Locus 1511

Sequence ID 2L_DroMel_CAF1
Location 4,094,117 – 4,094,232
Length 115
Max. P 0.982538
window2452 window2453 window2454

overview

Window 2

Location 4,094,117 – 4,094,216
Length 99
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 88.68
Mean single sequence MFE -27.10
Consensus MFE -17.82
Energy contribution -17.90
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -2.94
Structure conservation index 0.66
SVM decision value 0.53
SVM RNA-class probability 0.770014
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4094117 99 - 22407834
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCGCC----AUGGAGCCGAGACUCAUGCCAUUGCUAACCUUGCCUUCUCUACCAGAUGG----U
......((((((((.((.....)).))))))))(((..((((......----..))))..)))......((((((((.......))...........)))))----) ( -21.90)
>DroSec_CAF1 223463 98 - 1
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC----UUGGAGCGG-GACUCAUGCCAUUGCGAACCUUGCCUUCUCUACCAGAUGG----U
.......(((((((.((.....)).)))))))((((((..........----.))))))((-..(.((......)).)..))..(((.(((.....))).))----) ( -24.30)
>DroSim_CAF1 226347 98 - 1
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC----UUGGAGCCG-GACUCAUGCCAUUGCCAACCUUGCCUUCUCUACCAGAUGG----U
.......(((((((.((.....)).)))))))((((((..........----.)))))).(-(.(....)))............(((.(((.....))).))----) ( -21.60)
>DroEre_CAF1 231972 98 - 1
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCGCUCCUCCUCC----GUGGAGCCG-GACUCCUGCCAUGCCCAACCUAGCCAUCUCUGCCAGAUGG----U
.......(((((((.((.....)).)))))))(((((((.........----))))))).(-(.(....)))............(((((((.....))))))----) ( -29.20)
>DroYak_CAF1 237119 106 - 1
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUUCUUCGGAGGAGCCG-GUCUCCUGCCACUCGCAACCUAGCCAUCUCUACCAGAUGGUUGGU
.......(((((((.((.....)).)))))))((....(((((((......)))))))..(-((.....)))....))...((((((((((.....)))))))))). ( -38.50)
>consensus
AACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC____GUGGAGCCG_GACUCAUGCCAUUGCCAACCUUGCCUUCUCUACCAGAUGG____U
.......(((((((.((.....)).)))))))((((((...............))))))..........................((.(((.....))).))..... (-17.82 = -17.90 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,094,141 – 4,094,232
Length 91
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 90.98
Mean single sequence MFE -33.00
Consensus MFE -25.04
Energy contribution -24.92
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -3.03
Structure conservation index 0.76
SVM decision value 1.92
SVM RNA-class probability 0.982538
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4094141 91 + 22407834
UAGCAAUGGCAUGAGUCUCGGCUCCAU----GGCGGAGGAGUGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
..((((..(((.(..((((((((((((----..(....).)))))))(((((((.((.....)).))))))).......)))))..)))))))). ( -31.70)
>DroSec_CAF1 223487 90 + 1
UCGCAAUGGCAUGAGUC-CCGCUCCAA----GGAGGAGGAGUGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
.(((((((((....(..-(((((((..----......)))))))..)(((((((.((.....)).))))))).............)))).))))) ( -31.60)
>DroSim_CAF1 226371 90 + 1
UGGCAAUGGCAUGAGUC-CGGCUCCAA----GGAGGAGGAGUGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
..((((((((...(.((-(..(((...----.)))..))).).(((((((..((((..........))))...))))))).....)))).)))). ( -29.20)
>DroEre_CAF1 231996 90 + 1
UGGGCAUGGCAGGAGUC-CGGCUCCAC----GGAGGAGGAGCGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
...(((.(((((...((-(.(((((..----......))))).(((((((..((((..........))))...)))))))..))).)))))))). ( -32.10)
>DroYak_CAF1 237147 94 + 1
UGCGAGUGGCAGGAGAC-CGGCUCCUCCGAAGAAGGAGGAGUGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
.(((((..((.(....)-..((((((((......)))))))).(((((((..((((..........))))...))))))).....))..))))). ( -40.40)
>consensus
UGGCAAUGGCAUGAGUC_CGGCUCCAA____GGAGGAGGAGUGGAGCUUCAGCAGCUGGAGAAGAUGCUGAAAGAAGUUCGAGGAGCUGUUUGUG
....((..((..........(((((............))))).(((((((..((((..........))))...))))))).....))..)).... (-25.04 = -24.92 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,094,141 – 4,094,232
Length 91
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 90.98
Mean single sequence MFE -22.84
Consensus MFE -17.30
Energy contribution -17.38
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.87
Structure conservation index 0.76
SVM decision value 1.74
SVM RNA-class probability 0.975009
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4094141 91 - 22407834
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCGCC----AUGGAGCCGAGACUCAUGCCAUUGCUA
............((((.......(((((((.((.....)).)))))))((((((..........----.))))))))))................ ( -21.90)
>DroSec_CAF1 223487 90 - 1
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC----UUGGAGCGG-GACUCAUGCCAUUGCGA
.......((..((..........(((((((.((.....)).)))))))((((((..........----.))))))))-..))..(((....))). ( -22.10)
>DroSim_CAF1 226371 90 - 1
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC----UUGGAGCCG-GACUCAUGCCAUUGCCA
.......((.(((..........(((((((.((.....)).)))))))((((((..........----.)))))).)-))))............. ( -19.90)
>DroEre_CAF1 231996 90 - 1
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCGCUCCUCCUCC----GUGGAGCCG-GACUCCUGCCAUGCCCA
......(((.(((..........(((((((.((.....)).)))))))(((((((.........----))))))).)-))...)))......... ( -24.40)
>DroYak_CAF1 237147 94 - 1
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUUCUUCGGAGGAGCCG-GUCUCCUGCCACUCGCA
.......................(((((((.((.....)).)))))))((....(((((((......)))))))..(-((.....)))....)). ( -25.90)
>consensus
CACAAACAGCUCCUCGAACUUCUUUCAGCAUCUUCUCCAGCUGCUGAAGCUCCACUCCUCCUCC____GUGGAGCCG_GACUCAUGCCAUUGCCA
........((.............(((((((.((.....)).)))))))((((((...............))))))..........))........ (-17.30 = -17.38 +   0.08)

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 10:04:27 2006