Locus 579

Sequence ID	3L_DroMel_CAF1
Location	1,663,621 – 1,663,770
Length	149
Max. P	0.965176

overview

Window 3

Location	1,663,621 – 1,663,734
Length	113
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	82.41
Mean single sequence MFE	-27.10
Consensus MFE	-18.00
Energy contribution	-18.16
Covariance contribution	0.16
Combinations/Pair	1.13
Mean z-score	-2.02
Structure conservation index	0.66
SVM decision value	0.62
SVM RNA-class probability	0.801350
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1663621 113 + 23771897
AAAUUGCCAACAAGUUAUGAAAUUCCACAAAUUGUGAUUUGCAUGAAGCCGAAGCAGAAAUGGAAAAGGAACGA-GGAAAGG--AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGG
......((((............((((.....((((..(((.(((...((....))....))).)))....))))-.....))--))(((....)))(((((....))))).)))). ( -23.20)
>DroSec_CAF1 25765 112 + 1
AAAUUGCCAACAAGUUAUGAAAUUCCACAAAUUGUGGUUUGCAUGAAGCCG-GGCAGAAAUGGAAAAGGGAACA-GGAAACG--AAAGGAAGUCCUGCAGGAAGUCCUGCAUUGGG
...(((((......(((((.....((((.....))))....))))).....-)))))..........(....)(-(((..(.--...)....))))(((((....)))))...... ( -32.30)
>DroSim_CAF1 25856 96 + 1
AAAUUGCCAACAAGUUAUGAAAUUCCACAAAUUGUGAUUUGCAU-----------------GGAAAAGGGAACA-GGAAACG--AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGG
......((((...(((......((((((((((....)))))..)-----------------)))).....)))(-(((..(.--...)....))))(((((....))))).)))). ( -24.90)
>DroEre_CAF1 29306 103 + 1
AAAUUGCCAGCAAGUUAUGGAAUUCCACAAAUUGUGAUUUGCAUGAAGGC-----GGCAGCAGAAAAG-GAACA-------GGAAGAGGAAGUCCUGCAGGAAGCCCUGCAUUGGG
...(((((.((...(((((.((...(((.....)))..)).)))))..))-----)))))(((.....-....(-------(((........))))(((((....))))).))).. ( -28.20)
>DroYak_CAF1 26051 114 + 1
AAAUUGCCAACAAGUUAUGAAAUUCCACAAAUUGUGAUUUGCAUGAAGGCA-GGCAGAAGCAGAAAAA-GAACAAGAAAAAGGAAGAGGAAGUCCUGCAGGAAGCCCUGCACUGGG
...(((((..(...(((((((((..((.....))..)))).)))))..)..-)))))...(((.....-...........((((........))))(((((....))))).))).. ( -26.90)
>consensus
AAAUUGCCAACAAGUUAUGAAAUUCCACAAAUUGUGAUUUGCAUGAAGCC___GCAGAAACGGAAAAGGGAACA_GGAAACG__AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGG
......((((....(((((((((..((.....))..)))).)))))........................................(((....)))(((((....))))).)))). (-18.00 = -18.16 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	1,663,621 – 1,663,734
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	82.41
Mean single sequence MFE	-24.24
Consensus MFE	-18.66
Energy contribution	-18.70
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.34
Structure conservation index	0.77
SVM decision value	1.58
SVM RNA-class probability	0.965176
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1663621 113 - 23771897
CCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU--CCUUUCC-UCGUUCCUUUUCCAUUUCUGCUUCGGCUUCAUGCAAAUCACAAUUUGUGGAAUUUCAUAACUUGUUGGCAAUUU
