Locus 1301

Sequence ID 2L_DroMel_CAF1
Location 3,431,536 – 3,431,730
Length 194
Max. P 0.999928
window2130 window2131 window2132 window2133 window2134

overview

Window 0

Location 3,431,536 – 3,431,652
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.56
Mean single sequence MFE -24.64
Consensus MFE -18.37
Energy contribution -18.81
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.75
SVM decision value 0.74
SVM RNA-class probability 0.837633
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3431536 116 + 22407834
UUUAAGUUUUCAAUCGAACUGUGGUAUUUUUAAAAGGCACACACACACAC----ACCUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCC
....(((((......)))))...............(((.(((........----.....(((((((((((((..((.....)).....)))))))))))))...(((....))))))))) ( -23.70)
>DroSec_CAF1 20454 111 + 1
UUUAAGUUUCCAAACGAACUGUGGUAUU-UAAAAAGGCACACAC----AC----ACAUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCC
(((((((..(((.........))).)))-))))..(((.(((..----..----.(((.(((((((((((((..((.....)).....))))))))))))))))(((....))))))))) ( -26.20)
>DroSim_CAF1 20536 115 + 1
UUUAAGUUUCCAAACGAACUGUGGCAUU-UAAAAAGGCACACACACACAC----ACACAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCC
(((((((..(((.........))).)))-))))..(((.(((........----.....(((((((((((((..((.....)).....)))))))))))))...(((....))))))))) ( -24.60)
>DroEre_CAF1 20792 114 + 1
UUUAAGUUUCCAAACGAACGAUGGCAUU-UAAAAA-GCAUCCACACACAC----ACAUAUUUGCAUAUGGAAAUCAUUUCUCGUUCGAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCC
(((((((..(((.........))).)))-))))..-....((((......----.....((((((((((.(((((...........)))))))))))))))...(((....))))))).. ( -23.50)
>DroYak_CAF1 21921 118 + 1
UUUAAGUUUCCAAGCAAAGUGUGGUAUC-UAAAAA-GCACACACACACACAAACACUUAUUUGCAUAUGGAAAUCAUCUCUCGUUCAAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCC
.............((...(((((((...-......-)).)))))...(((.........(((((((((((((.....(....).....)))))))))))))...(((....)))))))). ( -25.20)
>consensus
UUUAAGUUUCCAAACGAACUGUGGUAUU_UAAAAAGGCACACACACACAC____ACAUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCC
...................................(((.(((.................(((((((((((((................)))))))))))))...(((....))))))))) (-18.37 = -18.81 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,431,576 – 3,431,690
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.49
Mean single sequence MFE -29.68
Consensus MFE -24.62
Energy contribution -25.02
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.83
SVM decision value 2.38
SVM RNA-class probability 0.993253
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3431576 114 + 22407834
ACACACACAC----ACCUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACGAA-AAUGAAAU-UUGGCCAUCGCAUUGAUGGUUG
..........----(((...((((((((((((..((.....)).....))))))))))))(((((((....))((((((((((.....-.......)-))))))))))))))...))).. ( -32.00)
>DroSec_CAF1 20493 110 + 1
ACAC----AC----ACAUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA-AAUGAAAU-UUGGCCAACGCAUUGAUGGUUG
....----.(----.(((.(((((((((((((..((.....)).....)))))))))))))))).)(((..((((((....((.((((-(......)-))))))....))))))..))). ( -27.60)
>DroSim_CAF1 20575 114 + 1
ACACACACAC----ACACAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA-AAUGAAAU-UUGGCCAACGCAUUGAUGGUUG
..........----...(((((((((((((((..((.....)).....))))))))))).((((((.......((...)).((.((((-(......)-))))))..)))))))))).... ( -26.70)
>DroEre_CAF1 20830 114 + 1
CCACACACAC----ACAUAUUUGCAUAUGGAAAUCAUUUCUCGUUCGAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCCAGGACCGA-AAUGAAAU-UUGGCCAUCGCAUUGAUGGGUG
