Locus 736

Sequence ID	X_DroMel_CAF1
Location	1,997,464 – 1,997,574
Length	110
Max. P	0.835421

overview

Window 2

Location	1,997,464 – 1,997,574
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.62
Mean single sequence MFE	-28.86
Consensus MFE	-14.44
Energy contribution	-14.84
Covariance contribution	0.40
Combinations/Pair	1.16
Mean z-score	-1.89
Structure conservation index	0.50
SVM decision value	0.73
SVM RNA-class probability	0.835421
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1997464 110 + 22224390
CGCCGCUGUGGUGUGCUCACUCACUCGCUUUCGCUCUGAAAGCUCAGUUCGCUCU------CUCUCCUGGGGAGCUUUCGCUCCGUGAUCAUUUUGAAUUCUUU----GAUGGAGGGGGG
.((.(((((((((....))).)))..((((((.....))))))..)))..)).((------((((((...(((((....)))))...((((............)----))))))))))). ( -36.90)
>DroSec_CAF1 29479 95 + 1
CGCCACUGUGGUGUACUCACUCACUCUCUUUCGCUCUGAAAGCUCAGUUUGCUCUCU----CUCUCCUGGGGAGCUUUCGCUCAGCGAUCAUAUGG-----UUU----------------
.((((..((((((....))).)))......(((((.(((((((((((....))..((----(......))))))))))))...))))).....)))-----)..---------------- ( -28.10)
>DroSim_CAF1 23684 93 + 1
CGCCACUGUAGUGUACUCACUCACUCUCUUUCGCUCUGAAAGCUCAGUUCGCUCU------CUCUCCUGGGGAGCUUUCGCUCAGCGAUCAUAUGG-----UUU----------------
.((((..((((((....)))).))......(((((.(((((((((((....))((------(......))))))))))))...))))).....)))-----)..---------------- ( -26.10)
>DroEre_CAF1 19257 104 + 1
AGCCACUGUAGAUUAC----UUACUCUUCUUCUCUCUGAAAGCUCAGUGCGCUCUCUCUCUCUCUCCAGGGGAGCUUUUGCUCAGCGAUCAUAUGG-----UUUUUUUUUUGG-------
(((((.(((.((((..----.........(((.....))).(((.((((.((((((.((........))))))))...)))).)))))))))))))-----))..........------- ( -21.10)
>DroYak_CAF1 29831 92 + 1
CGCUACUGUGGACUAC----GUGCUCUUCUGCUCUCUGAAAGCUCAGUGCGCUCUUU--CUCUCUGCAGAGGAGCUUUCGCUCAGCGAUCAUAUGG-----CU-----------------
.((((.(((((.....----..((((((((((.....(((((...((....))))))--).....))))))))))..((((...))))))))))))-----).----------------- ( -32.10)
>consensus
CGCCACUGUGGUGUACUCACUCACUCUCUUUCGCUCUGAAAGCUCAGUUCGCUCU_U____CUCUCCUGGGGAGCUUUCGCUCAGCGAUCAUAUGG_____UUU________________
..............................(((((.(((((((((((....))........(((....))))))))))))...)))))................................ (-14.44 = -14.84 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	1,997,464 – 1,997,574
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.62
Mean single sequence MFE	-28.76
Consensus MFE	-13.18
Energy contribution	-13.66
Covariance contribution	0.48
Combinations/Pair	1.14
Mean z-score	-1.81
Structure conservation index	0.46
SVM decision value	0.37
SVM RNA-class probability	0.707259
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1997464 110 - 22224390
CCCCCCUCCAUC----AAAGAAUUCAAAAUGAUCACGGAGCGAAAGCUCCCCAGGAGAG------AGAGCGAACUGAGCUUUCAGAGCGAAAGCGAGUGAGUGAGCACACCACAGCGGCG
.....(((((((----(............))))...(((((....)))))...)))).(------(((((.......))))))...((....))..(((.(((....))))))....... ( -35.90)
>DroSec_CAF1 29479 95 - 1
----------------AAA-----CCAUAUGAUCGCUGAGCGAAAGCUCCCCAGGAGAG----AGAGAGCAAACUGAGCUUUCAGAGCGAAAGAGAGUGAGUGAGUACACCACAGUGGCG
----------------...-----((((....(((((((((....))))..........----.((((((.......))))))..)))))......(((.(((....)))))).)))).. ( -31.60)
>DroSim_CAF1 23684 93 - 1
----------------AAA-----CCAUAUGAUCGCUGAGCGAAAGCUCCCCAGGAGAG------AGAGCGAACUGAGCUUUCAGAGCGAAAGAGAGUGAGUGAGUACACUACAGUGGCG
----------------...-----((((....(((((((((....)))).........(------(((((.......))))))..)))))......((.((((....)))))).)))).. ( -30.30)
>DroEre_CAF1 19257 104 - 1
-------CCAAAAAAAAAA-----CCAUAUGAUCGCUGAGCAAAAGCUCCCCUGGAGAGAGAGAGAGAGCGCACUGAGCUUUCAGAGAGAAGAAGAGUAA----GUAAUCUACAGUGGCU
-------............-----((((..(((..((..((.....((((...)))).......((((((.......)))))).............)).)----)..)))....)))).. ( -20.50)
>DroYak_CAF1 29831 92 - 1
-----------------AG-----CCAUAUGAUCGCUGAGCGAAAGCUCCUCUGCAGAGAG--AAAGAGCGCACUGAGCUUUCAGAGAGCAGAAGAGCAC----GUAGUCCACAGUAGCG
-----------------..-----..........(((((((....))))((((....))))--....)))((((((.((((.....))))....(..(..----...)..).)))).)). ( -25.50)
>consensus
________________AAA_____CCAUAUGAUCGCUGAGCGAAAGCUCCCCAGGAGAG____A_AGAGCGAACUGAGCUUUCAGAGCGAAAGAGAGUGAGUGAGUACACCACAGUGGCG
................................(((((((((....))))................(((((.......))))).............))))).................... (-13.18 = -13.66 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:33 2006