Locus 7210

Sequence ID 3L_DroMel_CAF1
Location 19,351,766 – 19,351,950
Length 184
Max. P 0.999938
window11708 window11709 window11710 window11711

overview

Window 8

Location 19,351,766 – 19,351,870
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 70.85
Mean single sequence MFE -28.78
Consensus MFE -16.83
Energy contribution -17.20
Covariance contribution 0.37
Combinations/Pair 1.24
Mean z-score -3.16
Structure conservation index 0.58
SVM decision value 4.68
SVM RNA-class probability 0.999938
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351766 104 + 23771897
AAAAUAUU------GCCGGUU--GU-------UUGUAACCCUUUCAAU-UAGUAGCUUGCUUUUGAGUUUGCAAACUUAUAUACAUAAAUACAUUUCCUUUCCUAUUGGAGAGGGAAACC
........------...((((--((-------((((((....(((((.-.(((.....))).))))).))))))))..................(((((((((....))))))))))))) ( -25.80)
>DroSec_CAF1 1920 113 + 1
AUAUUAUUGUAGGUGCCGGUU--GCUAUUAACUUGAAACCCUUUCAAU-UGGUAGCUAACUUAUGAGUUAGCAAACUUAUU----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACC
.((((...(((((((((((((--(....................))))-)))).(((((((....)))))))..)))))).----..))))..((((((((((....))))))))))... ( -32.65)
>DroSim_CAF1 1946 113 + 1
AUAUUAUUGUAGGUGCCAGUU--GAUUUUAACUUGAAACCCUUUCAAU-UGGUAGCUAACUUAUGAGUUAGCAAACUUAUU----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACC
.((((...(((((((((((((--((..................)))))-)))).(((((((....)))))))..)))))).----..))))..((((((((((....))))))))))... ( -36.57)
>DroYak_CAF1 5293 93 + 1
AAAAUAGG------GCCGUUUUAGU-------UUUUAA--------AUACAAUACCAUGCUUGUGGGUUUGCA--UUUAUU----UAAAUAGAUUUCUUUUCCCUUUGCAGAGGGAAGCC
.......(------((.......((-------((.(((--------((.(((..((((....))))..))).)--))))..----.)))).........(((((((....)))))))))) ( -20.10)
>consensus
AAAAUAUU______GCCGGUU__GU_______UUGAAACCCUUUCAAU_UAGUAGCUAACUUAUGAGUUAGCAAACUUAUU____UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACC
......................................................(((((((....))))))).....................((((((((((....))))))))))... (-16.83 = -17.20 +   0.37)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,351,791 – 19,351,910
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -30.77
Consensus MFE -21.38
Energy contribution -22.12
Covariance contribution 0.75
Combinations/Pair 1.19
Mean z-score -3.76
Structure conservation index 0.69
SVM decision value 3.20
SVM RNA-class probability 0.998721
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351791 119 + 23771897
CUUUCAAU-UAGUAGCUUGCUUUUGAGUUUGCAAACUUAUAUACAUAAAUACAUUUCCUUUCCUAUUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGUAUUCGUUUUACCAUUUUUGU
........-..(((((..(((....)))..))............(..((((((.......(((....)))((((((((((...))).)))))))...))))))..)..)))......... ( -23.90)
>DroSec_CAF1 1958 115 + 1
CUUUCAAU-UGGUAGCUAACUUAUGAGUUAGCAAACUUAUU----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGU
....(((.-((((((((((((....)))))))((((.....----........((((((((((....))))))))))((((.((((........))))))))..)))))))))...))). ( -36.10)
>DroSim_CAF1 1984 115 + 1
CUUUCAAU-UGGUAGCUAACUUAUGAGUUAGCAAACUUAUU----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGU
....(((.-((((((((((((....)))))))((((.....----........((((((((((....))))))))))((((.((((........))))))))..)))))))))...))). ( -36.10)
>DroYak_CAF1 5318 108 + 1
------AUACAAUACCAUGCUUGUGGGUUUGCA--UUUAUU----UAAAUAGAUUUCUUUUCCCUUUGCAGAGGGAAGCCUUAGGUAUUCCCUUACCUGGCUUCGCUUUACAUUCUUUGU
------..((((......((....(((.....(--(((((.----...)))))).......)))...))((((.((((((..(((((......))))))))))).)))).......)))) ( -27.00)
>consensus
CUUUCAAU_UAGUAGCUAACUUAUGAGUUAGCAAACUUAUU____UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGU
