Locus 3703

Sequence ID	3L_DroMel_CAF1
Location	10,769,375 – 10,769,506
Length	131
Max. P	0.680257

overview

Window 5

Location	10,769,375 – 10,769,474
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-19.52
Consensus MFE	-13.15
Energy contribution	-12.98
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-1.69
Structure conservation index	0.67
SVM decision value	0.30
SVM RNA-class probability	0.680257
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10769375 99 + 23771897
ACCCCC--UCUU----UACCAAUUUCUGGUGCGAACAUCG-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACA--
......--....----(((.......(((((((.....))-------------)))))..................((((((((((.....))))).)))))...........)))..-- ( -18.70)
>DroSec_CAF1 103022 101 + 1
ACCCCCCCUCUU----UACCAUUUUCUGGUGCGAACAUCG-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAGCGUACA--
.......(.(((----(.........(((((((.....))-------------)))))..................((((((((((.....))))).)))))......)))).)....-- ( -19.20)
>DroSim_CAF1 105918 98 + 1
ACCCCC---CUU----UCCCAAUUUCUGGUGCGAACAUCG-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAGCGUAGA--
.(..(.---(((----(.........(((((((.....))-------------)))))..................((((((((((.....))))).)))))......)))).)..).-- ( -18.80)
>DroEre_CAF1 107899 98 + 1
ACCCC-----UU----UCCCAAUUUCUGGUGCGAACAUCU-------------AGCCACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACACA
.....-----..----............((((((((....-------------......)))).............((((((((((.....))))).)))))...........))))... ( -16.40)
>DroYak_CAF1 119210 98 + 1
ACCCC---UCUU----UCCCAAUUUCUGGUGCGAACAUCG-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACA--
.....---....----..........(((((((.....))-------------)))))..................((((((((((.....))))).)))))................-- ( -18.50)
>DroAna_CAF1 104044 115 + 1
UUUUUU---UUUUUGUUGUUAAAGUUCGGUGUGAAAAUCUGCCAUCGAUUGCUCACUCUGUUCAACUUUCAACUUAUAGUUUUGCGACUUUCGCAGCAAGUGACACAGAAAAAACAUA--
...(((---(((((((.((((..(..(((.((((.((((.......))))..)))).)))..)..................(((((.....)))))....))))))))))))))....-- ( -25.50)
>consensus
ACCCCC___CUU____UCCCAAUUUCUGGUGCGAACAUCG_____________CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACA__
............................((((((((.......................)))).............((((((((((.....))))).)))))...........))))... (-13.15 = -12.98 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	10,769,409 – 10,769,506
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.86
Mean single sequence MFE	-13.30
Consensus MFE	-10.70
Energy contribution	-11.14
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-0.87
Structure conservation index	0.80
SVM decision value	0.00
SVM RNA-class probability	0.534300
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10769409 97 + 23771897
-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACA----------AAACAACAAAACAAAAAAAAAAAAAGGAAAGG
-------------............(((((......((((((((((.....))))).)))))...........((...----------..))......................))))). ( -13.40)
>DroSec_CAF1 103058 88 + 1
-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAGCGUACA----------AAAAAAUA--------AAAA-AAAAGGAAAGG
-------------............(((((......((((((((((.....))))).)))))((.(.....).))...----------........--------....-.....))))). ( -13.40)
>DroSim_CAF1 105951 89 + 1
-------------CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAGCGUAGA----------AAAAAAUA--------AAAAAAAAAGGAAAGG
-------------..(((((((...................(((((.....)))))...(((...)))..))))))).----------........--------................ ( -13.40)
>DroEre_CAF1 107930 104 + 1
-------------AGCCACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACACAGAUAUAUAAAA-AACAAAA--AAAAAAACAAAAGGAAAGG
-------------............(((((......((((((((((.....))))).)))))....((.....))................-.......--.............))))). ( -12.90)
>DroAna_CAF1 104081 100 + 1
GCCAUCGAUUGCUCACUCUGUUCAACUUUCAACUUAUAGUUUUGCGACUUUCGCAGCAAGUGACACAGAAAAAACAUA----------GAA----------AAAUAACAAAAAGGAAAGG
.((...((....))..((((((((.(((.((((.....))).((((.....))))).)))))).))))).........----------...----------............))..... ( -13.40)
>consensus
_____________CGCUACGUUCAACUUUCAACUUACAUUUUUGCGACUUUCGCAGCAAGUGACACACAAAACGUACA__________AAA_AACA_____AAAAAAAAAAAAGGAAAGG
.........................(((((......((((((((((.....))))).)))))....((.....)).......................................))))). (-10.70 = -11.14 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:44 2006