Locus 3762

Sequence ID 2L_DroMel_CAF1
Location 10,958,279 – 10,958,412
Length 133
Max. P 0.976029
window5920 window5921 window5922 window5923

overview

Window 0

Location 10,958,279 – 10,958,385
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.46
Mean single sequence MFE -24.49
Consensus MFE -12.35
Energy contribution -12.55
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.50
SVM decision value -0.03
SVM RNA-class probability 0.516451
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10958279 106 + 22407834
GAAACCCAUAAUAUUUUU-----------AAACCGAAUCAAAU-GAUUUUCGAAU-CCAGUUACGAACAUGCAAUUACACGGGGCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAACUG
....(((...........-----------.....(((((....-)))))((((((-...))).)))..............)))((((-(((((((....)))))))).....)))..... ( -23.60)
>DroSec_CAF1 41238 106 + 1
GAUUUCCCUUAUAUUUUU-----------AAACCGAUUCAAAU-GAUUUUCGAAU-CCAGUUACGAACAUGCAAUUACACGGGGCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAUCUG
.....(((..........-----------.....((((((((.-...))).))))-)..((.....))............)))((((-(((((((....)))))))).....)))..... ( -23.20)
>DroSim_CAF1 48214 106 + 1
GAUUUCCCUUAUAUUUUC-----------AAACCGAUUCAAAU-GAUUUUCGAAU-CGAGUUACGAACAUGCAAUUACACGGGCCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAUCUG
...........(((.(((-----------.((((((((((((.-...))).))))-)).)))..))).)))........((((..((-(((((((....)))))))))..))))...... ( -27.20)
>DroEre_CAF1 41960 94 + 1
GAAACCUAUAAUAUUUUU-----------UGGCCGAAUCAAAU-CAUUUUUGAAC-CCAGUUGCAU------------ACGGCGUUG-CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG
..................-----------..(((...(((((.-....)))))..-...((.....------------)))))(.((-(((.(((((((.....)))))))))))).).. ( -21.90)
>DroYak_CAF1 43390 104 + 1
AAAACG--CAAUAUAUUU-----------UAGCAGAAUCAAAU-AAUGGUUGAAU-CCAGUUACACACAUGCAAUUACACGGGGCUG-CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG
.....(--(.........-----------..(((.........-..(((......-)))..........)))........(((...(-(((((((....))))))))...)))))..... ( -23.60)
>DroAna_CAF1 49359 109 + 1
-----------CAUUUUUACGACGGAAUUCAGACAAACCAAGUACAUUUUUGAAUUUCUGUUACGAAUAUGCAAUUACACAAGGAUGCCAGGAUGAGCACAUCCUGCUUAUCUGCAUCUC
-----------(((.(((..(((((((((((((...............)))))).)))))))..))).)))...........((((((..(((((((((.....))))))))))))))). ( -27.46)
>consensus
GAAACCC_UAAUAUUUUU___________AAACCGAAUCAAAU_GAUUUUCGAAU_CCAGUUACGAACAUGCAAUUACACGGGGCAG_CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG
...............................................................................((((...(.(((((((....))))))))...))))...... (-12.35 = -12.55 +   0.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,958,279 – 10,958,385
