Locus 3142

Sequence ID	3R_DroMel_CAF1
Location	8,293,381 – 8,293,574
Length	193
Max. P	0.991556

overview

Window 0

Location	8,293,381 – 8,293,496
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-24.05
Consensus MFE	-15.30
Energy contribution	-15.67
Covariance contribution	0.37
Combinations/Pair	1.07
Mean z-score	-2.91
Structure conservation index	0.64
SVM decision value	2.27
SVM RNA-class probability	0.991556
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8293381 115 - 27905053
AAGUGAACACGUCGCUAAGCGAAAGCUAAGCAAAUAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGCAGUAAAGU-GCAAGUUAAAGUGAAUCAAUUAAAAGUAACCAGCAACC
...(((.(((...(((.(((....))).))).....(((..((((((((.....))))..(----(........))...))-))..)))...)))..))).................... ( -23.70)
>DroSim_CAF1 5013 117 - 1
AAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGCAUUGAAGU-GCAAGUUAAAGUGAAUCAAUUU-AAGUAACCAGCA-CC
...(((.(((...(((.(((....))).))).....(((..((((((((.....)))).......((((....))))..))-))..)))...)))..)))....-............-.. ( -25.30)
>DroEre_CAF1 5015 100 - 1
AAGUGAACACAUCGCUGAGCGAAAGCUAAGCAACCAAAUAAGCGCAGCUGAUCAAGCUAAA----CAAACUGCAGUGAAGU-------------G---CAAGUAAAAUAAACUAGCAAUC
.......(((...(((.(((....))).)))..............((((.....))))...----.........)))...(-------------(---(.(((.......))).)))... ( -21.80)
>DroYak_CAF1 4950 116 - 1
AACUGAAAACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGCAGUAACGUUGCAAGUUAAAGUGAAUCAAGUAACAGUAAUUAGGAAAC
.((((........(((.(((....))).)))...........(((((((.....))))...----.((..(((((.....)))))..))...)))..........))))........... ( -25.40)
>consensus
AAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA____CAAUCUGCAGUAAAGU_GCAAGUUAAAGUGAAUCAAGUAAAAGUAACCAGCAACC
.((((........(((.(((....))).)))..............((((.....))))..............))))............................................ (-15.30 = -15.67 +   0.37)

alignment

secondary structure

dotplot

Window 1

Location	8,293,420 – 8,293,536
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.72
Mean single sequence MFE	-25.62
Consensus MFE	-15.50
Energy contribution	-17.75
Covariance contribution	2.25
Combinations/Pair	1.20
Mean z-score	-2.60
Structure conservation index	0.60
SVM decision value	1.59
SVM RNA-class probability	0.965942
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8293420 116 - 27905053
GCGCUUCGUCUACGGAGCGACAAUUCAAUUUAAACAAGCAAAGUGAACACGUCGCUAAGCGAAAGCUAAGCAAAUAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGCAGUAAAG
((((((((....))))))(((..((((.(((........))).))))...)))(((.(((....))).)))............))((((.....))))...----............... ( -29.70)
>DroPse_CAF1 5303 102 - 1
CCGCCAGUUUCUCUUCGCAGCAAUUCAAUUCAAACAAGCGAAGAGAACACAUCUCAAAAGUGAAACAAAGCGAGCUACCAA------------AAGCCAAA----ACAACUGCAAAAA--
..((.(((((((((((((...................))))))))).(((.........))).........(.(((.....------------.))))...----..)))))).....-- ( -19.81)
>DroSec_CAF1 4983 120 - 1
CCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGCAUUAAAG
.(((((........)))))..................(((...((........(((.(((....))).)))..............((((.....)))).......))...)))....... ( -23.70)
>DroSim_CAF1 5050 120 - 1
CCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGCAUUGAAG
...(((((....((((((((......................(....).....(((.(((....))).)))..........))))((((.....))))..........))))...))))) ( -26.90)
>DroEre_CAF1 5039 116 - 1
CUGCUUGUUUCUUUUAGCGUCAUUUCAAUUCAAAGAAGCAAAGUGAACACAUCGCUGAGCGAAAGCUAAGCAACCAAAUAAGCGCAGCUGAUCAAGCUAAA----CAAACUGCAGUGAAG
((((..((((..((((((.((((((...(((...)))...))))))....((((((((((....)))..((..........)).)))).)))...))))))----.)))).))))..... ( -28.70)
>DroYak_CAF1 4990 116 - 1
CCGCUUGGUUCUCUUAGCGUCAAUUCAAUUCAAACAAGCAAACUGAAAACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGCAGUAACG
.(((((((((.((...((...................)).....)).)))...(((.(((....))).))).......)))))).((((.....))))...----............... ( -24.91)
>consensus
CCGCUUCGUUCUCUGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA____CAAUCUGCAGUAAAG
.(((((((....)))))))..................(((.............(((.(((....))).)))..............((((.....))))............)))....... (-15.50 = -17.75 +   2.25)