.((((((((((....))))).(((.((((...--.......-...................((....)).....((((((....)))))))))).))).......)))))...... ( -24.90)
>DroSec_CAF1 25765 112 - 1
CCCAAUGCAGGACUUCCUGCAGGACUUCCUUU--CGUUUCC-UGUUCCCUUUUCCAUUUCUGCC-CGGCUUCAUGCAAACCACAAUUUGUGGAAUUUCAUAACUUGUUGGCAAUUU
.....((((((....))))))((....))...--.......-..................((((-..((.....))...((((.....))))................)))).... ( -23.60)
>DroSim_CAF1 25856 96 - 1
CCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU--CGUUUCC-UGUUCCCUUUUCC-----------------AUGCAAAUCACAAUUUGUGGAAUUUCAUAACUUGUUGGCAAUUU
.((((((((((....)))))(((....)))..--.(((...-.(((((.......-----------------..((((((....))))))))))).....)))..)))))...... ( -20.30)
>DroEre_CAF1 29306 103 - 1
CCCAAUGCAGGGCUUCCUGCAGGACUUCCUCUUCC-------UGUUC-CUUUUCUGCUGCC-----GCCUUCAUGCAAAUCACAAUUUGUGGAAUUCCAUAACUUGCUGGCAAUUU
......((((((......((((((........)))-------)))..-...))))))((((-----((......))......(((.((((((....)))))).)))..)))).... ( -28.50)
>DroYak_CAF1 26051 114 - 1
CCCAGUGCAGGGCUUCCUGCAGGACUUCCUCUUCCUUUUUCUUGUUC-UUUUUCUGCUUCUGCC-UGCCUUCAUGCAAAUCACAAUUUGUGGAAUUUCAUAACUUGUUGGCAAUUU
..(((((((((....))))))(((........)))............-.....)))....((((-(((......)))....((((.((((((....)))))).)))).)))).... ( -23.90)
>consensus
CCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU__CGUUUCC_UGUUCCCUUUUCCACUUCUGC___GCCUUCAUGCAAAUCACAAUUUGUGGAAUUUCAUAACUUGUUGGCAAUUU
.....((((((....))))))((....))............................................(((.....((((.((((((....)))))).))))..))).... (-18.66 = -18.70 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	1,663,658 – 1,663,770
Length	112
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	82.08
Mean single sequence MFE	-34.66
Consensus MFE	-25.14
Energy contribution	-25.34
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.13
Structure conservation index	0.73
SVM decision value	1.08
SVM RNA-class probability	0.911788
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1663658 112 + 23771897
UUUGCAUGAAGCCGAAGCAGAAAUGGAAAAGGAACGA-GGAAAGG--AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGGCUUAAAGCUACGAGGGGCUCACUCGGCCAUGUCUUA
...(((((..(((((..((....))............-.......--...(..(((((((((((....))))).((((((.....))).)))))))))..))))))))))).... ( -33.40)
>DroSec_CAF1 25802 111 + 1
UUUGCAUGAAGCCG-GGCAGAAAUGGAAAAGGGAACA-GGAAACG--AAAGGAAGUCCUGCAGGAAGUCCUGCAUUGGGCUUAAAGCUUCGAGGGGCUCACUCGGCCAUGUCUUA
...(((((..((((-((((....)).....(((..(.-(....)(--((...((((((((((((....))))))..)))))).....)))...)..))).))))))))))).... ( -39.30)
>DroSim_CAF1 25893 95 + 1
UUUGCAU-----------------GGAAAAGGGAACA-GGAAACG--AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGGCUUAAAGCUACGAGGGGCUCACUCGGCCAUGUCUUA
...((((-----------------((....(((..((-(((..(.--...)....)))))...((.(((((......(((.....)))....))))))).)))..)))))).... ( -33.00)
>DroEre_CAF1 29343 102 + 1
