Locus 5254

Sequence ID 2R_DroMel_CAF1
Location 17,096,323 – 17,096,454
Length 131
Max. P 0.998835
window8391 window8392 window8393 window8394

overview

Window 1

Location 17,096,323 – 17,096,419
Length 96
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 70.12
Mean single sequence MFE -23.92
Consensus MFE -9.90
Energy contribution -11.68
Covariance contribution 1.78
Combinations/Pair 1.12
Mean z-score -3.06
Structure conservation index 0.41
SVM decision value 3.16
SVM RNA-class probability 0.998626
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17096323 96 + 20766785
AGUCAUAAAAUCACUGCACAAAAUGCACUCAAUUGCACUUACAGAUGCAGAUACUGUAUCUGUAUC-----------------------UGCAUCUGCAUCCUCAUCUGGUUGCUGUCA
.(.((...(((((..........((((......))))....(((((((((((((.......)))))-----------------------))))))))..........)))))..)).). ( -27.60)
>DroSec_CAF1 33564 82 + 1
AGUCAUAAAAUCACUGCACAAAAUGCACUCAAUUGCACUUACAGAUACAGAUACUGUAUCUGUAUC-----------------------UGCAUCUGUAUCCGCA--------------
..............((((.....))))..((..((((..(((((((((((...)))))))))))..-----------------------))))..))........-------------- ( -22.90)
>DroSim_CAF1 33791 96 + 1
AGUCAUAAAAUCACUGCACAAAAUGCACUCAAUUGCACUUACAGAUACAGAUACUGUAUCUGUAUC-----------------------UGCAUCUGUAUCCGCAUCUGGUCGCUGUCA
............((.((((...((((...((..((((..(((((((((((...)))))))))))..-----------------------))))..)).....))))...)).)).)).. ( -28.00)
>DroEre_CAF1 34155 119 + 1
AGUCGUAAAAUCACUGCACAAAACGCACUCAAUUGCACUUACAGAUACAGAUACUGUAUCUGCAUCAGCAUCGCCUCAGCCUCAGCAUUAGCAUCUGCAUCUGCAUAUGGUUUCUGUCA
.((.((......)).))(((((((((.......(((.....(((((((((...))))))))).....)))..((....))....)).....(((.(((....))).))))))).))).. ( -23.10)
>DroYak_CAF1 36117 108 + 1
AGUCGUAAAAUCACUGCAUGAAACGCACUCAAUUGCACUUACAUAUACAGAUACAGAUACAGACUCAG-----------AUACUGUAUCUGCAUCUGCGUCUGCAUCUGGUUGCUGUCA
............((.(((......(((......)))...........(((((.((((..((((..(((-----------(((...))))))..))))..)))).)))))..))).)).. ( -28.40)
>DroPer_CAF1 67083 84 + 1
AGUCAUAAAAUCAAUGCACAAAUUGCAU-GAAAUGUCCGUACUUAU-----------AUCUGUAUC-----------------------UGCAUCAGAGUCUGUAUCUGUUUGAUUUCA
.......(((((((((((.....)))))-...((((..((((....-----------....)))).-----------------------.))))((((.......))))..)))))).. ( -13.50)
>consensus
AGUCAUAAAAUCACUGCACAAAAUGCACUCAAUUGCACUUACAGAUACAGAUACUGUAUCUGUAUC_______________________UGCAUCUGCAUCCGCAUCUGGUUGCUGUCA
..............(((.......(((......)))...(((((((((((...)))))))))))..........................))).......................... ( -9.90 = -11.68 +   1.78)

