Locus 2818

Sequence ID	2L_DroMel_CAF1
Location	8,043,495 – 8,043,668
Length	173
Max. P	0.877861

overview

Window 0

Location	8,043,495 – 8,043,599
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	69.58
Mean single sequence MFE	-28.30
Consensus MFE	-15.37
Energy contribution	-16.82
Covariance contribution	1.45
Combinations/Pair	1.19
Mean z-score	-1.66
Structure conservation index	0.54
SVM decision value	0.90
SVM RNA-class probability	0.877861
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8043495 104 + 22407834
-------------AUCGAAAUAUUUUCAACAAUUUUCUGUGGAAAAUAAUUGGAAAUAUAGCGAAUCUC-CAGCAGCCGAAACCGGAUGCGCUGGUGGCCCGGGCC--CAGCGGCAAGUC
-------------.(((..((((((((((..((((((....))))))..))))))))))..))).....-..(((.(((....))).)))((((.((((....).)--)).))))..... ( -35.80)
>DroPse_CAF1 45752 119 + 1
CUGCUGUAAAUAAAUCGGAAUAUUUUCAAGAAGUUUUUAGCGAAAA-AAUUGCAAAUAAAACAAAUUUGUUCUCUGUCAAAUUCGGUCACGCCAGUGACCUAGGCCGCAGGCGCCUAGUU
..((((.((((......(((....))).....)))).))))((...-....((((((.......))))))......))......((((((....))))))((((((....).)))))... ( -25.72)
>DroSim_CAF1 2 104 + 1
-------------AUCGAAAUAUUUUCAACAAUUUUCCGUGGAAAAUAAUUGGAAAUAUAGCGAAUAUC-CAGCAGCCCAAACCGAAUGCGCUGGUGGCCCGGGCC--CAGCGGCAAGUC
-------------.(((..((((((((((..((((((....))))))..))))))))))..))).....-..(((..(......)..)))((((.((((....).)--)).))))..... ( -31.30)
>DroYak_CAF1 502 109 + 1
--------AAAAAAUCGAAAUAUUUUCAACAAUUUUCUUGCGAAAAUAAUUGGAAAUAUAGCGAAUAUU-CAGCAGACAAAACCAGAUGCGCUGGUGGCCCGGGCC--CAGCGGCAAGUC
--------......(((..((((((((((..((((((....))))))..))))))))))..))).....-..(((............)))((((.((((....).)--)).))))..... ( -29.30)
>DroAna_CAF1 1803 117 + 1
CACCUGUAAAUAAAUCGGAAUAUUUUCAUCAAUUUUUUGCCAAAAAUUAUUGAAACCAAAGUGAUCCUC-AAGCUGUUGAAACCGUUCCCGCUGGUGGCCCGGGCC--CAGCGCCAAUCC
................(((((..((((((((((..(((.....)))..)))))......(((.......-..)))..)))))..)))))((((((..((....)))--)))))....... ( -23.90)
>DroPer_CAF1 66464 119 + 1
CUGCUGUAAAUAAAUCGGAAUAUUUUCAACAAAUUUUUAGCGAAAA-AAUUGCAAAUAAAACAAAUUUGUUCUCUGUUAAAUUCGGUCACGCCAGUGACCUAGGCCGCAGGCGCCUAGUU
.(((((.((((......(((....))).....)))).)))))....-....((((((.......))))))..............((((((....))))))((((((....).)))))... ( -23.80)
>consensus
________AAUAAAUCGAAAUAUUUUCAACAAUUUUCUGGCGAAAAUAAUUGGAAAUAAAGCGAAUAUC_CAGCAGUCAAAACCGGACGCGCUGGUGGCCCGGGCC__CAGCGCCAAGUC
..............(((...(((((((((..((((((....))))))..)))))))))...))).........................(((((..(((....)))..)))))....... (-15.37 = -16.82 +   1.45)

