Locus 8384

Sequence ID	3L_DroMel_CAF1
Location	22,045,699 – 22,045,834
Length	135
Max. P	0.771190

overview

Window 1

Location	22,045,699 – 22,045,806
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.17
Mean single sequence MFE	-24.94
Consensus MFE	-15.39
Energy contribution	-16.28
Covariance contribution	0.89
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.62
SVM decision value	0.25
SVM RNA-class probability	0.651409
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22045699 107 - 23771897
UUGGUUUGGCAAUUUUGUAAGCGAAAU-UGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCGUCG-CUGGCU--------UU---UUUUGUGCCGCGCAGUUAUUAGAAGAAAAUGCUU
.......((((((((((....))))))-))))................((((((((.((((.((.(-(((((.--------..---.........)).)))).)).)))))))))))).. ( -29.50)
>DroPse_CAF1 43390 116 - 1
UUGGUUUGGCAAUUCUGUAAGCGAAAU-UGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCAUCGUCUCGUUUUUCUUCUUU---UUUUAUCCUGCGCAGUUAUUAGAAGAAAAUGCCU
..(((..(((((((.((....)).)))-))))....((((......((((((...............................---.........))))))......).)))....))). ( -19.90)
>DroGri_CAF1 30994 82 - 1
UUGGUUUGGCAAUUUUGUAAGCGAAAU-UGCCACUGUCUCGCAUU----CGUUGUCGUUUU--------------------------------UUGCGCAGUUAUUAGAAGAA-AUGCCG
..(((.(((((((((((....))))))-)))))(((.((((((..----((....))....--------------------------------.)))).))....))).....-..))). ( -22.90)
>DroEre_CAF1 31370 107 - 1
UUGGUUUGGCAAUUUUGUAAGCGAAAU-UGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCGUUG-CUGGCU--------UU---UUUUCUGCCGCGCAGUUAUUAGAAGAAAAUGCUU
.......((((((((((....))))))-))))................((((((((.(((...(((-(((((.--------..---......)))).)))).....))).)))))))).. ( -31.00)
>DroAna_CAF1 46394 106 - 1
UUGGUUUGGCAAUUUUGUAAGCGAAAU-UGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCAUCG-CUCGCU--------UU----UUUCUGCUGCGCAGUUAUUAGAAGAAAAUGUUU
.......((((((((((....))))))-))))................((((((((.((((.((.(-(((((.--------..----........))).))).)).)))))))))))).. ( -27.00)
>DroPer_CAF1 43194 120 - 1
UUGGUUUGGCAAUUCUGUAAGCGAAAUUUGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCAUCGUCUCGUUUUUCUUCUUUUUUUUUUAUCCUGCGCAGUUAUUAGAAGAAAAUGCCU
.......((((.((((...((((........)))).(((.((....((((((...........................................))))))..)).)))))))..)))). ( -19.33)
>consensus
UUGGUUUGGCAAUUUUGUAAGCGAAAU_UGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCAUCG_CUCGCU________UU___UUUUAUGCUGCGCAGUUAUUAGAAGAAAAUGCCU
.......((((((((((....)))))).))))((..((((......((((((...........................................))))))......).)))....)).. (-15.39 = -16.28 +   0.89)

