Locus 3223

Sequence ID	2L_DroMel_CAF1
Location	9,234,433 – 9,234,587
Length	154
Max. P	0.995820

overview

Window 9

Location	9,234,433 – 9,234,547
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	74.24
Mean single sequence MFE	-37.57
Consensus MFE	-24.04
Energy contribution	-24.68
Covariance contribution	0.64
Combinations/Pair	1.17
Mean z-score	-2.79
Structure conservation index	0.64
SVM decision value	2.62
SVM RNA-class probability	0.995820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9234433 114 + 22407834
UGGCCUACCAGCACCAGCAACUGCAGCAGCAGAUCAUCUCGCAUCGUUCCAUACAAAACAAGGCGGCGGCCACCGCUGCCGCACAAACGGCAAAUCUUGCUGCUGCCCUGCAGC
(((....)))......(((...((((((((((((....(((....(((........)))...((((((((....)))))))).....)))...))).)))))))))..)))... ( -40.30)
>DroVir_CAF1 106456 86 + 1
-------GC---------------AGCAACAGCUCAACUCCCAUCAUUCGCAUCAUAGCAAGGCAGCGG---CUGCCGCCGC---AACGGCGCAUAUUGCAGCUGCGCUGCAGC
-------((---------------(((......................((......))......((((---(((((((((.---..)))))......)))))))))))))... ( -32.80)
>DroSec_CAF1 64259 114 + 1
UGGCCUACCAGCACCAGCAACUGCAGCAGCAGAUCAUCUCGCAUCGUUCCAUACAAAACAAGGCGGCGGCCACCGCUGCCGCACAAACGGCAAAUCUUGCUGCUGCCCUGCAGC
(((....)))......(((...((((((((((((....(((....(((........)))...((((((((....)))))))).....)))...))).)))))))))..)))... ( -40.30)
>DroSim_CAF1 66126 114 + 1
UGGCCUACCAGCACCAGCAACUGCAGCAGCAGAUCAUCUCGCAUCGUUCCAUACAAAACAAGGCGGCGGCCACCGCUGCCGCACAAACGGCAAAUCUUGCUGCUGCCCUGCAGC
(((....)))......(((...((((((((((((....(((....(((........)))...((((((((....)))))))).....)))...))).)))))))))..)))... ( -40.30)
>DroEre_CAF1 71092 114 + 1
UGGCCUACCAGCAGUUGCAACUGCAACAGCAGAUCAUCUCGCAGCGUUCCAUACAAAACAAGGCGGCGGCCACAGCUGCCGCACACACGGCAAAUCUUGCUGCUGCCCUGCAGC
(((....)))...((((((.((((....))))........(((((.................((((((((....))))))))......((((.....)))))))))..)))))) ( -41.50)
>DroMoj_CAF1 117028 89 + 1
-------GC---------------AGCCGCAGCUCAACUCUCAUCAUUCGCAUCAUAGCAAAACAGCGGCAGCUGCCGCCGC---AACGGCGCACAUUGCAGCUGCAUUGCAGC
-------((---------------((..(((((((((............((......))......(((((....)))((((.---..))))))...))).)))))).))))... ( -30.20)
>consensus
UGGCCUACCAGCACCAGCAACUGCAGCAGCAGAUCAUCUCGCAUCGUUCCAUACAAAACAAGGCGGCGGCCACCGCUGCCGCACAAACGGCAAAUCUUGCUGCUGCCCUGCAGC
.........................((.((((.............(((........)))..(((((((((......(((((......)))))......))))))))))))).)) (-24.04 = -24.68 +   0.64)

alignment

secondary structure

dotplot

Window 0

Location	9,234,433 – 9,234,547
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.24
Mean single sequence MFE	-46.57
Consensus MFE	-31.57
Energy contribution	-31.30
Covariance contribution	-0.27
Combinations/Pair	1.36
Mean z-score	-2.29
Structure conservation index	0.68
SVM decision value	2.22
SVM RNA-class probability	0.990602
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9234433 114 - 22407834
GCUGCAGGGCAGCAGCAAGAUUUGCCGUUUGUGCGGCAGCGGUGGCCGCCGCCUUGUUUUGUAUGGAACGAUGCGAGAUGAUCUGCUGCUGCAGUUGCUGGUGCUGGUAGGCCA
((.((((.(((((((((.((((((((((....))))))(((((....)))))(((((.((((.....)))).)))))..)))))))))))))..))))....)).((....)). ( -51.80)
>DroVir_CAF1 106456 86 - 1
GCUGCAGCGCAGCUGCAAUAUGCGCCGUU---GCGGCGGCAG---CCGCUGCCUUGCUAUGAUGCGAAUGAUGGGAGUUGAGCUGUUGCU---------------GC-------
...(((((((((((.((((...(.(((((---(((((((...---))))))).((((......))))..)))))).))))))))).))))---------------))------- ( -38.40)
>DroSec_CAF1 64259 114 - 1
GCUGCAGGGCAGCAGCAAGAUUUGCCGUUUGUGCGGCAGCGGUGGCCGCCGCCUUGUUUUGUAUGGAACGAUGCGAGAUGAUCUGCUGCUGCAGUUGCUGGUGCUGGUAGGCCA
((.((((.(((((((((.((((((((((....))))))(((((....)))))(((((.((((.....)))).)))))..)))))))))))))..))))....)).((....)). ( -51.80)
>DroSim_CAF1 66126 114 - 1
GCUGCAGGGCAGCAGCAAGAUUUGCCGUUUGUGCGGCAGCGGUGGCCGCCGCCUUGUUUUGUAUGGAACGAUGCGAGAUGAUCUGCUGCUGCAGUUGCUGGUGCUGGUAGGCCA
((.((((.(((((((((.((((((((((....))))))(((((....)))))(((((.((((.....)))).)))))..)))))))))))))..))))....)).((....)). ( -51.80)
>DroEre_CAF1 71092 114 - 1
GCUGCAGGGCAGCAGCAAGAUUUGCCGUGUGUGCGGCAGCUGUGGCCGCCGCCUUGUUUUGUAUGGAACGCUGCGAGAUGAUCUGCUGUUGCAGUUGCAACUGCUGGUAGGCCA
(((((......))))).....(((((((....)))))))...((((((((..(((((..(((.....)))..))))).......((.(((((....))))).)).))).))))) ( -45.30)
>DroMoj_CAF1 117028 89 - 1
GCUGCAAUGCAGCUGCAAUGUGCGCCGUU---GCGGCGGCAGCUGCCGCUGUUUUGCUAUGAUGCGAAUGAUGAGAGUUGAGCUGCGGCU---------------GC-------
(((((((((..((.((.....))))))))---))))).((((((((.(((..(((((......))))).(((....))).))).))))))---------------))------- ( -40.30)
>consensus
GCUGCAGGGCAGCAGCAAGAUUUGCCGUUUGUGCGGCAGCGGUGGCCGCCGCCUUGUUUUGUAUGGAACGAUGCGAGAUGAUCUGCUGCUGCAGUUGCUGGUGCUGGUAGGCCA
........(((((((((.....((((((....))))))(((((....)))))(((((..(((.....)))..)))))......)))))))))...................... (-31.57 = -31.30 +  -0.27)

