Locus 3964

Sequence ID	3L_DroMel_CAF1
Location	11,508,053 – 11,508,198
Length	145
Max. P	0.999608

overview

Window 6

Location	11,508,053 – 11,508,164
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.93
Mean single sequence MFE	-28.55
Consensus MFE	-17.89
Energy contribution	-19.70
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-3.64
Structure conservation index	0.63
SVM decision value	3.78
SVM RNA-class probability	0.999608
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11508053 111 + 23771897
---U----UAAAAAACUUAAUUGCUUAGAAUGAACUGCAUGAGUUAGCCUUCAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAACUGAUCACUA--
---(----((((((.............((((((((.((.((((......)))).))))))))))((((((....(((((((....))))))))))))).)))))))............-- ( -25.70)
>DroSec_CAF1 14017 104 + 1
--------UAUAACACUUGAUUGCUUAGAAUGAACU-CAUGAAC-----UCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAUUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA--
--------.........((((..(((((((((((((-((....(-----((((((.....)))))))....))((((((((....))))))))))))))))))...)))..))))...-- ( -29.20)
>DroSim_CAF1 12358 103 + 1
---------AUAACACUUGAAUGCUUAGAAUGAACU-CAUGAAU-----UCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA--
---------....((((((((((.((((((((((((-(((...(-----((((.(.((((....))))).))))).....)))))))))))))))..)))))....))))).......-- ( -29.20)
>DroYak_CAF1 12392 109 + 1
UCAUUGGCCAAAACACUUGAUUGCUUAGAAUGAACG-UG----------UCACAGCGUUCAUUUUAGCCUCUGAAAAUGAACAAGUUCAUUUGGCUUCAUUUUCAAAAGUGAUCACAAGA
...(((((((((..(((((...(((.((((((((((-(.----------.....)))))))))))))).((.......)).)))))...)))))).((((((....))))))...))).. ( -30.10)
>consensus
________UAAAACACUUGAUUGCUUAGAAUGAACU_CAUGAAU_____UCAAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA__
.................(((((((((((((((((((.............((((.(.((((....))))).))))(((((((....))))))).))))))))))...)))))))))..... (-17.89 = -19.70 +   1.81)

alignment

secondary structure

dotplot

Window 7

Location	11,508,086 – 11,508,198
Length	112
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	83.29
Mean single sequence MFE	-24.46
Consensus MFE	-14.82
Energy contribution	-15.30
Covariance contribution	0.48
Combinations/Pair	1.22
Mean z-score	-2.21
Structure conservation index	0.61
SVM decision value	0.47
SVM RNA-class probability	0.750154
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11508086 112 + 23771897
GAGUUAGCCUUCAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAACUGAUCACUA---UGAUCAAGAAUUUGUCGCUGUGUUUUCUUAUUUU
(((..(((.....((((..((..(((((((....(((((((....))))))))))))))..........(((((....---.)))))......)).))))..)))..)))..... ( -24.20)
>DroSec_CAF1 14048 106 + 1
GAAC-----UCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAUUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA----GAUUAAUAAUUUGUCGCUGUGUUUUCCUAUUUU
(((.-----.((.((((......(((((((....(((((((....))))))))))))))..........(((((....----))))).........)))).))..)))....... ( -22.40)
>DroSim_CAF1 12388 107 + 1
GAAU-----UCAAAGCGUUCCUUUGAGCCAUUGAAAAUGAAUGAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA---UGAUCAAUAAUUUGUCGCUGUGUUUUCCUAUUUU
(((.-----.((.((((......(((((((....(((((((....))))))))))))))..........(((((....---.))))).........)))).))..)))....... ( -25.20)
>DroEre_CAF1 8380 106 + 1
---------UCGAAGCGUUCAUUUUAGCCUUCGGAAAUGAAUAGGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACCAGACUGAUGAACAAUUUGUCGCCGUGUUUUCUUAUUUU
---------..((((.(((......)))))))((..(..(((..((((((((((((((((((....))))))..)))))...))))))).)))..)..))............... ( -24.00)
>DroYak_CAF1 12430 106 + 1
---------UCACAGCGUUCAUUUUAGCCUCUGAAAAUGAACAAGUUCAUUUGGCUUCAUUUUCAAAAGUGAUCACAAGACUGAUCCACAAUUUGUCGCUGUGUUUUCUUAUUUU
---------.(((((((..((..((......(((((((((.((((....))))...)))))))))...(((((((......)))).)))))..)).)))))))............ ( -26.50)
>consensus
GA_______UCAAAGCGUUCAUUUGAGCCAUUGAAAAUGAAUAAGUUCAUUUUGGUUCAUUUUUAAAAGUGAUCACUA___UGAUCAACAAUUUGUCGCUGUGUUUUCUUAUUUU
..........((.((((......(((((((....(((((((....)))))))))))))).........(((((((......))))).)).......)))).))............ (-14.82 = -15.30 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:12 2006