Locus 4810

Sequence ID	X_DroMel_CAF1
Location	12,498,305 – 12,498,460
Length	155
Max. P	0.973670

overview

Window 6

Location	12,498,305 – 12,498,425
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.26
Mean single sequence MFE	-33.77
Consensus MFE	-23.29
Energy contribution	-23.47
Covariance contribution	0.19
Combinations/Pair	1.17
Mean z-score	-1.93
Structure conservation index	0.69
SVM decision value	0.00
SVM RNA-class probability	0.535351
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12498305 120 - 22224390
UCAUGAGUUUAAGUGCCCUGUUGGGUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUAGGAAACUGCCAGAAUUCUAGGCAACAGCAGGUGCAUGUUCUA
............(((((((((((((((((((((.((.....)).)))))))...)))........(((((((((..(((....)))...))).))).)))..))))))).))))...... ( -39.40)
>DroSec_CAF1 27782 120 - 1
UCAUGAGUUUAAGUGCCCUGUUGGAUAGUGAGUUUAGUUGAUAUGCUCACUUUAGCCUUUUUAUAGCCAGGUUCAAUAGGAAACUGCCAGAAUUCCAGGCAGUAGCAGGUGCAUAUUCCA
....((((....((((((((((((..(((((((.((.....)).)))))))....))........(((.(((((..(((....)))...)))..)).)))...)))))).)))))))).. ( -35.20)
>DroEre_CAF1 28873 119 - 1
UCAUGAGUUUAAGUGC-CUGUUGGGUAGUGAGUUUAUUUGAUGUGCUCACUUCAGCCAUUUUAUAGCCAAAUUCAAUAGGAAACUGCCAGAAUUCUACACAAUGGCAGGUGCAUUUUCUA
............(..(-((....((.(((((((...........))))))))).((((((.(.(((...(((((..(((....)))...)))))))).).)))))))))..)........ ( -30.60)
>DroYak_CAF1 23237 119 - 1
UCAUGAGUUUAAGUGC-CUGUUGGUUAGUGAGUUUAGUUGAUGUGCUCACUUCAGCCUUUUUAUAGCCAAGCUCAAUAGAAAAUGGCCAGAAUUCCAGACAAUAGCAGGUGCAUUUUCUA
............(..(-((((((((((((((((.((.....)).)))))))..))))........((((...((....))...))))................))))))..)........ ( -29.90)
>consensus
UCAUGAGUUUAAGUGC_CUGUUGGGUAGUGAGUUUAGUUGAUAUGCUCACUUCAGCCUUUUUAUAGCCAAGUUCAAUAGGAAACUGCCAGAAUUCCAGACAAUAGCAGGUGCAUUUUCUA
............(..(.(((((((..(((((((.((.....)).)))))))....))........(((.(((((..(((....)))...)))))...)))...))))))..)........ (-23.29 = -23.47 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	12,498,345 – 12,498,460
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.48
Mean single sequence MFE	-30.42
Consensus MFE	-26.02
Energy contribution	-25.14
Covariance contribution	-0.88
Combinations/Pair	1.15
Mean z-score	-2.44
Structure conservation index	0.86
SVM decision value	1.72
SVM RNA-class probability	0.973670
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12498345 115 + 22224390
CCUAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUACCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAAC-----
....(((..(((((((.....(((.....((((((.............)))))).(((....)))..)))...((((((........)))))).......)))))))....))).----- ( -30.92)
>DroSec_CAF1 27822 115 + 1
CCUAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCAUAUCAACUAAACUCACUAUCCAACAGGGCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAGCAGC-----
....(((..(((((((.....(((((...((((((.............))))))..((....)))).)))...((((((........)))))).......)))))))....))).----- ( -30.12)
>DroEre_CAF1 28913 119 + 1
CCUAUUGAAUUUGGCUAUAAAAUGGCUGAAGUGAGCACAUCAAAUAAACUCACUACCCAACAG-GCACUUAAACUCAUGAAAACGCACAUGAGGACAUGGGGCCGGGGCAACAACAGCUA
......................((((((.((((((.............)))))).(((....(-((.((((..((((((........))))))....))))))).)))......)))))) ( -32.12)
>DroYak_CAF1 23277 119 + 1
UCUAUUGAGCUUGGCUAUAAAAAGGCUGAAGUGAGCACAUCAACUAAACUCACUAACCAACAG-GCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAACAACAACAA
........(((..(((.......)))..)((((((.............))))))..((....(-((.((((..((((((........))))))....))))))).))))........... ( -28.52)
>consensus
CCUAUUGAACCUGGCUAUAAAAAGGCUAAAGUGAGCACAUCAACUAAACUCACUACCCAACAG_GCACUUAAACUCAUGAAAACGCACAUGAGGACAUGAGGCCGGGGCAACAAC_____
....(((..((((((........((....((((((.............))))))..)).........((((..((((((........))))))....)))))))))).)))......... (-26.02 = -25.14 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:39 2006