Locus 2830

Sequence ID 2R_DroMel_CAF1
Location 9,828,097 – 9,828,243
Length 146
Max. P 0.998080
window4677 window4678 window4679

overview

Window 7

Location 9,828,097 – 9,828,205
Length 108
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 93.22
Mean single sequence MFE -23.65
Consensus MFE -18.92
Energy contribution -19.68
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -3.51
Structure conservation index 0.80
SVM decision value 1.12
SVM RNA-class probability 0.917801
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9828097 108 - 20766785
GCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAAAUGCAAAAUGACAAAAAA-----AAACACAACAAAUAAUG
(((....)))......(((((((..((((((((((........))))))))))...)))))))....((((..........))))......-----................. ( -22.70)
>DroSec_CAF1 65731 113 - 1
GCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAAAUACAAAAUGACAAAAAAAUAAGAAACACAACAAAUACUG
(((....)))..(((((((((((..((((((((((........))))))))))...)))))))....((((..........))))..........)))).............. ( -24.40)
>DroSim_CAF1 67550 112 - 1
-CCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAAAUGCAAAAUGACAAAAAAAUAAGAAACACAACAAAUAAUG
-...(((((..((((.((....)).((((((((((........))))))))))....))))..))..((((..........))))..........)))............... ( -20.60)
>DroYak_CAF1 67826 111 - 1
GCCAUUCGGCUU-UUCGAUUUUUCUGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAAAUGCAAAACG-CAAAAUGACAAAAAACACAACAAAUAAUG
(((....)))..-...(((((((..((((((((((........))))))))))...)))))))....((((...(((.....)-))...)))).................... ( -26.90)
>consensus
GCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAAAUGCAAAAUGACAAAAAAAUAAGAAACACAACAAAUAAUG
(((....)))......(((((((..((((((((((........))))))))))...)))))))....((((..........))))............................ (-18.92 = -19.68 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,828,132 – 9,828,243
Length 111
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 83.90
Mean single sequence MFE -29.17
Consensus MFE -22.25
Energy contribution -22.75
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.76
SVM decision value 0.69
SVM RNA-class probability 0.823990
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9828132 111 + 20766785
UUUGACGUGGAAUUUUUGUGGCCAGCAAAAGUGUCUAAUUUCGCUGGCUGAAAAAUCGAAAAAGCCGAAUGGC-CGUAUAUAUAGCCACUUCAACGGC-AAUCACGCAGUUGU
.(((.((((((.(((((..(((((((.(((........))).)))))))))))).))......((((..((((-..(....)..))))......))))-...))))))).... ( -31.50)
>DroSec_CAF1 65771 113 + 1
UUUGACGUGGAAUUUUUGUGGCCAGCAAAAGUGUCUAAUUUCGCUGGCUGAAAAAUCGAAAAAGCCGAAUGGCCCGUAUGUAUAGCCACUUCAACAGCUAAACACGCAGUUGU
..(((.((((.((((((.((((((((.(((........))).)))))))))))))).......(((....)))............)))).)))((((((........)))))) ( -29.80)
>DroSim_CAF1 67590 88 + 1
UUUGACGUGGAAUUUUUGUGGCCAGCAAAAGUGUCUAAUUUCGCUGGCUGAAAAAUCGAAAAAGCCGAAUGG-------------------------CUAAACACGCAGUUGU
.(((.((((((.(((((..(((((((.(((........))).)))))))))))).)).....((((....))-------------------------))...))))))).... ( -26.50)
>DroYak_CAF1 67865 106 + 1
UUUGACGUGGAAUUUUUGUGGCCAGCAAAAGUGUCUAAUUUCGCUGGCAGAAAAAUCGAA-AAGCCGAAUGGCC-----AAAAAGCCACUUGAACAGC-AAUCACGCAGUUUU
.(((.((((((.(((((...((((((.(((........))).)))))).))))).))...-..(((((.((((.-----.....)))).)))....))-...))))))).... ( -28.90)
>consensus
UUUGACGUGGAAUUUUUGUGGCCAGCAAAAGUGUCUAAUUUCGCUGGCUGAAAAAUCGAAAAAGCCGAAUGGC______AUAUAGCCACUUCAACAGC_AAACACGCAGUUGU
.(((.((((((.(((((..(((((((.(((........))).)))))))))))).))......(((....))).............................))))))).... (-22.25 = -22.75 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,828,132 – 9,828,243
Length 111
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 83.90
Mean single sequence MFE -32.55
Consensus MFE -25.44
Energy contribution -27.38
Covariance contribution 1.94
Combinations/Pair 1.03
Mean z-score -3.63
Structure conservation index 0.78
SVM decision value 3.00
SVM RNA-class probability 0.998080
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9828132 111 - 20766785
ACAACUGCGUGAUU-GCCGUUGAAGUGGCUAUAUAUACG-GCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAA
......(((((...-((((....(((((((........)-))))))))))......(((((((..((((((((((........))))))))))...))))))).))))).... ( -36.00)
>DroSec_CAF1 65771 113 - 1
ACAACUGCGUGUUUAGCUGUUGAAGUGGCUAUACAUACGGGCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAA
....(((..(((.((((..(....)..)))).)))..)))(((....)))......(((((((..((((((((((........))))))))))...))))))).......... ( -33.70)
>DroSim_CAF1 67590 88 - 1
ACAACUGCGUGUUUAG-------------------------CCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAA
......(((((...((-------------------------((....)))).....(((((((..((((((((((........))))))))))...))))))).))))).... ( -26.20)
>DroYak_CAF1 67865 106 - 1
AAAACUGCGUGAUU-GCUGUUCAAGUGGCUUUUU-----GGCCAUUCGGCUU-UUCGAUUUUUCUGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAA
......(((((...-((((....(((((((....-----)))))))))))..-...(((((((..((((((((((........))))))))))...))))))).))))).... ( -34.30)
>consensus
ACAACUGCGUGAUU_GCUGUUGAAGUGGCUAUAU______GCCAUUCGGCUUUUUCGAUUUUUCAGCCAGCGAAAUUAGACACUUUUGCUGGCCACAAAAAUUCCACGUCAAA
......(((((....((((....((((((...........))))))))))......(((((((..((((((((((........))))))))))...))))))).))))).... (-25.44 = -27.38 +   1.94)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:32 2006