Locus 10259

Sequence ID	3R_DroMel_CAF1
Location	27,473,811 – 27,473,950
Length	139
Max. P	0.959014

overview

Window 0

Location	27,473,811 – 27,473,913
Length	102
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	73.98
Mean single sequence MFE	-30.37
Consensus MFE	-17.49
Energy contribution	-17.61
Covariance contribution	0.11
Combinations/Pair	1.18
Mean z-score	-1.99
Structure conservation index	0.58
SVM decision value	1.47
SVM RNA-class probability	0.956895
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27473811 102 - 27905053
GGCGCGCAUUUUCAACAGCUGAAGCUAA------------AGCUGCAGCUGAAAAGCUGAAGUGGAAAGCUGCACUGGGAGAAAUUAAACAGCCAUUCGAGG-UUUUAUCAAACA---
(((((((.((((((.(((((........------------)))))(((((....)))))...)))))))).))..((.((....))...))))).......(-(((....)))).--- ( -29.00)
>DroSec_CAF1 29625 106 - 1
GGCGCGCAUUUUGAACAGCUGAAGCUGA------------AACUCCAGCUGAAAAGCUGAAGUGGAAAGCUGCACUGGGAGAAAUUGCACAGCCAUUUGAAGAUUUAAUCAAUGCUUU
((((.(((((((...(((.((.((((..------------.(((.(((((....))))).)))....)))).)))))...)))).))).).)))..((((........))))...... ( -32.70)
>DroSim_CAF1 29552 106 - 1
GGCGCGCAUUUUCAACAGCUGAAGCUGA------------AGCUGCAGCUGAAAAGCUGAAGUGGAAAGCUGCACUGGGAGAAAUUGCACAGCCAUUCGAGGAUUUUAUCAAACCUUU
((((.(((.((((..(((.((.((((..------------.(((.(((((....))))).)))....)))).)))))...)))).))).).)))....((((.(((....))))))). ( -35.80)
>DroEre_CAF1 29562 94 - 1
GGCGCGCAUUUUCAACAGCUGAAG------------------CUGCAGCUGAAAAGCUGAAGUGGAAAGCUGCACCGCGGAAAACUGAAUGGCCAUUCGAGGAUUUCAUCCA------
((.((((.((((((.((((....)------------------)))(((((....)))))...)))))))).)).))..(((....((((...((......))..))))))).------ ( -31.30)
>DroYak_CAF1 30818 100 - 1
GGCGCGCAUUUUCAACAGCUGAAG------------------CUGCAGCUGAAAAGCUGAAGUGGAAAGCUGCACUGGCAAAAACUGUAUGGCCAUUUGAAGAUUUCAUCAGACUGUU
(((((((.((((((.((((....)------------------)))(((((....)))))...)))))))).))....(((.....)))...))).(((((.(....).)))))..... ( -28.90)
>DroAna_CAF1 43238 114 - 1
GGCGCGCAAUUUCAACAGCUGAAUCUGAAACUGAAUCUGAAGCUGAGGCUGAAAAGCCAAAGUGGGUGGCUAUACACUGAAAAACA----AGCUCUCGGAAUAAUUAAUUAGACUAAC
(((..............)))...(((((.......(((((((((..((((....))))....(.((((......)))).)......----)))).)))))........)))))..... ( -24.50)
>consensus
GGCGCGCAUUUUCAACAGCUGAAGCUGA____________AGCUGCAGCUGAAAAGCUGAAGUGGAAAGCUGCACUGGGAAAAACUGAACAGCCAUUCGAAGAUUUAAUCAAACC_UU
(((............((((((.((((..............)))).))))))...((((.........))))....................)))........................ (-17.49 = -17.61 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	27,473,847 – 27,473,950
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.47
Mean single sequence MFE	-38.03
Consensus MFE	-19.61
Energy contribution	-20.17
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.99
Structure conservation index	0.52
SVM decision value	1.50
SVM RNA-class probability	0.959014
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27473847 103 - 27905053
GAGCGACAAACUUGCAAAAGUU---UUGUUGGUGGCCAGCGGCGCGCAUUUUCAACAGCUGA-AGCUAA------------AGCUGCAGCUGAAAAGCUGAA-GUGGAAAGCUGCACUGG
.(.((((((((((....))).)---)))))).)..((((..(((.((.((((((.(((((..-......------------)))))(((((....)))))..-.))))))))))).)))) ( -35.80)
>DroPse_CAF1 35034 106 - 1
GAGCGAGAAACUUUCAAAAGUUUUUUUGUUGGUCGCCAGCGGCGCGCAUUUUCAACAGCUGAGAGCUG-------------AGCUGAAGCUGAAAAGCUGGAAGCUGGUAGCCAGAG-CU
.((((((((((((....)))))))))..(((((..(((((..(............(((((.(....).-------------))))).((((....)))).)..)))))..))))).)-)) ( -39.20)
>DroSec_CAF1 29665 103 - 1
GAGCGACAAACUUGCAAAAGUU---UUGUUGGUCGCCAGCGGCGCGCAUUUUGAACAGCUGA-AGCUGA------------AACUCCAGCUGAAAAGCUGAA-GUGGAAAGCUGCACUGG
((.((((((((((....))).)---)))))).)).((((..(((.((.((((...((((...-.)))).------------.(((.(((((....))))).)-)).))))))))).)))) ( -37.10)
>DroEre_CAF1 29596 97 - 1
GAGCGACAAACUUGCAAAAGUU---UUGUUGGUCGCCAGCGGCGCGCAUUUUCAACAGCUGA-AG------------------CUGCAGCUGAAAAGCUGAA-GUGGAAAGCUGCACCGC
((.((((((((((....))).)---)))))).))....((((.((((.((((((.((((...-.)------------------)))(((((....)))))..-.)))))))).)).)))) ( -40.00)
>DroAna_CAF1 43274 115 - 1
AAGCGACAAACUUGAUAAAGUU---UUGUUGGUCGCCAGCGGCGCGCAAUUUCAACAGCUGA-AUCUGAAACUGAAUCUGAAGCUGAGGCUGAAAAGCCAAA-GUGGGUGGCUAUACACU
..(((((((((((....)))))---).....))))).(((.((.(((........(((((((-.((.......)).))...))))).((((....))))...-))).)).)))....... ( -36.90)
>DroPer_CAF1 32901 106 - 1
GAGCGAGAAACUUUCAAAAGUUUUUUUGUUGGUCGCCAGCGGCGCGCAUUUUCAACAGCUGAGAGCUG-------------AGCUGAAGCUGAAAAGCUGGAAGCUGGUAGCCAGAG-CU
.((((((((((((....)))))))))..(((((..(((((..(............(((((.(....).-------------))))).((((....)))).)..)))))..))))).)-)) ( -39.20)
>consensus
GAGCGACAAACUUGCAAAAGUU___UUGUUGGUCGCCAGCGGCGCGCAUUUUCAACAGCUGA_AGCUG_____________AGCUGAAGCUGAAAAGCUGAA_GUGGAAAGCUACAC_CU
..(((...(((((....)))))...(((((((...))))))))))((........((((.....))))...................((((....))))...........))........ (-19.61 = -20.17 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:51 2006