Locus 1177

Sequence ID	2R_DroMel_CAF1
Location	4,682,700 – 4,682,878
Length	178
Max. P	0.729088

overview

Window 1

Location	4,682,700 – 4,682,799
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	82.12
Mean single sequence MFE	-38.80
Consensus MFE	-26.52
Energy contribution	-27.50
Covariance contribution	0.98
Combinations/Pair	1.30
Mean z-score	-1.42
Structure conservation index	0.68
SVM decision value	-0.03
SVM RNA-class probability	0.516833
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4682700 99 + 20766785
AGCUUGAGGCUGCGGACACCGAUGGCUUUGGUUUUAUGACUGGUGGCGCCUUAGCCGCUGGUGAGUUUGUCUCGCUUCCAGUCACCGGUUUCUGACGCA
........((..((((.((((.(((((..(((......((..(((((......)))))..))(((.....))))))...))))).)))).))))..)). ( -37.20)
>DroPse_CAF1 5937 96 + 1
AGCUGGUGGCACC---CCCAACUGGUUUGGGCUUGAUGGCUGGUGGAGGCUUGGCCGCCGGCGAGUUGGACUCGCUGCCAGUGAUCGGCUUCUGGCGUA
.((..(.(((...---(((((.....)))))..((((.((((((((.(((...))).))((((((.....)))))))))))).))))))).)..))... ( -45.30)
>DroSec_CAF1 5157 99 + 1
AGCUUGAGGCUGCGGACACCGAUGGCUUUGGUUUUAUGACUGGUGGCGCCUUAGCCGCUGGUGAGUUCGUCUCGCUUCCAGUCACCGGUUUUUGACGCA
.((..(((((.(((((((((((.....)))))....(.((..(((((......)))))..)).)))))))...)))))..((((........)))))). ( -36.90)
>DroEre_CAF1 5181 99 + 1
AGCUUGAAGCUGCGGAUACCGAUGGCUUUGGUUUUAUGGCUGGUGGCGCCUUAGUCGCUGGUGAGUUUGUCUCGCUUCCAGUCACCGGUUUCUGACGCA
........((..((((.((((.(((((..(((......((..(((((......)))))..))(((.....))))))...))))).)))).))))..)). ( -35.20)
>DroYak_CAF1 5065 99 + 1
AGCUUGACGCUGCGGACACCGAUGGCUUUGGUUUUAUGGCUGGUGGCGCCUUAGCUGCUGGUGAGUUUGUCUCGCUUCCAGUCACCGGUUUCUGACGCA
........((..((((.((((.(((((..(((......((..(..((......))..)..))(((.....))))))...))))).)))).))))..)). ( -35.00)
>DroPer_CAF1 5950 96 + 1
AGCUGGUGGCACC---CCCAACUGGUUUGGGCUUGAUGGCUGGUGGAGGCUUGGCCGCCGGCGAGUUGGACUCGCUGCCAGUAAUCGGCUUCUGGCGUA
.((..(.(((...---(((((.....)))))..((((.((((((((.(((...))).))((((((.....)))))))))))).))))))).)..))... ( -43.20)
>consensus
AGCUUGAGGCUGCGGACACCGAUGGCUUUGGUUUUAUGGCUGGUGGCGCCUUAGCCGCUGGUGAGUUUGUCUCGCUUCCAGUCACCGGUUUCUGACGCA
........((..((((.((((.(((((..(((......(((((((((......)))))))))(((.....))))))...))))).)))).))))..)). (-26.52 = -27.50 +   0.98)

alignment

secondary structure

dotplot

Window 2

Location	4,682,759 – 4,682,878
Length	119
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.06
Mean single sequence MFE	-42.88
Consensus MFE	-25.28
Energy contribution	-25.45
Covariance contribution	0.17
Combinations/Pair	1.38
Mean z-score	-1.94
Structure conservation index	0.59
SVM decision value	0.42
SVM RNA-class probability	0.729088
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4682759 119 - 20766785
AACCAGCAGCAACUGGCCAACAACCUUGCAAAGAUGGCGGUGCUCGGUUGCAUCGCCUUAGCUGGUUACAGCAUGGAGCUGCGUCAGAAACCGGUGACUGGAAGCGAGACAAACUCACC
(((((((.((((..((.......))))))......((((((((......))))))))...))))))).((((.....)))).(((.(...(((....).))...)..)))......... ( -41.10)
>DroVir_CAF1 3628 119 - 1
AACCAGCAGCAAUUGGCCAACAAUCUGGCCAAAAUGGCCGUGCUCGGCUGCAUAGCUCUGGCUGGCUACGACAUGGAGCUGCGCAACAAGCCCAUCACAGGCAACGAAUCCAGCUCGCC
.....(((((..(((((((......))))))).....(((((.(((...((.((((....))))))..)))))))).)))))((.....(((.......)))...((.......)))). ( -42.20)
>DroGri_CAF1 3812 119 - 1
AACCAGCAGCAGCUGGCUAACAAUUUGGCCAAAAUGGCCGUACUUGGCUGCAUCGCUCUCGCCGGCUACGGCAUGGAGUUGCGUAACAAACCGAUUACGGGCAGCGAAUCCAAUUCGCC
..(((((....)))))....(((..(((((.....)))))...)))(((((..(((.(((((((....))))...)))..))).......(((....))))))))((((...))))... ( -42.60)
>DroWil_CAF1 2834 119 - 1
AAUCAACAGCAGUUGGCAAACAAUUUGGCCAAAAUGGCUGUUCUGGGCUGCAUUGCUUUAGCCGGCUACCAAAUGGAGCUGCGCCACAAGCCCAUCACAGGCAGCGAAUCGAAUUCGCC
....((((((..(((((..........)))))....)))))).((((((((...))....(((((((.((....))))))).))....)))))).........((((((...)))))). ( -38.90)
>DroMoj_CAF1 3460 119 - 1
AACCAGCAGCAGUUGGCCAAUAACCUGGCCAAAAUGGCUGUGCUCGGCUGCAUAGCUUUGGCCGGCUACACCAUGGAGCUGCGCAACAAGCCAAUCACUGGUAGCGAGUCCAGCUCGCC
.(((((......(((((((......)))))))..(((((.(((.(((((.(((((((......))))).....)).))))).)))...)))))....))))).(((((.....))))). ( -50.90)
>DroAna_CAF1 7933 119 - 1
AACCAGCAGCAACUGGCCAACAACCUGGCCAAGAUGGCCGUUCUCGGGUGCAUUGCCUUGGCGGGCUAUAGCAUGGAGCUGCGCCAGAAACCAGUCACGGGCAGUGAGGCCAAUUCCCC
.............(((((....((((((((.....))))(....))))).(((((((((((((((((.........)))).)))))((......))..)))))))).)))))....... ( -41.60)
>consensus
AACCAGCAGCAACUGGCCAACAACCUGGCCAAAAUGGCCGUGCUCGGCUGCAUAGCUUUGGCCGGCUACAGCAUGGAGCUGCGCAACAAACCAAUCACAGGCAGCGAAUCCAACUCGCC
..((.(((((...((((((......))))))...((((((.....(((......))).....)))))).........)))))((.....))........))..(((((.....))))). (-25.28 = -25.45 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:22 2006