.......(((----.(((.((((((((((.(((((...........)))))))))))))))...........(((((((((((.....-.......)-)))))))))).....))).))) ( -32.20)
>DroYak_CAF1 21959 120 + 1
ACACACACACAAACACUUAUUUGCAUAUGGAAAUCAUCUCUCGUUCAAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCCAGGAACGAAAAUGAAAUUUUGGCCAUCGCAUUGAUGGUUG
.......(((((.......(((((((((((((.....(....).....)))))))))))))...........((((((((((((............))))))))))))..))).)).... ( -29.90)
>consensus
ACACACACAC____ACAUAUUUGCAUAUGGAAAUCAUUUCUUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA_AAUGAAAU_UUGGCCAUCGCAUUGAUGGUUG
...................(((((((((((((................)))))))))))))...........((((((((((................))))))))))............ (-24.62 = -25.02 +   0.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,431,576 – 3,431,690
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.49
Mean single sequence MFE -29.44
Consensus MFE -24.11
Energy contribution -24.11
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -1.96
Structure conservation index 0.82
SVM decision value 1.45
SVM RNA-class probability 0.954693
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3431576 114 - 22407834
CAACCAUCAAUGCGAUGGCCAA-AUUUCAUU-UUCGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAAGAAAUGAUUUCCAUAUGCAAAUAGGU----GUGUGUGUGU
..(((((((((((((((((((.-........-.......))))))........)))))))((((((((((((((...........))))).)))))))))...)))----).))...... ( -30.19)
>DroSec_CAF1 20493 110 - 1
CAACCAUCAAUGCGUUGGCCAA-AUUUCAUU-UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAAGAAAUGAUUUCCAUAUGCAAAUAUGU----GU----GUGU
............((.((((((.-...((...-..))...)))))).))...((.((((((((((((((((((((...........))))).)))))))))).))))----).----)).. ( -28.00)
>DroSim_CAF1 20575 114 - 1
CAACCAUCAAUGCGUUGGCCAA-AUUUCAUU-UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAAGAAAUGAUUUCCAUAUGCAAAUGUGU----GUGUGUGUGU
..(((((.....((.((((((.-...((...-..))...)))))).))......((((((((((((((((((((...........))))).)))))))))).))))----).))).)).. ( -28.80)
>DroEre_CAF1 20830 114 - 1
CACCCAUCAAUGCGAUGGCCAA-AUUUCAUU-UCGGUCCUGGCCACCGAAAAUUCGUAUUUUGCAUAUGAAAUCGAACGAGAAAUGAUUUCCAUAUGCAAAUAUGU----GUGUGUGUGG
(((.(((((...((.((((((.-...((...-..))...)))))).))......(((((((.(((((((((((((.........)))))).)))))))))))))))----).))).))). ( -30.90)
>DroYak_CAF1 21959 120 - 1
CAACCAUCAAUGCGAUGGCCAAAAUUUCAUUUUCGUUCCUGGCCACCGAAAAUUCGUAUUUUGCAUAUGAAAUUGAACGAGAGAUGAUUUCCAUAUGCAAAUAAGUGUUUGUGUGUGUGU
...(((((.....)))))........((((((((((((.(((...)))....(((((((.....)))))))...)))))).))))))....(((((((((((....)))))))))))... ( -29.30)
>consensus
CAACCAUCAAUGCGAUGGCCAA_AUUUCAUU_UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAAGAAAUGAUUUCCAUAUGCAAAUAUGU____GUGUGUGUGU
........(((((((((((((..................))))))........)))))))((((((((((((((...........))))).))))))))).................... (-24.11 = -24.11 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,431,612 – 3,431,730
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.95
Mean single sequence MFE -36.98
Consensus MFE -33.53
Energy contribution -34.29
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -3.13
Structure conservation index 0.91
SVM decision value 4.61
SVM RNA-class probability 0.999928
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3431612 118 + 22407834
UUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACGAA-AAUGAAAU-UUGGCCAUCGCAUUGAUGGUUGGCCAAAAGGCCGGCCUCAAACCAAUUUAUCACGAACGCAA
..((((.........((((((((....))))).((((((((((.....-.......)-))))))))))))((((.((((((((....)))))))))))).............)))).... ( -38.60)
>DroSec_CAF1 20525 118 + 1
UUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA-AAUGAAAU-UUGGCCAACGCAUUGAUGGUUGGCCAAAAGGCCGGCCUCAAACCAAUUUAUCACGAACGCAA
..((((.........(((......(((....))).((((((((..(..-...)...)-)))))))..)))((((.((((((((....)))))))))))).............)))).... ( -35.80)
>DroSim_CAF1 20611 118 + 1
UUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA-AAUGAAAU-UUGGCCAACGCAUUGAUGGUUGGCCAAAAGGCCGGCCUCAAACCAAUUUAUCACGAACGCAA
..((((.........(((......(((....))).((((((((..(..-...)...)-)))))))..)))((((.((((((((....)))))))))))).............)))).... ( -35.80)
>DroEre_CAF1 20866 118 + 1
UCGUUCGAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCCAGGACCGA-AAUGAAAU-UUGGCCAUCGCAUUGAUGGGUGGCCAAGAGGACGGGCUCAAACCAAUUUAUCACGAACGCAA
.(((((((((((((((.....))).....(((((((.......)))))-))))))))-(((((((((.((....)))))))))))(((......)))..............))))))... ( -33.50)
>DroYak_CAF1 21999 120 + 1
UCGUUCAAUUUCAUAUGCAAAAUACGAAUUUUCGGUGGCCAGGAACGAAAAUGAAAUUUUGGCCAUCGCAUUGAUGGUUGGCCAAAAGGCCGGCCUCAAACCAAUUUAUCACGAACGCAA
.(((((.........(((.......((....))(((((((((((............))))))))))))))((((.((((((((....)))))))))))).............)))))... ( -41.20)
>consensus
UUGUUCAAUUUCAUAUGCAAAAUGCGAAUUUUCGGUGGCCAGGACCAA_AAUGAAAU_UUGGCCAUCGCAUUGAUGGUUGGCCAAAAGGCCGGCCUCAAACCAAUUUAUCACGAACGCAA
.(((((.........((((((((....))))).(((((((((................))))))))))))((((.((((((((....)))))))))))).............)))))... (-33.53 = -34.29 +   0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,431,612 – 3,431,730
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.95
Mean single sequence MFE -35.76
Consensus MFE -28.73
Energy contribution -28.81
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.80
SVM decision value 1.69
SVM RNA-class probability 0.972296
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3431612 118 - 22407834
UUGCGUUCGUGAUAAAUUGGUUUGAGGCCGGCCUUUUGGCCAACCAUCAAUGCGAUGGCCAA-AUUUCAUU-UUCGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAA
....((((((((....(((((....((((((((....))))..(((((.....)))))....-........-........)))))))))....))))(((((......))))).)))).. ( -34.60)
>DroSec_CAF1 20525 118 - 1
UUGCGUUCGUGAUAAAUUGGUUUGAGGCCGGCCUUUUGGCCAACCAUCAAUGCGUUGGCCAA-AUUUCAUU-UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAA
....((((((((....(((((....((((((((.((((((((((((....)).)))))))))-).......-..)).)).)))))))))....))))(((((......))))).)))).. ( -38.80)
>DroSim_CAF1 20611 118 - 1
UUGCGUUCGUGAUAAAUUGGUUUGAGGCCGGCCUUUUGGCCAACCAUCAAUGCGUUGGCCAA-AUUUCAUU-UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAA
....((((((((....(((((....((((((((.((((((((((((....)).)))))))))-).......-..)).)).)))))))))....))))(((((......))))).)))).. ( -38.80)
>DroEre_CAF1 20866 118 - 1
UUGCGUUCGUGAUAAAUUGGUUUGAGCCCGUCCUCUUGGCCACCCAUCAAUGCGAUGGCCAA-AUUUCAUU-UCGGUCCUGGCCACCGAAAAUUCGUAUUUUGCAUAUGAAAUCGAACGA
...((((((.......(((((..(((......)))..(((((.(((((.....)))))((.(-(......)-).))...))))))))))...(((((((.....)))))))..)))))). ( -30.80)
>DroYak_CAF1 21999 120 - 1
UUGCGUUCGUGAUAAAUUGGUUUGAGGCCGGCCUUUUGGCCAACCAUCAAUGCGAUGGCCAAAAUUUCAUUUUCGUUCCUGGCCACCGAAAAUUCGUAUUUUGCAUAUGAAAUUGAACGA
...((((((.......(((((....((((((((....))))..(((((.....)))))......................)))))))))...(((((((.....)))))))..)))))). ( -35.80)
>consensus
UUGCGUUCGUGAUAAAUUGGUUUGAGGCCGGCCUUUUGGCCAACCAUCAAUGCGAUGGCCAA_AUUUCAUU_UUGGUCCUGGCCACCGAAAAUUCGCAUUUUGCAUAUGAAAUUGAACAA
....(((((((((...((((((.((((....))))..))))))..))))(((((.((((((..................)))))).(((....))).....))))).......))))).. (-28.73 = -28.81 +   0.08)

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 09:59:10 2006