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.46
Mean single sequence MFE -28.91
Consensus MFE -15.56
Energy contribution -16.23
Covariance contribution 0.67
Combinations/Pair 1.17
Mean z-score -1.99
Structure conservation index 0.54
SVM decision value 1.32
SVM RNA-class probability 0.942291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10958279 106 - 22407834
CAGUUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGCCCCGUGUAAUUGCAUGUUCGUAACUGG-AUUCGAAAAUC-AUUUGAUUCGGUUU-----------AAAAAUAUUAUGGGUUUC
(((((((.....(((((((((....)))))))-))....(((((....)))))...)))))))(-(.(((((....-.))))).)).....-----------.................. ( -30.80)
>DroSec_CAF1 41238 106 - 1
CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGCCCCGUGUAAUUGCAUGUUCGUAACUGG-AUUCGAAAAUC-AUUUGAAUCGGUUU-----------AAAAAUAUAAGGGAAAUC
............(((((((((....)))))))-))..(((((......))(((((..(((.(.(-(((((((....-.)))))))).).))-----------)..)))))..)))..... ( -30.00)
>DroSim_CAF1 48214 106 - 1
CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGGCCCGUGUAAUUGCAUGUUCGUAACUCG-AUUCGAAAAUC-AUUUGAAUCGGUUU-----------GAAAAUAUAAGGGAAAUC
............(((((((((....)))))))-))..(((((((....)))).((((.(((.((-(((((((....-.)))))))))))))-----------))).......)))..... ( -33.90)
>DroEre_CAF1 41960 94 - 1
CAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUG-CAACGCCGU------------AUGCAACUGG-GUUCAAAAAUG-AUUUGAUUCGGCCA-----------AAAAAUAUUAUAGGUUUC
(((.((((.....((((((((....)))))))-)........------------.)))).)))(-(((((((....-.)))))....))).-----------.................. ( -23.84)
>DroYak_CAF1 43390 104 - 1
CAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUG-CAGCCCCGUGUAAUUGCAUGUGUGUAACUGG-AUUCAACCAUU-AUUUGAUUCUGCUA-----------AAAUAUAUUG--CGUUUU
.((((((((....((((((((....)))))))-)(((..(((((....))))).........((-(.((((.....-..)))).)))))).-----------.......)))--))))). ( -29.80)
>DroAna_CAF1 49359 109 - 1
GAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUGGCAUCCUUGUGUAAUUGCAUAUUCGUAACAGAAAUUCAAAAAUGUACUUGGUUUGUCUGAAUUCCGUCGUAAAAAUG-----------
..(((((((((((((((((((....)))))).((((...(((((....)))))(((......)))........)))).....))))))))).....)))).........----------- ( -25.10)
>consensus
CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG_CAGCCCCGUGUAAUUGCAUGUUCGUAACUGG_AUUCAAAAAUC_AUUUGAUUCGGCUU___________AAAAAUAUUA_GGGUUUC
(((.(((......((((((((....))))))).).....(((((....)))))...))).)))....(((((......)))))..................................... (-15.56 = -16.23 +   0.67)

