Locus 3730

Sequence ID 3R_DroMel_CAF1
Location 10,123,819 – 10,124,131
Length 312
Max. P 0.892348
window5978 window5979 window5980 window5981

overview

Window 8

Location 10,123,819 – 10,123,939
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.83
Mean single sequence MFE -34.40
Consensus MFE -13.02
Energy contribution -17.38
Covariance contribution 4.36
Combinations/Pair 1.04
Mean z-score -1.94
Structure conservation index 0.38
SVM decision value 0.36
SVM RNA-class probability 0.703923
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10123819 120 + 27905053
UAAGAUUCGCAUCUCAAACUAGUUGAUAAUUUUAAAUUUCCCGCCAAGCUAAGACAAUCUGGCAACGCGUAAUGAAGGUGAAAGUGUUCCCAUUGGCUUAGUCAAUGGGAACAGGAGCUC
(((((((..((.((......)).))..)))))))...((((((((..((((........))))..((.....))..))))....(((((((((((((...)))))))))))))))))... ( -31.60)
>DroSec_CAF1 33082 117 + 1
AAAG-UACCAACGUAGGCCCAGUUGAUUAUUUCAAAUUUCCCGCCAAGCUAAGACAAUCUGGCAACGCG--GUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUC
..((-(.((....................(((((..((..((((...((((........))))...)))--)..))..))))).(((((((((((((...))))))))))))))).))). ( -39.80)
>DroSim_CAF1 29250 120 + 1
UAAGAUUCGCAUCUCAAUCUAGUUGAUAAUUUCAAACUUCCCGCCAAGCCAAGACAAUCUGGCAACGCGCAAUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUC
.....(((((............((((.....)))).((((.(((...((((........))))...)))....)))))))))..(((((((((((((...)))))))))))))....... ( -36.90)
>DroEre_CAF1 32811 107 + 1
UUAAGUUCGCUCGUAGGCGCAGUUGAUAGUUUCAAAUGUGCCGCCAAGAUAAGACGGUCUGGCAACGCGAAAUGAAGGUGACAGUGUUCCCGUUGGCUUUGUC-------------CCUC
.....(((((.....((((((.((((.....)))).))))))((((.(((......)))))))...)))))....(((.(((((.(((......))).)))))-------------))). ( -37.00)
>DroYak_CAF1 33468 106 + 1
UAAGGUUCGCUCGUAGGCGCAGUUGAAAAUUUUAAAUUUCGCGCCAAGAUA-GAUAGUCUGGCAACGCGAAAUGAAGGUGAAAGUGGUCCCUUUGGCUUUGUA-------------GCUC
........(((((.((((.................(((((((((((.(((.-....)))))))...)))))))(((((.((......))))))).)))))).)-------------)).. ( -26.70)
>consensus
UAAGAUUCGCACGUAGGCCCAGUUGAUAAUUUCAAAUUUCCCGCCAAGCUAAGACAAUCUGGCAACGCGAAAUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUC
.......(((............((((.....)))).......((((.............))))...)))...............(((((((((((((...)))))))))))))....... (-13.02 = -17.38 +   4.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,123,859 – 10,123,979
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.31
Mean single sequence MFE -36.58
Consensus MFE -21.77
Energy contribution -25.14
Covariance contribution 3.37
Combinations/Pair 1.10
Mean z-score -2.23
Structure conservation index 0.60
SVM decision value 0.97
SVM RNA-class probability 0.892348
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10123859 120 + 27905053
CCGCCAAGCUAAGACAAUCUGGCAACGCGUAAUGAAGGUGAAAGUGUUCCCAUUGGCUUAGUCAAUGGGAACAGGAGCUCACAUCGCAUUGAGAGCAAUUCCCCAUCUGGUAACAUUGCA
..((...((((........))))...))((((((.(((((....(((((((((((((...)))))))))))))(((((((.((......)).))))...))).))))).....)))))). ( -42.20)
>DroSec_CAF1 33121 118 + 1
CCGCCAAGCUAAGACAAUCUGGCAACGCG--GUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUCCCAUUAAGAGCACUUCCCCAUCUGGUAGCACUGCA
..((((.............))))...(((--(((.(((((....(((((((((((((...)))))))))))))(((((((............)))...)))).))))).....)))))). ( -41.52)
>DroSim_CAF1 29290 120 + 1
CCGCCAAGCCAAGACAAUCUGGCAACGCGCAAUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUCCCAUUAAGAGCACUUCCCCAUCUGGUAACACUGCA
..((...((((........))))...))(((.((.(((((....(((((((((((((...)))))))))))))(((((((............)))...)))).))))).....)).))). ( -37.70)
>DroEre_CAF1 32851 90 + 1
CCGCCAAGAUAAGACGGUCUGGCAACGCGAAAUGAAGGUGACAGUGUUCCCGUUGGCUUUGUC-------------CCUCACG-----------------CUGCAUCUGGUAACACUGCA
..((((.(((......)))))))...((........(....)((((((.(((...((..(((.-------------....)))-----------------..))...))).)))))))). ( -24.90)
>consensus
CCGCCAAGCUAAGACAAUCUGGCAACGCG_AAUGAAGGUGAAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUCCCAUUAAGAGCACUUCCCCAUCUGGUAACACUGCA
..((((.............)))).....((((((...((((...(((((((((((((...))))))))))))).....))))..................((......))...)))))). (-21.77 = -25.14 +   3.37)

