Locus 3916

Sequence ID X_DroMel_CAF1
Location 10,474,343 – 10,474,475
Length 132
Max. P 0.908787
window6424 window6425 window6426 window6427

overview

Window 4

Location 10,474,343 – 10,474,439
Length 96
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 82.26
Mean single sequence MFE -29.28
Consensus MFE -18.88
Energy contribution -19.48
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.33
Structure conservation index 0.64
SVM decision value 1.06
SVM RNA-class probability 0.908787
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10474343 96 + 22224390
CUGAAU-CAAUGAUAUUAAGUAAAGCAGAUGUCACGGAUGUAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGCGUUAACAGCGCGUAA
(((.((-(..(((((((..........)))))))..))).))).((.-(((((((.....)))))))..-----------......(((((((...))))))))).... ( -27.40)
>DroSec_CAF1 5134 95 + 1
CUGAAUCCAGAGAUC-UGAGUGUAGCAGAUGUCACGGAUGUAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGUGUUAACAGCGC-UAA
(((.((((.((.(((-((.......))))).))..)))).))).((.-(((((((.....)))))))..-----------......(((((((...)))))))))-... ( -31.40)
>DroSim_CAF1 5325 94 + 1
CUGAAU-UAGAGAUA-UGAGUGUAGCAGAUGUCACGGAUGCAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGUGUUAACAGCGC-UAA
......-........-......((((.((((.(((.......)))..-(((((((.....)))))))..-----------))))..(((((((...)))))))))-)). ( -25.40)
>DroEre_CAF1 6329 108 + 1
CUAAAU-CAAAACUAUUAAAUAUUGCAGAUGUCCCGGAUGAAGUGCAUGUUAAGGGUUAACCUUAACAUAGCCGCUGUUUAAUCCCGCUGUUGCGUUAACAGCACGUAA
......-...............((((.........((((..((((((((((((((.....))))))))).).)))).....)))).(((((((...)))))))..)))) ( -28.70)
>DroYak_CAF1 6847 107 + 1
CUGAAU-CAGUGAUAUUAAAUAUUGCAGAUGUCACAGAUAAAGUGCA-GUUAAGGGUUAACCUUAACAUAGCCGCUGGUUCAUCCUGCUGUUGCGUUAACAGCGCGUAA
.(((((-(((((...........((((..((((...))))...))))-(((((((.....))))))).....))))))))))....(((((((...)))))))...... ( -33.50)
>consensus
CUGAAU_CAGAGAUAUUAAGUAUAGCAGAUGUCACGGAUGAAGUGCA_GUUAAGGGUUAACCUUAACAU___________CAUCCCGCUGUUGCGUUAACAGCGCGUAA
........................((.((((.(((.......)))...(((((((.....))))))).............))))..(((((((...))))))))).... (-18.88 = -19.48 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,474,343 – 10,474,439
Length 96
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 82.26
Mean single sequence MFE -25.78
Consensus MFE -19.32
Energy contribution -19.56
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 0.97
SVM RNA-class probability 0.893119
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10474343 96 - 22224390
UUACGCGCUGUUAACGCAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUACAUCCGUGACAUCUGCUUUACUUAAUAUCAUUG-AUUCAG
.....(((((((.....))))))).((((-----------((((((((((((.....))))-(((((.......))).)).........)))))))))))).-...... ( -24.70)
>DroSec_CAF1 5134 95 - 1
UUA-GCGCUGUUAACACAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUACAUCCGUGACAUCUGCUACACUCA-GAUCUCUGGAUUCAG
.((-((((((((.....)))))).(((((-----------..(((((((.....)))))))-..(((.......))).)))))))))...(((-(....))))...... ( -27.80)
>DroSim_CAF1 5325 94 - 1
UUA-GCGCUGUUAACACAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUGCAUCCGUGACAUCUGCUACACUCA-UAUCUCUA-AUUCAG
.((-((((((((.....)))))).(((((-----------..(((((((.....)))))))-..(((.......))).)))))))))......-........-...... ( -25.20)
>DroEre_CAF1 6329 108 - 1
UUACGUGCUGUUAACGCAACAGCGGGAUUAAACAGCGGCUAUGUUAAGGUUAACCCUUAACAUGCACUUCAUCCGGGACAUCUGCAAUAUUUAAUAGUUUUG-AUUUAG
.....(((((((..(((....)))......)))))))((.(((((((((.....)))))))))))........((((((.................))))))-...... ( -24.83)
>DroYak_CAF1 6847 107 - 1
UUACGCGCUGUUAACGCAACAGCAGGAUGAACCAGCGGCUAUGUUAAGGUUAACCCUUAAC-UGCACUUUAUCUGUGACAUCUGCAAUAUUUAAUAUCACUG-AUUCAG
...(((((((((.....)))))).((.....)).)))((...(((((((.....)))))))-.)).((..(((.((((..................)))).)-))..)) ( -26.37)
>consensus
UUACGCGCUGUUAACGCAACAGCGGGAUG___________AUGUUAAGGUUAACCCUUAAC_UGCACUACAUCCGUGACAUCUGCUAUACUUAAUAUCUCUG_AUUCAG
....((((((((.....)))))).(((((.............(((((((.....)))))))...(((.......))).)))))))........................ (-19.32 = -19.56 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,474,379 – 10,474,475
