Locus 6041

Sequence ID 3R_DroMel_CAF1
Location 15,909,115 – 15,909,301
Length 186
Max. P 0.996127
window9852 window9853 window9854 window9855 window9856

overview

Window 2

Location 15,909,115 – 15,909,223
Length 108
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 71.89
Mean single sequence MFE -31.68
Consensus MFE -10.37
Energy contribution -10.73
Covariance contribution 0.37
Combinations/Pair 1.26
Mean z-score -2.15
Structure conservation index 0.33
SVM decision value 0.53
SVM RNA-class probability 0.771503
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15909115 108 - 27905053
CCACC----CACUUUUCCCUCCCAAUGAAACAAACACACACACACAUGCAAGGCCGUACGUUUGUAUAUGUGUGCGGUUGUCGGCUUUGCCGGGAAUUGGGGAAUAUUUGCA
...((----(.(..(((((.......((....(((.(.((((((.(((((((........))))))).)))))).)))).))(((...))))))))..)))).......... ( -33.90)
>DroSec_CAF1 26970 104 - 1
CCACC----CACAUUUCCCUCCCCAUGAAA----CACACACUCAUAUAAAAGGCCGUACGUAUGUAUAUGUGUGCGGUUGUCGGCUUUGCGGGGAAUUGGGGAAUAUUUGCA
.....----...((((((((((((((((..----.......))))....(((((((.(((..(((((....)))))..))))))))))..)))))...)))))))....... ( -32.50)
>DroSim_CAF1 16508 104 - 1
CCACC----CAUAUUUCCCUCCCCAUGAAA----CACACACUCAUAUAAAAGGCCGUACGUAUGUAUAUGUGUGCGGUUGUCGGCUUUGCGGGGAAUUGGGGAAUAUUUGCA
.....----.((((((((((((((((((..----.......))))....(((((((.(((..(((((....)))))..))))))))))..)))))...)))))))))..... ( -34.30)
>DroEre_CAF1 16075 91 - 1
CCACC----C-------------CUUGAAA----AACGCACACACAUGCAAGGCCGUAUGUAUGUAUGUGUGUGCGGUUGUCGGCUUUGCGGGGAAUUGGGGAAUAUUUGCA
...((----(-------------(......----..((((((((((((((..((.....)).))))))))))))))(((.((.((...)).)).))).)))).......... ( -35.30)
>DroYak_CAF1 17391 82 - 1
CCA----------------------UGAAA----CAACCACACACAUGCAAGGCCUUGUG----UAUAUGUGUGCGGUUGUCGGCUUUGCGGGGAAUUGGGGAAUAUUUGCA
(((----------------------....(----(((((.(((((((((((....)))).----...))))))).))))))(.((...)).).....)))............ ( -22.20)
>DroAna_CAF1 10053 97 - 1
CCAUCCUCCCUCUUGCCCCUC--UACGUCA----CUCACAC--------CAGCCCAUACCUAUAUGCAC-CGUGUGUCUGUGUGUGUGGCGGGGAAUUGGGGAAUAUUUGCA
......(((((....((((..--...((((----(.(((((--------.((..(((((..........-.))))).))))))).)))))))))....)))))......... ( -31.90)
>consensus
CCACC____CAC_UUUCCCUC__CAUGAAA____CACACACACACAUGCAAGGCCGUACGUAUGUAUAUGUGUGCGGUUGUCGGCUUUGCGGGGAAUUGGGGAAUAUUUGCA
.................................................(((((((.(((..(((((....)))))..))))))))))(((((..(((....))).))))). (-10.37 = -10.73 +   0.37)

