Locus 2674

Sequence ID X_DroMel_CAF1
Location 7,166,329 – 7,166,546
Length 217
Max. P 0.997713
window4377 window4378 window4379 window4380 window4381

overview

Window 7

Location 7,166,329 – 7,166,430
Length 101
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 82.90
Mean single sequence MFE -31.40
Consensus MFE -19.60
Energy contribution -20.56
Covariance contribution 0.96
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.62
SVM decision value 0.49
SVM RNA-class probability 0.757518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7166329 101 + 22224390
AACAGCGAUGUGUGGCAUUUUCUAACAGUUGCUGCUGCU----GUCGCAGGUUGCAGGUUGCAUGUUUUGUUGCAGU----UGCUGCAGCUUAUAUGACGCUUACAUUU
....(((((.(((((((........((((....)))).)----)))))).)))))((((..(((((...(((((((.----..)))))))..)))))..))))...... ( -32.80)
>DroSec_CAF1 33971 94 + 1
AACAGCGAUGUGUGGCAUUUUCCAACAGUUGCUGCUGUU----GUCGCAGGUUGCCGG-------UUUUGUGGCAGU----UGCUGCAGUUUCUAUGACGCUUGCAUUU
....((((.((((((((.....(((((((....))))))----)........))))((-------..(((..((...----.))..)))..))....)))))))).... ( -30.82)
>DroSim_CAF1 28184 94 + 1
AACAGCGAUGUGUGGCAUUUUCUAAUAGUUGCUGCUGCU----GUCGCAGGUUGCAGG-------UUUUGUGGCAGU----UGCUGCAGUUUCUAUGACGCUUACAUUU
...(((((((.....)))......((((..(((((.(((----((((((((.......-------.)))))))))))----....)))))..))))..))))....... ( -30.10)
>DroEre_CAF1 34824 85 + 1
AACAGCGAUGUGUGGCAUUUUCCAAGAGUUGCUG----------UCGCAGGUUGCAGG-------CUUUGUGGCAGU-------UGCAGGUUCUAUGACGCUUGCAUUU
.((((((((...(((......)))...)))))))----------).((((((((((.(-------((....)))...-------)))).(((....))))))))).... ( -27.20)
>DroYak_CAF1 35960 99 + 1
AACAGCGAUGUGUGGCAUUUUCUAACAGUUGCUGCAGUCGCAGGUUGCAGGUUGCAGG-------CUUUGUGGCAGUUCUAUGCUGCAGGUUCUGUGACGCUUG---UU
(((((((((.((..(((............)))..))))))).....((..((..(((.-------.((((..(((......)))..))))..)))..)))).))---)) ( -36.10)
>consensus
AACAGCGAUGUGUGGCAUUUUCUAACAGUUGCUGCUGCU____GUCGCAGGUUGCAGG_______UUUUGUGGCAGU____UGCUGCAGGUUCUAUGACGCUUGCAUUU
..(((((((...(((......)))...)))))))............((((((.(((((........))))).(((((.....)))))............)))))).... (-19.60 = -20.56 +   0.96)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,166,394 – 7,166,509
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 72.45
Mean single sequence MFE -34.18
Consensus MFE -14.67
Energy contribution -15.85
Covariance contribution 1.18
Combinations/Pair 1.20
Mean z-score -2.06
Structure conservation index 0.43
SVM decision value 1.28
SVM RNA-class probability 0.939115
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7166394 115 + 22224390
GUUGCAGU----UGCUGCAGCUUAUAUGACGCUUACAUUUGUUAUAUGUAUCUGCCACUGGGGGUUUUCCGUCAAUAUUGCAGGUUGCAUAGCUUAUGCUGCAGCUUCUAUU-GAUGACU
((((((((----.((((((((..((((((((........))))))))((((((((...(((.((....)).))).....))))).))).........))))))))....)))-).)))). ( -35.90)
>DroSec_CAF1 34029 115 + 1
GUGGCAGU----UGCUGCAGUUUCUAUGACGCUUGCAUUUGUUAUAUGUAUCUGCCACUAGGGGUUUUCCGUCGAUGUUGCAGGUUGCAUAGCUAAUGCUGCAACUUCUAUU-GAUAACU
((((.(((----(((.((.(((.....)))))..(((((.((..(((((((((((.((..((((....)).))...)).))))).)))))))).))))).)))))).)))).-....... ( -32.80)
>DroSim_CAF1 28242 115 + 1
GUGGCAGU----UGCUGCAGUUUCUAUGACGCUUACAUUUGUUAUAAGUAUCUGCCACUAGGGGUUUUCCAUCGAUGUUGCAGGUUGCAUAGCUUAUGCUGCAACUUCUAUU-GAUAACU
(((((((.----((((........(((((((........))))))))))).)))))))..(((....)))(((((((..(.((((((((..((....)))))))))))))))-))).... ( -33.30)
>DroEre_CAF1 34876 95 + 1
GUGGCAGU-------UGCAGGUUCUAUGACGCUUGCAUUUGGU----GUAUCUGCUGCUGGGA-UUUUUCCUGGAUGUCGCAGGUUGCAUAGCUUAUGCUGCAGCUA-------------
((((((..-------.((((((......(((((.......)))----))))))))..(..(((-....)))..).)))))).(((((((..((....))))))))).------------- ( -33.60)
>DroYak_CAF1 36022 101 + 1
GUGGCAGUUCUAUGCUGCAGGUUCUGUGACGCUUG---UUGCU----GUG-----------CG-UUGAUGUUGCAGGUUGCAGGUUGCACAGCUUGUGUGGCAGCUUCCCUAGGAUGACG
(..(((......)))..)(((..((((.((((...---..(((----(((-----------((-....(((........)))...))))))))..)))).))))....)))......... ( -35.30)
>consensus
GUGGCAGU____UGCUGCAGGUUCUAUGACGCUUGCAUUUGUUAUA_GUAUCUGCCACUAGGGGUUUUCCGUCGAUGUUGCAGGUUGCAUAGCUUAUGCUGCAGCUUCUAUU_GAUAACU
...(((((.....)))))............((..(((((...........(((......)))...........))))).))(((((((..(((....))))))))))............. (-14.67 = -15.85 +   1.18)

