Locus 5447

Sequence ID	X_DroMel_CAF1
Location	14,182,333 – 14,182,471
Length	138
Max. P	0.985586

overview

Window 1

Location	14,182,333 – 14,182,431
Length	98
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	91.43
Mean single sequence MFE	-21.29
Consensus MFE	-18.18
Energy contribution	-18.54
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.21
Structure conservation index	0.85
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14182333 98 + 22224390
CUAAAGGAGUUGGCUAACAUCGGCAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGU---UUUUUGCACAACUUGAUGCUUUCGCAAAU
......((((((((.(((...(....)...(((..(((((((((.....)))))))))..)))....))---)....)).))))))..(((....)))... ( -21.70)
>DroSec_CAF1 92754 98 + 1
CUAAAGGAGUUGGCUAAUAUCGGCAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGC---UUUUUGCACAACUUGAUGCCUUCGCAAAU
......((((((((.......(....)((((((..(((((((((.....)))))))))........)))---)))..)).))))))..(((....)))... ( -21.10)
>DroSim_CAF1 70270 98 + 1
CUAAAGGAGUUGGCUAACAUCGGCAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGU---UUUUUGCACAACUUGAUGCCUUCGCAAAU
......((((((((.(((...(....)...(((..(((((((((.....)))))))))..)))....))---)....)).))))))..(((....)))... ( -21.20)
>DroEre_CAF1 82458 92 + 1
UUAAAGCAGUUGGCUAACAUCGGUAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUCGUAUUCGC---UUCUUGCACAACUUGGU------GAAAAU
....(((.....)))..(((((((......(((..(((((((((.....)))))))))..)))....((---.....))...)).))))------)..... ( -18.00)
>DroYak_CAF1 83053 101 + 1
UUAAAGGAGUUGGCUAACAUCGGCAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUCGUAUUCGCCUUUUUUUGCACAACUUGAUGCUUUUGCAAAU
......((((((((.......(((...((.(((..(((((((((.....)))))))))..))).)).))).......)).))))))..(((....)))... ( -24.44)
>consensus
CUAAAGGAGUUGGCUAACAUCGGCAACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGC___UUUUUGCACAACUUGAUGCCUUCGCAAAU
......((((((((.......(....)...(((..(((((((((.....)))))))))..)))..............)).))))))..(((....)))... (-18.18 = -18.54 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	14,182,357 – 14,182,471
Length	114
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	88.66
Mean single sequence MFE	-28.22
Consensus MFE	-20.80
Energy contribution	-22.08
Covariance contribution	1.28
Combinations/Pair	1.09
Mean z-score	-2.36
Structure conservation index	0.74
SVM decision value	1.03
SVM RNA-class probability	0.904149
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14182357 114 + 22224390
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGU---UUUUUGCACAACUUGAUGCUUUCGCAAAUGGCGAAAAUGUCAAAGGAAAUUGUGUAGAAAUGUUGGUGA
((((..(((..(((((((((.....)))))))))..)))......---(((((((((((((((((..((((((.....))))))..))).)))....)))))))))))))))..... ( -30.40)
>DroSec_CAF1 92778 112 + 1
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGC---UUUUUGCACAACUUGAUGCCUUCGCAAAUGGCGAAAAUGUCAAAGGAAAUAGUGUAGAAAUUUUGGU--
..(((((..((.((((((....((.((((((((((((((....((---.....)).........(((....)))....))))))))))))))))...)))))).))..)))))..-- ( -27.40)
>DroSim_CAF1 70294 112 + 1
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGU---UUUUUGCACAACUUGAUGCCUUCGCAAAUGGCGAAAAUGUCAAAGGAAAUUGUGUAGAAAUUUUGGU--
..(((((((..(((((((((.....)))))))))..)))......---((((((((((((((((((..(((((.....)))))..)))).)))....))))))))))).))))..-- ( -28.10)
>DroEre_CAF1 82482 97 + 1
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUCGUAUUCGC---UUCUUGCACAACUUGGU------GAAAAUGGCGAAAAUGUCAAACGAAAUUGUGUAGA-----------
.((((.(((((.......)))))..((((((((((((((.(((((---(.............)))------)))....)))))))))))))).....)))).....----------- ( -25.02)
>DroYak_CAF1 83077 117 + 1
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUCGUAUUCGCCUUUUUUUGCACAACUUGAUGCUUUUGCAAAUGGCGAAAAUGUCAAAGGAAAUUGUGUAGAAAUGUUGAUGA
.......((((((((((..((((..(((((((((((((....)(((....((((((.(((.....).)).)))))).))))))))))))))).......))))...)))))))))). ( -30.20)
>consensus
AACAAAGCGUUAACAUUAAACGCCAUUUGAUGUUUUUGUAUUCGC___UUUUUGCACAACUUGAUGCCUUCGCAAAUGGCGAAAAUGUCAAAGGAAAUUGUGUAGAAAUGUUGGU__
......(((..(((((((((.....)))))))))..))).........(((((((((((.((((((..(((((.....)))))..))))))......)))))))))))......... (-20.80 = -22.08 +   1.28)

alignment

secondary structure

dotplot

Window 3

Location	14,182,357 – 14,182,471
Length	114
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	88.66
Mean single sequence MFE	-23.82
Consensus MFE	-19.22
Energy contribution	-20.02
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.42
Structure conservation index	0.81
SVM decision value	2.01
SVM RNA-class probability	0.985586
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14182357 114 - 22224390
UCACCAACAUUUCUACACAAUUUCCUUUGACAUUUUCGCCAUUUGCGAAAGCAUCAAGUUGUGCAAAAA---ACGAAUACAAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
................((((....(.((((((((..((((((((((....))......((((.......---)))).............))))))))...)))))))).)..)))). ( -24.50)
>DroSec_CAF1 92778 112 - 1
--ACCAAAAUUUCUACACUAUUUCCUUUGACAUUUUCGCCAUUUGCGAAGGCAUCAAGUUGUGCAAAAA---GCGAAUACAAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
--........................((((((((..((((((((((....)).....((..(((.....---)))...)).........))))))))...))))))))......... ( -24.60)
>DroSim_CAF1 70294 112 - 1
--ACCAAAAUUUCUACACAAUUUCCUUUGACAUUUUCGCCAUUUGCGAAGGCAUCAAGUUGUGCAAAAA---ACGAAUACAAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
--..............((((....(.((((((((..((((((((((....))......((((.......---)))).............))))))))...)))))))).)..)))). ( -23.40)
>DroEre_CAF1 82482 97 - 1
-----------UCUACACAAUUUCGUUUGACAUUUUCGCCAUUUUC------ACCAAGUUGUGCAAGAA---GCGAAUACGAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
-----------.....((((...((((.((((((..((((((((..------.....((..(((.....---)))...)).........))))))))...))))))))))..)))). ( -22.99)
>DroYak_CAF1 83077 117 - 1
UCAUCAACAUUUCUACACAAUUUCCUUUGACAUUUUCGCCAUUUGCAAAAGCAUCAAGUUGUGCAAAAAAAGGCGAAUACGAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
................((((....(.((((((((..(((((((((.....((((......)))).........((....)).......)))))))))...)))))))).)..)))). ( -23.60)
>consensus
__ACCAAAAUUUCUACACAAUUUCCUUUGACAUUUUCGCCAUUUGCGAAAGCAUCAAGUUGUGCAAAAA___GCGAAUACAAAAACAUCAAAUGGCGUUUAAUGUUAACGCUUUGUU
..........................((((((((..((((((((((....)).....((..(((........)))...)).........))))))))...))))))))......... (-19.22 = -20.02 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:06 2006