alignment

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secondary structure

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Window 2

Location 17,096,323 – 17,096,419
Length 96
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 70.12
Mean single sequence MFE -30.85
Consensus MFE -16.50
Energy contribution -18.17
Covariance contribution 1.67
Combinations/Pair 1.26
Mean z-score -3.24
Structure conservation index 0.53
SVM decision value 3.25
SVM RNA-class probability 0.998835
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17096323 96 - 20766785
UGACAGCAACCAGAUGAGGAUGCAGAUGCA-----------------------GAUACAGAUACAGUAUCUGCAUCUGUAAGUGCAAUUGAGUGCAUUUUGUGCAGUGAUUUUAUGACU
.....(((.((......)).((((((((((-----------------------(((((.......)))))))))))))))((((((......))))))...)))............... ( -32.40)
>DroSec_CAF1 33564 82 - 1
--------------UGCGGAUACAGAUGCA-----------------------GAUACAGAUACAGUAUCUGUAUCUGUAAGUGCAAUUGAGUGCAUUUUGUGCAGUGAUUUUAUGACU
--------------((((..((((((((((-----------------------(((((.......)))))))))))))))..))))..(.(.(((((...))))).).).......... ( -30.50)
>DroSim_CAF1 33791 96 - 1
UGACAGCGACCAGAUGCGGAUACAGAUGCA-----------------------GAUACAGAUACAGUAUCUGUAUCUGUAAGUGCAAUUGAGUGCAUUUUGUGCAGUGAUUUUAUGACU
.....(((..(((.((((..((((((((((-----------------------(((((.......)))))))))))))))..)))).)))..)))........................ ( -33.40)
>DroEre_CAF1 34155 119 - 1
UGACAGAAACCAUAUGCAGAUGCAGAUGCUAAUGCUGAGGCUGAGGCGAUGCUGAUGCAGAUACAGUAUCUGUAUCUGUAAGUGCAAUUGAGUGCGUUUUGUGCAGUGAUUUUACGACU
((((((((......((((((((((((((((..(((...(((.........)))...))).....)))))))))))))))).(..(......)..).)))))).)).............. ( -37.20)
>DroYak_CAF1 36117 108 - 1
UGACAGCAACCAGAUGCAGACGCAGAUGCAGAUACAGUAU-----------CUGAGUCUGUAUCUGUAUCUGUAUAUGUAAGUGCAAUUGAGUGCGUUUCAUGCAGUGAUUUUACGACU
.....(((..((.(((((((..(((((((((((.(((...-----------))).)))))))))))..))))))).))....))).....(((.(((.((((...))))....)))))) ( -38.10)
>DroPer_CAF1 67083 84 - 1
UGAAAUCAAACAGAUACAGACUCUGAUGCA-----------------------GAUACAGAU-----------AUAAGUACGGACAUUUC-AUGCAAUUUGUGCAUUGAUUUUAUGACU
(((((((((.((((.......)))).....-----------------------.........-----------....(((((((......-......))))))).)))))))))..... ( -13.50)
>consensus
UGACAGCAACCAGAUGCAGAUGCAGAUGCA_______________________GAUACAGAUACAGUAUCUGUAUCUGUAAGUGCAAUUGAGUGCAUUUUGUGCAGUGAUUUUAUGACU
..............(((((((((((((((....................................))))))))))))))).(((.((((.(.((((.....)))).))))).))).... (-16.50 = -18.17 +   1.67)