alignment

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secondary structure

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Window 9

Location 7,166,394 – 7,166,509
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 72.45
Mean single sequence MFE -26.10
Consensus MFE -11.46
Energy contribution -11.76
Covariance contribution 0.30
Combinations/Pair 1.25
Mean z-score -2.23
Structure conservation index 0.44
SVM decision value 1.87
SVM RNA-class probability 0.980633
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7166394 115 - 22224390
AGUCAUC-AAUAGAAGCUGCAGCAUAAGCUAUGCAACCUGCAAUAUUGACGGAAAACCCCCAGUGGCAGAUACAUAUAACAAAUGUAAGCGUCAUAUAAGCUGCAGCA----ACUGCAAC
.......-..(((..((((((((.((....((((...((((..(((((..((.....)).))))))))).(((((.......))))).))))....)).)))))))).----.))).... ( -31.20)
>DroSec_CAF1 34029 115 - 1
AGUUAUC-AAUAGAAGUUGCAGCAUUAGCUAUGCAACCUGCAACAUCGACGGAAAACCCCUAGUGGCAGAUACAUAUAACAAAUGCAAGCGUCAUAGAAACUGCAGCA----ACUGCCAC
.(((.((-....((.((((((((((.....))))....)))))).))....)).))).....(((((((...(((.......)))...((..((.......))..)).----.))))))) ( -26.10)
>DroSim_CAF1 28242 115 - 1
AGUUAUC-AAUAGAAGUUGCAGCAUAAGCUAUGCAACCUGCAACAUCGAUGGAAAACCCCUAGUGGCAGAUACUUAUAACAAAUGUAAGCGUCAUAGAAACUGCAGCA----ACUGCCAC
.(((.((-....((.(((((((((((...)))))....)))))).))....)).))).....(((((((...((((((.....)))))).((..(((...)))..)).----.))))))) ( -28.80)
>DroEre_CAF1 34876 95 - 1
-------------UAGCUGCAGCAUAAGCUAUGCAACCUGCGACAUCCAGGAAAAA-UCCCAGCAGCAGAUAC----ACCAAAUGCAAGCGUCAUAGAACCUGCA-------ACUGCCAC
-------------..(((((.(((((...)))))..((((.(....))))).....-.....)))))......----......((((.(.((......)))))))-------........ ( -21.90)
>DroYak_CAF1 36022 101 - 1
CGUCAUCCUAGGGAAGCUGCCACACAAGCUGUGCAACCUGCAACCUGCAACAUCAA-CG-----------CAC----AGCAA---CAAGCGUCACAGAACCUGCAGCAUAGAACUGCCAC
..((.(((...))).(((((.......(((((((....(((.....))).......-.)-----------)))----)))..---..((.((......)))))))))...))........ ( -22.50)
>consensus
AGUCAUC_AAUAGAAGCUGCAGCAUAAGCUAUGCAACCUGCAACAUCGACGGAAAACCCCCAGUGGCAGAUAC_UAUAACAAAUGCAAGCGUCAUAGAAACUGCAGCA____ACUGCCAC
...............(((((((......(((((.....(((.........((.....))......(((...............)))..))).)))))...)))))))............. (-11.46 = -11.76 +   0.30)

