Locus 3773

Sequence ID X_DroMel_CAF1
Location 10,005,688 – 10,005,925
Length 237
Max. P 0.998747
window6194 window6195 window6196 window6197 window6198 window6199

overview

Window 4

Location 10,005,688 – 10,005,780
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 87.32
Mean single sequence MFE -28.03
Consensus MFE -21.73
Energy contribution -22.07
Covariance contribution 0.34
Combinations/Pair 1.07
Mean z-score -3.28
Structure conservation index 0.78
SVM decision value 1.33
SVM RNA-class probability 0.942994
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005688 92 + 22224390
UAACUGCAAAAUGUAAUUUUGUGGAAAUCACAAAAUGUGUGAGUGUGUGUGGAAUGAGAGCCGCACGCAAACACACAGAAUGCCCACACUGC
.....(((.......((((((((.....))))))))(((((..(((((((((........)))))))))..)))))....)))......... ( -31.20)
>DroSec_CAF1 11232 92 + 1
UAACUGCAAAAUGUAAUUUUGUGGAAAUCACAAAAUGUUUGAGUGUGUGUGGGAUGAGGACCACACGCAAACACACAGAAUGCCCACACUGC
.....(((.......((((((((.....))))))))((.((..(((((((((........)))))))))..)).))....)))......... ( -26.70)
>DroYak_CAF1 8422 87 + 1
UAACUGCAAAAUGUAAUUUUGUGGAAAUCACAAAACGAGUGUGUGUGUGU-----GAGAGCCACACGCAAACAAGCGGAGUACCCACACUGC
...((((.........(((((((.....))))))).(..((((((((.((-----....))))))))))..)..)))).............. ( -26.20)
>consensus
UAACUGCAAAAUGUAAUUUUGUGGAAAUCACAAAAUGUGUGAGUGUGUGUGG_AUGAGAGCCACACGCAAACACACAGAAUGCCCACACUGC
.....(((...(((..(((((((.....)))))))(((.((..(((((((((........)))))))))..)).)))........))).))) (-21.73 = -22.07 +   0.34)

alignment

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secondary structure

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Window 5

Location 10,005,688 – 10,005,780
Length 92
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 87.32
Mean single sequence MFE -26.67
Consensus MFE -20.70
Energy contribution -20.93
Covariance contribution 0.23
Combinations/Pair 1.17
Mean z-score -3.04
Structure conservation index 0.78
SVM decision value 1.18
SVM RNA-class probability 0.927529
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005688 92 - 22224390
GCAGUGUGGGCAUUCUGUGUGUUUGCGUGCGGCUCUCAUUCCACACACACUCACACAUUUUGUGAUUUCCACAAAAUUACAUUUUGCAGUUA
((((.(((........(((((..((.(((.((........)).))).))..)))))((((((((.....))))))))..))).))))..... ( -27.70)
>DroSec_CAF1 11232 92 - 1
GCAGUGUGGGCAUUCUGUGUGUUUGCGUGUGGUCCUCAUCCCACACACACUCAAACAUUUUGUGAUUUCCACAAAAUUACAUUUUGCAGUUA
((((.(((........((.((..((.((((((........)))))).))..)).))((((((((.....))))))))..))).))))..... ( -26.10)
>DroYak_CAF1 8422 87 - 1
GCAGUGUGGGUACUCCGCUUGUUUGCGUGUGGCUCUC-----ACACACACACACUCGUUUUGUGAUUUCCACAAAAUUACAUUUUGCAGUUA
((((((((((....))((......))(((((......-----.))))).)))))..((((((((.....)))))))).......)))..... ( -26.20)
>consensus
GCAGUGUGGGCAUUCUGUGUGUUUGCGUGUGGCUCUCAU_CCACACACACUCACACAUUUUGUGAUUUCCACAAAAUUACAUUUUGCAGUUA
((((((((((....(((..((....))..))).......)))))))..........((((((((.....)))))))).......)))..... (-20.70 = -20.93 +   0.23)