alignment

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secondary structure

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Window 0

Location 10,123,899 – 10,124,019
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.89
Mean single sequence MFE -27.24
Consensus MFE -13.26
Energy contribution -16.30
Covariance contribution 3.04
Combinations/Pair 1.05
Mean z-score -2.00
Structure conservation index 0.49
SVM decision value 0.31
SVM RNA-class probability 0.682341
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10123899 120 + 27905053
AAAGUGUUCCCAUUGGCUUAGUCAAUGGGAACAGGAGCUCACAUCGCAUUGAGAGCAAUUCCCCAUCUGGUAACAUUGCAGCACGUAGUAAACAGAAAAUCACAAUUGGAUCGAAAAAUC
....(((((((((((((...)))))))))))))(((((((.((......)).))))...)))(((((((.....(((((.....)))))...))))..........)))........... ( -33.50)
>DroSec_CAF1 33159 120 + 1
AAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUCCCAUUAAGAGCACUUCCCCAUCUGGUAGCACUGCAGCACGUAGUAAACAAAAAAUCACAAUUGGAUCGAAAAAUC
....(((((((((((((...))))))))))))).........((((.(((..(((((((.........))).))(((((.....)))))..........))..))).))))......... ( -29.70)
>DroSim_CAF1 29330 120 + 1
AAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUCCCAUUAAGAGCACUUCCCCAUCUGGUAACACUGCAGCACGUAGUAAACAGAAAAUCACAAUUGGAUCGAAAAAUC
....(((((((((((((...)))))))))))))(((((((............)))...))))(((((((.....(((((.....)))))...))))..........)))........... ( -30.70)
>DroEre_CAF1 32891 90 + 1
ACAGUGUUCCCGUUGGCUUUGUC-------------CCUCACG-----------------CUGCAUCUGGUAACACUGCAGCACGUAGUAAACAGAAAAUCACAAUUGGAUCGAAAAAUC
....((.(((.((((((..(((.-------------....)))-----------------..)).((((.....(((((.....)))))...))))......)))).))).))....... ( -17.40)
>DroYak_CAF1 33547 90 + 1
AAAGUGGUCCCUUUGGCUUUGUA-------------GCUCACG-----------------CUGCAUCUGGUAACACUGCAGCACGUAGUAAACAGAAAAUCACAAUUGGAUCGAAAAAUC
....((((((..(((....((((-------------((....)-----------------)))))((((.....(((((.....)))))...))))......)))..))))))....... ( -24.90)
>consensus
AAAGUGUUCCCAUUGGCUUUGUCAAUGGGAACAGGAACUCACAUC_CAUU_AGAGCA_UUCCCCAUCUGGUAACACUGCAGCACGUAGUAAACAGAAAAUCACAAUUGGAUCGAAAAAUC
...(((.((((((((((...))))))))))...................................((((.....(((((.....)))))...))))....)))................. (-13.26 = -16.30 +   3.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,124,019 – 10,124,131