alignment

secondary structure

dotplot

Window 1

Location	8,043,495 – 8,043,599
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	69.58
Mean single sequence MFE	-30.08
Consensus MFE	-16.51
Energy contribution	-16.98
Covariance contribution	0.48
Combinations/Pair	1.20
Mean z-score	-1.47
Structure conservation index	0.55
SVM decision value	0.43
SVM RNA-class probability	0.734222
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8043495 104 - 22407834
GACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUCCGGUUUCGGCUGCUG-GAGAUUCGCUAUAUUUCCAAUUAUUUUCCACAGAAAAUUGUUGAAAAUAUUUCGAU-------------
....(((.((((--(((....))..))))))))((((((.......))))-))...(((..((((((.((((.((((((....)))))).)))).))))))..))).------------- ( -32.90)
>DroPse_CAF1 45752 119 - 1
AACUAGGCGCCUGCGGCCUAGGUCACUGGCGUGACCGAAUUUGACAGAGAACAAAUUUGUUUUAUUUGCAAUU-UUUUCGCUAAAAACUUCUUGAAAAUAUUCCGAUUUAUUUACAGCAG
..........(((((((...((((((....))))))(((.(((.(((((((((....)))))..)))))))..-..))))))..........((.(((((........))))).)))))) ( -24.80)
>DroSim_CAF1 2 104 - 1
GACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUUCGGUUUGGGCUGCUG-GAUAUUCGCUAUAUUUCCAAUUAUUUUCCACGGAAAAUUGUUGAAAAUAUUUCGAU-------------
......((((..--((((((((((............)))))))))))).)-)....(((..((((((.((((.((((((....)))))).)))).))))))..))).------------- ( -32.80)
>DroYak_CAF1 502 109 - 1
GACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUCUGGUUUUGUCUGCUG-AAUAUUCGCUAUAUUUCCAAUUAUUUUCGCAAGAAAAUUGUUGAAAAUAUUUCGAUUUUUU--------
(((..(((((((--(((....))..)))))......)))...))).....-.....(((..((((((.((((.((((((....)))))).)))).))))))..)))......-------- ( -31.10)
>DroAna_CAF1 1803 117 - 1
GGAUUGGCGCUG--GGCCCGGGCCACCAGCGGGAACGGUUUCAACAGCUU-GAGGAUCACUUUGGUUUCAAUAAUUUUUGGCAAAAAAUUGAUGAAAAUAUUCCGAUUUAUUUACAGGUG
...((((.((((--..((((.........))))..)))).))))..((((-(..(((....(((((((((.((((((((....)))))))).))))).....))))...)))..))))). ( -30.00)
>DroPer_CAF1 66464 119 - 1
AACUAGGCGCCUGCGGCCUAGGUCACUGGCGUGACCGAAUUUAACAGAGAACAAAUUUGUUUUAUUUGCAAUU-UUUUCGCUAAAAAUUUGUUGAAAAUAUUCCGAUUUAUUUACAGCAG
..((((((.......))))))(((((....)))))(((((..((((((.......))))))..))))).((((-(((.....)))))))(((((.(((((........))))).))))). ( -28.90)
>consensus
GACUUGCCGCUG__GGCCCGGGCCACCAGCGCAACCGGUUUUGACAGCUG_GAAAUUCGCUAUAUUUCCAAUUAUUUUCGCCAAAAAAUUGUUGAAAAUAUUCCGAUUUAUU________
.......((((...(((....)))...)))).........................(((...(((((.((((.((((((....)))))).)))).)))))...))).............. (-16.51 = -16.98 +   0.48)

alignment

secondary structure

dotplot

Window 2

Location	8,043,561 – 8,043,668
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	66.69
Mean single sequence MFE	-40.75
Consensus MFE	-18.10
Energy contribution	-18.35
Covariance contribution	0.25
Combinations/Pair	1.21
Mean z-score	-1.52
Structure conservation index	0.44
SVM decision value	0.08
SVM RNA-class probability	0.571641
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8043561 107 - 22407834
--UAACUGGUUG-CCGUUU-UGGCCGUUUAGAUUUG-CUCUAGCCAGCGC------ACGCUGGCUGCUGCCAUUGCUCACGACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUCCGGUU
--.((((((.((-(.(((.-(((((..........(-(..((((((((..------..))))))))..))....(((((((......)).))--)))...)))))..)))))).)))))) ( -45.20)
>DroPse_CAF1 45831 115 - 1
--GCACUAGGAGACCAUUG-GUACUAUUUACAUCCGGAUUUUGCCAGCUUUUUUUGCCCCUGGU--CUUACAUUGCAUCGAACUAGGCGCCUGCGGCCUAGGUCACUGGCGUGACCGAAU
--(((....(((((((.((-(((..((((......))))..)))))((.......))...))))--)))....))).(((..((((((.......))))))(((((....)))))))).. ( -37.10)
>DroSim_CAF1 68 107 - 1
--UCACUGGUUG-CCGUUU-UGGCCGUUUAGAUUUG-CUCUAGCCAGCGC------CCGCUGGCUGCUGCCAUUGCUCACGACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUUCGGUU
--..((((..((-(.(((.-(((((..........(-(..((((((((..------..))))))))..))....(((((((......)).))--)))...)))))..))))))..)))). ( -42.10)
>DroYak_CAF1 573 107 - 1
--UCACUGGUUG-CCGUUU-UGGCCGUUUACAAUUG-CUCCAGCCAGCGC------CCGCUGGCACCUGCCAUUGCUCCCGACUUGCCGCUG--GGCCCGGGCCACCAGCGCAUCUGGUU
--..((..(.((-(.....-.(((.(((..((((.(-(....((((((..------..))))))....)).)))).....)))..)))((((--(((....))..)))))))).)..)). ( -38.90)
>DroAna_CAF1 1882 108 - 1
AAUCACUGA--G-CCAUUUCUUGGCAAUUAGACUCG-CUGCGGGCAGCGU------CCGCCAGUUACUUCCGUUGCACACGGAUUGGCGCUG--GGCCCGGGCCACCAGCGGGAACGGUU
....((((.--(-(((.....)))).......((((-(((..(((..((.------.(.(((((..(.(((((.....)))))..)..))))--))..)).)))..)))))))..)))). ( -44.10)
>DroPer_CAF1 66543 115 - 1
--GCACUAGGAGACCAUUG-GUACUAUUUACAUCCGGAUUUUGCCAGCUUUUUUUGCCCCUGGU--CUUACAUUGCAUCGAACUAGGCGCCUGCGGCCUAGGUCACUGGCGUGACCGAAU
--(((....(((((((.((-(((..((((......))))..)))))((.......))...))))--)))....))).(((..((((((.......))))))(((((....)))))))).. ( -37.10)
>consensus
__UCACUGGUUG_CCAUUU_UGGCCAUUUACAUUCG_CUCUAGCCAGCGC______CCGCUGGCU_CUGCCAUUGCACACGACUUGCCGCUG__GGCCCGGGCCACCAGCGCAACCGGUU
..........................................(((((((........))))))).......................((((...(((....)))...))))......... (-18.10 = -18.35 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:02 2006