Locus 4425

Sequence ID X_DroMel_CAF1
Location 11,681,509 – 11,681,646
Length 137
Max. P 0.998065
window7273 window7274 window7275

overview

Window 3

Location 11,681,509 – 11,681,616
Length 107
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 75.30
Mean single sequence MFE -31.62
Consensus MFE -15.91
Energy contribution -16.92
Covariance contribution 1.00
Combinations/Pair 1.28
Mean z-score -1.94
Structure conservation index 0.50
SVM decision value 0.66
SVM RNA-class probability 0.815347
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11681509 107 - 22224390
UUGGCGAUCGU---UUU------GGUCGUUU---UGUGUGUAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAAAAUAUUUGAGCCAAGAUGGGUCAAGGUUUUCUCGAUUAG
(((((..((((---(((------((((((((---((((((((((((((..((((....))))..)))).))))))))))))))....)).))))))))))))))............... ( -35.90)
>DroPse_CAF1 7721 107 - 1
CUAGCCAUCAUCGCUUAACACAUCAUCGCUUAAAUGUAUGCAUUGGCUUGC------------CGGCCAAGUAUGCAUAAAAUAUUUGACUGGAGAUGGGUCAAGGUUGUCCCAAAUUG
....((((((..((.............))....((((((((.((((((...------------.))))))))))))))........))).)))...((((.((....)).))))..... ( -26.92)
>DroSec_CAF1 7996 107 - 1
UUGGCGAUCGU---UUG------GGCCGUUU---UGUGUGCAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAAAAUAUUUGAGCCAAGAUGGGUCAAGGUUUUCUCGAUUAG
.....(((((.---..(------((((((((---((((((.(((((((....))))))))((....))......)))))))))..((((.((.....)).)))))))))...))))).. ( -36.80)
>DroSim_CAF1 9846 107 - 1
UUGGCGAUCGU---UUU------GGCCGUUU---UGUGUGCAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAAAAUAUUUGAGCCAAGAUGGGUCAAGGUUUUCUCGAUUAG
.....(((((.---...------((((((((---((((((.(((((((....))))))))((....))......)))))))))..((((.((.....)).))))))))....))))).. ( -36.00)
>DroEre_CAF1 7353 100 - 1
CUGGUGGC--U---UUU------GGCCGUUU---UGUGUGCAUUGGCUAGU----CAGCCGGUGGGCCAAAUAUGCAUAAAAUAUUUGUGUUAAGAUGGGUCAAGGUU-GCUCGAUUGU
(.((..((--(---((.------(.((((((---((.((.((((((((...----.)))))))).))(((((((.......)))))))...)))))))).).))))).-.)).)..... ( -34.00)
>DroYak_CAF1 10623 87 - 1
CUGGCGAUCGU---UUU------GGCCGUUU---UGUAUGCAUUGGCUAGC-------------------GUAUGCAUAAAAUAUUUGAGUCAAGAUGGGUCAAGGUU-UCUCGAUUAU
.((((..((((---(((------(((((..(---..(((((((..(....)-------------------..)))))))....)..)).)))))))))))))).....-.......... ( -20.10)
>consensus
CUGGCGAUCGU___UUU______GGCCGUUU___UGUGUGCAUUGGCCAGU____CAGUCGGUGGGCCAAAUAUGCAUAAAAUAUUUGAGCCAAGAUGGGUCAAGGUUUUCUCGAUUAG
........................(((.........((((((((((((..((((....))))..)))))...)))))))......((((.((.....)).)))))))............ (-15.91 = -16.92 +   1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,681,548 – 11,681,646
Length 98
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 79.83
Mean single sequence MFE -23.45
Consensus MFE -15.53
Energy contribution -16.84
Covariance contribution 1.31
Combinations/Pair 1.05
Mean z-score -2.72
Structure conservation index 0.66
SVM decision value 2.41
SVM RNA-class probability 0.993568
