Locus 6109

Sequence ID	3L_DroMel_CAF1
Location	16,206,681 – 16,206,874
Length	193
Max. P	0.995081

overview

Window 1

Location	16,206,681 – 16,206,794
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.78
Mean single sequence MFE	-38.49
Consensus MFE	-33.44
Energy contribution	-33.80
Covariance contribution	0.36
Combinations/Pair	1.09
Mean z-score	-2.12
Structure conservation index	0.87
SVM decision value	2.54
SVM RNA-class probability	0.995081
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16206681 113 - 23771897
GGCCCAAAACGCCGAGCUGCAGCCUGCAGUUGCGCUCUCUGCGGAGAGAAAGUAGCUAGUAAGAGAGA-------AGGUUGUCGGUGUGCGUGAAUUUCGGAAGGAUGUGGUAGAAAGUA
.(((((..((((...((((((((((((((((((.(((((....)))))...)))))).))........-------)))))).))))..))))....(((....))))).)))........ ( -38.00)
>DroSec_CAF1 25565 113 - 1
GGCCCAAAACGCCGAGCUGCAGCCUGCAGUUGCGCUCUCUGCGGAGAGAAAGUAGCUAGUAAGAGAGA-------AGGUUGUCGGUGUGCGUGAAUUUCGGAAGGAUGUGGUAGAAAGUA
.(((((..((((...((((((((((((((((((.(((((....)))))...)))))).))........-------)))))).))))..))))....(((....))))).)))........ ( -38.00)
>DroSim_CAF1 27442 113 - 1
GGCCCAAAACGCCGAGCUGCAGCCUGCAGUUGCGCUCUCUGCGGAGAGAAAGUAGCUAGUAAGAGAGA-------AGGUUGUCGGUGUGCGUGAAUUUCGGAAGGAUGUGGUAUAAAGUA
.(((((..((((...((((((((((((((((((.(((((....)))))...)))))).))........-------)))))).))))..))))....(((....))))).)))........ ( -38.00)
>DroEre_CAF1 25070 119 - 1
GGCCCAAAACGCCGAGCUGCAGCCUGCAGUUGCGCUCUCCGCG-AGAGAAAGUAGCUAGUAAGAGAGAGAGAGAGAGGCUGUCGGUGUGCGUGAAUUUCGGAAGGAUGUGGCAGAAAGUA
.(((((..((((...((((((((((((((((((.(((((...)-))))...)))))).))...............)))))).))))..))))....(((....))))).)))........ ( -39.86)
>DroYak_CAF1 61967 112 - 1
GGCCCACAACGGCGAGCUGCAGUCUGCAGUUGCGCUCUCAGCG-AGAGAAAGUAGCUAGUAAGAGAGA-------AGGUUGUCGGUGUGCGUAAAUUUCGGAAGGAUGUGGGAGAAAGUA
..((((((.((((((.((.(..(((((((((((.(((((...)-))))...)))))).)).)))..).-------)).))))))............(((....)))))))))........ ( -38.60)
>consensus
GGCCCAAAACGCCGAGCUGCAGCCUGCAGUUGCGCUCUCUGCGGAGAGAAAGUAGCUAGUAAGAGAGA_______AGGUUGUCGGUGUGCGUGAAUUUCGGAAGGAUGUGGUAGAAAGUA
.(((((..((((...((((((((((((((((((.(((((....)))))...)))))).))...............)))))).))))..))))....(((....))))).)))........ (-33.44 = -33.80 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	16,206,721 – 16,206,834
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.78
Mean single sequence MFE	-38.92
Consensus MFE	-36.10
Energy contribution	-36.86
Covariance contribution	0.76
Combinations/Pair	1.06
Mean z-score	-1.11
Structure conservation index	0.93
SVM decision value	0.13
SVM RNA-class probability	0.600158
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16206721 113 + 23771897
AACCU-------UCUCUCUUACUAGCUACUUUCUCUCCGCAGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAG
.....-------...(((..............(((((....))))).((((((((((.(((((((((((.((((.........)))))))))))))..))...))))))))))....))) ( -39.60)
>DroSec_CAF1 25605 113 + 1
AACCU-------UCUCUCUUACUAGCUACUUUCUCUCCGCAGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAG
.....-------...(((..............(((((....))))).((((((((((.(((((((((((.((((.........)))))))))))))..))...))))))))))....))) ( -39.60)
>DroSim_CAF1 27482 113 + 1
AACCU-------UCUCUCUUACUAGCUACUUUCUCUCCGCAGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCUGUCGAG
.....-------...(((..............(((((....))))).((((((((((.(((((((((((.((((.........)))))))))))))..))...))))))))))....))) ( -40.00)
>DroEre_CAF1 25110 119 + 1
AGCCUCUCUCUCUCUCUCUUACUAGCUACUUUCUCU-CGCGGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGUGCUGCAAGGACAUUGCAGUUGCCGUCGAG
...(((.......((((((.....((..........-.)))))))).((((((((((.(((((((.(((.((((.........))))))).)))))..))...))))))))))....))) ( -36.90)
>DroYak_CAF1 62007 112 + 1
AACCU-------UCUCUCUUACUAGCUACUUUCUCU-CGCUGAGAGCGCAACUGCAGACUGCAGCUCGCCGUUGUGGGCCAAUGAACUGGAGCUGCAAGGACAUUGCAGUUGCCGUCGAG
.....-------...(((.............((((.-....))))(.((((((((((.((((((((((((......)))((......))))))))).))....)))))))))))...))) ( -38.50)
>consensus
AACCU_______UCUCUCUUACUAGCUACUUUCUCUCCGCAGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAG
...............(((......(((.((((........)))))))((((((((((.(((((((((((.((((.........))))))))))))).))....))))))))))....))) (-36.10 = -36.86 +   0.76)

