Locus 5962

Sequence ID X_DroMel_CAF1
Location 15,367,435 – 15,367,698
Length 263
Max. P 0.991465
window9674 window9675 window9676 window9677 window9678 window9679

overview

Window 4

Location 15,367,435 – 15,367,555
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -34.62
Consensus MFE -33.05
Energy contribution -33.18
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -1.58
Structure conservation index 0.95
SVM decision value 0.53
SVM RNA-class probability 0.770862
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367435 120 + 22224390
CACCCUCUUAUCAGCCCCAACCCGAGUUUAUUUUUAUCGUACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAA
((((.((..((((((..((...(((...........)))...))..))))))...))....(((((((((..(((.(((.....))))))....))))))))).....))))........ ( -35.40)
>DroSec_CAF1 250 120 + 1
CACCCUCUUAUCAGACCCAACCCGAGUUUAUUUUUAUCGCACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAA
((((.((..(((((...((...(((...........)))...))...)))))...))....(((((((((..(((.(((.....))))))....))))))))).....))))........ ( -32.30)
>DroSim_CAF1 2750 120 + 1
CACCCUCUUAUCAGCCCCAACCCGAGUUUAUUUUUAUCGCACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAUAGGUGAAAUGCAA
((((.((..((((((..((...(((...........)))...))..))))))...))....(((((((((..(((.(((.....))))))....))))))))).....))))........ ( -35.40)
>DroEre_CAF1 7368 117 + 1
CGCCCUCUUAUCAGCCCCAACCCGAGUUUAUUUUUAUCGCACUG---CUGAUUAUGAAAUUCCUUUGGCAAAGGCUCUGUGAGGCAGGCCAAAGUGCCAAAGGUUAAAGGUGAAAGGUAA
((((.((..((((((.......(((...........)))....)---)))))...))....(((((((((..(((.(((.....))))))....))))))))).....))))........ ( -35.40)
>consensus
CACCCUCUUAUCAGCCCCAACCCGAGUUUAUUUUUAUCGCACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAA
((((.((..((((((..((...(((...........)))...))..))))))...))....(((((((((..(((.(((.....))))))....))))))))).....))))........ (-33.05 = -33.18 +   0.13)

alignment

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secondary structure

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Window 5

Location 15,367,435 – 15,367,555
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -35.85
Consensus MFE -31.25
Energy contribution -32.50
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.87
SVM decision value 0.69
SVM RNA-class probability 0.823857
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367435 120 - 22224390
UUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGUACGAUAAAAAUAAACUCGGGUUGGGGCUGAUAAGAGGGUG
........(((((((..(.(((((((...(((((((.....))).)))).))))))).).........((((((..(((..(((...........)))..)))..))))))..))))))) ( -38.70)
>DroSec_CAF1 250 120 - 1
UUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGUGCGAUAAAAAUAAACUCGGGUUGGGUCUGAUAAGAGGGUG
........(((((((..(.(((((((...(((((((.....))).)))).))))))).).........((((((..((((.(((...........))).)))).).)))))..))))))) ( -33.30)
>DroSim_CAF1 2750 120 - 1
UUGCAUUUCACCUAUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGUGCGAUAAAAAUAAACUCGGGUUGGGGCUGAUAAGAGGGUG
........(((((....(.(((((((...(((((((.....))).)))).))))))).).........((((((..((((.(((...........))).))))..))))))....))))) ( -36.00)
>DroEre_CAF1 7368 117 - 1
UUACCUUUCACCUUUAACCUUUGGCACUUUGGCCUGCCUCACAGAGCCUUUGCCAAAGGAAUUUCAUAAUCAG---CAGUGCGAUAAAAAUAAACUCGGGUUGGGGCUGAUAAGAGGGCG
..........(((((..(((((((((....((((((.....))).)))..))))))))).........(((((---(..(.(((...........))).).....)))))).)))))... ( -35.40)
>consensus
UUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGUGCGAUAAAAAUAAACUCGGGUUGGGGCUGAUAAGAGGGUG
........(((((((..(.(((((((...(((((((.....))).)))).))))))).).........((((((..(((..(((...........)))..)))..))))))..))))))) (-31.25 = -32.50 +   1.25)

alignment

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secondary structure

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Window 6

Location 15,367,475 – 15,367,578
Length 103
Sequences 3
Columns 107
Reading direction forward
Mean pairwise identity 86.27
Mean single sequence MFE -28.00
Consensus MFE -25.17
Energy contribution -25.06
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.90
SVM decision value 1.11
SVM RNA-class probability 0.916258
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367475 103 + 22224390
ACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAAA----AGGUAAUAGGGGAUGGAGCUGU
.(((.((((..((((......((((((((...(((.((...(((....))).)).)))....))))))))......)))).----.)))).)))............. ( -26.20)
>DroSec_CAF1 290 91 + 1
ACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAAA----AGGCAACAGG------------
.(((.((((..((((......((((((((...(((.((...(((....))).)).)))....))))))))......)))).----.)))).))).------------ ( -29.90)
>DroSim_CAF1 2790 96 + 1
ACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAUAGGUGAAAUGCAAAACAAAUGCAACAGGG-----------
.(((.(((...((((((....(((((((((..(((.(((.....))))))....)))))))))))))))((.....)).........))).)))..----------- ( -27.90)
>consensus
ACUGCUGCUGAUUAUGAAAUUCUUUUGGCAAAGGCUCUGUGGGGCAGGCCCAAGUGCCAAAGGUUAAAGGUGAAAUGUAAA____AGGCAACAGGG___________
.(((.((((..((((......(((((((((..(((.(((.....))))))....)))))))))......)))).............)))).)))............. (-25.17 = -25.06 +  -0.11)