alignment

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secondary structure

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Window 0

Location 7,166,430 – 7,166,546
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.76
Mean single sequence MFE -32.94
Consensus MFE -14.80
Energy contribution -15.40
Covariance contribution 0.60
Combinations/Pair 1.32
Mean z-score -2.08
Structure conservation index 0.45
SVM decision value 1.48
SVM RNA-class probability 0.957627
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7166430 116 + 22224390
GUUAUAUGUAUCUGCCACUGGGGGUUUUCCGUCAAUAUUGCAGGUUGCAUAGCUUAUGCUGCAGCUUCUAUU-GAUGACUAAUU---UAUUGUUGCUUGCUUGCUUGAGCAAGUUGCUUU
(((((......((((...(((.((....)).))).....))))((((((..((....)))))))).......-.))))).....---....((.((((((((....)))))))).))... ( -31.50)
>DroSec_CAF1 34065 116 + 1
GUUAUAUGUAUCUGCCACUAGGGGUUUUCCGUCGAUGUUGCAGGUUGCAUAGCUAAUGCUGCAACUUCUAUU-GAUAACUAAUU---UGUUGUUGCUUGAUUGCUUAAGCAAGUGGCUUU
.............((((((...((((.((.((.((.((((((((((((...)).))).))))))).)).)).-)).))))....---......(((((((....)))))))))))))... ( -32.20)
>DroSim_CAF1 28278 116 + 1
GUUAUAAGUAUCUGCCACUAGGGGUUUUCCAUCGAUGUUGCAGGUUGCAUAGCUUAUGCUGCAACUUCUAUU-GAUAACUAAUU---UGUUGUUGCUUGAUUGCUUAAGCAAGUGGCUUU
.............((((((((.((....))(((((((..(.((((((((..((....)))))))))))))))-)))..)))...---.....((((((((....)))))))))))))... ( -31.80)
>DroEre_CAF1 34909 95 + 1
GGU----GUAUCUGCUGCUGGGA-UUUUUCCUGGAUGUCGCAGGUUGCAUAGCUUAUGCUGCAGCUA-------------------AUAUUGUUGCAUGAAUGUGUCAGCAAGUGGCU-C
.((----((((((((..(..(((-....)))..).....))))).)))))(((....)))..(((((-------------------...(((((((((....))).)))))).)))))-. ( -32.40)
>DroYak_CAF1 36059 104 + 1
GCU----GUG-----------CG-UUGAUGUUGCAGGUUGCAGGUUGCACAGCUUGUGUGGCAGCUUCCCUAGGAUGACGCAUUCGCUGCUGCUGCUUGAAUGUUUCAAGAAGUGGCUUU
((.----(((-----------((-((...(((((....((((((((....))))))))..))))).(((...))).)))))))..)).((..((.(((((.....))))).))..))... ( -36.80)
>consensus
GUUAUA_GUAUCUGCCACUAGGGGUUUUCCGUCGAUGUUGCAGGUUGCAUAGCUUAUGCUGCAGCUUCUAUU_GAUAACUAAUU___UGUUGUUGCUUGAUUGCUUAAGCAAGUGGCUUU
...........((((.((...((.....))......)).))))(((((..(((....))))))))..........................((..((((..........))))..))... (-14.80 = -15.40 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,166,430 – 7,166,546
