Locus 2515

Sequence ID X_DroMel_CAF1
Location 6,685,312 – 6,685,441
Length 129
Max. P 0.990408
window4109 window4110 window4111

overview

Window 9

Location 6,685,312 – 6,685,407
Length 95
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 61.54
Mean single sequence MFE -31.81
Consensus MFE -14.40
Energy contribution -14.64
Covariance contribution 0.24
Combinations/Pair 1.29
Mean z-score -1.76
Structure conservation index 0.45
SVM decision value 0.63
SVM RNA-class probability 0.806399
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6685312 95 + 22224390
UU----------AACUUUCUU--AAGUUA-AG----AUAUGUUGCUCAACUUACGUGCAAAGUGUGUGGCCACUGGGCCUGAGAUCUACG-----UCCCAACCCAGAGACCAG---ACCC
((----------(((((....--))))))-).----.....((((.(.......).))))...((.(((.(.(((((..((.(((....)-----)).)).))))).).))).---)).. ( -23.00)
>DroSec_CAF1 15062 111 + 1
UGAUAUG-AUAUAUGUCUCUUCAGAGUUA-AG----AUAAGUUGCCCAACUUACGUGCAAAGUGUGUGGUCACUGGGCCUGGGAUCUGCGUCGCGUCCCAGCCCAGAGACCAG---ACCC
(((...(-((....)))...)))..((..-.(----.((((((....)))))))..)).....((.(((((.((((((.((((((..((...)))))))))))))).))))).---)).. ( -39.20)
>DroEre_CAF1 14805 110 + 1
UGAUAUA-ACAUAUCUUCUUU-CAGGUAAGUGACUGAUGUGCUGCCCAACUUACGUGCAAAGUGUUUGGUCACUGGGCCUGGGAUCUACG-----UCCCAACCCAGAGAUUUG---ACCC
.(((((.-..)))))..((((-((.((((((.................)))))).)).)))).(((..(((.(((((..((((((....)-----))))).))))).)))..)---)).. ( -32.33)
>DroYak_CAF1 14766 109 + 1
UGAAAUAUGCAUAUCU-CUUU-CAAAUUA-UGACUUUAUUUUGGCCCAACUUACGUGCAAAGUAUUUGGUCACUGGGCCUGGGAUCUCCG-----UCCCAACCCAGAGAAUGG---ACCC
.............(((-..((-(......-(((((.(((((((..(........)..)))))))...)))))(((((..((((((....)-----))))).))))).))).))---)... ( -27.90)
>DroAna_CAF1 15627 95 + 1
-------------GUUUCUAC-CAGCCAAG----------GGCGUCCAACCUACCUCUUGAAGGUUCGAUCUCUGGGCCUGGGGC-ACCAUGGGCCACCAACCCAGAGAUGCGCCAACCA
-------------........-....((((----------((.((.......))))))))..(((((((((((((((..((((((-.(....)))).))).))))))))).))..)))). ( -36.60)
>consensus
UGA_AU____AUAUCUUCUUU_CAAGUUA_AG____AUAUGUUGCCCAACUUACGUGCAAAGUGUUUGGUCACUGGGCCUGGGAUCUACG_____UCCCAACCCAGAGACCAG___ACCC
...................................................................((((.(((((..(((((...........))))).))))).))))......... (-14.40 = -14.64 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,685,312 – 6,685,407
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 61.54
Mean single sequence MFE -36.34
Consensus MFE -18.00
Energy contribution -17.04
Covariance contribution -0.96
Combinations/Pair 1.47
Mean z-score -2.35
Structure conservation index 0.50
SVM decision value 2.19
SVM RNA-class probability 0.989883
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6685312 95 - 22224390
GGGU---CUGGUCUCUGGGUUGGGA-----CGUAGAUCUCAGGCCCAGUGGCCACACACUUUGCACGUAAGUUGAGCAACAUAU----CU-UAACUU--AAGAAAGUU----------AA
..((---.(((((.(((((((((((-----......))))).)))))).))))).))(((((.(...(((((((((........----))-))))))--).)))))).----------.. ( -33.80)
>DroSec_CAF1 15062 111 - 1
GGGU---CUGGUCUCUGGGCUGGGACGCGACGCAGAUCCCAGGCCCAGUGACCACACACUUUGCACGUAAGUUGGGCAACUUAU----CU-UAACUCUGAAGAGACAUAUAU-CAUAUCA
