Locus 4677

Sequence ID	X_DroMel_CAF1
Location	12,195,072 – 12,195,256
Length	184
Max. P	0.934791

overview

Window 3

Location	12,195,072 – 12,195,184
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.42
Mean single sequence MFE	-35.03
Consensus MFE	-15.76
Energy contribution	-18.07
Covariance contribution	2.31
Combinations/Pair	1.24
Mean z-score	-2.25
Structure conservation index	0.45
SVM decision value	1.24
SVM RNA-class probability	0.934791
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12195072 112 - 22224390
GGGCGGGUAGGUGCGGCAG---GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAUGGCAGCGCUGAAGCGAUGGCUUACAGUGCGGCAAAAAUCG-----UUGGUAAUAGAAUG
.(((((.....(((.((..---....((((((((((((...((....))......))))))))))))((((((((....)))).)))))).)))....)))-----))............ ( -42.80)
>DroSec_CAF1 21377 112 - 1
GGGCGGCUGGGUGCGGCAG---GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAUGGAAGCGCUGAAGCGAUGGCUUACAGUGCGGCAAAAAUCG-----UUGUUAAUAAAAAG
.((((((...(..((((((---.....))))))..)...................((((......((((((((((....)))).)))))).)))).....)-----)))))......... ( -37.50)
>DroSim_CAF1 22601 112 - 1
GGGCGGGUGGGUGCGGCAG---GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAUGGAAGCGCUGAAGCGAUGGCUUACAGUGCGGCAAAAAUCG-----UUGGUAAUAAAAAG
.((((((((.(..((((((---.....))))))..)..........)))......((((......((((((((((....)))).)))))).))))...)))-----))............ ( -37.00)
>DroEre_CAF1 20767 95 - 1
GAGGCGGUGGGAGUGGCAG---GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAU-----------------GGCGUACAGUGCGGCAAAAAUCU-----GUGGUUACAAAGAG
....(..((..(.(.((((---(((.((((((((((((...((....))......))))))-----------------)))((.....)))))...)))))-----)).))..))..).. ( -26.80)
>DroYak_CAF1 5952 112 - 1
CUGAGGGCGGGUGUGGCAG---GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAUGGGAGCGCUCAAGCGAUGGCUUACAGUGCGCCAAAAAUCC-----GUGAUAAUAAAAUG
......((((((.((((..---....(((.((((((((...((....))......)))))))).)))((.(((((....))))...).))))))...))))-----))............ ( -37.70)
>DroAna_CAF1 33355 118 - 1
CGGCAGCCAGAUCCUGGAGCAUAGGGAGUGGCAUCCACAAGGUAAACACAAAUUGUUGCAUGGGUGCAGUGAUGCGGAGAUGGGCACUGAA--AGAAAUUCUAAAGGUGUUAUUAAGAUA
(.((.((((..(((((.....)))))..))))...................((..(((((....)))))..)))).).....((((((...--((.....))...))))))......... ( -28.40)
>consensus
GGGCGGGUGGGUGCGGCAG___GUUGGCUGCCGUGCAAAAGGUAAACACAAAUUGUUGCAUGGAAGCGCUGAAGCGAUGGCUUACAGUGCGGCAAAAAUCG_____GUGGUAAUAAAAAG
..........(((((((((.....((..((((........))))..))....)))))))))....((((((((((....)))).)))))).............................. (-15.76 = -18.07 +   2.31)

alignment

secondary structure

dotplot

Window 4

Location	12,195,147 – 12,195,256
Length	109
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	84.85
Mean single sequence MFE	-37.16
Consensus MFE	-23.94
Energy contribution	-25.06
Covariance contribution	1.12
Combinations/Pair	1.18
Mean z-score	-2.14
Structure conservation index	0.64
SVM decision value	0.36
SVM RNA-class probability	0.705955
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12195147 109 - 22224390
AAUGAAGCUCGAAAUGAAAAGCCAGCCCAUGCAAAAAACGGCAAGGGGGGCGUGGUCG---U-----GGGUGAAUGUGAGGGGCGGGUAGGUGCGGCAGGUUGGCUGCCGUGCAAAA
......(((((..((((...(((..(((.(((........))).))).)))....)))---)-----................)))))..(..((((((.....))))))..).... ( -36.77)
>DroSec_CAF1 21452 107 - 1
AAUGAAGCUCGAAAUGAAAAGCCAGCCCAUGCAAAAACCGGCAAGG-GGGCGUGGUCG---U-----GGGUGAAUGUG-GGGGCGGCUGGGUGCGGCAGGUUGGCUGCCGUGCAAAA
...................((((.((((..(((...(((.((....-..........)---)-----.)))...))).-.))))))))..(..((((((.....))))))..).... ( -38.24)
>DroSim_CAF1 22676 107 - 1
AAUGAAGCUCGAAAUGAAAAGCCAGCCCAUGCAAAAAACGGCAAGG-GGGCGUGGUCG---U-----GGGCGAAUGUG-GGGGCGGGUGGGUGCGGCAGGUUGGCUGCCGUGCAAAA
......((((....(....)(((.((((((((.....(((.(....-.).))).).))---)-----)))).......-..)))))))..(..((((((.....))))))..).... ( -37.40)
>DroEre_CAF1 20825 106 - 1
AAUGAAGCUCGAAAUGAAAAGCCAGCCAGUGCAAAAAACAGCAAGG-G-GCGUGGCUG---U-----GGGCGGGUGUG-GGAGGCGGUGGGAGUGGCAGGUUGGCUGCCGUGCAAAA
......(((((........((((((((..(((........)))...-)-)).))))).---)-----))))..(..((-(.((.(..(..(.....)..)..).)).)))..).... ( -34.20)
>DroYak_CAF1 6027 114 - 1
AAUGAAGCUCGAAAUGAAAAGCCAGCCUGUGCAAAAAACAGCCAGG-C-GGGUGGGCGGUGUUGGUUAAGGGGGCGUG-GCUGAGGGCGGGUGUGGCAGGUUGGCUGCCGUGCAAAA
......((((..........(((.(((((.((........))))))-)-.))).(((.(((((.........))))).-)))..))))..(..((((((.....))))))..).... ( -39.20)
>consensus
AAUGAAGCUCGAAAUGAAAAGCCAGCCCAUGCAAAAAACGGCAAGG_GGGCGUGGUCG___U_____GGGCGAAUGUG_GGGGCGGGUGGGUGCGGCAGGUUGGCUGCCGUGCAAAA
......((((..........((((((((.(((........)))....)))).))))...........))))...................(..((((((.....))))))..).... (-23.94 = -25.06 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:45 2006