UUUGCAUGAAGGC-----GGCAGCAGAAAAG-GAACA-------GGAAGAGGAAGUCCUGCAGGAAGCCCUGCAUUGGGCUUAAAGCUACGAGGGGCCCACUCGGCCAUGUCUUA
........(((((-----((((((.......-...((-------(((........)))))....((((((......))))))...))).(((((....).)))))))..))))). ( -33.10)
>DroYak_CAF1 26088 113 + 1
UUUGCAUGAAGGCA-GGCAGAAGCAGAAAAA-GAACAAGAAAAAGGAAGAGGAAGUCCUGCAGGAAGCCCUGCACUGGGCUUAAAGCUACGAGGAGCCCACUCGGCCAUGUCUUA
........((((((-(((...(((.......-...(........).......((((((((((((....))))))..))))))...))).((((.......))))))).)))))). ( -34.50)
>consensus
UUUGCAUGAAGCC___GCAGAAACGGAAAAGGGAACA_GGAAACG__AAAGGAAGUCCUGCAGGAAGCCCUGCAUUGGGCUUAAAGCUACGAGGGGCUCACUCGGCCAUGUCUUA
...(((((............................................((((((((((((....))))))..)))))).......((((.......))))..))))).... (-25.14 = -25.34 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	1,663,658 – 1,663,770
Length	112
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	82.08
Mean single sequence MFE	-29.72
Consensus MFE	-18.42
Energy contribution	-19.02
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.62
SVM decision value	0.12
SVM RNA-class probability	0.595516
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1663658 112 - 23771897
UAAGACAUGGCCGAGUGAGCCCCUCGUAGCUUUAAGCCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU--CCUUUCC-UCGUUCCUUUUCCAUUUCUGCUUCGGCUUCAUGCAAA
..(((.((((..(((.((((.....((((....((((((......)))))).))))((((.......)--)))....-..)))))))..)))).)))((....)).......... ( -31.30)
>DroSec_CAF1 25802 111 - 1
UAAGACAUGGCCGAGUGAGCCCCUCGAAGCUUUAAGCCCAAUGCAGGACUUCCUGCAGGACUUCCUUU--CGUUUCC-UGUUCCCUUUUCCAUUUCUGCC-CGGCUUCAUGCAAA
..(((.((((..(((.((((....(((((....(((.((..((((((....)))))))).)))..)))--)).....-.)))).)))..)))).)))...-..((.....))... ( -29.00)
>DroSim_CAF1 25893 95 - 1
UAAGACAUGGCCGAGUGAGCCCCUCGUAGCUUUAAGCCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU--CGUUUCC-UGUUCCCUUUUCC-----------------AUGCAAA
...(.(((((..(((.((((.....((((....((((((......)))))).))))(((....)))..--.......-.)))).)))..))-----------------))))... ( -27.30)
>DroEre_CAF1 29343 102 - 1
UAAGACAUGGCCGAGUGGGCCCCUCGUAGCUUUAAGCCCAAUGCAGGGCUUCCUGCAGGACUUCCUCUUCC-------UGUUC-CUUUUCUGCUGCC-----GCCUUCAUGCAAA
...((...(((.(((.(....))))(((((...((((((......))))))...((((((........)))-------)))..-.......))))).-----))).))....... ( -30.50)
>DroYak_CAF1 26088 113 - 1
UAAGACAUGGCCGAGUGGGCUCCUCGUAGCUUUAAGCCCAGUGCAGGGCUUCCUGCAGGACUUCCUCUUCCUUUUUCUUGUUC-UUUUUCUGCUUCUGCC-UGCCUUCAUGCAAA
(((((...((..(((..((.((((.((((....((((((......)))))).))))))))))..)))..))....)))))...-.......((....)).-(((......))).. ( -30.50)
>consensus
UAAGACAUGGCCGAGUGAGCCCCUCGUAGCUUUAAGCCCAAUGCAGGGCUUCCUGCAGGACUUCCUUU__CGUUUCC_UGUUCCCUUUUCCACUUCUGC___GCCUUCAUGCAAA
...(.(((((.((((.(....)))))..((...((((((......))))))...))(((....)))........................................))))))... (-18.42 = -19.02 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:49 2006