Locus 203

Sequence ID 3L_DroMel_CAF1
Location 570,310 – 570,466
Length 156
Max. P 0.967925
window298 window299 window300

overview

Window 8

Location 570,310 – 570,402
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.31
Mean single sequence MFE -32.00
Consensus MFE -18.08
Energy contribution -18.78
Covariance contribution 0.70
Combinations/Pair 1.20
Mean z-score -2.05
Structure conservation index 0.56
SVM decision value 1.62
SVM RNA-class probability 0.967925
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 570310 92 + 23771897
UUGCGCCCGCUUAGCUGCCAAUUCCCAUCGGCU--------------------------UCU--CCUCGGGGAGCAGUACAUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUG
..(((.((((((((.((((...((((...((..--------------------------...--))...))))((((.((((....))))..)))))))).))))))))......))).. ( -35.10)
>DroPse_CAF1 844 102 + 1
UUGAGCAUUCUUAGCUGCCAAUUCGCUCGCGUUCAUUU-----UUGCU-----------UUUUUUGCCACCGCGGAGUACAUCAAAAUGUUG--GCGGCAAUUAAACAGAAUUCUCGCUG
..(((.(((((..(((((((....(((((((.......-----.))).-----------.....(((....)))))))((((....))))))--)))))........))))).))).... ( -23.80)
>DroSec_CAF1 1750 92 + 1
UUGCGCCCGUUUAGCUGCCAAUUCCCAUCGGCU--------------------------UCU--CCUCGGGGAGCAGUACAUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUAAUCGCUG
..(((.((((((((.((((...((((...((..--------------------------...--))...))))((((.((((....))))..)))))))).))))))))......))).. ( -32.70)
>DroSim_CAF1 1765 92 + 1
UUGCGCCCGCUUAGCUGCCAAUUCCCAUCGGCU--------------------------UCU--CCUCGGGGAGCAGUACAUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUG
..(((.((((((((.((((...((((...((..--------------------------...--))...))))((((.((((....))))..)))))))).))))))))......))).. ( -35.10)
>DroEre_CAF1 1803 118 + 1
UUGCGCCCGCUUAGCUGCCAAUUCCCAUCGGUUCCUCGGUUCCUCGGUUCCUCGGCUCCUCU--CCUCGGGGAGCAGUACAUCAAAAUGUUUGUGCGGCAAUUAAGCGGAAUGAUCGCUG
..(((.((((((((.((((..........((..((..(....)..))..))...(((((((.--....))))))).(((((..........))))))))).))))))))......))).. ( -41.50)
>DroPer_CAF1 852 101 + 1
UUGAGCAUUCUUAGCUGCCAAUUCGCUCGCGUUCAUUU-----UUGCU-----------UU-UUUGCCACCGCGGAGUACAUCAAAAUGUUG--GCGGCAAUUAAACAGAAUUCUCGUUG
..(((.(((((..(((((((....(((((((.......-----.))).-----------..-..(((....)))))))((((....))))))--)))))........))))).))).... ( -23.80)
>consensus
UUGCGCCCGCUUAGCUGCCAAUUCCCAUCGGCU__________________________UCU__CCUCGGGGAGCAGUACAUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUG
......((((((((.((((...((((...((.................................))...))))(((..((((....))))...))))))).))))))))........... (-18.08 = -18.78 +   0.70)