alignment

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secondary structure

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Window 2

Location 10,958,308 – 10,958,412
Length 104
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 74.00
Mean single sequence MFE -29.60
Consensus MFE -15.55
Energy contribution -15.55
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.53
SVM decision value 0.59
SVM RNA-class probability 0.792605
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10958308 104 + 22407834
AAU-GAUUUUCGAAU-CCAGUUACGAACAUGCAAUUACACGGGGCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAACUG--ACUGCAGGAGAUAUGUGUGCGGCACAG
...-....(((((((-...))).))))..(((...((((((...(((-(((((((....)))))))))..((((((....--..)))))).)...))))))..)))... ( -32.40)
>DroSec_CAF1 41267 104 + 1
AAU-GAUUUUCGAAU-CCAGUUACGAACAUGCAAUUACACGGGGCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAUCUG--ACUGCAGGAGAUAUGUGUGCGGCACAG
...-....(((((((-...))).))))..(((...((((((...(((-(((((((....)))))))))..((((((....--..)))))).)...))))))..)))... ( -32.20)
>DroSim_CAF1 48243 104 + 1
AAU-GAUUUUCGAAU-CGAGUUACGAACAUGCAAUUACACGGGCCAG-CAGGAUGGGCACAUCCUGCUUAUCUGCAUCUG--ACUGCAGGAGAUAUGUGUGCGGCACAG
..(-((((....)))-))...........(((...((((((....((-(((((((....)))))))))..((((((....--..)))))).....))))))..)))... ( -32.10)
>DroEre_CAF1 41989 80 + 1
AAU-CAUUUUUGAAC-CCAGUUGCAU------------ACGGCGUUG-CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG--ACUGCAG------------CCGCAUAG
..(-((....)))..-...((((((.------------.(((...((-(((.(((((((.....)))))))))))).)))--..)))))------------)....... ( -24.60)
>DroYak_CAF1 43417 89 + 1
AAU-AAUGGUUGAAU-CCAGUUACACACAUGCAAUUACACGGGGCUG-CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG--GCUGCAG---------------GAUAG
...-.........((-((.((..(.((.(((((........((...(-(((((((....))))))))...))))))).))--)..)).)---------------))).. ( -23.70)
>DroAna_CAF1 49388 104 + 1
AGUACAUUUUUGAAUUUCUGUUACGAAUAUGCAAUUACACAAGGAUGCCAGGAUGAGCACAUCCUGCUUAUCUGCAUCUCCUGCUGCAGGAAGCAUCAUCCUGG-----
....((((((((......(((.........)))......))))))))(((((((((((...((((((......(((.....))).)))))).)).)))))))))----- ( -32.60)
>consensus
AAU_GAUUUUCGAAU_CCAGUUACGAACAUGCAAUUACACGGGGCAG_CAGGAUGAGCACAUCCUGCUUAUCUGCAUCUG__ACUGCAGGAGAUAUGUGUGCGGCACAG
..............................................(.(((((((....))))))))....(((((........))))).................... (-15.55 = -15.55 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,958,308 – 10,958,412
Length 104
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 74.00
Mean single sequence MFE -29.83
Consensus MFE -17.41
Energy contribution -17.77
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.12
Structure conservation index 0.58
SVM decision value 1.76
SVM RNA-class probability 0.976029
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10958308 104 - 22407834
CUGUGCCGCACACAUAUCUCCUGCAGU--CAGUUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGCCCCGUGUAAUUGCAUGUUCGUAACUGG-AUUCGAAAAUC-AUU
.((((.....)))).............--(((((((.....(((((((((....)))))))-))....(((((....)))))...)))))))(-(((....))))-... ( -30.10)
>DroSec_CAF1 41267 104 - 1
CUGUGCCGCACACAUAUCUCCUGCAGU--CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGCCCCGUGUAAUUGCAUGUUCGUAACUGG-AUUCGAAAAUC-AUU
..((((...((((.......(((((..--....)))))...(((((((((....)))))))-)).....))))....)))).((((.......-...))))....-... ( -30.30)
>DroSim_CAF1 48243 104 - 1
CUGUGCCGCACACAUAUCUCCUGCAGU--CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG-CUGGCCCGUGUAAUUGCAUGUUCGUAACUCG-AUUCGAAAAUC-AUU
..((((...((((.......(((((..--....)))))...(((((((((....)))))))-)).....))))....)))).((((.......-...))))....-... ( -30.30)
>DroEre_CAF1 41989 80 - 1
CUAUGCGG------------CUGCAGU--CAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUG-CAACGCCGU------------AUGCAACUGG-GUUCAAAAAUG-AUU
.(((((((------------(((((..--....)))).....((((((((....)))))))-)...)))))------------))).......-...........-... ( -29.70)
>DroYak_CAF1 43417 89 - 1
CUAUC---------------CUGCAGC--CAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUG-CAGCCCCGUGUAAUUGCAUGUGUGUAACUGG-AUUCAACCAUU-AUU
.....---------------.((...(--(((.((((.(...((((((((....)))))))-).....(((((....)))))).)))).))))-...))......-... ( -27.20)
>DroAna_CAF1 49388 104 - 1
-----CCAGGAUGAUGCUUCCUGCAGCAGGAGAUGCAGAUAAGCAGGAUGUGCUCAUCCUGGCAUCCUUGUGUAAUUGCAUAUUCGUAACAGAAAUUCAAAAAUGUACU
-----(((((((((.((.((((((.(((.....)))......))))))...)))))))))))......(((((....)))))(((......)))............... ( -31.40)
>consensus
CUGUGCCGCACACAUAUCUCCUGCAGU__CAGAUGCAGAUAAGCAGGAUGUGCCCAUCCUG_CAGCCCCGUGUAAUUGCAUGUUCGUAACUGG_AUUCAAAAAUC_AUU
....................(((((........)))))....((((((((....))))))).).....(((((....)))))........................... (-17.41 = -17.77 +   0.36)

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 11:00:26 2006