..((---((((((.((((((((((((........).))))).)))))).)))).....((((.....((((..((....))...----))-)).....))))))))......-....... ( -40.10)
>DroEre_CAF1 14805 110 - 1
GGGU---CAAAUCUCUGGGUUGGGA-----CGUAGAUCCCAGGCCCAGUGACCAAACACUUUGCACGUAAGUUGGGCAGCACAUCAGUCACUUACCUG-AAAGAAGAUAUGU-UAUAUCA
.(((---((.....(((((((((((-----......))))).))))))))))).....((((.((.((((((..(((.........))))))))).))-))))..(((((..-.))))). ( -34.30)
>DroYak_CAF1 14766 109 - 1
GGGU---CCAUUCUCUGGGUUGGGA-----CGGAGAUCCCAGGCCCAGUGACCAAAUACUUUGCACGUAAGUUGGGCCAAAAUAAAGUCA-UAAUUUG-AAAG-AGAUAUGCAUAUUUCA
.(((---(((.((.(((((((((((-----......))))).)))))).)).............((....)))))))).........(((-.....))-)..(-(((((....)))))). ( -33.40)
>DroAna_CAF1 15627 95 - 1
UGGUUGGCGCAUCUCUGGGUUGGUGGCCCAUGGU-GCCCCAGGCCCAGAGAUCGAACCUUCAAGAGGUAGGUUGGACGCC----------CUUGGCUG-GUAGAAAC-------------
.((((((((..((((((((((((.((((....).-)))))).)))))))))((.(((((((....)).))))).))))))----------...)))).-........------------- ( -40.10)
>consensus
GGGU___CUAAUCUCUGGGUUGGGA_____CGGAGAUCCCAGGCCCAGUGACCAAACACUUUGCACGUAAGUUGGGCAACAUAU____CA_UAACUUG_AAAGAAGAUAU____AU_UCA
..........(((.(((((((((((...........))))).)))))).)))......(((.((......)).)))............................................ (-18.00 = -17.04 +  -0.96)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,685,335 – 6,685,441
Length 106
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 87.00
Mean single sequence MFE -47.70
Consensus MFE -43.56
Energy contribution -43.88
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.46
Structure conservation index 0.91
SVM decision value 2.21
SVM RNA-class probability 0.990408
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6685335 106 - 22224390
------ACUGGAACUGGCCAGCUGGGCGCAGUGCGAGGAUGGGUCUGGUCUCUGGGUUGGGA-----CGUAGAUCUCAGGCCCAGUGGCCACACACUUUGCACGUAAGUUGAGCAAC
------..(((......)))(((.(((...((((((((....((.(((((.(((((((((((-----......))))).)))))).))))).)).))))))))....))).)))... ( -46.00)
>DroSec_CAF1 15096 111 - 1
------UCUGGAACUGGCCAGCUGGGCGCAGUGCGAGGAUGGGUCUGGUCUCUGGGCUGGGACGCGACGCAGAUCCCAGGCCCAGUGACCACACACUUUGCACGUAAGUUGGGCAAC
------........((.((((((....((.((((((((....((.(((((.((((((((((((........).))))).)))))).))))).)).)))))))))).)))))).)).. ( -53.00)
>DroEre_CAF1 14843 106 - 1
------ACUGGAACUGGCCAGCUGGACGCAGUGCGAGGAUGGGUCAAAUCUCUGGGUUGGGA-----CGUAGAUCCCAGGCCCAGUGACCAAACACUUUGCACGUAAGUUGGGCAGC
------.......(((.((((((....((.((((((((...(((((.....(((((((((((-----......))))).))))))))))).....)))))))))).)))))).))). ( -47.60)
>DroYak_CAF1 14803 112 - 1
GCAGCGACUGGAACUGGCCAGCUGGACGCAGUGCGAGGAUGGGUCCAUUCUCUGGGUUGGGA-----CGGAGAUCCCAGGCCCAGUGACCAAAUACUUUGCACGUAAGUUGGGCCAA
..............(((((((((....((.((((((((...((((......(((((((((((-----......))))).)))))).)))).....)))))))))).)))).))))). ( -44.20)
>consensus
______ACUGGAACUGGCCAGCUGGACGCAGUGCGAGGAUGGGUCUAGUCUCUGGGUUGGGA_____CGUAGAUCCCAGGCCCAGUGACCAAACACUUUGCACGUAAGUUGGGCAAC
........(((......)))(((.(((...((((((((....((.(((((.(((((((((((...........))))).)))))).))))).)).))))))))....))).)))... (-43.56 = -43.88 +   0.31)

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 10:36:40 2006