alignment

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secondary structure

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Window 3

Location 15,909,154 – 15,909,261
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 79.19
Mean single sequence MFE -26.38
Consensus MFE -15.96
Energy contribution -17.21
Covariance contribution 1.25
Combinations/Pair 1.19
Mean z-score -1.79
Structure conservation index 0.61
SVM decision value 0.27
SVM RNA-class probability 0.663738
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15909154 107 + 27905053
ACACAUAUACAAACGUACGGCCUUGCAUGUGUGUGUGUGUUUGUUUCAUUGGGAGGGAAAAGUGGGUGGAGAUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAG
............((((((......(((((((((..(((((...(((((((.(..........).)))))))...)))))..))))))))).....))))))...... ( -28.40)
>DroSec_CAF1 27009 103 + 1
ACACAUAUACAUACGUACGGCCUUUUAUAUGAGUGUGUG----UUUCAUGGGGAGGGAAAUGUGGGUGGGGAUCUUACGUGGGCAUAUGCUAAAAGUAUGUACAAAG
.......(((((((......(((((..((((((......----.))))))..)))))..(((((((.......))))))).(((....)))....)))))))..... ( -24.90)
>DroSim_CAF1 16547 103 + 1
ACACAUAUACAUACGUACGGCCUUUUAUAUGAGUGUGUG----UUUCAUGGGGAGGGAAAUAUGGGUGGGGAUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAG
.........((..((((...(((((..((((((......----.))))))..)))))...))))..))...........(((((((((.......)))))))))... ( -25.20)
>DroEre_CAF1 16114 90 + 1
ACACACAUACAUACAUACGGCCUUGCAUGUGUGUGCGUU----UUUCAAG-------------GGGUGGGGAUCGUACGUGUGCAUAUGCUAAAAGUAUGUACAAAG
...........(((((((......(((((((((..((((----(..((..-------------...))..))....)))..))))))))).....)))))))..... ( -27.60)
>DroYak_CAF1 17430 81 + 1
ACACAUAUA----CACAAGGCCUUGCAUGUGUGUGGUUG----UUUCA------------------UGGGGAUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAG
....(((((----(....(((..((((..(((((((((.----((...------------------.)).)))))))))..))))...)))....))))))...... ( -25.80)
>consensus
ACACAUAUACAUACGUACGGCCUUGCAUGUGUGUGUGUG____UUUCAUGGGGAGGGAAA__UGGGUGGGGAUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAG
...........(((((((......(((((((..((((((....((((((................))))))....))))))..))))))).....)))))))..... (-15.96 = -17.21 +   1.25)

