Locus 9260

Sequence ID 3R_DroMel_CAF1
Location 24,678,306 – 24,678,565
Length 259
Max. P 0.992770
window14808 window14809 window14810 window14811

overview

Window 8

Location 24,678,306 – 24,678,420
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.47
Mean single sequence MFE -35.14
Consensus MFE -27.66
Energy contribution -27.82
Covariance contribution 0.16
Combinations/Pair 1.09
Mean z-score -3.23
Structure conservation index 0.79
SVM decision value 2.35
SVM RNA-class probability 0.992770
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24678306 114 - 27905053
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCUACGAAAGGAAAAUA----CAUACAUUCGAAUGUGUGUAUUUUUAUGGAGCCUUAGUGUGUAUAUGGGGGUGU--
..(((((....)..............(((((.(((.((.((.((((.(....)(((((((----(((((((....))))))))))))))....)))))).)).))).)))))))))..-- ( -37.10)
>DroSec_CAF1 19222 114 - 1
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCUGCGAAAGGAAAAUA----CAGGCAUCCGAAUGUGUGUAUUUUUAUGGAGCCUUAGUGUGUAUAUGGGGGUGU--
..(((((....)..............(((((.(((.((.((.((((.((....(((((((----((.((((....)))).))))))))).)).)))))).)).))).)))))))))..-- ( -36.10)
>DroSim_CAF1 19306 114 - 1
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCUGCGAAAGGAAAAUA----CAUGCAUCCGAAUGUGAGUAUUUUUAUGGAGCCUUAGUGUGUAUAUGGGGGUGU--
..(((((....)..............(((((.(((.((.((.((((.((....(((((((----(.(((((....))))).)))))))).)).)))))).)).))).)))))))))..-- ( -32.20)
>DroEre_CAF1 20733 114 - 1
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCUGCAAAAGGAAAAUA----UAUGCAUCCGAAUGUGUGUAUUUUUAUGGAGCCUCUGUGUGUAUAUGGGGGUGU--
..(((((....)..............(((((.(((.(((...((((.((....(((((((----(((((((....)))))))))))))).)).))))..))).))).)))))))))..-- ( -37.30)
>DroYak_CAF1 19816 120 - 1
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCAGCAAAAGGAAAAUACAUGUAUGCAACCGAAUGUGUGUAUUUUUAUGGAGCCUUAGUGUGUAUAUGGGGGUGCCU
.((((((....)..............(((((.(((.((.((.(((..((....(((((((((..(((........)))..))))))))).))..))))).)).))).))))).)).))). ( -33.00)
>consensus
UGGCCCGGCAACAAUAAAUACUUCAACUAUAAAUAGGCAAAUGGCUGCGAAAGGAAAAUA____CAUGCAUCCGAAUGUGUGUAUUUUUAUGGAGCCUUAGUGUGUAUAUGGGGGUGU__
..(((((....)..............(((((.(((.((....((((.((....(((((((....(((((((....)))))))))))))).)).))))...)).))).))))))))).... (-27.66 = -27.82 +   0.16)

alignment

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secondary structure

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Window 9

Location 24,678,420 – 24,678,539
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.65
Mean single sequence MFE -43.92
Consensus MFE -40.02
Energy contribution -39.90
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -1.23
Structure conservation index 0.91
SVM decision value 0.03
SVM RNA-class probability 0.550463
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24678420 119 + 27905053
CUCGUGGCAUGCUCAAGUGGCCACUCGAGGG-GGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCGAGAAGUGGUAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
...((((((.....(((((.((.((....))-)).)))))....))))))(((((((.....))(((...)))))))).((((((((((...((((....))))......)))))))))) ( -43.10)
>DroSec_CAF1 19336 120 + 1
CUCGUGGCAUGCUCAAGUGGCCACUCGAGGGGGGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
...((((((.....(((((.((.((....)).)).)))))....))))))(((((((.....))(((...)))))))).((((((((((...((((....))))......)))))))))) ( -44.40)
>DroSim_CAF1 19420 118 + 1
CUCGUGGCAUGCUCAAGUGGCCACUCGAGG--GGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
...((((((.....(((((.((........--)).)))))....))))))(((((((.....))(((...)))))))).((((((((((...((((....))))......)))))))))) ( -42.40)
>DroEre_CAF1 20847 118 + 1
CUCGUGGCAUGCUCAAGUGGACACUCGUGG--GGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
.(((((((((((((..((((((...(((((--.((........)).)))))..))))))....)))).)))))))))..((((((((((...((((....))))......)))))))))) ( -47.10)
>DroYak_CAF1 19936 118 + 1
CUCGUGGCAUGCUCAAGUGGCCACUCGUGG--GGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
...((((((.....(((((.((.(....).--)).)))))....))))))(((((((.....))(((...)))))))).((((((((((...((((....))))......)))))))))) ( -42.60)
>consensus
CUCGUGGCAUGCUCAAGUGGCCACUCGAGG__GGGCACUUUAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUU
...((((((.....(((((.((.(....)...)).)))))....))))))(((((((.....))(((...)))))))).((((((((((...((((....))))......)))))))))) (-40.02 = -39.90 +  -0.12)

