Locus 3095

Sequence ID	3R_DroMel_CAF1
Location	8,172,638 – 8,172,784
Length	146
Max. P	0.614994

overview

Window 3

Location	8,172,638 – 8,172,753
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	87.31
Mean single sequence MFE	-21.95
Consensus MFE	-19.23
Energy contribution	-19.03
Covariance contribution	-0.19
Combinations/Pair	1.07
Mean z-score	-1.45
Structure conservation index	0.88
SVM decision value	0.11
SVM RNA-class probability	0.589610
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8172638 115 + 27905053
UGGUGUGCCCACUCACAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGGCUUUUUGAAUGACAUCGCUUGAACUU-UUCAAGCAAUAAAGUA-ACGUACAAUAAUA---AUUUUCUU
.(((((...(((......))).)))))....(((((..((((((((((((((((((..((......))((((((....-.))))))...))))).-.)))).)))))))---))))))). ( -21.60)
>DroVir_CAF1 150994 106 + 1
--GCGUGCGCGCUCAUAUGUGAACAUUUAUUGGAAAACAUUAUAAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUUUUUCAAGCUAUAAAGUCCAGGGACAAUAAC------------
--(((....)))....(((....)))(((((.((((((((........)))..))))).)))))....(((((((....)))))))......(((....)))......------------ ( -20.10)
>DroPse_CAF1 102910 116 + 1
--GUGUGCCCACUCAUAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUU-UUCAAGCAAUAAAGUA-ACGCACAAUAAUACAUAUUUCCCU
--.(((((.(((......))).((.((((((...........(((((((........)))))))....((((((....-.)))))))))))))).-..)))))................. ( -21.10)
>DroGri_CAF1 134159 105 + 1
--GCGUGCGCGCUCAUAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUU-UUCAAGCAAUAAAGUCCAGGCACAAUAAC------------
--..((((.(((......)))........(((((........(((((((........)))))))....((((((....-.)))))).......)))))))))......------------ ( -23.50)
>DroMoj_CAF1 138070 106 + 1
--GCGUGCGCGCUCAUAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUUUUUCAAGCAAUAAAGUCCAGGCACAAUAAC------------
--..((((.(((......)))........(((((........(((((((........)))))))....(((((((....))))))).......)))))))))......------------ ( -24.30)
>DroPer_CAF1 104283 116 + 1
--GUGUGCCCACUCAUAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUU-UUCAAGCAAUAAAGUA-ACGCACAAUAAUACAUAUUUCCCU
--.(((((.(((......))).((.((((((...........(((((((........)))))))....((((((....-.)))))))))))))).-..)))))................. ( -21.10)
>consensus
__GCGUGCCCACUCAUAUGUGAACAUUUAUUGGAAAACAUUAUUAUUUAUGACUUUUUGAAUGACAUCGCUUGAACUU_UUCAAGCAAUAAAGUA_ACGCACAAUAAC____________
....((((.(((......))).((..(((((.((((((((........)))..))))).)))))....(((((((....)))))))......))....)))).................. (-19.23 = -19.03 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	8,172,678 – 8,172,784
Length	106
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	80.34
Mean single sequence MFE	-22.08
Consensus MFE	-13.14
Energy contribution	-13.83
Covariance contribution	0.70
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.59
SVM decision value	0.17
SVM RNA-class probability	0.614994
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8172678 106 - 27905053
-GAAAAAAUUGUG---CGCUCGCUAUUUCCGUUAUAAGAAAAU---UAUUAUUGUACGU-UACUUUAUUGCUUGAA-AAGUUCAAGCGAUGUCAUUCAAAAAGCCAUAAAUAAUA
-.......(((((---.(((.........(((.((((......---..))))...))).-.....((((((((((.-....))))))))))..........))))))))...... ( -18.60)
>DroPse_CAF1 102948 109 - 1
-GCAGGCAUUUUU---UUUUAACAAUUUCCGCUGGAGGGAAAUAUGUAUUAUUGUGCGU-UACUUUAUUGCUUGAA-AAGUUCAAGCGAUGUCAUUCAAAAAGUCAUAAAUAAUA
-...(((......---...((((.((((((.......))))))..((((....))))))-))...((((((((((.-....))))))))))...........))).......... ( -22.50)
>DroEre_CAF1 67101 104 - 1
-GAAAAA-UUGAG---AGCUCGCAAUUUCCGUUAUAAGGAAAU----AUUAUUGUACGU-UACUUUAUUGCUUGAA-AAGUUCAAGCGAUGUCAUUCAAAAAGCCAUAAAUAAUA
-......-(((((---(((..(((((((((.......))))..----...)))))..))-)....((((((((((.-....))))))))))...)))))................ ( -19.40)
>DroYak_CAF1 66125 104 - 1
-GAAAAA-AUGCG---AACUCGCAAUUUCCGUUAUAAGGAAAU----AUUAUUGUACGU-UACUUUAUUGCUUGAA-AAGUUCAAGCGAUGUCAUUCAAAAAGCCAUAAAUAAUA
-(((...-.((((---....))))((((((.......))))))----............-.....((((((((((.-....))))))))))...))).................. ( -21.70)
>DroMoj_CAF1 138108 101 - 1
AUAAAAAAUUGAAGUCCCGCCGCAAUAUCCGUU--------------GUUAUUGUGCCUGGACUUUAUUGCUUGAAAAAGUUCAAGCGAUGUCAUUCAAAAAGUCAUAAAUAAUA
........(((((((((.(.(((((((......--------------..))))))).).))))..(((((((((((....)))))))))))...)))))................ ( -27.80)
>DroPer_CAF1 104321 109 - 1
-GCAGGCAUUUUU---UUUUAACAAUUUCCGCUGGAGGGAAAUAUGUAUUAUUGUGCGU-UACUUUAUUGCUUGAA-AAGUUCAAGCGAUGUCAUUCAAAAAGUCAUAAAUAAUA
-...(((......---...((((.((((((.......))))))..((((....))))))-))...((((((((((.-....))))))))))...........))).......... ( -22.50)
>consensus
_GAAAAAAUUGUG___AGCUCGCAAUUUCCGUUAUAAGGAAAU____AUUAUUGUACGU_UACUUUAUUGCUUGAA_AAGUUCAAGCGAUGUCAUUCAAAAAGCCAUAAAUAAUA
.....................((.((((((.......))))))......................(((((((((((....)))))))))))...........))........... (-13.14 = -13.83 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:58 2006