Locus 4534

Sequence ID 2L_DroMel_CAF1
Location 12,975,423 – 12,975,636
Length 213
Max. P 0.986032
window7144 window7145 window7146 window7147

overview

Window 4

Location 12,975,423 – 12,975,543
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.26
Mean single sequence MFE -28.12
Consensus MFE -21.99
Energy contribution -23.43
Covariance contribution 1.44
Combinations/Pair 1.10
Mean z-score -1.63
Structure conservation index 0.78
SVM decision value 0.28
SVM RNA-class probability 0.666019
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975423 120 - 22407834
ACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUAAGUUUUUGUAGAGCCCACAGCUCCCAAAUUUUUCGAUUAU
(((....((((...((.............((((..((((....))))..))))(((((((.....)))))))..))..))))....))).((((.....))))................. ( -27.20)
>DroSec_CAF1 20055 119 - 1
ACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUAAGUUUUUGGAGAGUCCACAGCUCUCG-AUUUUUCGAUUAU
..............((((...((((..(.((((..((((....))))..))))(((((((.....)))))))...)..))))...)))).((((.....))))(((-(....)))).... ( -30.30)
>DroSim_CAF1 21218 119 - 1
ACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUAAGUUUUUGGAGAGUCCACAGCUCUCG-AUUUUUCGAUUAU
..............((((...((((..(.((((..((((....))))..))))(((((((.....)))))))...)..))))...)))).((((.....))))(((-(....)))).... ( -30.30)
>DroYak_CAF1 23041 108 - 1
CCACAUUCUCAUCACUAAUUUCUGGCUUGGCCCUCUGUCAGCUGACAAAGGGCAGGUGUAUCUGCUGCAUUUACAGGUUAAG-----------UCCACAGCUCCCU-AUUUUUCGAUUAU
......................((((((((((((.((((....)))).)))))(((((((.....))))))).)))))))..-----------.............-............. ( -24.70)
>consensus
ACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUAAGUUUUUGGAGAGUCCACAGCUCCCG_AUUUUUCGAUUAU
..........(((........((((....(((((.((((....)))).)))))(((((((.....))))))).))))...........((((((.....)))))).........)))... (-21.99 = -23.43 +   1.44)

alignment

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secondary structure

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Window 5

Location 12,975,463 – 12,975,583
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.72
Mean single sequence MFE -32.85
Consensus MFE -31.17
Energy contribution -30.80
Covariance contribution -0.37
Combinations/Pair 1.06
Mean z-score -2.45
Structure conservation index 0.95
SVM decision value 2.03
SVM RNA-class probability 0.986032
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975463 120 + 22407834
UAACCUGUAAAUGUAGCAGAUACACCUGCCCCUUGUCAGCUGACAGAGGGCUGAGCAAGAAAUUAGUGAUAAGAAAAUGUUCACCUUUAUCUUCGCCCUUUUGCAGCCAGCAUUUAACAA
.....(((((((((.((((......)))).........((((..(((((((((((((.....(((....))).....))))))...........)))))))..))))..)))))).))). ( -31.80)
>DroSec_CAF1 20094 120 + 1
UAACCUGUAAAUGUAGCAGAUACACCUGCCCCUUGUCAGCUGACAGAGGGCUGAGCAAGAAAUUAGUGAUAAGAAAAUGUUCACCUUUAUCUUUGCCCUUUUCCAGCCAGCAUUUAACAA
.....(((((((((.((((......)))).........((((..(((((((((((((.....(((....))).....))))))...........)))))))..))))..)))))).))). ( -31.70)
>DroSim_CAF1 21257 120 + 1
UAACCUGUAAAUGUAGCAGAUACACCUGCCCCUUGUCAGCUGACAGAGGGCUGAGCAAGAAAUUAGUGAUAAGAAAAUGUUCACCUUUAUCUUCGCCCUUUUCCAGCCAGCAUUUAACAA
.....(((((((((.((((......)))).........((((..(((((((((((((.....(((....))).....))))))...........)))))))..))))..)))))).))). ( -31.70)
>DroYak_CAF1 23069 120 + 1
UAACCUGUAAAUGCAGCAGAUACACCUGCCCUUUGUCAGCUGACAGAGGGCCAAGCCAGAAAUUAGUGAUGAGAAUGUGGUCACCUUUAUCUUUGCCCUUUUGCAGCCAGCAUUUUACAA
....(((((((.((((.(((((.....((((((((((....))))))))))...((((.(..(((....)))...).))))......)))))))))...))))))).............. ( -36.20)
>consensus
UAACCUGUAAAUGUAGCAGAUACACCUGCCCCUUGUCAGCUGACAGAGGGCUGAGCAAGAAAUUAGUGAUAAGAAAAUGUUCACCUUUAUCUUCGCCCUUUUCCAGCCAGCAUUUAACAA
.....(((((((((.((((......)))).........((((..(((((((.(((....(((...((((...........)))).)))..))).)))))))..))))..)))))).))). (-31.17 = -30.80 +  -0.37)