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.21
Mean single sequence MFE -43.96
Consensus MFE -31.90
Energy contribution -32.30
Covariance contribution 0.40
Combinations/Pair 1.21
Mean z-score -1.63
Structure conservation index 0.73
SVM decision value 0.03
SVM RNA-class probability 0.551201
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10124019 112 - 27905053
GACGGAGAGAGUGGGAGCGGGUGGG------UUGGCGUCUCUACCGCCCACU--GCUCAGCCUGCCAACGAAUUGCGCUAAUAUUUGCACACGCGAGUGCUCUGUUUUAUGGCAAUUUGC
...((..((.((..((((((.((((------(.((........)))))))))--)))).)))).))..((((((((((........)).(((....)))............)))))))). ( -39.20)
>DroSec_CAF1 33279 117 - 1
GACGGAGAGAGUGGGAGUGGGUGGGG-UGGGGUGGCGUUUCUACCUUCCACC--GCGCAGUCUGCCAACGAAUUGCGCUAAUAUUUGCACACGCGAGUGCUCUGUAUUAUGGCAAUUUGC
...........(((.((...(((.((-((((((((.....)))))..)))))--.)))...)).))).((((((((..((((((..((((......))))...))))))..)))))))). ( -44.10)
>DroSim_CAF1 29450 117 - 1
GACGGAGAGAGUGGGAGUGGGUGGGG-UGAGGUGGCGUCUCUACCUUCCACC--GCGCAGUCUGCCAACGAAUUGCGCUAAUAUUUGCACACGCGAGUGCUCUGUUUUAUGGCAAUUUGC
(((((((...(((.((((((((((..-.(((((((.....))))))))))))--(((((((.((....)).)))))))...))))).)))((....)).))))))).............. ( -42.90)
>DroEre_CAF1 32981 120 - 1
GAGAGAGAGAGUGGUAGUGGGUGGGUUUGGGGUGGCGUCUUUACCGCCCACCUCUCUCACCCUGCCAACAAAUUGCGCUAAUAUUUGCACACGCGAGUGCACUGUUUUAUGGCAAUUUGC
...........(((((..(((((((...(((((((((.......)).))))))).)))))))))))).((((((((((........)).(((....)))............)))))))). ( -46.40)
>DroYak_CAF1 33637 119 - 1
UAGAGAGAGAGUGGGAGUGGGUGGGU-UGUGGUGGCGUCUUUACCGCCCAGCCCUCUCACUCUGCUAAUAAAUUGCGCUAAUAUUUGCACACGCGAGUGCACUGUUUUAUGGCAAUUUGC
.....((((((((((((.((.(((((-.((((........)))).))))).)))))))))))).))..((((((((((........)).(((....)))............)))))))). ( -47.20)
>consensus
GACGGAGAGAGUGGGAGUGGGUGGGG_UGGGGUGGCGUCUCUACCGCCCACC__GCUCAGUCUGCCAACGAAUUGCGCUAAUAUUUGCACACGCGAGUGCUCUGUUUUAUGGCAAUUUGC
...((..(((.((((....(((((((....(((((.....))))))))))))...)))).))).))..((((((((((........)).(((....)))............)))))))). (-31.90 = -32.30 +   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 11:08:40 2006