..............(((((((....)))))))........................(((((((....)))))))((((((((((((........)))))))...)))))........... (-21.38 = -22.12 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,351,791 – 19,351,910
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -28.62
Consensus MFE -17.51
Energy contribution -19.45
Covariance contribution 1.94
Combinations/Pair 1.14
Mean z-score -3.30
Structure conservation index 0.61
SVM decision value 2.23
SVM RNA-class probability 0.990726
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351791 119 - 23771897
ACAAAAAUGGUAAAACGAAUACAGGUGAGGGAAUACCUAAGGUUUCCCUCUCCAAUAGGAAAGGAAAUGUAUUUAUGUAUAUAAGUUUGCAAACUCAAAAGCAAGCUACUA-AUUGAAAG
.......(((((....(((((((...(((((((.(((...))))))))))(((....))).......)))))))..........((((((..........)))))))))))-........ ( -28.80)
>DroSec_CAF1 1958 115 - 1
ACAAAAAUGGUAAAACGAACCCAGGUGAGGGAAUACCUAAGGUUUCCCUCUCCACUAGGAAAGGAAAUGUAUUUA----AAUAAGUUUGCUAACUCAUAAGUUAGCUACCA-AUUGAAAG
.......(((((((((.......((.(((((((.(((...)))))))))).)).((.....))............----.....))))(((((((....))))))))))))-........ ( -30.50)
>DroSim_CAF1 1984 115 - 1
ACAAAAAUGGUAAAACGAACCCAGGUGAGGGAAUACCUAAGGUUUCCCUCUCCACUAGGAAAGGAAAUGUAUUUA----AAUAAGUUUGCUAACUCAUAAGUUAGCUACCA-AUUGAAAG
.......(((((((((.......((.(((((((.(((...)))))))))).)).((.....))............----.....))))(((((((....))))))))))))-........ ( -30.50)
>DroYak_CAF1 5318 108 - 1
ACAAAGAAUGUAAAGCGAAGCCAGGUAAGGGAAUACCUAAGGCUUCCCUCUGCAAAGGGAAAAGAAAUCUAUUUA----AAUAAA--UGCAAACCCACAAGCAUGGUAUUGUAU------
........((((.((.(((((((((((......)))))..)))))).)).)))).....................----.....(--(((((..(((......)))..))))))------ ( -24.70)
>consensus
ACAAAAAUGGUAAAACGAACCCAGGUGAGGGAAUACCUAAGGUUUCCCUCUCCAAUAGGAAAGGAAAUGUAUUUA____AAUAAGUUUGCAAACUCAUAAGCAAGCUACCA_AUUGAAAG
........((((...........((.(((((((.(((...)))))))))).))...................................((((((......)))))))))).......... (-17.51 = -19.45 +   1.94)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,351,830 – 19,351,950
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.97
Mean single sequence MFE -22.60
Consensus MFE -16.31
Energy contribution -16.75
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -2.56
Structure conservation index 0.72
SVM decision value 0.91
SVM RNA-class probability 0.880181
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19351830 120 + 23771897
AUACAUAAAUACAUUUCCUUUCCUAUUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGUAUUCGUUUUACCAUUUUUGUCUCUGUUUUAUCCUCCUUUUAUCUCUUCGAGCUGCCCCUC
....(..((((((.......(((....)))((((((((((...))).)))))))...))))))..)..........................................(((......))) ( -19.10)
>DroSec_CAF1 1997 115 + 1
U----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGUCUCUCUUUCAUCC-CCUUUUAUCUCUUCGAGCUGCCCCUC
.----........((((((((((....))))))))))......((((..(((......))).......))))......((..(((........-..............)))..))..... ( -21.65)
>DroSim_CAF1 2023 115 + 1
U----UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGUCUCUCUUUCAUCC-CCUUUUAUCUCUUCGAGCUGCCGCUC
.----........((((((((((....))))))))))......((((..(((......))).......)))).....................-..............((((....)))) ( -25.40)
>DroYak_CAF1 5350 116 + 1
U----UAAAUAGAUUUCUUUUCCCUUUGCAGAGGGAAGCCUUAGGUAUUCCCUUACCUGGCUUCGCUUUACAUUCUUUGUCUCUGUUUUAUCCUUCUUUUAUCUCUUCGAGCUGCCCCUC
(----..((.((((.............((((((.((((((..(((((......))))))))))).....(((.....)))))))))..............)))).))..).......... ( -24.23)
>consensus
U____UAAAUACAUUUCCUUUCCUAGUGGAGAGGGAAACCUUAGGUAUUCCCUCACCUGGGUUCGUUUUACCAUUUUUGUCUCUCUUUCAUCC_CCUUUUAUCUCUUCGAGCUGCCCCUC
................(((((((....)))))))((((((((((((........)))))))...))))).......................................(((......))) (-16.31 = -16.75 +   0.44)

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 12:40:56 2006