alignment

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secondary structure

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dotplot

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Window 9

Location 570,310 – 570,402
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.31
Mean single sequence MFE -32.25
Consensus MFE -17.25
Energy contribution -18.20
Covariance contribution 0.95
Combinations/Pair 1.12
Mean z-score -1.98
Structure conservation index 0.53
SVM decision value 1.30
SVM RNA-class probability 0.939257
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 570310 92 - 23771897
CAGCGAUCAUUCCGCUUAAUUGCCGCAGAAACAUUUUGAUGUACUGCUCCCCGAGG--AGA--------------------------AGCCGAUGGGAAUUGGCAGCUAAGCGGGCGCAA
..(((.....((((((((.(((((((((..((((....)))).))))((((...((--...--------------------------..))...))))...))))).))))))))))).. ( -36.60)
>DroPse_CAF1 844 102 - 1
CAGCGAGAAUUCUGUUUAAUUGCCGC--CAACAUUUUGAUGUACUCCGCGGUGGCAAAAAA-----------AGCAA-----AAAUGAACGCGAGCGAAUUGGCAGCUAAGAAUGCUCAA
..(((...(((.(((((..(((((((--(.((((....)))).......))))))))...)-----------)))).-----.)))...)))(((((..((((...))))...))))).. ( -24.90)
>DroSec_CAF1 1750 92 - 1
CAGCGAUUAUUCCGCUUAAUUGCCGCAGAAACAUUUUGAUGUACUGCUCCCCGAGG--AGA--------------------------AGCCGAUGGGAAUUGGCAGCUAAACGGGCGCAA
..(((.....((((.(((.(((((((((..((((....)))).))))((((...((--...--------------------------..))...))))...))))).))).))))))).. ( -30.00)
>DroSim_CAF1 1765 92 - 1
CAGCGAUCAUUCCGCUUAAUUGCCGCAGAAACAUUUUGAUGUACUGCUCCCCGAGG--AGA--------------------------AGCCGAUGGGAAUUGGCAGCUAAGCGGGCGCAA
..(((.....((((((((.(((((((((..((((....)))).))))((((...((--...--------------------------..))...))))...))))).))))))))))).. ( -36.60)
>DroEre_CAF1 1803 118 - 1
CAGCGAUCAUUCCGCUUAAUUGCCGCACAAACAUUUUGAUGUACUGCUCCCCGAGG--AGAGGAGCCGAGGAACCGAGGAACCGAGGAACCGAUGGGAAUUGGCAGCUAAGCGGGCGCAA
..(((.....((((((((.((((((((...((((....))))..)))((((...((--...((..((..(....)..))..))......))...))))...))))).))))))))))).. ( -40.00)
>DroPer_CAF1 852 101 - 1
CAACGAGAAUUCUGUUUAAUUGCCGC--CAACAUUUUGAUGUACUCCGCGGUGGCAAA-AA-----------AGCAA-----AAAUGAACGCGAGCGAAUUGGCAGCUAAGAAUGCUCAA
....(((.(((((((((..(((((((--(.((((....)))).......)))))))).-.)-----------)))..-----........((..((......)).))..))))).))).. ( -25.40)
>consensus
CAGCGAUCAUUCCGCUUAAUUGCCGCAGAAACAUUUUGAUGUACUGCUCCCCGAGG__AGA__________________________AACCGAUGGGAAUUGGCAGCUAAGCGGGCGCAA
..(((.....((((((((.((((((((...((((....))))..)))..........................................((....))....))))).))))))))))).. (-17.25 = -18.20 +   0.95)

alignment

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secondary structure

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dotplot

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Window 0

Location 570,362 – 570,466
Length 104
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 88.99
Mean single sequence MFE -38.48
Consensus MFE -27.31
Energy contribution -27.50
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -2.09
Structure conservation index 0.71
SVM decision value 0.46
SVM RNA-class probability 0.744221
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 570362 104 + 23771897
AUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUGCCAAGGUGGCCGGAGGUGUGCG-------AAAGUGGUUUUCCAUGGAAG--GAAAUACCUUCGCGCCUCUUCC----
..........((((((.........)))))).....((..(....)..)).(((((.(((((-------((...((((((((......)--)))).))))))))))..)))))---- ( -35.50)
>DroSec_CAF1 1802 104 + 1
AUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUAAUCGCUGCCAAGGUGGCCGGAGGUGUGCG-------AAGGUGGUUUUCCAUGGAAG--GAAAUACCUUCGCGCCUCUUCC----
..........((((((.........)))))).....((..(....)..)).(((((.(((((-------((((((.(((((....))))--)...)))))))))))..)))))---- ( -41.40)
>DroSim_CAF1 1817 104 + 1
AUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUGCCAAGGUGGCCGGAGGUGUGCG-------AAGGUGGUUUUCCAUGGAAG--GAAAUACCUUCGCGCCUCUUCC----
..........((((((.........)))))).....((..(....)..)).(((((.(((((-------((((((.(((((....))))--)...)))))))))))..)))))---- ( -41.40)
>DroEre_CAF1 1881 117 + 1
AUCAAAAUGUUUGUGCGGCAAUUAAGCGGAAUGAUCGCUGCCAAGGUGGCCGAAGGUGUGCGAAAUGCGAAAGUGGUUUUCCAUGAAAGUGGUUUUCCCCUUGCGCCUCUUCCCCCC
..........(((.(((((.((((.......)))).))))))))((.((..(((((.((((((...((....))((....((((....))))....))..)))))).))))))))). ( -35.60)
>consensus
AUCAAAAUGUUUCUGCGGCAAUUAAGCGGAAUGAUCGCUGCCAAGGUGGCCGGAGGUGUGCG_______AAAGUGGUUUUCCAUGGAAG__GAAAUACCUUCGCGCCUCUUCC____
..............(((((.((((.......)))).)))))..(((.((((((((((((.............((((....))))..........))))))))).))).)))...... (-27.31 = -27.50 +   0.19)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:53 2006