Locus 1420

Sequence ID	3R_DroMel_CAF1
Location	4,106,318 – 4,106,441
Length	123
Max. P	0.992356

overview

Window 5

Location	4,106,318 – 4,106,420
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.36
Mean single sequence MFE	-34.55
Consensus MFE	-22.04
Energy contribution	-21.85
Covariance contribution	-0.19
Combinations/Pair	1.08
Mean z-score	-2.76
Structure conservation index	0.64
SVM decision value	0.38
SVM RNA-class probability	0.713360
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4106318 102 - 27905053
CCGA------ACGGAGCCGAACAAUUUGUGUAAUUGACAAAUUGACGGCAGCGCU-UUGUGCGGAAGCGUUCAAAGCCGUAAAUUGUCGCUAACAAGA--GCGACACU--CC-A------
....------..(((((((..((((((((.......)))))))).)))).(((((-((((((....)))..))))).)))....(((((((......)--)))))).)--))-.------ ( -38.80)
>DroPse_CAF1 12180 107 - 1
-CGA------UGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCU-UUGUGCGGAAGCGUUCGAAGCCGUAAAUUGUCGCUAACAAGA--GCAAGGCG--AC-ACGGCUA
-...------..((((.((((((((((((.......)))))))).((....)).)-))).((....))))))..((((((.....((((((.......--....))))--))-)))))). ( -33.20)
>DroGri_CAF1 14694 104 - 1
-AGC------CGAGACCUAAACAAUUUGUGUAAUUGACAAAUUGACGGCGACGCUUUUGUGCGGAAGCGUUCAAAGCCGUAAAUUGUCGCUAACAAGAGAGCUCGAUC--CC-A------
-...------((((((.....((((((((.......))))))))((((((((((((((....)))))))))....))))).....)))(((........))))))...--..-.------ ( -30.80)
>DroWil_CAF1 2637 100 - 1
----------GGAGACCUAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCU-UUGUGCGGAAGCGUUCAAAGCCGUAAAUUGUCGCUAACAAGA--GCGACACA--CACAC-----
----------(....).....((((((((.......))))))))(((((((((((-((.....))))))))....)))))....(((((((......)--))))))..--.....----- ( -32.90)
>DroAna_CAF1 12987 110 - 1
CCAAGUCCAGGGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAGCGCU-UUGUGCGGAAGCGUUCAAAGCCGUAAAUUGUCGCUAACAAGA--GCGACACUCUCC-A------
..........(((((......((((((((.......))))))))(((((((((((-((.....))))))))....)))))....(((((((......)--)))))).)))))-.------ ( -38.40)
>DroPer_CAF1 12257 107 - 1
-CGA------UGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCU-UUGUGCGGAAGCGUUCGAAGCCGUAAAUUGUCGCUAACAAGA--GCAAGGCG--AC-ACGGCUA
-...------..((((.((((((((((((.......)))))))).((....)).)-))).((....))))))..((((((.....((((((.......--....))))--))-)))))). ( -33.20)
>consensus
_CGA______GGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCU_UUGUGCGGAAGCGUUCAAAGCCGUAAAUUGUCGCUAACAAGA__GCGACACG__CC_A______
.............(((.....((((((((.......))))))))(((((((((((.((....)).))))))....))))).....)))................................ (-22.04 = -21.85 +  -0.19)

