Locus 694

Sequence ID	2R_DroMel_CAF1
Location	3,412,266 – 3,412,412
Length	146
Max. P	0.988643

overview

Window 2

Location	3,412,266 – 3,412,372
Length	106
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	81.87
Mean single sequence MFE	-32.38
Consensus MFE	-19.60
Energy contribution	-22.08
Covariance contribution	2.48
Combinations/Pair	1.09
Mean z-score	-3.09
Structure conservation index	0.61
SVM decision value	2.13
SVM RNA-class probability	0.988643
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3412266 106 + 20766785
CGUGGCCACCAAGUGCAUUCUUUGCGAGCGCCAAACAAGUUCCACUUCCACUUACAACUCCACUUGAAGCACCACUCGCAGCUCCACUUGGAGCUCCAGUUGGCCA
..((((((.((((((((.....)))((((.........))))...................))))).......(((.(.((((((....))))))).))))))))) ( -30.40)
>DroSec_CAF1 42452 82 + 1
CGUGGCCACCAAGUGCAUUCUUUGCGAGCGCCAAACCAGUUCCACUUCCACUUACAGCUCCACU------------------------UGGAGCUCCAGUUGGCCA
..((((((.((((((((.....)))((((.........)))).......))))..((((((...------------------------.))))))...).)))))) ( -26.20)
>DroSim_CAF1 41693 106 + 1
CGUGGCCACCAAGUGCAUUCUUCGCGAGCGCCAAACCAGUUCCACUUCCACUUACAGCUCCACUUGGAGCUCCACUUGGAGCUCCACUUGGAGCUCCAGUUGGCCA
..((((((.(((((((.......))((((.........)))).......))))..(((((((..(((((((((....)))))))))..)))))))...).)))))) ( -45.20)
>DroEre_CAF1 42973 93 + 1
CGUGGCCACCAAGUGCAUUCUUUGCGAGCGCCAAACCAGUUCCACUUCCACUCACACCUCCACUUGAGG------------CUCCACUCGCAGCUCCAGUGG-GCA
.((((.....(((((((.....)))((((.........)))).)))))))).......((((((.(..(------------((.(....).)))..))))))-).. ( -22.30)
>DroYak_CAF1 45619 106 + 1
UGUGGCCACCAAGUGCAUUCUUUGCGAGCGCCAAACCAGUGCCACUUCCACUAACAGCUCCACUUGGAGCUCUACUUGGAGCUCUACUUGCAGCUCCAGUUGGCCA
..(((((..((((((((.....)))((((.((((...((((.......))))...((((((....))))))....)))).)))).))))).(((....)))))))) ( -37.80)
>consensus
CGUGGCCACCAAGUGCAUUCUUUGCGAGCGCCAAACCAGUUCCACUUCCACUUACAGCUCCACUUGAAGC_C_ACU_G_AGCUCCACUUGGAGCUCCAGUUGGCCA
..(((((...(((((((.....)))((((.........)))).))))..(((...(((((((..((.((((((....)))))).))..)))))))..))).))))) (-19.60 = -22.08 +   2.48)