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11681548 98 + 22224390
UUAUGCAUAUUUGGCCCACCGACUGGCCAACUGGCCAAUACACACAAAACGACCAAAACGAUCGCCAACCACUUGGCCAACAGAC-GAAAAUUCAGACG
..........((((((.......(((((....)))))............(((.(.....).)))..........)))))).....-............. ( -18.60)
>DroSec_CAF1 8035 88 + 1
UUAUGCAUAUUUGGCCCACCGACUGGCCAACUGGCCAAUGCACACAAAACGGCCCAAACGAUCGCCAACCACUUGGCCAACAGAC-GCA----------
...(((....((((((........)))))).(((((((((....))....(((..........)))......)))))))......-)))---------- ( -23.50)
>DroSim_CAF1 9885 83 + 1
UUAUGCAUAUUUGGCCCACCGACUGGCCAACUGGCCAAUGCACACAAAACGGCCAAAACGAUCGCCAACCACUUGGCCAACAG----------------
...(((((..((((....)))).(((((....))))))))))........((((((................)))))).....---------------- ( -23.79)
>DroEre_CAF1 7391 91 + 1
UUAUGCAUAUUUGGCCCACCGGCUG----ACUAGCCAAUGCACACAAAACGGCCAAAA--GCCACCAG-CACUUGGCCAACAGA-CAAAAGGCCGAAAG
.........(((((((....((((.----...))))..............((((((..--((.....)-)..))))))......-.....))))))).. ( -27.90)
>consensus
UUAUGCAUAUUUGGCCCACCGACUGGCCAACUGGCCAAUGCACACAAAACGGCCAAAACGAUCGCCAACCACUUGGCCAACAGA__GAA__________
...(((((..((((....)))).(((((....))))))))))........((((((................))))))..................... (-15.53 = -16.84 +   1.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,681,548 – 11,681,646
Length 98
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 79.83
Mean single sequence MFE -34.35
Consensus MFE -25.50
Energy contribution -26.00
Covariance contribution 0.50
Combinations/Pair 1.16
Mean z-score -2.85
Structure conservation index 0.74
SVM decision value 3.00
SVM RNA-class probability 0.998065
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11681548 98 - 22224390
CGUCUGAAUUUUC-GUCUGUUGGCCAAGUGGUUGGCGAUCGUUUUGGUCGUUUUGUGUGUAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAA
((.(..((....(-(..(((..(((....)))..)))..)).))..).))..(((((((((((((((..((((....))))..)))).))))))))))) ( -34.90)
>DroSec_CAF1 8035 88 - 1
----------UGC-GUCUGUUGGCCAAGUGGUUGGCGAUCGUUUGGGCCGUUUUGUGUGCAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAA
----------(((-((...((((((.(.((..((((.(.(.....(((((...((....)).))))).).).))))..)).).))))))..)))))... ( -36.00)
>DroSim_CAF1 9885 83 - 1
----------------CUGUUGGCCAAGUGGUUGGCGAUCGUUUUGGCCGUUUUGUGUGCAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAA
----------------...((((((.(.((..((((.(.....(((((((...((....)).))))))).).))))..)).).)))))).......... ( -32.20)
>DroEre_CAF1 7391 91 - 1
CUUUCGGCCUUUUG-UCUGUUGGCCAAGUG-CUGGUGGC--UUUUGGCCGUUUUGUGUGCAUUGGCUAGU----CAGCCGGUGGGCCAAAUAUGCAUAA
.....(((((.(((-.((((((((((((..-(.((((((--.....))))))....)..).)))))))).----))).))).)))))............ ( -34.30)
>consensus
__________UUC__UCUGUUGGCCAAGUGGUUGGCGAUCGUUUUGGCCGUUUUGUGUGCAUUGGCCAGUUGGCCAGUCGGUGGGCCAAAUAUGCAUAA
...................((((((.(.((((((((.(.....(((((((...((....)).))))))).).)))))))).).)))))).......... (-25.50 = -26.00 +   0.50)

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 11:24:46 2006