alignment

secondary structure

dotplot

Window 6

Location	4,106,347 – 4,106,441
Length	94
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	76.45
Mean single sequence MFE	-23.23
Consensus MFE	-15.75
Energy contribution	-16.42
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	0.68
SVM decision value	2.09
SVM RNA-class probability	0.987681
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4106347 94 + 27905053
ACGGCUUUGAACGCUUCCGCACAAAGCGCUGCCGUCAAUUUGUCAAUUACACAAAUUGUUCGGCUCCGU------UCGGUUCCCCCAUCUC-AAAAGCCAC
..(((((((((((....(((.....)))..((((.((((((((.......))))))))..))))..)))------))((.....)).....-.)))))).. ( -30.80)
>DroPse_CAF1 12215 86 + 1
ACGGCUUCGAACGCUUCCGCACAAAGCGUUGCCGUCAAUUUGUCAAUUACACAAAUUGUUUGGGUCCCA------UCG--UCCCCCGA-------CAACAA
(((((....(((((((.......)))))))))))).(((((((.......)))))))(((.(((..(..------..)--..))).))-------)..... ( -22.80)
>DroWil_CAF1 2668 79 + 1
ACGGCUUUGAACGCUUCCGCACAAAGCGUUGCCGUCAAUUUGUCAAUUACACAAAUUGUUUAGGUCUCC---------------CCGA-------CAGAAU
(((((....(((((((.......))))))))))))((((((((.......)))))))).....(((...---------------..))-------)..... ( -20.20)
>DroMoj_CAF1 2841 90 + 1
ACGGCUUUGAACGCUUCCGCACAAUGCGUCGCCGUCAAUUUGUCAAUUACACAAAUUGUUUAGCUCUCG------ACU--CGCCACGACACCAAC---CAC
..(((.((((..(((..(((.....))).......((((((((.......))))))))...)))..)))------)..--.)))...........---... ( -17.20)
>DroAna_CAF1 13018 83 + 1
ACGGCUUUGAACGCUUCCGCACAAAGCGCUGCCGUCAAUUUGUCAAUUACACAAAUUGUUUGGGUCCCCCUGGACUUGGAUCC------------------
(((((......(((((.......)))))..)))))((((((((.......))))))))((..(((((....)))))..))...------------------ ( -25.20)
>DroPer_CAF1 12292 86 + 1
ACGGCUUCGAACGCUUCCGCACAAAGCGUUGCCGUCAAUUUGUCAAUUACACAAAUUGUUUGGGUCCCA------UCG--UCCCCCGA-------AACCAA
(((((....(((((((.......))))))))))))((((((((.......))))))))((((((.....------...--...)))))-------)..... ( -23.20)
>consensus
ACGGCUUUGAACGCUUCCGCACAAAGCGUUGCCGUCAAUUUGUCAAUUACACAAAUUGUUUGGGUCCCA______UCG__UCCCCCGA________A_CAA
(((((....(((((((.......))))))))))))((((((((.......))))))))........................................... (-15.75 = -16.42 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	4,106,347 – 4,106,441
Length	94
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	76.45
Mean single sequence MFE	-31.35
Consensus MFE	-21.36
Energy contribution	-21.17
Covariance contribution	-0.19
Combinations/Pair	1.10
Mean z-score	-3.01
Structure conservation index	0.68
SVM decision value	2.32
SVM RNA-class probability	0.992356
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4106347 94 - 27905053
GUGGCUUUU-GAGAUGGGGGAACCGA------ACGGAGCCGAACAAUUUGUGUAAUUGACAAAUUGACGGCAGCGCUUUGUGCGGAAGCGUUCAAAGCCGU
..((((((.-......((....))((------(((..((((..((((((((.......)))))))).))))..(((.....)))....))))))))))).. ( -35.00)
>DroPse_CAF1 12215 86 - 1
UUGUUG-------UCGGGGGA--CGA------UGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCUUUGUGCGGAAGCGUUCGAAGCCGU
..((((-------((((((..--(..------..)..)))...((((((((.......)))))))).)))))))(((((((((....)))..))))))... ( -35.30)
>DroWil_CAF1 2668 79 - 1
AUUCUG-------UCGG---------------GGAGACCUAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCUUUGUGCGGAAGCGUUCAAAGCCGU
....((-------((((---------------(....))....((((((((.......)))))))).)))))..(((((((((....)))..))))))... ( -28.60)
>DroMoj_CAF1 2841 90 - 1
GUG---GUUGGUGUCGUGGCG--AGU------CGAGAGCUAAACAAUUUGUGUAAUUGACAAAUUGACGGCGACGCAUUGUGCGGAAGCGUUCAAAGCCGU
..(---(((.(((((((.(..--((.------(....)))...((((((((.......)))))))).).))))))).....((....))......)))).. ( -28.60)
>DroAna_CAF1 13018 83 - 1
------------------GGAUCCAAGUCCAGGGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAGCGCUUUGUGCGGAAGCGUUCAAAGCCGU
------------------((((....)))).((....))....((((((((.......))))))))(((((((((((((.....))))))))....))))) ( -29.10)
>DroPer_CAF1 12292 86 - 1
UUGGUU-------UCGGGGGA--CGA------UGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCUUUGUGCGGAAGCGUUCGAAGCCGU
..((((-------((((((..--(..------..)..)))...((((((((.......)))))))).....((((((((.....))))))))))))))).. ( -31.50)
>consensus
GUG_U________UCGGGGGA__CGA______GGGGACCCAAACAAUUUGUGUAAUUGACAAAUUGACGGCAACGCUUUGUGCGGAAGCGUUCAAAGCCGU
...........................................((((((((.......))))))))(((((((((((((.....))))))))....))))) (-21.36 = -21.17 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:06 2006