Locus 4337

Sequence ID	2L_DroMel_CAF1
Location	12,418,330 – 12,418,467
Length	137
Max. P	0.886697

overview

Window 3

Location	12,418,330 – 12,418,435
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.13
Mean single sequence MFE	-32.50
Consensus MFE	-22.42
Energy contribution	-21.78
Covariance contribution	-0.64
Combinations/Pair	1.19
Mean z-score	-1.08
Structure conservation index	0.69
SVM decision value	0.12
SVM RNA-class probability	0.592122
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12418330 105 + 22407834
GG--GGGUUAUAACCCUCCAGGGAGGCCCUGCGGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCUGAUUCUGAUGGUUUCUAGUCUGCCGUUGCAGU---AGUUCU
((--((((....)))).))..((((...((((((((....((.(((...((((((.((((.....))))........))))))...))))).)))))))).---..)))) ( -32.10)
>DroPse_CAF1 330723 80 + 1
-----------AUGCCUCCAGGGAGGCCUUGCAGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCU----CUGAU------------GCUGCUGCAGC---AGUUCU
-----------..(((((....))))).((((((((.....((........))(((((((.....))))----)))..------------..)))))))).---...... ( -32.40)
>DroEre_CAF1 240662 107 + 1
AG--GGGGGAUAACCCUCCAGGGAGGCCCUGCGGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCCGAUUCUGAUGGUU-UUCGUCUGCCGUUGCAGUAGUAGUUCU
.(--(((((....))))))((((..((.((((((((....((.(((...((((((..(((.....))).........)))))-)..))))).))))))))..))..)))) ( -34.90)
>DroYak_CAF1 251170 106 + 1
AGAAGGGGGUUAACCCUCCAGGGAGGCCCUGCGGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCUGAUUCUGAUGGUU-UUGGUCUGCCGUUGCAGU---AGUUCU
....(((((....)))))(((((...)))))....(((((((..((..(..((((((((((.((.........))..)))))-)))))..)..))..).))---)))).. ( -34.50)
>DroAna_CAF1 228704 94 + 1
-U--GG----CGCACCUCCAGGGAGGCCUUGCAGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCUGAUGGUGA---UU-UUGA--UGCUGUUGCAGU---GAUUCU
-.--.(----((((((((....))))...))).))((((((....((....((((.((((.....))))..))))..---..-.)).--(((....)))))---)))).. ( -28.70)
>DroPer_CAF1 333474 80 + 1
-----------AUGCCUCCAGGGAGGCCUUGCAGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCU----CUGAU------------GCUGCUGCAGC---AGUUCU
-----------..(((((....))))).((((((((.....((........))(((((((.....))))----)))..------------..)))))))).---...... ( -32.40)
>consensus
_G__GG____UAACCCUCCAGGGAGGCCCUGCAGCGAUUACGUGACAUUGAACCAGAGCCAAAGUGGCUGAUUCUGAU__UU_UU_G__UGCCGUUGCAGU___AGUUCU
..............((((....))))..((((((((.....((........))(((((((.....))))....)))................)))))))).......... (-22.42 = -21.78 +  -0.64)