alignment

secondary structure

dotplot

Window 1

Location	9,234,467 – 9,234,587
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.77
Mean single sequence MFE	-42.39
Consensus MFE	-24.09
Energy contribution	-24.65
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-2.22
Structure conservation index	0.57
SVM decision value	0.97
SVM RNA-class probability	0.892437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9234467 120 + 22407834
CAUCUCGCAUCGUUCCAUACAAAACAAGGCGGCGGCCACCGCUGCCGCACAAACGGCAAAUCUUGCUGCUGCCCUGCAGCGAUCGGCUGCCAUUAUGAAUGCGGUGGCAUCGCCGAUCUC
......((...((.....))....((.(((((((((......(((((......)))))......))))))))).))..))(((((((((((((..(....)..))))))..))))))).. ( -48.90)
>DroVir_CAF1 106468 114 + 1
CAACUCCCAUCAUUCGCAUCAUAGCAAGGCAGCGG---CUGCCGCCGC---AACGGCGCAUAUUGCAGCUGCGCUGCAGCGCUCGGCCGCCAUUAUGAAUGCGGUGGCAUCGCCGAUUCC
........(((..(((((((((((...(((.((((---(....)))))---..((((((....((((((...)))))))))).)))))....))))).)))))).(((...))))))... ( -45.90)
>DroPse_CAF1 80164 111 + 1
CAACUCUCAUCAUUCUCUCCA---CAAGGCAGCGGCCGC---CGCCGCAGCCACGGCCAACAUCGCAGCUGCGCUGCAACGCUCGG---CCAUUAUGAAUGCGGUGGCGUCGCCGAUCUC
................((((.---...)).))(((((((---(((((((..((.((((......(((((...))))).......))---))....))..))))))))))..))))..... ( -41.72)
>DroMoj_CAF1 117040 114 + 1
CAACUCUCAUCAUUCGCAUCAUAGCAAAACAGCGGCAGCUGCCGCCGC---AACGGCGCACAUUGCAGCUGCAUUGCAGCGAUCGG---CCAUUAUGAACGCGGUGGCAUCGCCGAUUCC
........(((....(((.....((......)).(((((((((((((.---..)))))......))))))))..))).(((((..(---((((..(....)..)))))))))).)))... ( -40.20)
>DroAna_CAF1 64618 117 + 1
CAACUCGCACCAUUCUAUCCAAAAUAAGGCAGCGGCCAC---UGCCGCUCACCCGACAAACAUUGCAGCCGCGCUGCAGCGAUCGACCGCCAUUAUGAAUGCGGUGGCAUCGCCGAUCUC
......((...................((.((((((...---.))))))...)).........((((((...))))))))((((.(((((..........)))))(((...))))))).. ( -35.90)
>DroPer_CAF1 80252 111 + 1
CAACUCUCAUCAUUCUCUCCA---CAAGGCAGCGGCCGC---CGCCGCAGCCACGGCCAACAUCGCAGCUGCGCUGCAACGCUCGG---CCAUUAUGAAUGCGGUGGCGUCGCCGAUCUC
................((((.---...)).))(((((((---(((((((..((.((((......(((((...))))).......))---))....))..))))))))))..))))..... ( -41.72)
>consensus
CAACUCUCAUCAUUCUCUCCA_A_CAAGGCAGCGGCCGC___CGCCGCA__AACGGCAAACAUUGCAGCUGCGCUGCAGCGAUCGG___CCAUUAUGAAUGCGGUGGCAUCGCCGAUCUC
...............................(((((.......))))).....((((...((((((.(((((...)))))....(.....).........)))))).....))))..... (-24.09 = -24.65 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:21 2006