Locus 4598

Sequence ID	3L_DroMel_CAF1
Location	13,137,763 – 13,137,960
Length	197
Max. P	0.999262

overview

Window 6

Location	13,137,763 – 13,137,880
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.67
Mean single sequence MFE	-26.98
Consensus MFE	-24.31
Energy contribution	-23.91
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-1.40
Structure conservation index	0.90
SVM decision value	0.58
SVM RNA-class probability	0.789330
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137763 117 + 23771897
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUCUCCGAAA---AGCCCGCUCCCAAAACCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAA
................(((((((......)))))))...(((((.((((((...........---((....))..........)))))).....)))))((((((.....)))))).... ( -23.60)
>DroSec_CAF1 125519 117 + 1
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUAUCCAAAA---AGCCCGCUCCCAAAACCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAA
................(((((((......)))))))...(((((.((((((...........---((....))..........)))))).....)))))((((((.....)))))).... ( -26.30)
>DroSim_CAF1 125438 117 + 1
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUCUCCAAAA---AGCCCGCUCCCAAAACCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAA
................(((((((......)))))))...(((((.((((((...........---((....))..........)))))).....)))))((((((.....)))))).... ( -26.30)
>DroEre_CAF1 122288 120 + 1
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUCUCCAAAAAGAAGCCCCCGCCCAAAGCCGGGGUCUCCGCAGCCAGGCCAAUUUAAAAUUGGCAAAA
.............((((....)))).(((...((((((.((((((.(((....(((......))).(((((.((.....)).))))).......))).))))))))))))....)))... ( -32.50)
>DroYak_CAF1 126674 105 + 1
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUCCCCAAAACCAGG---------------AGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAA
................(((((((......)))))))...(((((.((((((..(((.........))---------------))))))).....)))))((((((.....)))))).... ( -26.20)
>consensus
AUCUUUAGUCUUUGAACAAAUGUUUGUGCAUAUUUGAACUUGGCCAGGCCCAGUCUCCAAAA___AGCCCGCUCCCAAAACCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAA
................(((((((......)))))))...(((((.((((((................................)))))).....)))))((((((.....)))))).... (-24.31 = -23.91 +  -0.40)

