Locus 2670

Sequence ID	2R_DroMel_CAF1
Location	9,420,000 – 9,420,108
Length	108
Max. P	0.878635

overview

Window 2

Location	9,420,000 – 9,420,108
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.01
Mean single sequence MFE	-31.95
Consensus MFE	-26.66
Energy contribution	-26.72
Covariance contribution	0.06
Combinations/Pair	1.22
Mean z-score	-1.87
Structure conservation index	0.83
SVM decision value	0.90
SVM RNA-class probability	0.878635
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9420000 108 + 20766785
UCAAUGAUCUUGUGCUCGUGCUGUUGGCGAUCCAGUUCCUCCUUGACCGACGGCAGGUCACUGCCAUAGUCAGCGGCAAGCAAUUGUUUCUGCAACA--CGAAAACAAUC----------
.........((((..((((((((((((((.((.((......)).)).)...(((((....)))))...)))))))))..(((........)))...)--)))..))))..---------- ( -33.70)
>DroVir_CAF1 12086 113 + 1
UCAAUGAUCUUGUGCUCGUGCUGUUGACGAUCCAGUUCCUCCUUGACCGAUGGCAGAUCACUGCCAUAGUCAGCGGCAAGCAAUUGUUUCUACAAAA--AAGAGGAAAUU-A---UAGA-
.......((((.((((..(((((((((((.((.((......)).)).).(((((((....))))))).)))))))))))))).((((....))))..--)))).......-.---....- ( -33.40)
>DroGri_CAF1 12794 107 + 1
UCGAUGAUCUUGUGCUCGUGCUGUUGACGAUCCAGUUCCUCCUUGACCGAUGGCAGAUCACUGCCAUAGUCGGCGGCAAGCAAUUGUUUCUGCAAAU--UACAAAUAAU-----------
.........(((((((..(((((((((((.((.((......)).)).).(((((((....))))))).)))))))))))))..((((....))))..--.)))).....----------- ( -31.50)
>DroWil_CAF1 9950 117 + 1
UCAAUAAUCUUGUGCUCAUGCUGUUGACGAUCCAGUUCAUCCUUGACCGAUGGCAAAUCACUGCCAUAGUCAGCGGCUAGCAAUUGUUUCUAUAAA---UGAUGACAAUCCAAAUUAGUU
....((((.(((((((...(((((((((......(.(((....))).).((((((......)))))).))))))))).))))((((((((......---.)).)))))).)))))))... ( -31.00)
>DroMoj_CAF1 19536 112 + 1
UCAAUGAUUUUAUGUUCGUGCUGUUGACGAUCCAGUUCCUCCUUGACAGAUGGCAGGUCACUGCCAUAGUCAGCGGCAAGCAAUUGUUUCUAGAAUCACAACAAUAAG-------UAGU-
....(((((((((((...((((((((((......(((.......)))..(((((((....))))))).)))))))))).)))........))))))))..........-------....- ( -33.00)
>DroAna_CAF1 9155 103 + 1
UCGAUGAUCUUGUGCUCGUGCUGUUGCCGGUCCAGUUCCUCCUUCACCGAUGGCAAGUCGCUGCCAUAGUCGGCGGCAAGCAAUUGUUUCUACAAUG-------AUAAUU----------
......(((((((((...(((((((((((((..((......))..))).((((((......))))))....)))))).))))...))....)))).)-------))....---------- ( -29.10)
>consensus
UCAAUGAUCUUGUGCUCGUGCUGUUGACGAUCCAGUUCCUCCUUGACCGAUGGCAGAUCACUGCCAUAGUCAGCGGCAAGCAAUUGUUUCUACAAAA__AAAAAAAAAU___________
............((((..((((((((((((......))...........(((((((....))))))).)))))))))))))).((((....))))......................... (-26.66 = -26.72 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	9,420,000 – 9,420,108
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.01
Mean single sequence MFE	-30.42
Consensus MFE	-24.70
Energy contribution	-25.07
Covariance contribution	0.36
Combinations/Pair	1.17
Mean z-score	-1.22
Structure conservation index	0.81
SVM decision value	0.12
SVM RNA-class probability	0.593019
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9420000 108 - 20766785
----------GAUUGUUUUCG--UGUUGCAGAAACAAUUGCUUGCCGCUGACUAUGGCAGUGACCUGCCGUCGGUCAAGGAGGAACUGGAUCGCCAACAGCACGAGCACAAGAUCAUUGA
----------..((((.((((--(((((..((..((.((.(((.((..((((((((((((....))))))).))))).))))))).))..)).....))))))))).))))......... ( -36.90)
>DroVir_CAF1 12086 113 - 1
-UCUA---U-AAUUUCCUCUU--UUUUGUAGAAACAAUUGCUUGCCGCUGACUAUGGCAGUGAUCUGCCAUCGGUCAAGGAGGAACUGGAUCGUCAACAGCACGAGCACAAGAUCAUUGA
-((((---(-((.........--..)))))))......((((((..((((...(((((((....)))))))(((((.((......)).)))))....)))).))))))(((.....))). ( -33.60)
>DroGri_CAF1 12794 107 - 1
-----------AUUAUUUGUA--AUUUGCAGAAACAAUUGCUUGCCGCCGACUAUGGCAGUGAUCUGCCAUCGGUCAAGGAGGAACUGGAUCGUCAACAGCACGAGCACAAGAUCAUCGA
-----------....(((((.--....)))))......((((((((.(((((((((((((....))))))).))))..)).))..(((.........)))..))))))............ ( -29.00)
>DroWil_CAF1 9950 117 - 1
AACUAAUUUGGAUUGUCAUCA---UUUAUAGAAACAAUUGCUAGCCGCUGACUAUGGCAGUGAUUUGCCAUCGGUCAAGGAUGAACUGGAUCGUCAACAGCAUGAGCACAAGAUUAUUGA
......((((((((((..((.---......)).))))))(((....((((((((((((((....))))))).))))...(((((......)))))...)))...))).))))........ ( -28.20)
>DroMoj_CAF1 19536 112 - 1
-ACUA-------CUUAUUGUUGUGAUUCUAGAAACAAUUGCUUGCCGCUGACUAUGGCAGUGACCUGCCAUCUGUCAAGGAGGAACUGGAUCGUCAACAGCACGAACAUAAAAUCAUUGA
-....-------....((((((((((.((((...(((....)))((..((((.(((((((....)))))))..)))).)).....)))))))).)))))).................... ( -28.50)
>DroAna_CAF1 9155 103 - 1
----------AAUUAU-------CAUUGUAGAAACAAUUGCUUGCCGCCGACUAUGGCAGCGACUUGCCAUCGGUGAAGGAGGAACUGGACCGGCAACAGCACGAGCACAAGAUCAUCGA
----------....((-------((((((....)))))((((((..(((......))).((...(((((...(((..((......))..))))))))..)).))))))...)))...... ( -26.30)
>consensus
___________AUUAUUUGUA__UUUUGUAGAAACAAUUGCUUGCCGCUGACUAUGGCAGUGACCUGCCAUCGGUCAAGGAGGAACUGGAUCGUCAACAGCACGAGCACAAGAUCAUUGA
......................................((((((..((((...(((((((....)))))))(((((.((......)).)))))....)))).))))))............ (-24.70 = -25.07 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:54 2006