Locus 6174

Sequence ID X_DroMel_CAF1
Location 15,744,754 – 15,745,026
Length 272
Max. P 0.995884
window10056 window10057 window10058 window10059 window10060

overview

Window 6

Location 15,744,754 – 15,744,870
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -36.54
Consensus MFE -31.36
Energy contribution -32.60
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.28
Structure conservation index 0.86
SVM decision value 0.08
SVM RNA-class probability 0.575558
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15744754 116 - 22224390
CAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCUCUGAAUCCUUAAGCUUUUUCUGGGAAGCG---AGCUUUUG
..((.((((...((..-((((((((((.(((((.(((.((((..........)))).))).))))))))).(((..(((...)))..)))..)))))))).)))).)).---........ ( -37.20)
>DroSec_CAF1 3763 116 - 1
CAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCUCUGAAUCCUUAAGCUUUUUCUGCGAAGCG---AGCUUUUG
.(((.((.((.((.((-((((((((((.(((((.(((.((((..........)))).))).))))))))).(((..(((...)))..)))..)))..))))))).)).)---)))).... ( -33.60)
>DroSim_CAF1 3773 116 - 1
CAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCUCUGAAUCCUUAAGCUUUUUCUGGGAAGCG---AGCUUUUG
..((.((((...((..-((((((((((.(((((.(((.((((..........)))).))).))))))))).(((..(((...)))..)))..)))))))).)))).)).---........ ( -37.20)
>DroEre_CAF1 3604 117 - 1
CAGCAUCCCUCUGACG-GUAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUU-AAAAGUUUUCUCUGAAUCCUUAAGCUUUUUCUGGGAAGCA-GAAGCUUUUG
((((...((.(((((.-.........))))).))(((((((.(((......))).))))))))))).(-(((((((...((((..((((............))))..))-)))))))))) ( -37.70)
>DroYak_CAF1 3699 118 - 1
CAGCAUCCCUCUGACGCGAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGCGCUGUU-AAAAGUUUUCUCCGAAUCCUUAAGCUU-UUCUGGGAAGCAAGAAGCUUUUG
((((...((.(((((((....))...))))).)).((((((.(((......))).)))))).)))).(-((((((((.((..(..((((.......-....))))..).))))))))))) ( -37.00)
>consensus
CAGCAUCCCUCUGACG_GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCUCUGAAUCCUUAAGCUUUUUCUGGGAAGCG___AGCUUUUG
..((.((((...((...((((((((((.(((((.(((.((((..........)))).))).))))))))).(((..(((...)))..)))..)))))))).)))).))............ (-31.36 = -32.60 +   1.24)

alignment

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secondary structure

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Window 7

Location 15,744,791 – 15,744,910
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.65
Mean single sequence MFE -36.50
Consensus MFE -34.18
Energy contribution -34.22
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.00
Structure conservation index 0.94
SVM decision value 2.63
SVM RNA-class probability 0.995884
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15744791 119 - 22224390
UUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCU
(((....)))...................(((((((((......))))).)))).(-((((((((((.(((((.(((.((((..........)))).))).)))))))))...))))))) ( -36.90)
>DroSec_CAF1 3800 119 - 1
UUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCU
(((....)))...................(((((((((......))))).)))).(-((((((((((.(((((.(((.((((..........)))).))).)))))))))...))))))) ( -36.90)
>DroSim_CAF1 3810 119 - 1
UUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCU
(((....)))...................(((((((((......))))).)))).(-((((((((((.(((((.(((.((((..........)))).))).)))))))))...))))))) ( -36.90)
>DroEre_CAF1 3643 118 - 1
UUCUUCGGCAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GUAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUU-AAAAGUUUUCU
...((((.........))))...........((..(((((((((...((.(((((.-.........))))).))(((((((.(((......))).)))))))))))).-...))))..)) ( -33.10)
>DroYak_CAF1 3738 119 - 1
UUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACGCGAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGCGCUGUU-AAAAGUUUUCU
......(..(((.((((((..........(((((((((......))))).))))(((....)))...))((((.(((.((((..........)))).))).)))))))-)...)))..). ( -38.70)
>consensus
UUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG_GAAAGCGAAGUCGGCGGACGCGAGUGUUCCACUCAACUCUCGUGUGCUGUUUCAAAGUUUUCU
...((((.........)))).........(((((((((......))))).))))...((((((.....(((((.(((.((((..........)))).))).))))).......)))))). (-34.18 = -34.22 +   0.04)

alignment

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secondary structure

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Window 8

Location 15,744,831 – 15,744,950
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.99
Mean single sequence MFE -32.54
Consensus MFE -30.24
Energy contribution -30.64
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.28
Structure conservation index 0.93
SVM decision value 0.28
SVM RNA-class probability 0.667947
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15744831 119 - 22224390
CGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGA
((((.(((((((....)))))))...((.((.((.(((..(((((((.........)))..........(((((((((......))))).)))).)-)))..))))).))))...)))). ( -31.60)
>DroSec_CAF1 3840 118 - 1
CGUGAAUGAAAAAUGAUUUUCGUACAGCACGUCUC-UGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGA
.((..(((((((....)))))))...)).(((.((-((((..(((((....((((.....)))).....(((((((((......))))).))))..-.....)))))..)))))).))). ( -33.60)
>DroSim_CAF1 3850 119 - 1
CGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GAAAGCGAAGUCGGCGGACGCGA
((((.(((((((....)))))))...((.((.((.(((..(((((((.........)))..........(((((((((......))))).)))).)-)))..))))).))))...)))). ( -31.60)
>DroEre_CAF1 3682 118 - 1
CGUGAAUGAA-AAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGCAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG-GUAAGCGAAGUCGGCGGACGCGA
..((.(((((-(.....)))))).)).(.(((((.(((.((((((((.........)))).........(((((((((......))))).))))..-......)))).))).))))).). ( -30.20)
>DroYak_CAF1 3777 120 - 1
CGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACGCGAAAGCGAAGUCGGCGGACGCGA
..((.(((((((....))))))).)).(.(((((.(((.((((((((.........)))).........(((((((((......))))).)))).((....)))))).))).))))).). ( -35.70)
>consensus
CGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUACAGCAUCCCUCUGACG_GAAAGCGAAGUCGGCGGACGCGA
..((.(((((((....))))))).)).(.(((((.(((.((((((((.........)))).........(((((((((......))))).)))).........)))).))).))))).). (-30.24 = -30.64 +   0.40)