alignment

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secondary structure

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Window 4

Location 15,909,154 – 15,909,261
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 79.19
Mean single sequence MFE -17.22
Consensus MFE -13.53
Energy contribution -14.09
Covariance contribution 0.56
Combinations/Pair 1.24
Mean z-score -1.48
Structure conservation index 0.79
SVM decision value 0.41
SVM RNA-class probability 0.726596
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15909154 107 - 27905053
CUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAUCUCCACCCACUUUUCCCUCCCAAUGAAACAAACACACACACACAUGCAAGGCCGUACGUUUGUAUAUGUGU
.................(((((((((.(((((((..((..............................................))..))))))).))))))))).. ( -19.15)
>DroSec_CAF1 27009 103 - 1
CUUUGUACAUACUUUUAGCAUAUGCCCACGUAAGAUCCCCACCCACAUUUCCCUCCCCAUGAAA----CACACACUCAUAUAAAAGGCCGUACGUAUGUAUAUGUGU
.................((((((((..(((((.(.....)...........(((....((((..----.......)))).....)))...)))))..)))))))).. ( -13.30)
>DroSim_CAF1 16547 103 - 1
CUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAUCCCCACCCAUAUUUCCCUCCCCAUGAAA----CACACACUCAUAUAAAAGGCCGUACGUAUGUAUAUGUGU
.................(((((((((.(((((((.................(((....((((..----.......)))).....))).))))))).))))))))).. ( -18.07)
>DroEre_CAF1 16114 90 - 1
CUUUGUACAUACUUUUAGCAUAUGCACACGUACGAUCCCCACCC-------------CUUGAAA----AACGCACACACAUGCAAGGCCGUAUGUAUGUAUGUGUGU
.................(((((((((.(((((((..(.......-------------.((....----)).(((......)))..)..))))))).))))))))).. ( -21.90)
>DroYak_CAF1 17430 81 - 1
CUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAUCCCCA------------------UGAAA----CAACCACACACAUGCAAGGCCUUGUG----UAUAUGUGU
.................(((((((((((..((((.....))------------------))...----...((............))...))))----))))))).. ( -13.70)
>consensus
CUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAUCCCCACCCA__UUUCCCUCCCCAUGAAA____CACACACACACAUGCAAGGCCGUACGUAUGUAUAUGUGU
.................(((((((((.(((((((..(................................................)..))))))).))))))))).. (-13.53 = -14.09 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,909,187 – 15,909,301
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.94
Mean single sequence MFE -31.42
Consensus MFE -19.94
Energy contribution -20.38
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -3.19
Structure conservation index 0.63
SVM decision value 2.66
SVM RNA-class probability 0.996127
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15909187 114 + 27905053
UGUGUGUUUGUUUCAUUGGGAGGGAAAAGUG----GGUGGAG--AUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUGUGUGUGAAUGU
.....(((..(..((((((((((.(((...(----((.((((--((((....(((((((((.......))))))))).....)))))))))))..))).))))))))))...)..))).. ( -38.70)
>DroSim_CAF1 16580 110 + 1
UGUGUG----UUUCAUGGGGAGGGAAAUAUG----GGUGGGG--AUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUGUGUGUGAAUGU
......----...(((..(((((.(((((.(----((.((..--((((....(((((((((.......))))))))).....))))..)))))))))).)))))..)))........... ( -33.30)
>DroEre_CAF1 16147 97 + 1
UGCGUU----UUUCAAG-------------G----GGUGGGG--AUCGUACGUGUGCAUAUGCUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUGUGUGUGAAUGU
.(((.(----(..((..-------------.----..))..)--).)))((((.(((((((((((((((.....((((((..........))))))....))))))))))))))).)))) ( -27.70)
>DroYak_CAF1 17459 92 + 1
UGGUUG----UUUCA----------------------UGGGG--AUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUGUGUGUGAAUGU
(((((.----((...----------------------.)).)--)))).((((.(((((((((((((((.....((((((..........))))))....))))))))))))))).)))) ( -24.30)
>DroAna_CAF1 10116 112 + 1
UGUGAG----UGACGUA--GAGGGGCAAGAGGGAGGAUGGGGCUAUCAUACGUGUGCAUAUGGUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUA--UGUGAAUGU
......----(.(((((--((((((((((((((((((((....)))).....(((((((((.......))))))))).........)))))))...)))))))))..))--))).).... ( -33.10)
>consensus
UGUGUG____UUUCAUG__GAGGG__A___G____GGUGGGG__AUCAUACGUGUGCAUAUGCUAAAAGUAUGUACAAAGAUUGAUUUCCCUUUGUUUGCCUUUUAGUGUGUGUGAAUGU
.................................................((((.(((((((((((((((.....((((((..........))))))....))))))))))))))).)))) (-19.94 = -20.38 +   0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,909,187 – 15,909,301
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.94
Mean single sequence MFE -16.30
Consensus MFE -13.98
Energy contribution -14.38
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.78
Structure conservation index 0.86
SVM decision value 2.65
SVM RNA-class probability 0.996062
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15909187 114 - 27905053
ACAUUCACACACACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAU--CUCCACC----CACUUUUCCCUCCCAAUGAAACAAACACACA
...((((......(((((((....(((((((........))))))).....)))))))((((((....))))))..--.......----................))))........... ( -17.40)
>DroSim_CAF1 16580 110 - 1
ACAUUCACACACACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAU--CCCCACC----CAUAUUUCCCUCCCCAUGAAA----CACACA
...((((......(((((((....(((((((........))))))).....)))))))((((((....))))))..--.......----................)))).----...... ( -17.40)
>DroEre_CAF1 16147 97 - 1
ACAUUCACACACACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUAGCAUAUGCACACGUACGAU--CCCCACC----C-------------CUUGAAA----AACGCA
...((((......(((((((....(((((((........))))))).....)))))))..((((....))))....--.......----.-------------..)))).----...... ( -13.10)
>DroYak_CAF1 17459 92 - 1
ACAUUCACACACACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAU--CCCCA----------------------UGAAA----CAACCA
...((((......(((((((....(((((((........))))))).....)))))))((((((....))))))..--.....----------------------)))).----...... ( -17.40)
>DroAna_CAF1 10116 112 - 1
ACAUUCACA--UACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUACCAUAUGCACACGUAUGAUAGCCCCAUCCUCCCUCUUGCCCCUC--UACGUCA----CUCACA
.........--........((((((((((((........)))))))............((((((....))))))..................)))))....--.......----...... ( -16.20)
>consensus
ACAUUCACACACACUAAAAGGCAAACAAAGGGAAAUCAAUCUUUGUACAUACUUUUAGCAUAUGCACACGUAUGAU__CCCCACC____C___U__CCCUC__CAUGAAA____CACACA
.............(((((((....(((((((........))))))).....)))))))((((((....)))))).............................................. (-13.98 = -14.38 +   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 12:11:09 2006