alignment

secondary structure

dotplot

Window 2

Location	8,293,456 – 8,293,574
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.85
Mean single sequence MFE	-31.92
Consensus MFE	-16.49
Energy contribution	-18.13
Covariance contribution	1.64
Combinations/Pair	1.19
Mean z-score	-2.69
Structure conservation index	0.52
SVM decision value	0.31
SVM RNA-class probability	0.684028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8293456 118 - 27905053
CGAAUGUUCGCGAAAAGAGCGC-AGC-AGUAUAAAUAGAGGCGCUUCGUCUACGGAGCGACAAUUCAAUUUAAACAAGCAAAGUGAACACGUCGCUAAGCGAAAGCUAAGCAAAUAAACA
.((.((((((((.......)))-.((-.((.(((((.(((.(((((((....)))))))....))).))))).))..)).....)))))..))(((.(((....))).)))......... ( -37.20)
>DroSec_CAF1 5023 118 - 1
CGAAUGUUCGCGAAAAGAGCGC-CGG-AGUAUAAAUAGAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACA
.((.((((((((((..(((((.-(..-............).)))))..))).....((...................))...)))))))..))(((.(((....))).)))......... ( -28.25)
>DroSim_CAF1 5090 119 - 1
CGAAUGUUCGCGAAAAGAGCGCCCGG-AGUAUAAAUAGAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACA
.((.(((((((.....(((((..(((-..(.......)..)))...))))).....((...................))...)))))))..))(((.(((....))).)))......... ( -28.21)
>DroEre_CAF1 5075 119 - 1
CGAAUGUUCUCGAAAGGAGCGC-CGGGUGUAUAAAUAGCGCUGCUUGUUUCUUUUAGCGUCAUUUCAAUUCAAAGAAGCAAAGUGAACACAUCGCUGAGCGAAAGCUAAGCAACCAAAUA
.((.(((((.(..(((.(((((-...((......)).))))).)))((((((((.................))))))))...).)))))..))(((.(((....))).)))......... ( -32.83)
>DroYak_CAF1 5026 118 - 1
CGAAUGUUCGCGAAAAGAGCGC-CGG-AGUAUAAAUAGGGCCGCUUGGUUCUCUUAGCGUCAAUUCAAUUCAAACAAGCAAACUGAAAACAUCGCUAAGCGAAAGCUAAGCAAACAAACA
.((((...(((...(((((.((-((.-(((............))))))).))))).)))...))))...........................(((.(((....))).)))......... ( -29.20)
>DroPer_CAF1 5479 118 - 1
CGAAGUUUCGAACGGAGAGCGG-CCA-GGUAUAAAUACAGCCGCCAGUUUCUCUUCGCAGCAAUUCAAUUCAAACAAGCGAAGAGAACACAUCUCAAAAGUGAAACAAAGCGAGCUACCA
....((((((....((((((((-(..-.(((....))).)))))..((((((((((((...................)))))))))).)).)))).....)))))).............. ( -35.81)
>consensus
CGAAUGUUCGCGAAAAGAGCGC_CGG_AGUAUAAAUAGAGCCGCUUCGUUCUCUGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACA
.((((((((.......))))...................(.(((((((....))))))).)......))))......((..(((((.....))))).(((....)))..))......... (-16.49 = -18.13 +   1.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:05 2006