alignment

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secondary structure

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Window 9

Location 15,744,870 – 15,744,990
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -27.30
Consensus MFE -23.40
Energy contribution -24.44
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.32
Structure conservation index 0.86
SVM decision value 0.02
SVM RNA-class probability 0.545670
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15744870 120 - 22224390
AUCAGCUAAUUGUUCCACACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....(((......((((((((....)))))))).....((((.((((((....)))))).)))).)))..((((((((..(((....))).((((.....))))......)))))))).. ( -28.60)
>DroSec_CAF1 3879 119 - 1
AUCAGCUAAUUGUUCCGCACACAUUUGUGGUGGGUAUUUACGUGAAUGAAAAAUGAUUUUCGUACAGCACGUCUC-UGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....(((......(((((.(((....))))))))....((((.((((........)))).)))).)))..(((((-(...(((....))).......(((........))).)))))).. ( -24.20)
>DroSim_CAF1 3889 120 - 1
AUCAGCUAAUUGUUCCACACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....(((......((((((((....)))))))).....((((.((((((....)))))).)))).)))..((((((((..(((....))).((((.....))))......)))))))).. ( -28.60)
>DroEre_CAF1 3721 119 - 1
AUCAGCUAAUUGUUCAGCACACAUUUGUGUGGGCAAUUUACGUGAAUGAA-AAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGCAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....((((((((((((.((((....)))))))))))))((((.((((((.-..)))))).)))).)))..((((((((((......)))........(((........)))))))))).. ( -26.90)
>DroYak_CAF1 3817 120 - 1
AUCAGCUAAUUGUUCCGCACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....(((......((((((((....)))))))).....((((.((((((....)))))).)))).)))..((((((((..(((....))).((((.....))))......)))))))).. ( -28.20)
>consensus
AUCAGCUAAUUGUUCCGCACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUCUUCUUCGGGAAUAUAACGAAUAUAAAAUUUCAGGGGAUUA
....(((......((((((((....)))))))).....((((.((((((....)))))).)))).)))..((((((((..(((....))).((((.....))))......)))))))).. (-23.40 = -24.44 +   1.04)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,744,910 – 15,745,026
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.19
Mean single sequence MFE -31.46
Consensus MFE -24.56
Energy contribution -24.92
Covariance contribution 0.36
Combinations/Pair 1.09
Mean z-score -2.32
Structure conservation index 0.78
SVM decision value 1.51
SVM RNA-class probability 0.960192
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15744910 116 - 22224390
GAUUCCAA---U-UAGCAAGUGGCGGGCGAGAACAAUUGAAUCAGCUAAUUGUUCCACACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUC
........---.-..(((((.((((.(((.(((((((((.......)))))))))).(((((....))))).......((((.((((((....)))))).))))..)).)))).))))). ( -33.60)
>DroSec_CAF1 3919 115 - 1
GAUUCCAA---U-UGGCAAGUGGCGGGCGAGAACAAUUGAAUCAGCUAAUUGUUCCGCACACAUUUGUGGUGGGUAUUUACGUGAAUGAAAAAUGAUUUUCGUACAGCACGUCUC-UGUC
...((((.---.-..(((((((....(((.(((((((((.......))))))))))))...)))))))..)))).....(((((.(((((((....)))))))....)))))...-.... ( -32.80)
>DroSim_CAF1 3929 116 - 1
GAUUCCAA---U-UGGCAAGUGGCGGGCGAGAACAAUUGAAUCAGCUAAUUGUUCCACACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUC
........---.-.((((((.((((.(((.(((((((((.......)))))))))).(((((....))))).......((((.((((((....)))))).))))..)).)))).)))))) ( -35.20)
>DroEre_CAF1 3761 117 - 1
AAUUCCAAGAAUUUCG--AUUUCAAGACAAGAACAAUUGAAUCAGCUAAUUGUUCAGCACACAUUUGUGUGGGCAAUUUACGUGAAUGAA-AAUUAUUUUCGUACAGCACGUCUCUUGUC
........(((.....--..)))..(((((((...............(((((((((.((((....))))))))))))).(((((.(((((-(.....))))))....))))).))))))) ( -26.80)
>DroYak_CAF1 3857 113 - 1
AAUUCCAA---UUUAG----CAAACGACAAGAACAAUUGAAUCAGCUAAUUGUUCCGCACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUC
........---.....----.....((((((((((((((.......)))))))((((((((....))))))))......(((((.(((((((....)))))))....))))).))))))) ( -28.90)
>consensus
GAUUCCAA___U_UAGCAAGUGGCGGGCGAGAACAAUUGAAUCAGCUAAUUGUUCCGCACACAUUUGUGUGGGUAAUUUACGUGAAUGAAAAAUUAUUUUCGUACAGCACGUCUCUUGUC
.........................((((((((((((((.......)))))))((((((((....))))))))......(((((.(((((((....)))))))....))))).))))))) (-24.56 = -24.92 +   0.36)

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 12:06:25 2006