGAAGUUUUCGU---GUGGACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUGAAAA
..(((((((((((((.((........(((((((....)))))))((((((---(..(.(.....))..))))))).))))))).))))))))(((..(((.((....)))))..)))... ( -37.50)
>DroSim_CAF1 179965 117 + 1
GAACUGUUUGCAUGAAGUCGUUUACUGCUUUGUAGUCACGAAGUUUUCGU---GCAUACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUGAAAA
(((((((((((((((..((((..(((((...))))).))))..(((((((---(((.((.....))))))))))))..))))).))))))))))...(((.((....)))))........ ( -41.90)
>DroEre_CAF1 168204 109 + 1
GUACUGCUUGUGCGAAACAGUUUACUGCUUUGUUGGCACGAAGC-----------ACACUGCUUGUAGGACAAGAAACUCAUGUAAAGCAGUACAAAACCAGUUCAAACGGAAACUAAAC
(((((((((.((((...((((....((((((((....)))))))-----------).))))((((.....)))).......)))))))))))))...............(....)..... ( -30.50)
>DroYak_CAF1 175942 110 + 1
UAACUGCUUGUGUGGUACAGUUUACUGCUUCGCUGGCACGAAGCUCUUGUUAAGCGUACUGCUUGUGG-------AACGUAUGUAAAGCAGG--AAAUCCACUUCAAACGGAAG-UGGAU
...((((((..(..((((.((((((.((((((......))))))....).)))))))))..)......-------.((....)).)))))).--..(((((((((.....))))-))))) ( -37.20)
>consensus
GAACUGCUUGCGUGAAGCAGUUUACUGCUUUGUUGGCACGAAGCUCUCGU___GCAUACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUUAAAA
.((((((((((((((...........((((((......)))))).................((((.....))))....)))))).))))))))....(((.........)))........ (-13.72 = -15.64 +   1.92)

alignment

secondary structure

dotplot

Window 7

Location	18,053,454 – 18,053,564
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.50
Mean single sequence MFE	-31.66
Consensus MFE	-15.82
Energy contribution	-19.42
Covariance contribution	3.60
Combinations/Pair	1.27
Mean z-score	-2.39
Structure conservation index	0.50
SVM decision value	2.46
SVM RNA-class probability	0.994232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18053454 110 - 23771897
UACUAAUUUCCGUUUGAACUGGAUUUGAACUGCUUGGCAUGCGUUUUUCGUGCAACAAGCAGUAUGC---ACAUGAGCUUCGUGCGAAUAAAGCAGUUAACAUCUUCACGCAA-------
...........((.(((...((((...((((((((.(((((.((((...(((((((.....)).)))---))..))))..))))).....))))))))...))))))).))..------- ( -29.70)
>DroSec_CAF1 168120 117 - 1
UUUUCAUUUCCGUUUGAACUGGAUUUGAACUGCUUGGCAUGAGUUUCUCGUGCAACAAGCAGUCCAC---ACGAAAACUUCGCACCAACAAAGCAGUAAACGACUUCAUGCAAGCAGUUG
...(((..((((.......))))..)))((((((((.(((((((((.(((((..((.....))...)---))))))))...((.........))...........))))))))))))).. ( -31.10)
>DroSim_CAF1 179965 117 - 1
UUUUCAUUUCCGUUUGAACUGGAUUUGAACUGCUUGGCAUGAGUUUCUCGUGCAACAAGCAGUAUGC---ACGAAAACUUCGUGACUACAAAGCAGUAAACGACUUCAUGCAAACAGUUC
...............((((((.......(((((((((((((((...)))))))..)))))))).(((---(.(((....((((...(((......))).)))).))).))))..)))))) ( -35.90)
>DroEre_CAF1 168204 109 - 1
GUUUAGUUUCCGUUUGAACUGGUUUUGUACUGCUUUACAUGAGUUUCUUGUCCUACAAGCAGUGU-----------GCUUCGUGCCAACAAAGCAGUAAACUGUUUCGCACAAGCAGUAC
..(((((((......)))))))....((((((((((((((......((((.....))))..))))-----------)....((((.....((((((....)))))).))))))))))))) ( -28.40)
>DroYak_CAF1 175942 110 - 1
AUCCA-CUUCCGUUUGAAGUGGAUUU--CCUGCUUUACAUACGUU-------CCACAAGCAGUACGCUUAACAAGAGCUUCGUGCCAGCGAAGCAGUAAACUGUACCACACAAGCAGUUA
(((((-((((.....)))))))))..--.(((((((((((((...-------....((((.....)))).......(((((((....))))))).)))...))))......))))))... ( -33.20)
>consensus
UUUUAAUUUCCGUUUGAACUGGAUUUGAACUGCUUGGCAUGAGUUUCUCGUGCAACAAGCAGUAUGC___ACAAAAGCUUCGUGCCAACAAAGCAGUAAACGACUUCACGCAAGCAGUUC
...........(((((...((((.(((.(((((((((((((((...)))))))..)))))))).............((((.((....)).))))......))).))))..)))))..... (-15.82 = -19.42 +   3.60)