alignment

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secondary structure

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Window 3

Location 17,096,363 – 17,096,454
Length 91
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 64.60
Mean single sequence MFE -31.62
Consensus MFE -10.32
Energy contribution -13.68
Covariance contribution 3.36
Combinations/Pair 1.27
Mean z-score -4.15
Structure conservation index 0.33
SVM decision value 2.78
SVM RNA-class probability 0.997019
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17096363 91 + 20766785
ACAGAUGCAGAUAC-UGUAUCUGUAUC-----------------------UGCAUCUGCAUCCUCAUCUGGUUGCUGUCAAAUCUAGCUAUCGA--GUGCAGACUU---AAGGCAUUCAU
.(((((((((((((-.......)))))-----------------------))))))))...........(((.((((.......)))).)))((--((((......---...)))))).. ( -32.70)
>DroSim_CAF1 33831 91 + 1
ACAGAUACAGAUAC-UGUAUCUGUAUC-----------------------UGCAUCUGUAUCCGCAUCUGGUCGCUGUCAAAUCCAGCCAUCGA--GUGCAGACUU---AAGGCAUUCAU
((((((.(((((((-.......)))))-----------------------)).)))))).((.(((..((((.((((.......)))).)))).--.))).))...---........... ( -29.80)
>DroEre_CAF1 34195 114 + 1
ACAGAUACAGAUAC-UGUAUCUGCAUCAGCAUCGCCUCAGCCUCAGCAUUAGCAUCUGCAUCUGCAUAUGGUUUCUGUCAAAUCCAGCAAUCGA--GUGCAGACUU---AAGGCAUUCAU
.(((((((((...)-))))))))..........((((..((....((....))....)).(((((((.(((((.(((.......))).))))).--)))))))...---.))))...... ( -34.50)
>DroYak_CAF1 36157 103 + 1
ACAUAUACAGAUAC-AGAUACAGACUCAG-----------AUACUGUAUCUGCAUCUGCGUCUGCAUCUGGUUGCUGUCAAAUCCAGCAAUCGA--GUGCAGACUU---AAGGCAUUCAU
.......(((((.(-((((((((......-----------...))))))))).))))).(((((((..(((((((((.......))))))))).--.)))))))..---........... ( -43.20)
>DroAna_CAF1 45490 79 + 1
ACAAAUGCAGAUACGUGUAUCUGUAUC-----------------------UGU------------------CGGCUGACAAAUUCCAAAUUCCACAUGGCAGAUUGUGGUAGAUACUUAU
....(((((((((....))))))))).-----------------------(((------------------(....))))...........(((((........)))))........... ( -17.90)
>consensus
ACAGAUACAGAUAC_UGUAUCUGUAUC_______________________UGCAUCUGCAUCCGCAUCUGGUUGCUGUCAAAUCCAGCAAUCGA__GUGCAGACUU___AAGGCAUUCAU
...((((((((((....))))))))))........................((.(((((((.......((((.((((.......)))).))))...)))))))(((...)))))...... (-10.32 = -13.68 +   3.36)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,096,363 – 17,096,454
Length 91
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 64.60
Mean single sequence MFE -34.28
Consensus MFE -9.89
Energy contribution -12.45
Covariance contribution 2.56
Combinations/Pair 1.32
Mean z-score -4.07
Structure conservation index 0.29
SVM decision value 2.51
SVM RNA-class probability 0.994754
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17096363 91 - 20766785
AUGAAUGCCUU---AAGUCUGCAC--UCGAUAGCUAGAUUUGACAGCAACCAGAUGAGGAUGCAGAUGCA-----------------------GAUACAGAUACA-GUAUCUGCAUCUGU
.....(((.((---((((((((..--......)).))))))))..))).((......))..(((((((((-----------------------(((((.......-)))))))))))))) ( -33.60)
>DroSim_CAF1 33831 91 - 1
AUGAAUGCCUU---AAGUCUGCAC--UCGAUGGCUGGAUUUGACAGCGACCAGAUGCGGAUACAGAUGCA-----------------------GAUACAGAUACA-GUAUCUGUAUCUGU
...........---..((((((((--(.(.(.((((.......)))).)).)).)))))))(((((((((-----------------------(((((.......-)))))))))))))) ( -36.10)
>DroEre_CAF1 34195 114 - 1
AUGAAUGCCUU---AAGUCUGCAC--UCGAUUGCUGGAUUUGACAGAAACCAUAUGCAGAUGCAGAUGCUAAUGCUGAGGCUGAGGCGAUGCUGAUGCAGAUACA-GUAUCUGUAUCUGU
.....((((((---(.(((((((.--.......(((.......)))........)))))))((....((....))....)))))))))........(((((((((-(...)))))))))) ( -36.79)
>DroYak_CAF1 36157 103 - 1
AUGAAUGCCUU---AAGUCUGCAC--UCGAUUGCUGGAUUUGACAGCAACCAGAUGCAGACGCAGAUGCAGAUACAGUAU-----------CUGAGUCUGUAUCU-GUAUCUGUAUAUGU
...........---..((((((((--(.(.((((((.......))))))).)).)))))))((((((((((((((((...-----------......))))))))-))))))))...... ( -45.80)
>DroAna_CAF1 45490 79 - 1
AUAAGUAUCUACCACAAUCUGCCAUGUGGAAUUUGGAAUUUGUCAGCCG------------------ACA-----------------------GAUACAGAUACACGUAUCUGCAUUUGU
....((((((.(((((........)))))......(.(((((((....)------------------)))-----------------------))).)))))))................ ( -19.10)
>consensus
AUGAAUGCCUU___AAGUCUGCAC__UCGAUUGCUGGAUUUGACAGCAACCAGAUGCAGAUGCAGAUGCA_______________________GAUACAGAUACA_GUAUCUGUAUCUGU
..............((((((((..........)).))))))..............((((((((((((((.....................................)))))))))))))) ( -9.89 = -12.45 +   2.56)

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 11:40:18 2006