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.76
Mean single sequence MFE -25.84
Consensus MFE -7.95
Energy contribution -7.95
Covariance contribution 0.00
Combinations/Pair 1.31
Mean z-score -2.75
Structure conservation index 0.31
SVM decision value 2.91
SVM RNA-class probability 0.997713
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7166430 116 - 22224390
AAAGCAACUUGCUCAAGCAAGCAAGCAACAAUA---AAUUAGUCAUC-AAUAGAAGCUGCAGCAUAAGCUAUGCAACCUGCAAUAUUGACGGAAAACCCCCAGUGGCAGAUACAUAUAAC
...((..(((((....)))))...)).......---.....((((((-((((..((((........)))).(((.....))).)))))).((.......))..))))............. ( -22.50)
>DroSec_CAF1 34065 116 - 1
AAAGCCACUUGCUUAAGCAAUCAAGCAACAACA---AAUUAGUUAUC-AAUAGAAGUUGCAGCAUUAGCUAUGCAACCUGCAACAUCGACGGAAAACCCCUAGUGGCAGAUACAUAUAAC
...(((((((((((.(....).)))))......---.....(((.((-....((.((((((((((.....))))....)))))).))....)).)))....))))))............. ( -28.90)
>DroSim_CAF1 28278 116 - 1
AAAGCCACUUGCUUAAGCAAUCAAGCAACAACA---AAUUAGUUAUC-AAUAGAAGUUGCAGCAUAAGCUAUGCAACCUGCAACAUCGAUGGAAAACCCCUAGUGGCAGAUACUUAUAAC
...(((((((((((.(....).)))))......---.....(((.((-....((.(((((((((((...)))))....)))))).))....)).)))....))))))............. ( -28.80)
>DroEre_CAF1 34909 95 - 1
G-AGCCACUUGCUGACACAUUCAUGCAACAAUAU-------------------UAGCUGCAGCAUAAGCUAUGCAACCUGCGACAUCCAGGAAAAA-UCCCAGCAGCAGAUAC----ACC
.-......(((((((.....))).))))...(((-------------------(.(((((.(((((...)))))..((((.(....))))).....-.....))))).)))).----... ( -23.80)
>DroYak_CAF1 36059 104 - 1
AAAGCCACUUCUUGAAACAUUCAAGCAGCAGCAGCGAAUGCGUCAUCCUAGGGAAGCUGCCACACAAGCUGUGCAACCUGCAACCUGCAACAUCAA-CG-----------CAC----AGC
..........(((((.....)))))..(((((.((....))....(((...))).))))).......(((((((....(((.....))).......-.)-----------)))----))) ( -25.20)
>consensus
AAAGCCACUUGCUGAAGCAAUCAAGCAACAACA___AAUUAGUCAUC_AAUAGAAGCUGCAGCAUAAGCUAUGCAACCUGCAACAUCGACGGAAAACCCCCAGUGGCAGAUAC_UAUAAC
........((((............(((((..........................))))).((((.....)))).....))))..................................... ( -7.95 =  -7.95 +   0.00)

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 10:40:41 2006