alignment

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secondary structure

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Window 6

Location 10,005,740 – 10,005,856
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -44.82
Consensus MFE -39.29
Energy contribution -39.35
Covariance contribution 0.06
Combinations/Pair 1.15
Mean z-score -5.02
Structure conservation index 0.88
SVM decision value 3.15
SVM RNA-class probability 0.998597
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005740 116 + 22224390
AAUGAGAGCCGCACGCAAACACACAGAAUGCCCACACUGCGUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGGGUCGCCGACGACCAACCCCCCGUAAA
..........(((..(.........)..))).(((((((((((((((((((.......((((....)))))))))))))))))))))))(((((....)))))............. ( -44.21)
>DroSec_CAF1 11284 98 + 1
GAUGAGGACCACACGCAAACACACAGAAUGCCCACACUGCGUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGG---------------CCCCCC---AA
..((.((.......(((..(.....)..)))((((((((((((((((((((.......((((....))))))))))))))))))))))))---------------..)).)---). ( -40.81)
>DroEre_CAF1 11825 110 + 1
AAAGAGAGCCACACGCAAAUAACCAGAAUGCUCACACUGCGUAUUAGUAAUCCGACUGGCAAGCAAUUGCGUUGCUCAUACGCAGUGUGGGUCGCCCACGGCCACC---CC---AA
.....((((....................))))(((((((((((.((((((.......((((....)))))))))).)))))))))))((((.(((...))).)))---).---.. ( -38.96)
>DroYak_CAF1 8472 109 + 1
---GAGAGCCACACGCAAACAAGCGGAGUACCCACACUGCGUAUGAGUAAUCCGACUGGCAAGCAAUCGCGUUACUCAUACGCAGUGUGGGUCGCCGACGGCCACC-CCCC---AA
---..(.(((....((......))((.(.((((((((((((((((((((((.(((.((.....)).))).))))))))))))))))))))))).))...))))...-....---.. ( -55.30)
>consensus
AAUGAGAGCCACACGCAAACAAACAGAAUGCCCACACUGCGUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGGGUCGCCGACGGCCACC_CCCC___AA
.............................((((((((((((((((((((((.(((.((.....)).))).))))))))))))))))))))))........................ (-39.29 = -39.35 +   0.06)

alignment

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secondary structure

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Window 7

Location 10,005,740 – 10,005,856
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -52.18
Consensus MFE -36.66
Energy contribution -37.23
Covariance contribution 0.56
Combinations/Pair 1.21
Mean z-score -4.81
Structure conservation index 0.70
SVM decision value 3.21
SVM RNA-class probability 0.998747
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005740 116 - 22224390
UUUACGGGGGGUUGGUCGUCGGCGACCCACACUGCGUAUGAGUAACGCAAUUGCUUGCCAGUCGGAUUACUCAUACGCAGUGUGGGCAUUCUGUGUGUUUGCGUGCGGCUCUCAUU
......((((((((((((....))))(((((((((((((((((((.((....))...((....)).)))))))))))))))))))(((..(.....)..)))...))))))))... ( -54.20)
>DroSec_CAF1 11284 98 - 1
UU---GGGGGG---------------CCACACUGCGUAUGAGUAACGCAAUUGCUUGCCAGUCGGAUUACUCAUACGCAGUGUGGGCAUUCUGUGUGUUUGCGUGUGGUCCUCAUC
..---.(((((---------------(((((((((((((((((((.((....))...((....)).)))))))))))))))(..(((((.....)))))..)..)))))))))... ( -50.20)
>DroEre_CAF1 11825 110 - 1
UU---GG---GGUGGCCGUGGGCGACCCACACUGCGUAUGAGCAACGCAAUUGCUUGCCAGUCGGAUUACUAAUACGCAGUGUGAGCAUUCUGGUUAUUUGCGUGUGGCUCUCUUU
..---((---(((.((((..((..(((((((((((((((((((((.....)))))).((....)).......))))))))))))........)))..))..)).)).))))).... ( -42.60)
>DroYak_CAF1 8472 109 - 1
UU---GGGG-GGUGGCCGUCGGCGACCCACACUGCGUAUGAGUAACGCGAUUGCUUGCCAGUCGGAUUACUCAUACGCAGUGUGGGUACUCCGCUUGUUUGCGUGUGGCUCUC---
..---.(((-(((.((((((((.((((((((((((((((((((((..((((((.....))))))..))))))))))))))))))))).).))).......))).)).))))))--- ( -61.71)
>consensus
UU___GGGG_GGUGGCCGUCGGCGACCCACACUGCGUAUGAGUAACGCAAUUGCUUGCCAGUCGGAUUACUCAUACGCAGUGUGGGCAUUCUGUGUGUUUGCGUGUGGCUCUCAUU
.........((((.((.....)).))))(((((((((((((((((.((....))...((....)).)))))))))))))))))((((....(((......)))....))))..... (-36.66 = -37.23 +   0.56)