alignment

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secondary structure

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Window 0

Location 24,678,459 – 24,678,565
Length 106
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 95.94
Mean single sequence MFE -32.08
Consensus MFE -29.88
Energy contribution -29.76
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.22
Structure conservation index 0.93
SVM decision value 0.48
SVM RNA-class probability 0.754201
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24678459 106 + 27905053
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCGAGAAGUGGUAACGCAACUGGUUGUAAUCCAGCCGCUUCUUGGACU------GUAGCUUUUCCUGCUCUCAAU
..((((((...(((.......)))))))))(..((((((((((((((((...((((....))))......)))))))))))).))------))..)................ ( -31.50)
>DroSec_CAF1 19376 106 + 1
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUUAGACU------GUAGCUUUUCCUGCUCUCAUU
.....((((.((.((((......))))...))..)))).((((((((((...((((....))))......)))))))))).((..------((((......))))..))... ( -29.60)
>DroSim_CAF1 19458 106 + 1
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUUGGACU------GUAGCUUUUCCUGCUCUCAUU
..((((((...(((.......)))))))))(..((((((((((((((((...((((....))))......)))))))))))).))------))..)................ ( -33.40)
>DroEre_CAF1 20885 106 + 1
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUUGGACU------GUAGCUUUUCCUGCUCUCAUU
..((((((...(((.......)))))))))(..((((((((((((((((...((((....))))......)))))))))))).))------))..)................ ( -33.40)
>DroYak_CAF1 19974 112 + 1
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUUGGACUUCAGCUUUAGCUUUUCCUGCUCUCAUU
..((((((...(((.......)))))))))((...((((((((((((((...((((....))))......)))))))))))).))...))...(((.......)))...... ( -32.50)
>consensus
UAAUUGCCACGCCGUCCAUCCUGGGGCAAUGUCAUGGCCAAGAAGUGGCAACGCAACUGGUUGUAAUCCAGCCGCUUCUUGGACU______GUAGCUUUUCCUGCUCUCAUU
..((((((...(((.......))))))))).....((((((((((((((...((((....))))......)))))))))))).))........(((.......)))...... (-29.88 = -29.76 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 24,678,459 – 24,678,565
Length 106
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 95.94
Mean single sequence MFE -33.84
Consensus MFE -29.94
Energy contribution -30.34
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.34
SVM RNA-class probability 0.694956
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24678459 106 - 27905053
AUUGAGAGCAGGAAAAGCUAC------AGUCCAAGAAGCGGCUGGAUUACAACCAGUUGCGUUACCACUUCUCGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
................(((((------.(((((....((((((((.......))))))))........((((.((.((......)).)).)))))))))...)))))..... ( -32.10)
>DroSec_CAF1 19376 106 - 1
AAUGAGAGCAGGAAAAGCUAC------AGUCUAAGAAGCGGCUGGAUUACAACCAGUUGCGUUGCCACUUCUUGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
................(((((------..........((((((((.......))))))))(((((((..((((((.((......))..))))))))).)))))))))..... ( -33.80)
>DroSim_CAF1 19458 106 - 1
AAUGAGAGCAGGAAAAGCUAC------AGUCCAAGAAGCGGCUGGAUUACAACCAGUUGCGUUGCCACUUCUUGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
................(((((------..........((((((((.......))))))))(((((((..((((((.((......))..))))))))).)))))))))..... ( -33.80)
>DroEre_CAF1 20885 106 - 1
AAUGAGAGCAGGAAAAGCUAC------AGUCCAAGAAGCGGCUGGAUUACAACCAGUUGCGUUGCCACUUCUUGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
................(((((------..........((((((((.......))))))))(((((((..((((((.((......))..))))))))).)))))))))..... ( -33.80)
>DroYak_CAF1 19974 112 - 1
AAUGAGAGCAGGAAAAGCUAAAGCUGAAGUCCAAGAAGCGGCUGGAUUACAACCAGUUGCGUUGCCACUUCUUGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
..........(((..(((....)))....))).....((((((((.......))))))))((((((((.((........))....(((((.....))..))))))))))).. ( -35.70)
>consensus
AAUGAGAGCAGGAAAAGCUAC______AGUCCAAGAAGCGGCUGGAUUACAACCAGUUGCGUUGCCACUUCUUGGCCAUGACAUUGCCCCAGGAUGGACGGCGUGGCAAUUA
................(((((................((((((((.......))))))))(((((((.((((.((.((......)).)).))))))).)))))))))..... (-29.94 = -30.34 +   0.40)

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 13:30:12 2006