alignment

secondary structure

dotplot

Window 4

Location	12,418,330 – 12,418,435
Length	105
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.13
Mean single sequence MFE	-29.47
Consensus MFE	-18.25
Energy contribution	-17.37
Covariance contribution	-0.89
Combinations/Pair	1.16
Mean z-score	-1.70
Structure conservation index	0.62
SVM decision value	0.74
SVM RNA-class probability	0.839167
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12418330 105 - 22407834
AGAACU---ACUGCAACGGCAGACUAGAAACCAUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCCGCAGGGCCUCCCUGGAGGGUUAUAACCC--CC
......---.......((((.(((..((.....)).(((((((((.....)))..))))))...)))..(....)))))(((((...)))))..((((....))))--.. ( -28.30)
>DroPse_CAF1 330723 80 - 1
AGAACU---GCUGCAGCAGC------------AUCAG----AGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCUGCAAGGCCUCCCUGGAGGCAU-----------
......---..((((((.(.------------(((((----((((.....))))))))).)........(....)))))))..(((((....)))))..----------- ( -34.30)
>DroEre_CAF1 240662 107 - 1
AGAACUACUACUGCAACGGCAGACGAA-AACCAUCAGAAUCGGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCCGCAGGGCCUCCCUGGAGGGUUAUCCCCC--CU
................((((.(((((.-.....)).(((((((((.....))))..)))))...)))..(....)))))(((((...))))).((((.......))--)) ( -28.30)
>DroYak_CAF1 251170 106 - 1
AGAACU---ACUGCAACGGCAGACCAA-AACCAUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCCGCAGGGCCUCCCUGGAGGGUUAACCCCCUUCU
.(((((---(((((....)))).....-.............((((.....)))).))))))...((..((....))..))((((...))))((((((......)))))). ( -28.30)
>DroAna_CAF1 228704 94 - 1
AGAAUC---ACUGCAACAGCA--UCAA-AA---UCACCAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCUGCAAGGCCUCCCUGGAGGUGCG----CC--A-
......---...((..((((.--....-..---..((((..((((.....)))).))))..........(....)))))....(((((....))))))).----..--.- ( -23.30)
>DroPer_CAF1 333474 80 - 1
AGAACU---GCUGCAGCAGC------------AUCAG----AGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCUGCAAGGCCUCCCUGGAGGCAU-----------
......---..((((((.(.------------(((((----((((.....))))))))).)........(....)))))))..(((((....)))))..----------- ( -34.30)
>consensus
AGAACU___ACUGCAACAGCA__C_AA_AA__AUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAAUCGCCGCAAGGCCUCCCUGGAGGGUUA____CC__C_
..........((....((((.....................((((.....))))..(((((........).))))))))..)).((((....)))).............. (-18.25 = -17.37 +  -0.89)

alignment

secondary structure

dotplot

Window 5

Location	12,418,365 – 12,418,467
Length	102
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	76.75
Mean single sequence MFE	-29.43
Consensus MFE	-16.05
Energy contribution	-15.88
Covariance contribution	-0.17
Combinations/Pair	1.16
Mean z-score	-2.04
Structure conservation index	0.55
SVM decision value	0.94
SVM RNA-class probability	0.886697
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12418365 102 - 22407834
ACGG-UGACUCGAA---CUCUCGUCGUCUGUGAUUGAGAACU---ACUGCAACGGCAGACUAGAAACCAUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
...(-((((..(((---(..((...((((((..(((((....---.)).)))..))))))..))......((((....(((.....)))))))))))...))))).... ( -28.10)
>DroPse_CAF1 330749 86 - 1
GUGGAUGACUCAGCCCGCUCUCA----CCGUGAUUGAGAACU---GCUGCAGCAGC------------AUCAG----AGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
((((..........)))).....----.((((((...(((((---((((...))))------------).(((----((((.....)))))))))))...))))))... ( -32.10)
>DroEre_CAF1 240697 104 - 1
ACGG-UGACUCGAA---CACUCGUCGUCUGUGAUUGAGAACUACUACUGCAACGGCAGACGAA-AACCAUCAGAAUCGGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
...(-((((..(((---(.....((((((((..(((((........)).)))..)))))))).-......((((....(((.....)))))))))))...))))).... ( -32.30)
>DroYak_CAF1 251207 101 - 1
ACGG-UGACUCGAA---CUCUCGUCGUCUGUGAUUGAGAACU---ACUGCAACGGCAGACCAA-AACCAUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
...(-((((..(((---(.......((((((..(((((....---.)).)))..))))))...-......((((....(((.....)))))))))))...))))).... ( -27.60)
>DroAna_CAF1 228734 94 - 1
GUGG-UGACUCAAA---G--UCAUUGUCUAUGAUUGAGAAUC---ACUGCAACAGCA--UCAA-AA---UCACCAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
(..(-(((.((..(---(--((((.....))))))..)).))---))..).......--....-..---..((((..((((.....)))).)))).............. ( -24.40)
>DroPer_CAF1 333500 86 - 1
GUGGAUGACUCAGCCCGCUCUCA----CCGUGAUUGAGAACU---GCUGCAGCAGC------------AUCAG----AGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
((((..........)))).....----.((((((...(((((---((((...))))------------).(((----((((.....)))))))))))...))))))... ( -32.10)
>consensus
ACGG_UGACUCAAA___CUCUCAUCGUCUGUGAUUGAGAACU___ACUGCAACAGCA__C_AA_AA__AUCAGAAUCAGCCACUUUGGCUCUGGUUCAAUGUCACGUAA
............................((((((...((((.......((....))..............(((....((((.....)))))))))))...))))))... (-16.05 = -15.88 +  -0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:23 2006