Locus 4098

Sequence ID	3R_DroMel_CAF1
Location	11,196,153 – 11,196,256
Length	103
Max. P	0.992039

overview

Window 1

Location	11,196,153 – 11,196,256
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	67.91
Mean single sequence MFE	-32.86
Consensus MFE	-19.92
Energy contribution	-20.65
Covariance contribution	0.73
Combinations/Pair	1.24
Mean z-score	-2.31
Structure conservation index	0.61
SVM decision value	2.30
SVM RNA-class probability	0.992039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11196153 103 + 27905053
AUCUCCACCACGUCUUGGGUUUG---CUCU---UCC-----UCUUCAGGCUCCAUGUG----AGACUUGCAUUGCGUCCAACAUGCCUCUCUGAUGUUGGUCGCCUUGCAAGUCCUAC--
........(((((...(((((((---....---...-----....))))))).)))))----.((((((((..(((.(((((((.........))))))).)))..))))))))....-- ( -36.00)
>DroVir_CAF1 6881 102 + 1
AGCACUGCCAGCUGGUCAAC---GGGCAAAGUAUUC-----U------CCUGCAACGG----GGCCAUGCAAUGGGUCCAGCAUGUAUCGGCUAUGUUGGGCCCCCUGCAAGACCACUGC
........(((.(((((...---.(((..((....)-----)------((((...)))----)))).((((..(((((((((((((....)).)))))))))))..)))).)))))))). ( -40.90)
>DroSec_CAF1 6765 103 + 1
AUCUCCACCACGUCUUGGGCUUG---CUCU---UUC-----UCUUCCGGCUCCAUGUG----AGACUUGCAUUGCGUCCAACAGGCCUCUCUGAUGUCGGUCGCCUUGCAAGUCCUAC--
........(((((...(((((..---....---...-----......))))).)))))----.((((((((..(((.((.(((...........))).)).)))..))))))))....-- ( -30.06)
>DroSim_CAF1 5899 103 + 1
AUCUCUACUACGUCUUGGGUUUG---CUCU---UUC-----UCUUCUGGCUCCAUGUG----AGACUUGCAUUGCGUCCAACAGGCCUCUCUGAUGUCGGUCGCCUUGCAAGUCCUAC--
.................((...(---((..---...-----......))).))..(((----.((((((((..(((.((.(((...........))).)).)))..)))))))).)))-- ( -26.40)
>DroYak_CAF1 6217 103 + 1
ACCUCCACCAAGUCCUGGAUGUG---CUCU---UUC-----AUUGGUGGCACGAUGUG----AGACUUGCAUUGCGUCCAACAUGCCUCUCUGAUGUUGGUCGCCUUGCAAGUCCUAC--
....(((((((.....(((....---.)))---...-----.)))))))......(((----.((((((((..(((.(((((((.........))))))).)))..)))))))).)))-- ( -39.90)
>DroAna_CAF1 6486 112 + 1
AUCUCCACCAAGUGGUUGGGAUU---CUCA---ACCUUCUCCAUCAUGCCUUCAUCUGUCGUGGGCUUGCAGUGCGUCCAACUGAUCUGUCUGAUGUUGGUCACCUCACAAGUUUCAC--
.....(((((((((((((((...---))))---))).......(((((.(.......).))))))))))..))).(.(((((..(((.....)))))))).)................-- ( -23.90)
>consensus
AUCUCCACCACGUCUUGGGUUUG___CUCU___UUC_____UCUUCUGGCUCCAUGUG____AGACUUGCAUUGCGUCCAACAGGCCUCUCUGAUGUUGGUCGCCUUGCAAGUCCUAC__
...............................................................((((((((..(((.((((((...........)))))).)))..))))))))...... (-19.92 = -20.65 +   0.73)

alignment

secondary structure

dotplot

Window 2

Location	11,196,153 – 11,196,256
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.91
Mean single sequence MFE	-33.37
Consensus MFE	-22.85
Energy contribution	-22.13
Covariance contribution	-0.72
Combinations/Pair	1.45
Mean z-score	-1.67
Structure conservation index	0.68
SVM decision value	1.67
SVM RNA-class probability	0.970937
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11196153 103 - 27905053
--GUAGGACUUGCAAGGCGACCAACAUCAGAGAGGCAUGUUGGACGCAAUGCAAGUCU----CACAUGGAGCCUGAAGA-----GGA---AGAG---CAAACCCAAGACGUGGUGGAGAU
--((..((((((((..(((.((((((((......).))))))).)))..)))))))).----.)).....((((.....-----...---)).)---)....(((........))).... ( -34.30)
>DroVir_CAF1 6881 102 - 1
GCAGUGGUCUUGCAGGGGGCCCAACAUAGCCGAUACAUGCUGGACCCAUUGCAUGGCC----CCGUUGCAGG------A-----GAAUACUUUGCCC---GUUGACCAGCUGGCAGUGCU
((((((.(((((((((((((((((.....(((........))).....)))...))))----)).)))))))------)-----...))).(((((.---(((....))).)))))))). ( -37.70)
>DroSec_CAF1 6765 103 - 1
--GUAGGACUUGCAAGGCGACCGACAUCAGAGAGGCCUGUUGGACGCAAUGCAAGUCU----CACAUGGAGCCGGAAGA-----GAA---AGAG---CAAGCCCAAGACGUGGUGGAGAU
--((..((((((((..(((.((((((...........)))))).)))..)))))))).----.)).(((.(((....).-----(..---....---)..)))))............... ( -31.90)
>DroSim_CAF1 5899 103 - 1
--GUAGGACUUGCAAGGCGACCGACAUCAGAGAGGCCUGUUGGACGCAAUGCAAGUCU----CACAUGGAGCCAGAAGA-----GAA---AGAG---CAAACCCAAGACGUAGUAGAGAU
--((..((((((((..(((.((((((...........)))))).)))..)))))))).----.)).(((.(((......-----...---.).)---)....)))............... ( -28.40)
>DroYak_CAF1 6217 103 - 1
--GUAGGACUUGCAAGGCGACCAACAUCAGAGAGGCAUGUUGGACGCAAUGCAAGUCU----CACAUCGUGCCACCAAU-----GAA---AGAG---CACAUCCAGGACUUGGUGGAGGU
--((..((((((((..(((.((((((((......).))))))).)))..)))))))).----.))(((...(((((((.-----...---.((.---....))......))))))).))) ( -40.30)
>DroAna_CAF1 6486 112 - 1
--GUGAAACUUGUGAGGUGACCAACAUCAGACAGAUCAGUUGGACGCACUGCAAGCCCACGACAGAUGAAGGCAUGAUGGAGAAGGU---UGAG---AAUCCCAACCACUUGGUGGAGAU
--......((((((..(((.((((((((.....)))..))))).)))..)))))).((((..((.(((....)))..)).....(((---((..---.....))))).....)))).... ( -27.60)
>consensus
__GUAGGACUUGCAAGGCGACCAACAUCAGAGAGGCAUGUUGGACGCAAUGCAAGUCU____CACAUGGAGCCAGAAGA_____GAA___AGAG___CAAACCCAAGACGUGGUGGAGAU
.....(((((((((..(((.((((((((.....))..)))))).)))..))))))))).............................................................. (-22.85 = -22.13 +  -0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:04 2006