alignment

secondary structure

dotplot

Window 3

Location	16,206,754 – 16,206,874
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.81
Mean single sequence MFE	-42.23
Consensus MFE	-36.24
Energy contribution	-36.12
Covariance contribution	-0.12
Combinations/Pair	1.12
Mean z-score	-1.26
Structure conservation index	0.86
SVM decision value	0.13
SVM RNA-class probability	0.597175
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16206754 120 + 23771897
AGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAGUGACAUUACGAAAAGCAAGAACAUCAGCAGGCGGGCAGGA
.....((((((((((((.(((((((((((.((((.........)))))))))))))..))...))))))))))((((..(((....))).....((..........)).)))).)).... ( -41.00)
>DroSec_CAF1 25638 120 + 1
AGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAGUGACAUUACGAAAGGCAAGAACAGCAGCAGGCAGGCAGGA
.......((..((((..(((((.((((((((...((((........))))((((((((.....))))))))..)))))))).......(....).........)))))..)))))).... ( -43.90)
>DroSim_CAF1 27515 120 + 1
AGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCUGUCGAGUGACAUUACGAAAGGCAAGAACAGCAGCAGGCAGGCAGGA
.......((..((((..(((((.(.((.((.(((((....((((.(((((((((((((.....))))))).....))))))..)))).))))).))..)).).)))))..)))))).... ( -42.90)
>DroEre_CAF1 25149 116 + 1
GGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGUGCUGCAAGGACAUUGCAGUUGCCGUCGAGUGACAUUACGAAAGGCAGGAACAGCGGCAGGCGGG----A
...........((((..(((((.(.((.((.(((((....((((.(((((.(((((((.....)))))))......)))))..)))).))))).))..)).).)))))..)))).----. ( -41.10)
>DroYak_CAF1 62039 116 + 1
UGAGAGCGCAACUGCAGACUGCAGCUCGCCGUUGUGGGCCAAUGAACUGGAGCUGCAAGGACAUUGCAGUUGCCGUCGAGUGACAUUACGAAAGGCAAGACCAGCGGCAGGCAGG----A
.....((((((((((((.((((((((((((......)))((......))))))))).))....)))))))))).((((..........(....)..........))))..))...----. ( -42.25)
>consensus
AGAGAGCGCAACUGCAGGCUGCAGCUCGGCGUUUUGGGCCAAUGAACUCGGGCUGCAAGGACAUUGCAGUUGCCGUCGAGUGACAUUACGAAAGGCAAGAACAGCAGCAGGCAGGCAGGA
...........((((..(((((.((((((....)))))).((((.(((((((((((((.....))))))).....))))))..))))................)))))..))))...... (-36.24 = -36.12 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:15 2006