alignment

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secondary structure

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Window 8

Location 10,005,780 – 10,005,896
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 87.03
Mean single sequence MFE -33.36
Consensus MFE -27.80
Energy contribution -28.05
Covariance contribution 0.25
Combinations/Pair 1.08
Mean z-score -2.32
Structure conservation index 0.83
SVM decision value 1.55
SVM RNA-class probability 0.962924
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005780 116 + 22224390
GUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGGGUCGCCGACGACCAACCCCCCGUAAAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCUA
(((((((((((.......((((....)))))))))))))))(((...(((((((....)))))........(((((((((((...))))).))))))....))...)))....... ( -35.21)
>DroSec_CAF1 11324 98 + 1
GUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGG---------------CCCCCC---AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCCA
(((((((((((.......((((....)))))))))))))))((.((((((---------------(.....---........)))))))......(((((....)))))...)).. ( -29.33)
>DroEre_CAF1 11865 110 + 1
GUAUUAGUAAUCCGACUGGCAAGCAAUUGCGUUGCUCAUACGCAGUGUGGGUCGCCCACGGCCACC---CC---AAAUGUAUGCUAUAGAUUUUCGCAUGUCAAUAUGCUUAGCCA
.................(((((((((((((((.((.((((((...((.((((.(((...))).)))---))---)..)))))).....(.....)))))).)))).))))).))). ( -32.10)
>DroYak_CAF1 8509 112 + 1
GUAUGAGUAAUCCGACUGGCAAGCAAUCGCGUUACUCAUACGCAGUGUGGGUCGCCGACGGCCACC-CCCC---AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCUA
(((((((((((.(((.((.....)).))).)))))))))))((.(.(.((((.(((...))).)))-).))---((((((((...))))))))..(((((....)))))...)).. ( -36.80)
>consensus
GUAUGAGUAAUCCGACUGGCAAGCAAUUGCGUUACUCAUACGCAGUGUGGGUCGCCGACGGCCACC_CCCC___AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCCA
(((((((((((.(((.((.....)).))).)))))))))))(((((((((((((....)))))..............(((((((...........))))).)).))))))..)).. (-27.80 = -28.05 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,005,816 – 10,005,925
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.65
Mean single sequence MFE -27.23
Consensus MFE -16.60
Energy contribution -17.91
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -2.25
Structure conservation index 0.61
SVM decision value 0.95
SVM RNA-class probability 0.888061
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10005816 109 + 22224390
CAUACGCAGUGUGGGUCGCCGACGACCAACCCCCCGUAAAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCUAUCCGCCCCACU----------GCUGUGAUUUCU-CAUCCA
((((.((((((.(((.((...................(((((((((...))))))))).(((((....))))).........)))))))))----------))))))......-...... ( -27.60)
>DroSec_CAF1 11360 92 + 1
CAUACGCAGUGUGG---------------CCCCCC---AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCCAUCCGCCCUACU----------GCUGUGACUUCUCCAUCCA
((((.((((((.((---------------(.....---((((((((...))))))))..(((((....)))))..........))).))))----------))))))............. ( -23.60)
>DroEre_CAF1 11901 113 + 1
CAUACGCAGUGUGGGUCGCCCACGGCCACC---CC---AAAUGUAUGCUAUAGAUUUUCGCAUGUCAAUAUGCUUAGCCAUCCGACCCACUGCAGUGCACCGCUGUGAUUCCU-CAUCCA
....((((((((((((((.....(((....---..---((((.(((...))).))))..(((((....)))))...)))...))))))))(((...)))..))))))......-...... ( -30.10)
>DroYak_CAF1 8545 105 + 1
CAUACGCAGUGUGGGUCGCCGACGGCCACC-CCCC---AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCUAUCCACCCAACU----------GCUGUGAUUCCU-CAUCCA
((((.(((((.(((((....((..((....-....---((((((((...))))))))..(((((....)))))...))..)).))))))))----------))))))......-...... ( -27.60)
>consensus
CAUACGCAGUGUGGGUCGCCGACGGCCACC_CCCC___AAAUGUAUGCUAUACAUUUUUGCAUGUCAAUAUGCUUAGCCAUCCGCCCCACU__________GCUGUGAUUCCU_CAUCCA
....((((((((((((.((...................((((((((...))))))))..(((((....)))))...)).))))))................))))))............. (-16.60 = -17.91 +   1.31)

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 11:08:05 2006