Length 96
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 81.72
Mean single sequence MFE -28.35
Consensus MFE -22.54
Energy contribution -22.82
Covariance contribution 0.28
Combinations/Pair 1.10
Mean z-score -1.42
Structure conservation index 0.79
SVM decision value -0.04
SVM RNA-class probability 0.510992
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10474379 96 + 22224390
AUGUAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGCGUUAACAGCGCGUAACGGGACUGCCGCUCUCUUUGUCCAG-CCCCCCUC--CGA
..((..(((.-(((((((.....)))))))..-----------......(((((((...))))))))))..))(((.(((..((.......)).)))-))).....--... ( -28.50)
>DroSec_CAF1 5170 97 + 1
AUGUAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGUGUUAACAGCGC-UAACGGGACUGCCGCUCUCUUUGUCAAU-CCCCCCUCACCAA
..((...((.-(((((((.....)))))))..-----------......(((((((...)))))))))-..))((((.((.((.......)).)).)-))).......... ( -25.10)
>DroSim_CAF1 5360 97 + 1
AUGCAGUGCA-GUUAAGGGUUAACCUUAACAU-----------CAUCCCGCUGUUGUGUUAACAGCGC-UAACGGGACUGCCGCUCUCUUUGUCAAU-CCCCCCUCACCGA
..(((((...-(((((((.....)))))))..-----------...((((.((((((....)))))).-...)))))))))................-............. ( -26.80)
>DroEre_CAF1 6365 110 + 1
AUGAAGUGCAUGUUAAGGGUUAACCUUAACAUAGCCGCUGUUUAAUCCCGCUGUUGCGUUAACAGCACGUAACGGGACUGCCGCGCUCUCUU-UUGUGUCCCCCUCUCUCU
.....(.(((((((((((.....))))))))).)))((((((......(((....)))..)))))).......(((((..............-....)))))......... ( -31.57)
>DroYak_CAF1 6883 110 + 1
AUAAAGUGCA-GUUAAGGGUUAACCUUAACAUAGCCGCUGGUUCAUCCUGCUGUUGCGUUAACAGCGCGUAACGGGACUGCCGCUCUCUUUGCCCGUCUUCCCCUCUCUCA
.(((((.((.-(((((((.....))))))).........(((...(((((....(((((.....)))))...)))))..)))))...)))))................... ( -29.80)
>consensus
AUGAAGUGCA_GUUAAGGGUUAACCUUAACAU___________CAUCCCGCUGUUGCGUUAACAGCGCGUAACGGGACUGCCGCUCUCUUUGUCAAU_CCCCCCUCACCCA
....((.((..(((((((.....)))))))...............(((((....(((((.....)))))...))))).....)).))........................ (-22.54 = -22.82 +   0.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,474,379 – 10,474,475
Length 96
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 81.72
Mean single sequence MFE -33.09
Consensus MFE -21.66
Energy contribution -21.70
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.63
Structure conservation index 0.65
SVM decision value -0.03
SVM RNA-class probability 0.518965
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10474379 96 - 22224390
UCG--GAGGGGGG-CUGGACAAAGAGAGCGGCAGUCCCGUUACGCGCUGUUAACGCAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUACAU
...--....((((-(((..............)))))))(((((.(((((((.....))))))).).))-----------))(((((((.....)))))))-.......... ( -30.44)
>DroSec_CAF1 5170 97 - 1
UUGGUGAGGGGGG-AUUGACAAAGAGAGCGGCAGUCCCGUUA-GCGCUGUUAACACAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUACAU
.(((((((.((((-.(((((......((((...((((((...-.)((((((.....))))))))))).-----------.))))...)))))))))...)-).)))))... ( -32.90)
>DroSim_CAF1 5360 97 - 1
UCGGUGAGGGGGG-AUUGACAAAGAGAGCGGCAGUCCCGUUA-GCGCUGUUAACACAACAGCGGGAUG-----------AUGUUAAGGUUAACCCUUAAC-UGCACUGCAU
.(((((((.((((-.(((((......((((...((((((...-.)((((((.....))))))))))).-----------.))))...)))))))))...)-).)))))... ( -33.60)
>DroEre_CAF1 6365 110 - 1
AGAGAGAGGGGGACACAA-AAGAGAGCGCGGCAGUCCCGUUACGUGCUGUUAACGCAACAGCGGGAUUAAACAGCGGCUAUGUUAAGGUUAACCCUUAACAUGCACUUCAU
.....((((.........-.......(((...(((((((((...(((.......)))..))))))))).....)))((.(((((((((.....))))))))))).)))).. ( -36.20)
>DroYak_CAF1 6883 110 - 1
UGAGAGAGGGGAAGACGGGCAAAGAGAGCGGCAGUCCCGUUACGCGCUGUUAACGCAACAGCAGGAUGAACCAGCGGCUAUGUUAAGGUUAACCCUUAAC-UGCACUUUAU
....((((((((...((..(.....)..))....))))....(((((((((.....)))))).((.....)).)))((...(((((((.....)))))))-.)).)))).. ( -32.30)
>consensus
UCGGAGAGGGGGG_AUGGACAAAGAGAGCGGCAGUCCCGUUACGCGCUGUUAACGCAACAGCGGGAUG___________AUGUUAAGGUUAACCCUUAAC_UGCACUACAU
..............................(((((((((.....)((((((.....)))))))))))..............(((((((.....))))))).)))....... (-21.66 = -21.70 +   0.04)

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 11:11:39 2006