alignment

secondary structure

dotplot

Window 2

Location	22,045,735 – 22,045,834
Length	99
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	79.34
Mean single sequence MFE	-15.75
Consensus MFE	-11.72
Energy contribution	-11.58
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-1.26
Structure conservation index	0.74
SVM decision value	0.38
SVM RNA-class probability	0.711877
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22045735 99 + 23771897
AGCCAGCGACGAAAAUGAAAACGCAGAAAAACGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAGGACUUUGAAUUCCAAUUGCAAAG-----------A
..((.(((.............)))................((((((((........))))))))..........)).((((((((....))).)))))-----------. ( -16.02)
>DroVir_CAF1 37641 84 + 1
-----------AAAACGAUAACG----AGUGCGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAUGACUUUGAAUUCCAAUUGCAAAG-----------A
-----------..........(.----..(((((......((((((((........))))))))....((((......))))........)))))..)-----------. ( -14.60)
>DroGri_CAF1 31020 84 + 1
-----------AAAACGACAACG----AAUGCGAGACAGUGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAUGACUUUGAAUUCCAAUUGCGCCG-----------A
-----------..........((----..(((((.....(((((((((........)))))))))...((((......))))........))))).))-----------. ( -14.60)
>DroWil_CAF1 44865 82 + 1
----------------AAAAACGCACA-AAACGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAGGACUUUGAAUUCCAAUUGCAAAG-----------C
----------------......(((..-............((((((((........))))))))..........(((........)))...)))....-----------. ( -14.50)
>DroMoj_CAF1 41180 84 + 1
-----------AAAACGAUAACG----AGUGCGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAUGACUUUGAAUUCCAAUUGCGAUG-----------A
-----------............----..(((((......((((((((........))))))))....((((......))))........)))))...-----------. ( -13.60)
>DroAna_CAF1 46429 110 + 1
AGCGAGCGAUGAAAAUGAAAACGCAGAAAAACGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAGGACUUUGAAUUCCAAUUGCAAAGUUGGAAAGUACA
.(((..(.((....)))....))).......((((.....((((((((........))))))))...((.....))..))))..((((((((....))))))))...... ( -21.20)
>consensus
___________AAAACGAAAACG____AAAACGAGACAGCGGCAAUUUCGCUUACAAAAUUGCCAAACCAAAAAGGACUUUGAAUUCCAAUUGCAAAG___________A
......................................((((((((((........))))))))....((((......))))..........))................ (-11.72 = -11.58 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	22,045,735 – 22,045,834
Length	99
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.34
Mean single sequence MFE	-19.94
Consensus MFE	-17.00
Energy contribution	-16.62
Covariance contribution	-0.39
Combinations/Pair	1.11
Mean z-score	-1.31
Structure conservation index	0.85
SVM decision value	0.53
SVM RNA-class probability	0.771190
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22045735 99 - 23771897
U-----------CUUUGCAAUUGGAAUUCAAAGUCCUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCGUCGCUGGCU
.-----------....((....((((.((((((....))))))...((((((((((....))))))))))............))))(((.............)))..)). ( -20.32)
>DroVir_CAF1 37641 84 - 1
U-----------CUUUGCAAUUGGAAUUCAAAGUCAUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGCACU----CGUUAUCGUUUU-----------
.-----------...(((.....((((.(((((....)))))))))((((((((((....))))))))))........)))..----............----------- ( -18.60)
>DroGri_CAF1 31020 84 - 1
U-----------CGGCGCAAUUGGAAUUCAAAGUCAUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCACUGUCUCGCAUU----CGUUGUCGUUUU-----------
.-----------.((((((((.(((..((((((....))))))..(((((((((((....)))))))))))..........))----))))).))))..----------- ( -21.70)
>DroWil_CAF1 44865 82 - 1
G-----------CUUUGCAAUUGGAAUUCAAAGUCCUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGUUU-UGUGCGUUUUU----------------
(-----------(....(((..(((........)))...)))....((((((((((....)))))))))))).....(((..-...))).....---------------- ( -19.20)
>DroMoj_CAF1 41180 84 - 1
U-----------CAUCGCAAUUGGAAUUCAAAGUCAUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGCACU----CGUUAUCGUUUU-----------
.-----------....((.....((((.(((((....)))))))))((((((((((....))))))))))........))...----............----------- ( -18.30)
>DroAna_CAF1 46429 110 - 1
UGUACUUUCCAACUUUGCAAUUGGAAUUCAAAGUCCUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGUUUUUCUGCGUUUUCAUUUUCAUCGCUCGCU
......((((((........)))))).((((((....))))))...((((((((((....))))))))))................(((.............)))..... ( -21.52)
>consensus
U___________CUUUGCAAUUGGAAUUCAAAGUCAUUUUUGGUUUGGCAAUUUUGUAAGCGAAAUUGCCGCUGUCUCGCAUU____CGUUUUCGUUUU___________
................((.........((((((....))))))..(((((((((((....))))))))))).......)).............................. (-17.00 = -16.62 +  -0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:01 2006