alignment

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secondary structure

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Window 6

Location 12,975,463 – 12,975,583
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.72
Mean single sequence MFE -38.05
Consensus MFE -35.11
Energy contribution -34.80
Covariance contribution -0.31
Combinations/Pair 1.09
Mean z-score -2.63
Structure conservation index 0.92
SVM decision value 1.99
SVM RNA-class probability 0.985071
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975463 120 - 22407834
UUGUUAAAUGCUGGCUGCAAAAGGGCGAAGAUAAAGGUGAACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUA
((((.(((((.((((((((...((((.((((....(((((...........)))))....)))))))).((((..((((....))))..))))...))))...))))))))))))).... ( -38.10)
>DroSec_CAF1 20094 120 - 1
UUGUUAAAUGCUGGCUGGAAAAGGGCAAAGAUAAAGGUGAACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUA
((((.(((((.((((.(((...((((((.((....(((((...........)))))....)))))))).((((..((((....))))..)))).......)))))))))))))))).... ( -38.40)
>DroSim_CAF1 21257 120 - 1
UUGUUAAAUGCUGGCUGGAAAAGGGCGAAGAUAAAGGUGAACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUA
((((.(((((.((((.(((...((((.((((....(((((...........)))))....)))))))).((((..((((....))))..)))).......)))))))))))))))).... ( -38.40)
>DroYak_CAF1 23069 120 - 1
UUGUAAAAUGCUGGCUGCAAAAGGGCAAAGAUAAAGGUGACCACAUUCUCAUCACUAAUUUCUGGCUUGGCCCUCUGUCAGCUGACAAAGGGCAGGUGUAUCUGCUGCAUUUACAGGUUA
(((((((.(((.((((((......))).(((((..(((((........)))))...........(((((.((((.((((....)))).))))))))).)))))))))))))))))).... ( -37.30)
>consensus
UUGUUAAAUGCUGGCUGCAAAAGGGCAAAGAUAAAGGUGAACAUUUUCUUAUCACUAAUUUCUUGCUCAGCCCUCUGUCAGCUGACAAGGGGCAGGUGUAUCUGCUACAUUUACAGGUUA
((((.(((((.((((.......((((.((((....(((((...........)))))....)))))))).(((((.((((....)))).)))))..........))))))))))))).... (-35.11 = -34.80 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,975,543 – 12,975,636
Length 93
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.18
Mean single sequence MFE -23.47
Consensus MFE -19.27
Energy contribution -19.17
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -2.04
Structure conservation index 0.82
SVM decision value 1.50
SVM RNA-class probability 0.959436
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12975543 93 - 22407834
---------------------------UUUGCUUUAUUCUGUUUUUUCGACUGCAAUGGAGGGAAAAUAGAAGAGGAAAAUUGUUAAAUGCUGGCUGCAAAAGGGCGAAGAUAAAGGUGA
---------------------------((((((((.(((((((((..(..(......)..)..)))))))))................(((.....)))..))))))))........... ( -21.80)
>DroSim_CAF1 21337 120 - 1
AUCAUCGAAACGCUUAAGGUUGGACAUUUUGCUUUAUUCUGUUUUUUCGACUGCAAUGGAGGGAAAAUAGAAGAGGAAAAUUGUUAAAUGCUGGCUGGAAAAGGGCGAAGAUAAAGGUGA
.(((((....(((((..(((..(.(((((.(((((.(((((((((..(..(......)..)..)))))))))...)))....)).))))))..)))......)))))........))))) ( -29.40)
>DroYak_CAF1 23149 93 - 1
---------------------------UUUGCUUUAUUCUGUUUUAACGACUGCAAUGGAGGGAAAAUAGAGGAGGAAAAUUGUAAAAUGCUGGCUGCAAAAGGGCAAAGAUAAAGGUGA
---------------------------((((((((.(((((((((..(..(......)..)..)))))))))................(((.....)))..))))))))........... ( -19.20)
>consensus
___________________________UUUGCUUUAUUCUGUUUUUUCGACUGCAAUGGAGGGAAAAUAGAAGAGGAAAAUUGUUAAAUGCUGGCUGCAAAAGGGCGAAGAUAAAGGUGA
...........................((((((((.(((((((((..(..(......)..)..)))))))))................(((.....)))..))))))))........... (-19.27 = -19.17 +  -0.11)

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 11:20:26 2006