Locus 1539

Sequence ID X_DroMel_CAF1
Location 4,449,335 – 4,449,495
Length 160
Max. P 0.982806
window2518 window2519 window2520

overview

Window 8

Location 4,449,335 – 4,449,455
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.15
Mean single sequence MFE -35.08
Consensus MFE -31.67
Energy contribution -32.11
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.77
Structure conservation index 0.90
SVM decision value 1.93
SVM RNA-class probability 0.982806
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4449335 120 + 22224390
UCGGGCGAAGAAGUGCCCACAAAUUUGCGGUUGCUCCAUCUGGUUGCCGAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAAGGGAAGUCACAUCGGUAACAAGUAAGUGGAUGCCGCAAA
..(((((......))))).....((((((((...(((((((.((((((((..((((...............(((.......)))..))))..)))))))).))...))))).)))))))) ( -42.33)
>DroSec_CAF1 50888 119 + 1
UCGGGCGAAGAAGUGCCCACAAAUUUGCGGUUGCUCCAUCUGGUCGCCGAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAAGGGAAGUCACAUCGGUAACA-GUAAGUGGAUGCCGCAAA
..(((((......))))).....((((((((...((((((((...(((((..((((...............(((.......)))..))))..)))))..))-)...))))).)))))))) ( -39.53)
>DroSim_CAF1 52171 119 + 1
UCGGGCGAAGAAGUGCCCACAAAUUUGCGGUUGCUCCAUCUGGUCGCCGAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAAGGGAAGUCACAUCGGUAACA-GUAAGUGGAUGCCGCAAA
..(((((......))))).....((((((((...((((((((...(((((..((((...............(((.......)))..))))..)))))..))-)...))))).)))))))) ( -39.53)
>DroEre_CAF1 52718 119 + 1
UCGGGCGAAGAAGUACCCACAAAUUUGCGGUUGCUCCAUCUGGUCACCAAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAAGGGAAGUCACAUCGGUAGCA-GUAAGUGGAUGCCACAAA
...((((.....(((.((.((....)).)).)))((((((((.(.(((..(((.....)))......((..(((.......)))..))......)))).))-)...)))))))))..... ( -25.70)
>DroYak_CAF1 51459 119 + 1
UCGGGCGACGAAGUACCCACAAAUUUGCGGUUGCUCCAUCUGGUCACCGAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAUGGGAAGUUACAUCGGUAACA-GUAAGUGGAUGCCACAAA
((((((((.(.((((.((.((....)).)).)))).).))..((((......))))..............))))))..........(((((....))))).-....((((...))))... ( -28.30)
>consensus
UCGGGCGAAGAAGUGCCCACAAAUUUGCGGUUGCUCCAUCUGGUCGCCGAGUUGAUAAAAUAAAUAUGCGGCCCGAAAAAAGGGAAGUCACAUCGGUAACA_GUAAGUGGAUGCCGCAAA
..(((((......))))).....((((((((...((((.((.((.(((((..((((...............(((.......)))..))))..))))).)).....)))))).)))))))) (-31.67 = -32.11 +   0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,449,335 – 4,449,455
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.15
Mean single sequence MFE -32.15
Consensus MFE -28.68
Energy contribution -28.40
Covariance contribution -0.28
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.89
SVM decision value 0.77
SVM RNA-class probability 0.845610
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4449335 120 - 22224390
UUUGCGGCAUCCACUUACUUGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCAACCAGAUGGAGCAACCGCAAAUUUGUGGGCACUUCUUCGCCCGA
(((((((..((((....((.(((.((((((((.(..(((.......)))..)))))..............)))).))).)).))))....)))))))....(((((........))))). ( -31.93)
>DroSec_CAF1 50888 119 - 1
UUUGCGGCAUCCACUUAC-UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCAGAUGGAGCAACCGCAAAUUUGUGGGCACUUCUUCGCCCGA
(((((((..((((((...-.((..((((((((.(..(((.......)))..)))))..............))))..)).)).))))....)))))))....(((((........))))). ( -32.53)
>DroSim_CAF1 52171 119 - 1