alignment

secondary structure

dotplot

Window 7

Location	13,137,803 – 13,137,920
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.67
Mean single sequence MFE	-26.60
Consensus MFE	-23.97
Energy contribution	-23.73
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.90
SVM decision value	2.53
SVM RNA-class probability	0.995003
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137803 117 + 23771897
UGGCCAGGCCCAGUCUCCGAAA---AGCCCGCUCCCAAAACCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
((((..(((....((...))..---.))).........((((.(((....)))......((((((.....))))))....))))..)))).............((..((.....))..)) ( -24.30)
>DroSec_CAF1 125559 117 + 1
UGGCCAGGCCCAGUAUCCAAAA---AGCCCGCUCCCAAAACCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
((((.((((((...........---((....))..........))))))....((((..((((((.....))))))....))))..)))).............((..((.....))..)) ( -25.80)
>DroSim_CAF1 125478 117 + 1
UGGCCAGGCCCAGUCUCCAAAA---AGCCCGCUCCCAAAACCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
((((.((((((...........---((....))..........))))))....((((..((((((.....))))))....))))..)))).............((..((.....))..)) ( -25.80)
>DroEre_CAF1 122328 120 + 1
UGGCCAGGCCCAGUCUCCAAAAAGAAGCCCCCGCCCAAAGCCGGGGUCUCCGCAGCCAGGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
(((((.(((....(((......))).(((((.((.....)).))))).......))).)))))........(((((..........)))))............((..((.....))..)) ( -31.40)
>DroYak_CAF1 126714 105 + 1
UGGCCAGGCCCAGUCCCCAAAACCAGG---------------AGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
((((.((((((..(((.........))---------------)))))))....((((..((((((.....))))))....))))..)))).............((..((.....))..)) ( -25.70)
>consensus
UGGCCAGGCCCAGUCUCCAAAA___AGCCCGCUCCCAAAACCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGG
((((.((((((................................))))))....((((..((((((.....))))))....))))..)))).............((..((.....))..)) (-23.97 = -23.73 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	13,137,803 – 13,137,920
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.67
Mean single sequence MFE	-39.22
Consensus MFE	-30.10
Energy contribution	-30.14
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.77
SVM decision value	0.94
SVM RNA-class probability	0.886104
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137803 117 - 23771897
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCUGGUUUUGGGAGCGGGCU---UUUCGGAGACUGGGCCUGGCCA
............((..((..(((((((....))).))))..))..))..........(((((.(((((((....))).((((((.((((......---)))).)))))).)))).))))) ( -39.40)
>DroSec_CAF1 125559 117 - 1
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGGCCCUGGUUUUGGGAGCGGGCU---UUUUGGAUACUGGGCCUGGCCA
((.(((.....))).))...((((((((.(((((..........)))))....)))))))).(((((....((((((..((((..((((....))---))..))))...))))))))))) ( -37.80)
>DroSim_CAF1 125478 117 - 1
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGGCCCUGGUUUUGGGAGCGGGCU---UUUUGGAGACUGGGCCUGGCCA
((.(((.....))).))...((((((((.(((((..........)))))....)))))))).(((((....((((((.((((((.((((......---)))).))))))))))))))))) ( -38.70)
>DroEre_CAF1 122328 120 - 1
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCCUGGCUGCGGAGACCCCGGCUUUGGGCGGGGGCUUCUUUUUGGAGACUGGGCCUGGCCA
............((..((..(((((((....))).))))..))..))..........(((((.((((..((((.((((.((.....)).)))))))).....(....)..)))).))))) ( -44.50)
>DroYak_CAF1 126714 105 - 1
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCU---------------CCUGGUUUUGGGGACUGGGCCUGGCCA
((.(((.....))).))...((((((((.(((((..........)))))....)))))))).((((((((....))).---------------...((((..(....)..)))).))))) ( -35.70)
>consensus
CCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCUGGUUUUGGGAGCGGGCU___UUUUGGAGACUGGGCCUGGCCA
............((..((..(((((((....))).))))..))..))..........(((((.(((((((....))).........................(....)..)))).))))) (-30.10 = -30.14 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	13,137,840 – 13,137,960
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.96
Mean single sequence MFE	-33.14
Consensus MFE	-30.98
Energy contribution	-30.98
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-1.95
Structure conservation index	0.93
SVM decision value	2.88
SVM RNA-class probability	0.997543
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137840 120 + 23771897
CCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAAGAGAAAGGGGGAGCAGCUGGCACGCUGAUGGCAUGC
.(((.(.((((((((((..((((((.....))))))....))))..................(((..((.....))...))).........)))))))..)))(((.((.....)).))) ( -33.50)
>DroSec_CAF1 125596 118 + 1
CCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAAG--AAAGGGGGAGCAGCUGGCACGCUGAUGGCAUGC
.(((.((..((((((((..((((((.....))))))....))))..................(((..((.....))...)))...--...))))..))..)))(((.((.....)).))) ( -34.50)
>DroSim_CAF1 125515 118 + 1
CCAGGGCCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAAG--AAAGGGGGAGCAGCUGGCACGCUGAUGGCAUGC
.(((.((..((((((((..((((((.....))))))....))))..................(((..((.....))...)))...--...))))..))..)))(((.((.....)).))) ( -34.50)
>DroEre_CAF1 122368 118 + 1
CCGGGGUCUCCGCAGCCAGGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAGG--AAAGGGGGAGCAGCUGGCACGCUGAUGGCAUGC
.(((.....))).((((..((((((.....))))))....))))..((((............(((.((.....((....))....--...)).))).((((......)))).)))).... ( -30.00)
>DroYak_CAF1 126741 116 + 1
--AGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAGG--AAGGGGGAAGCAGCUGGCACGCUGAUGGCAUGC
--...((((((((..((..((((((.....))))))....((.....)).............(((..((.....))...))).))--...)))))..((((......))))..))).... ( -33.20)
>consensus
CCAGGGUCUCCCCAGCCAAGCCAAUUUAAAAUUGGCAAAAGGUUAAGCCAAAAAACUAACAAUCCACCGAAAAUCGAAGGGAAAG__AAAGGGGGAGCAGCUGGCACGCUGAUGGCAUGC
.(((.((..((((((((..((((((.....))))))....))))..................(((..((.....))...)))........))))..))..)))(((.((.....)).))) (-30.98 = -30.98 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,137,840 – 13,137,960
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.96
Mean single sequence MFE	-36.58
Consensus MFE	-34.06
Energy contribution	-34.50
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.93
SVM decision value	3.47
SVM RNA-class probability	0.999262
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13137840 120 - 23771897
GCAUGCCAUCAGCGUGCCAGCUGCUCCCCCUUUCUCUUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCUGG
((((((.....))))))(((...((((((.........(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))......))))))...))). ( -38.60)
>DroSec_CAF1 125596 118 - 1
GCAUGCCAUCAGCGUGCCAGCUGCUCCCCCUUU--CUUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGGCCCUGG
((((((.....))))))(((..((..((((..(--(..(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))..))..))))..)).))). ( -38.80)
>DroSim_CAF1 125515 118 - 1
GCAUGCCAUCAGCGUGCCAGCUGCUCCCCCUUU--CUUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGGCCCUGG
((((((.....))))))(((..((..((((..(--(..(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))..))..))))..)).))). ( -38.80)
>DroEre_CAF1 122368 118 - 1
GCAUGCCAUCAGCGUGCCAGCUGCUCCCCCUUU--CCUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCCUGGCUGCGGAGACCCCGG
((((((.....))))))(((((...........--...(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))..)))))(((.....))). ( -32.00)
>DroYak_CAF1 126741 116 - 1
GCAUGCCAUCAGCGUGCCAGCUGCUUCCCCCUU--CCUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCU--
((((((.....))))))........((((((..--((.(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))..))..)))).))....-- ( -34.70)
>consensus
GCAUGCCAUCAGCGUGCCAGCUGCUCCCCCUUU__CUUUCCCUUCGAUUUUCGGUGGAUUGUUAGUUUUUUGGCUUAACCUUUUGCCAAUUUUAAAUUGGCUUGGCUGGGGAGACCCUGG
((((((.....))))))(((...((((((.........(((..(((.....))).)))..((((((((.(((((..........)))))....))))))))......))))))...))). (-34.06 = -34.50 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:01 2006