Locus 1543

Sequence ID 2L_DroMel_CAF1
Location 4,162,408 – 4,162,515
Length 107
Max. P 0.693720
window2495 window2496

overview

Window 5

Location 4,162,408 – 4,162,515
Length 107
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 79.61
Mean single sequence MFE -21.00
Consensus MFE -6.96
Energy contribution -6.96
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.33
SVM decision value 0.32
SVM RNA-class probability 0.688892
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4162408 107 + 22407834
UUUUUAUUGGUCGCUGCAUUAUGCAUGUUUGUCACACAUUUAAUUAUUCAC--ACUCGCACAU--------ACGCCAUUUCUUCCCACCUCCUGUAUGCGUGUGUGUGUGUGUGUAU
.......((((.((.((((.....))))..)).)).))..........(((--((.(((((((--------((((......................))))))))))).)))))... ( -26.85)
>DroSec_CAF1 292586 103 + 1
U-UUUAUUUGUCGCUGCAUUAUGCAUGUUUGUCACACAUUUAAUUAUUCAC--ACUCGCACAU--------AC-CUAUUUCUUGCCACCUCCUGUAUGCGAGUG--UGUGUGUGUAU
.-..........(((((.....))).))....((((((..........(((--(((((((.((--------(.-..................))).))))))))--))))))))... ( -23.11)
>DroSim_CAF1 295221 94 + 1
U-UUUAUUUGUCGCUGCAUUAUGCAUGUUUGUCACACAUUUAAUUAUUCAC--ACUCGCACAU--------AC-CCAUUUCU-------UCCUGUAUGCG--UG--UGUGUGUGUAU
.-......(((.((.((((.....))))..)).)))........(((.(((--((.(((.(((--------((-........-------....))))).)--))--.))))).))). ( -19.40)
>DroEre_CAF1 309755 107 + 1
U-UUCAUUUGUCGCUGCAUUAUGCAUAUUUGUCACACAUUUAAUUAUUCACAUACUCGCACAUAUGUGUGUAC-CUCUUUUCUGCCACCCC------GCUCAUG--UGUGUGUGUAU
.-..((..(((.((........)))))..))....................((((.((((((((((.(((...-................)------)).))))--)))))).)))) ( -21.31)
>DroYak_CAF1 314915 92 + 1
U-UUUAUUCGCCGCUGCAUUAUGCAUGUUUGUCACACAUUUAAUUAUUCAC--ACUCGCACAU--------AC-CUAUUUUCUGUCCCC---------AUC--G--UGUGUGUGUGU
.-..........(((((.....))).))....................(((--((.(((((..--------..-...............---------...--)--)))).))))). ( -14.35)
>consensus
U_UUUAUUUGUCGCUGCAUUAUGCAUGUUUGUCACACAUUUAAUUAUUCAC__ACUCGCACAU________AC_CUAUUUCUUGCCACCUCCUGUAUGCGC_UG__UGUGUGUGUAU
..............(((.....)))............................((.((((((............................................)))))).)).. ( -6.96 =  -6.96 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,162,408 – 4,162,515
Length 107
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 79.61
Mean single sequence MFE -22.16
Consensus MFE -6.10
Energy contribution -6.10
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.28
SVM decision value 0.33
SVM RNA-class probability 0.693720
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4162408 107 - 22407834
AUACACACACACACACACGCAUACAGGAGGUGGGAAGAAAUGGCGU--------AUGUGCGAGU--GUGAAUAAUUAAAUGUGUGACAAACAUGCAUAAUGCAGCGACCAAUAAAAA
.....(((((((((((.((((((.(.(..((........))..).)--------.)))))).))--)))..........)))))).......(((.....))).............. ( -24.10)
>DroSec_CAF1 292586 103 - 1
AUACACACACA--CACUCGCAUACAGGAGGUGGCAAGAAAUAG-GU--------AUGUGCGAGU--GUGAAUAAUUAAAUGUGUGACAAACAUGCAUAAUGCAGCGACAAAUAAA-A
...((((((((--((((((((((......((........))..-..--------.)))))))))--)))..........)))))).......(((.....)))............-. ( -26.40)
>DroSim_CAF1 295221 94 - 1
AUACACACACA--CA--CGCAUACAGGA-------AGAAAUGG-GU--------AUGUGCGAGU--GUGAAUAAUUAAAUGUGUGACAAACAUGCAUAAUGCAGCGACAAAUAAA-A
.....(((((.--(.--(((((((....-------(....)..-))--------))))).).))--))).........(((((((.....)))))))..................-. ( -21.70)
>DroEre_CAF1 309755 107 - 1
AUACACACACA--CAUGAGC------GGGGUGGCAGAAAAGAG-GUACACACAUAUGUGCGAGUAUGUGAAUAAUUAAAUGUGUGACAAAUAUGCAUAAUGCAGCGACAAAUGAA-A
...((((((((--((((..(------(..(((.(........)-.))).(((....)))))..))))))..........)))))).......(((.....)))............-. ( -20.70)
>DroYak_CAF1 314915 92 - 1
ACACACACACA--C--GAU---------GGGGACAGAAAAUAG-GU--------AUGUGCGAGU--GUGAAUAAUUAAAUGUGUGACAAACAUGCAUAAUGCAGCGGCGAAUAAA-A
.(((((.(.((--(--(.(---------(....))........-..--------.)))).).))--))).........(((((((.....)))))))..(((....)))......-. ( -17.90)
>consensus
AUACACACACA__CA_GCGCAUACAGGAGGUGGCAAGAAAUAG_GU________AUGUGCGAGU__GUGAAUAAUUAAAUGUGUGACAAACAUGCAUAAUGCAGCGACAAAUAAA_A
...((((((......................................................................)))))).......(((.....))).............. ( -6.10 =  -6.10 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:08 2006