alignment

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secondary structure

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Window 7

Location 15,367,475 – 15,367,578
Length 103
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 86.27
Mean single sequence MFE -24.57
Consensus MFE -22.47
Energy contribution -23.13
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.38
Structure conservation index 0.91
SVM decision value 2.27
SVM RNA-class probability 0.991465
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367475 103 - 22224390
ACAGCUCCAUCCCCUAUUACCU----UUUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGU
...(((.(..............----....................(((((((...(((((((.....))).)))).))))))).(.....).......).)))... ( -19.70)
>DroSec_CAF1 290 91 - 1
------------CCUGUUGCCU----UUUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGU
------------.(((((((..----....................(((((((...(((((((.....))).)))).))))))).(.....).......))))))). ( -26.20)
>DroSim_CAF1 2790 96 - 1
-----------CCCUGUUGCAUUUGUUUUGCAUUUCACCUAUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGU
-----------..(((((((...((.....))............(.(((((((...(((((((.....))).)))).))))))).).............))))))). ( -27.80)
>consensus
___________CCCUGUUGCCU____UUUACAUUUCACCUUUAACCUUUGGCACUUGGGCCUGCCCCACAGAGCCUUUGCCAAAAGAAUUUCAUAAUCAGCAGCAGU
.............(((((((..........................(((((((...(((((((.....))).)))).))))))).(.....).......))))))). (-22.47 = -23.13 +   0.67)

alignment

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secondary structure

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Window 8

Location 15,367,555 – 15,367,658
Length 103
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 82.72
Mean single sequence MFE -22.77
Consensus MFE -20.10
Energy contribution -20.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.93
Structure conservation index 0.88
SVM decision value -0.03
SVM RNA-class probability 0.516205
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367555 103 - 22224390
UUUGCUGUGGUGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUUGCAUUGUUGGUCUGUCACCCCGCACCGCUUCACAGCUCCAUCCCCUAUUACCU----U
...((((((((((((......)))...........(((((((((((........).))))))))))........)))..)))))).................----. ( -24.70)
>DroSec_CAF1 370 86 - 1
UUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC-----------------CCUGUUGCCU----U
..(((.(((((((.(((((...(((..(....((.....))....)..)))...))))).)))))))...)))..-----------------..........----. ( -21.80)
>DroSim_CAF1 2870 91 - 1
UUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC----------------CCCUGUUGCAUUUGUU
..(((.(((((((.(((((...(((..(....((.....))....)..)))...))))).)))))))...)))..----------------................ ( -21.80)
>consensus
UUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC________________CCCUGUUGCCU____U
..((((((.(.((((......)))).).)))....(((((((((((........).))))))))))....))).................................. (-20.10 = -20.10 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,367,578 – 15,367,698
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -30.68
Consensus MFE -29.31
Energy contribution -29.88
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.40
Structure conservation index 0.96
SVM decision value 0.06
SVM RNA-class probability 0.562435
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15367578 120 - 22224390
UUGUAAAGCAAACAAUUGUCGAAAAAUUAUUGCUGCCUCAUUUGCUGUGGUGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUUGCAUUGUUGGUCUGUCACCCCGCACCGCUUC
.((((((((((....(((((((((((((...((..((.((.....)).))..))..)))))((........)))))))))).)))))))))).....(((.((......)).)))..... ( -30.20)
>DroSec_CAF1 381 115 - 1
UUGUAAAGCAAACAAUUGUCGAAAAAUUAUUGCUGCCUCAUUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC-----
.......((.......(((((((........((((((.((.....)).))))))((.....)).)))))))....(((((((((((........).))))))))))....))...----- ( -30.90)
>DroSim_CAF1 2886 115 - 1
UUGUAAAGCAAACAAUUGUCGAAAAAUUAUUGCUGCCUCAUUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC-----
.......((.......(((((((........((((((.((.....)).))))))((.....)).)))))))....(((((((((((........).))))))))))....))...----- ( -30.90)
>DroEre_CAF1 7521 117 - 1
UUGUAAAGCAAACAAUUGUCGAAAAAUUAUUGCUGCCUCAUUUGCUGUGGCGGCCC-AUUUGGCUUUGACACCUUUGACAGAUUGCUUUGCAUUGUUGGUCUGUCACCCCUCACCC--UC
.((((((((((....((((((((........((((((.((.....)).))))))((-....))..........)))))))).)))))))))).....(((.....)))........--.. ( -30.70)
>consensus
UUGUAAAGCAAACAAUUGUCGAAAAAUUAUUGCUGCCUCAUUUGCUGUGGCGGCCCAAUUUGGCUUUGACACCUUUGACAGAUUGCUUAGCAUUGUUGGUCUGUCACCCCGCACC_____
.((((((((((....((((((((........((((((.((.....)).)))))).......((........)))))))))).)))))))))).(((.((........)).)))....... (-29.31 = -29.88 +   0.56)

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 12:00:39 2006