alignment

secondary structure

dotplot

Window 8

Location	18,053,487 – 18,053,602
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.39
Mean single sequence MFE	-23.52
Consensus MFE	-7.12
Energy contribution	-9.08
Covariance contribution	1.96
Combinations/Pair	1.06
Mean z-score	-2.12
Structure conservation index	0.30
SVM decision value	1.46
SVM RNA-class probability	0.956355
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18053487 115 + 23771897
AAGCUCAUGU---GCAUACUGCUUGUUGCACGAAAAACGCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUUAGUAAUCAUGC-AAUCCUGC-AUUUAUUUAUUUGUAUAUCAUUA
..((.....(---((((((((((((.(((.........)))...)))))))).....(((.((....)))))...........))))-).....))-....................... ( -22.90)
>DroSec_CAF1 168160 116 + 1
AAGUUUUCGU---GUGGACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUGAAAAAUCAUGCCAAUCCUGC-AUUUAUUUAUUUUUAUAACAUUA
...(((((((---.(((((((((((..(((.(((...))).))))))))))))))..(((.((....))))).)))))))...((((.......))-))..................... ( -28.20)
>DroSim_CAF1 180005 113 + 1
AAGUUUUCGU---GCAUACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUGAAAAAUCAUGC-AAUC--GC-AUUUAUUUAUUUUUAUAACAUUA
..((.....(---((((.(((((((..(((.(((...))).))))))))))((((..(((.((....)))))..)))).....))))-)...--))-....................... ( -23.90)
>DroEre_CAF1 168244 103 + 1
AAGC-----------ACACUGCUUGUAGGACAAGAAACUCAUGUAAAGCAGUACAAAACCAGUUCAAACGGAAACUAAACAU------AAUUUCACUAAACAUUUAUUUCUAUAAUAUUC
....-----------..(((((((.....(((.(.....).))).))))))).................(....).......------................................ ( -11.10)
>DroYak_CAF1 175982 103 + 1
AAGCUCUUGUUAAGCGUACUGCUUGUGG-------AACGUAUGUAAAGCAGG--AAAUCCACUUCAAACGGAAG-UGGAUGC------AAUCUUGC-AUUUAUUUAUUUCUAUAAUAUUU
..(((.......))).......((((((-------((.(((.((((((((((--(.(((((((((.....))))-)))))..------..))))))-.))))).)))))))))))..... ( -31.50)
>consensus
AAGCUCUCGU___GCAUACUGCUUGUUGCACGAGAAACUCAUGCCAAGCAGUUCAAAUCCAGUUCAAACGGAAAUUAAAAAUCAUGC_AAUCCUGC_AUUUAUUUAUUUCUAUAACAUUA
.................((((((((..(((.((.....)).))))))))))).....(((.........)))................................................ ( -7.12 =  -9.08 +   1.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:50 2006