Locus 6373

Sequence ID 3L_DroMel_CAF1
Location 17,060,869 – 17,060,997
Length 128
Max. P 0.948307
window10210 window10211 window10212

overview

Window 0

Location 17,060,869 – 17,060,970
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 80.87
Mean single sequence MFE -28.40
Consensus MFE -17.81
Energy contribution -18.17
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.63
SVM decision value 0.54
SVM RNA-class probability 0.776379
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17060869 101 - 23771897
AGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUUGCCAUUCUGCCAUUUGGCCAUUUGGCCAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
.(.((((.....((((((..((((..(.((((..(.((......)).)..)))).)..))))....)))))).(........)....)))).)........ ( -30.60)
>DroSec_CAF1 19259 77 - 1
AGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAU------------------------UUGGCCAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
.(.((((..........(((((((((..(((..------------------------..)))....))).))))))...........)))).)........ ( -21.60)
>DroSim_CAF1 20627 93 - 1
AGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUGGCCAUUCUGCCAU--------UUGGCCAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
.(.((((..........(((((((((..((((..((((......)))).--------.))))....))).))))))...........)))).)........ ( -31.10)
>DroEre_CAF1 18887 84 - 1
AGG-GCCAUU--------UUGCCAUUUGGCCAUUUGGCCAUUCUGCCAU--------UUGGCCAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
..(-((....--------..)))...((((((..((((......)))).--------.))))))((((...((((.(..........).))))...)))). ( -32.50)
>DroYak_CAF1 20322 77 - 1
AGGGGCCAUU--------UUGCCAUUUUGCCAUUUGGCC--------AU--------UUGGCAAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
.(.((((...--------((((((..(.(((....))).--------).--------.))))))..((((......)))).......)))).)........ ( -26.20)
>consensus
AGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUGGCCAUUCUGCCAU________UUGGCCAUCGAUGGGCGGACAUUAACAACAGGCCGCAAUUCGAG
.(.((((..........(((((((((..((((..........................))))....))).))))))...........)))).)........ (-17.81 = -18.17 +   0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,060,902 – 17,060,997
Length 95
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 84.06
Mean single sequence MFE -29.98
Consensus MFE -19.82
Energy contribution -20.49
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.16
Structure conservation index 0.66
SVM decision value 1.38
SVM RNA-class probability 0.948307
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17060902 95 + 23771897
UCGAUGGCCAAAUGGCCAAAUGGCAGAAUGGCAAAAUGGCAAAAUGGCAGAAUGGGAGAAUGGCCCCUCUGCCCCCACCGAUAGCUGUCAUAAUU
....(((((....))))).(((((((....((......)).....((((((..(((........)))))))))...........))))))).... ( -31.90)
>DroSim_CAF1 20660 86 + 1
UCGAUGGCCAA--------AUGGCAGAAUGGCCAAAUGGCAAAAUGGCAGAAUGGGAGAAUGGCCCCUCUGCC-CCACCUAUAGCUGUCAUAAUU
......((((.--------.((((......))))..))))...(((((((.(((((.(...(((......)))-.).)))))..))))))).... ( -28.50)
>DroEre_CAF1 18920 77 + 1
UCGAUGGCCAA--------AUGGCAGAAUGGCCAAAUGGCCAAAUGGCAA--------AAUGGC-CCUCUGCC-CCACCGAUAGCUGUCAUAAUU
..((((((...--------..((((((..(((((....(((....)))..--------..))))-).))))))-.........))))))...... ( -29.54)
>consensus
UCGAUGGCCAA________AUGGCAGAAUGGCCAAAUGGCAAAAUGGCAGAAUGGGAGAAUGGCCCCUCUGCC_CCACCGAUAGCUGUCAUAAUU
..((((((.............((((((..(((((....((......))............)))))..))))))..........))))))...... (-19.82 = -20.49 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,060,902 – 17,060,997
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 84.06
Mean single sequence MFE -33.07
Consensus MFE -20.44
Energy contribution -21.97
Covariance contribution 1.53
Combinations/Pair 1.04
Mean z-score -3.62
Structure conservation index 0.62
SVM decision value 1.37
SVM RNA-class probability 0.947242
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17060902 95 - 23771897
AAUUAUGACAGCUAUCGGUGGGGGCAGAGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUUGCCAUUCUGCCAUUUGGCCAUUUGGCCAUCGA
..............((((((..((((((((((.......))).))))))).....((((..(.((((..........)))).)..)))))))))) ( -33.00)
>DroSim_CAF1 20660 86 - 1
AAUUAUGACAGCUAUAGGUGG-GGCAGAGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUGGCCAUUCUGCCAU--------UUGGCCAUCGA
................((((.-((((((((((.......))).))))))).....((((..((((......)))).--------.)))))))).. ( -32.20)
>DroEre_CAF1 18920 77 - 1
AAUUAUGACAGCUAUCGGUGG-GGCAGAGG-GCCAUU--------UUGCCAUUUGGCCAUUUGGCCAUUCUGCCAU--------UUGGCCAUCGA
..............(((((((-((((((((-((((..--------(.(((....))).)..))))).)))))))..--------....))))))) ( -34.00)
>consensus
AAUUAUGACAGCUAUCGGUGG_GGCAGAGGGGCCAUUCUCCCAUUCUGCCAUUUUGCCAUUUGGCCAUUCUGCCAU________UUGGCCAUCGA
.....(((..((((..((..(.((((((((((.......))).)))))))...)..))...((((......))))..........))))..))). (-20.44 = -21.97 +   1.53)

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 12:16:50 2006