UUUGCGGCAUCCACUUAC-UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCAGAUGGAGCAACCGCAAAUUUGUGGGCACUUCUUCGCCCGA
(((((((..((((((...-.((..((((((((.(..(((.......)))..)))))..............))))..)).)).))))....)))))))....(((((........))))). ( -32.53)
>DroEre_CAF1 52718 119 - 1
UUUGUGGCAUCCACUUAC-UGCUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUUGGUGACCAGAUGGAGCAACCGCAAAUUUGUGGGUACUUCUUCGCCCGA
...((.(((((.......-.......))))).))..........((((((............(((((.....)))))...((.((((...(((((....)))))...)))).)))))))) ( -29.74)
>DroYak_CAF1 51459 119 - 1
UUUGUGGCAUCCACUUAC-UGUUACCGAUGUAACUUCCCAUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGUGACCAGAUGGAGCAACCGCAAAUUUGUGGGUACUUCGUCGCCCGA
.(((.(((..........-.((((((((.((.....(((.......)))..(.(((.......)))).))))))))))..(((((((...(((((....)))))...))))))))))))) ( -34.00)
>consensus
UUUGCGGCAUCCACUUAC_UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCAGAUGGAGCAACCGCAAAUUUGUGGGCACUUCUUCGCCCGA
(((((((..((((.............((((((....(((.......)))...))))))...........((.(....).)).))))....)))))))....(((((........))))). (-28.68 = -28.40 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,449,375 – 4,449,495
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.13
Mean single sequence MFE -31.19
Consensus MFE -23.78
Energy contribution -23.02
Covariance contribution -0.76
Combinations/Pair 1.20
Mean z-score -1.65
Structure conservation index 0.76
SVM decision value 0.02
SVM RNA-class probability 0.542026
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4449375 120 - 22224390
UUGGACGUAGGGUGCUCCUGAUUUGCUUAUCGCAAGUACUUUUGCGGCAUCCACUUACUUGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCAACCA
.(((..((.((((.......((((((.....)))))).....((((((............(((((....)))))...((.......))))))))..............)))).))..))) ( -27.90)
>DroSec_CAF1 50928 119 - 1
UUGGGCGUAGGGUGCUGCUGAUUUGCUUAUCGCAAGUACUUUUGCGGCAUCCACUUAC-UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCA
.(((.(((.(((((((((..((((((.....))))))......)))))))))......-.......((((((.(..(((.......)))..)))))))...............))).))) ( -34.40)
>DroSim_CAF1 52211 119 - 1
UUGUACGUAGGGUGCUGCUGAUUUGCUUAUCGCAAGUACUUUUGCGGCAUCCACUUAC-UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCA
..(((.((.(((((((((..((((((.....))))))......))))))))))).)))-.((..((((((((.(..(((.......)))..)))))..............))))..)).. ( -34.43)
>DroEre_CAF1 52758 119 - 1
UUGAAUGUAGGGUGCUCCCGAUUUGCUUAUCGCAAGAACAUUUGUGGCAUCCACUUAC-UGCUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUUGGUGACCA
.........((((((.((((((((((.....))))).(((((.((((((.........-)))))).))))).............)))))..)))).......(((((.....))))))). ( -30.60)
>DroYak_CAF1 51499 119 - 1
UUGGAAGUAGGGUUCUCCCGAUUUGCUUAUCGCAAAUACUUUUGUGGCAUCCACUUAC-UGUUACCGAUGUAACUUCCCAUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGUGACCA
..((((((((((....)))..(((((.....))))))))))))((((...))))....-.((((((((.((.....(((.......)))..(.(((.......)))).)))))))))).. ( -28.60)
>consensus
UUGGACGUAGGGUGCUCCUGAUUUGCUUAUCGCAAGUACUUUUGCGGCAUCCACUUAC_UGUUACCGAUGUGACUUCCCUUUUUUCGGGCCGCAUAUUUAUUUUAUCAACUCGGCGACCA
..........(((....(((((((((.....)))))......((((((............(((((....)))))...((.......))))))))................))))..))). (-23.78 = -23.02 +  -0.76)

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 10:12:51 2006