alignment

secondary structure

dotplot

Window 3

Location	3,412,266 – 3,412,372
Length	106
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	81.87
Mean single sequence MFE	-39.10
Consensus MFE	-30.05
Energy contribution	-32.16
Covariance contribution	2.11
Combinations/Pair	1.09
Mean z-score	-2.44
Structure conservation index	0.77
SVM decision value	1.81
SVM RNA-class probability	0.978332
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3412266 106 - 20766785
UGGCCAACUGGAGCUCCAAGUGGAGCUGCGAGUGGUGCUUCAAGUGGAGUUGUAAGUGGAAGUGGAACUUGUUUGGCGCUCGCAAAGAAUGCACUUGGUGGCCACG
(((((((((.(((((((....)))))).).)))......(((((((..(((.(..((((..((.(((....))).))..))))..).))).))))))))))))).. ( -39.80)
>DroSec_CAF1 42452 82 - 1
UGGCCAACUGGAGCUCCA------------------------AGUGGAGCUGUAAGUGGAAGUGGAACUGGUUUGGCGCUCGCAAAGAAUGCACUUGGUGGCCACG
...(((..((.((((((.------------------------...)))))).))..)))..((((.((..(....(((.((.....)).)))..)..))..)))). ( -29.70)
>DroSim_CAF1 41693 106 - 1
UGGCCAACUGGAGCUCCAAGUGGAGCUCCAAGUGGAGCUCCAAGUGGAGCUGUAAGUGGAAGUGGAACUGGUUUGGCGCUCGCGAAGAAUGCACUUGGUGGCCACG
...(((..((.(((((((..(((((((((....)))))))))..))))))).))..)))..((((.((..(....(((.((.....)).)))..)..))..)))). ( -52.60)
>DroEre_CAF1 42973 93 - 1
UGC-CCACUGGAGCUGCGAGUGGAG------------CCUCAAGUGGAGGUGUGAGUGGAAGUGGAACUGGUUUGGCGCUCGCAAAGAAUGCACUUGGUGGCCACG
...-(((((.(.....).))))).(------------(((((((((.(..(((((((....((.(((....))).))))))))).....).))))))).))).... ( -32.70)
>DroYak_CAF1 45619 106 - 1
UGGCCAACUGGAGCUGCAAGUAGAGCUCCAAGUAGAGCUCCAAGUGGAGCUGUUAGUGGAAGUGGCACUGGUUUGGCGCUCGCAAAGAAUGCACUUGGUGGCCACA
((((((.((((((((........))))))((((.((((.((((..((.((..((......))..)).))...)))).))))(((.....))))))))))))))).. ( -40.70)
>consensus
UGGCCAACUGGAGCUCCAAGUGGAGCU_C_AGU_G_GCUCCAAGUGGAGCUGUAAGUGGAAGUGGAACUGGUUUGGCGCUCGCAAAGAAUGCACUUGGUGGCCACG
(((((.((..((((((((..((((((((......))))))))..)))))))....((((..((.(((....))).))..))))...........)..))))))).. (-30.05 = -32.16 +   2.11)

alignment

secondary structure

dotplot

Window 4

Location	3,412,304 – 3,412,412
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-39.78
Consensus MFE	-30.61
Energy contribution	-33.04
Covariance contribution	2.43
Combinations/Pair	1.15
Mean z-score	-2.15
Structure conservation index	0.77
SVM decision value	1.52
SVM RNA-class probability	0.960803
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3412304 108 - 20766785
UUACGGCUCUUUGCCAGCGGCGUCUCCAAUGCAUCCGCUUUGGCCAACUGGAGCUCCAAGUGGAGCUGCGAGUGGUGCUUCAAGUGGAGUUGUAAGUGGAAGUGGAAC
....(((.....)))....((((.....)))).(((((((...(((..((.(((((((..((((((.((.....))))))))..))))))).))..)))))))))).. ( -41.70)
>DroSec_CAF1 42490 84 - 1
UUACGGCUCUUUGCCAGCGGCGUCUCCAAUGCAUCCGCUUUGGCCAACUGGAGCUCCA------------------------AGUGGAGCUGUAAGUGGAAGUGGAAC
....(((.....)))....((((.....)))).(((((((...(((..((.((((((.------------------------...)))))).))..)))))))))).. ( -32.00)
>DroSim_CAF1 41731 107 - 1
NNNNNNCUC-UUGCCAGCGGCGUCUCCAAUGCAUCCGCUUUGGCCAACUGGAGCUCCAAGUGGAGCUCCAAGUGGAGCUCCAAGUGGAGCUGUAAGUGGAAGUGGAAC
.........-..(((...)))............(((((((...(((..((.(((((((..(((((((((....)))))))))..))))))).))..)))))))))).. ( -50.00)
>DroEre_CAF1 43011 95 - 1
UUACGGCUCUUUGCCAGCGGCGUCUCCAAUGCAUCCGCUUUGC-CCACUGGAGCUGCGAGUGGAG------------CCUCAAGUGGAGGUGUGAGUGGAAGUGGAAC
....(((.....)))....((((.....)))).((((((((..-(((((.(.....).))))).(------------((((.....))))).......)))))))).. ( -32.50)
>DroYak_CAF1 45657 107 - 1
-UACGGCUCUUUGCCAGCGGCAUCUCCAAUGCAUCCGCUUUGGCCAACUGGAGCUGCAAGUAGAGCUCCAAGUAGAGCUCCAAGUGGAGCUGUUAGUGGAAGUGGCAC
-...(((.....))).((.((((.....))))...((((((.((.((((((((((........))))))).....((((((....))))))))).)).)))))))).. ( -42.70)
>consensus
UUACGGCUCUUUGCCAGCGGCGUCUCCAAUGCAUCCGCUUUGGCCAACUGGAGCUCCAAGUGGAGCU_C_AGU_G_GCUCCAAGUGGAGCUGUAAGUGGAAGUGGAAC
....(((.....)))....((((.....)))).((((((((.((....((.(((((((..((((((((......))))))))..))))))).)).)).)))))))).. (-30.61 = -33.04 +   2.43)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:50 2006