Locus 1485

Sequence ID 3L_DroMel_CAF1
Location 4,326,740 – 4,326,934
Length 194
Max. P 0.717212
window2312 window2313 window2314

overview

Window 2

Location 4,326,740 – 4,326,856
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 93.11
Mean single sequence MFE -36.00
Consensus MFE -29.86
Energy contribution -30.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.83
SVM decision value 0.22
SVM RNA-class probability 0.638836
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4326740 116 - 23771897
AGACUUACGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCACUGGGGGCAAUGUCAAUUUGCGUCGGCCAAGGGAACAGUCAGUCAUCAGUGGACAUCAUCGUCAUCCACUA
.((((.(((((..((((((((.(((.(((.(((.....))))))..))).))).)))))....))))).(((...(....).)))))))...((((((...........)))))). ( -37.60)
>DroSec_CAF1 13397 112 - 1
AGACAUAUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCACUGGGGGCAAUGUCAAUUUGCGUCGGCCAAGGGAACAG----UCAUCAGUGGACAUCAUCGUCAUCCACUA
.(((..(((((..((((((((.(((.(((.(((.....))))))..))).))).)))))....))))).......(....).)----))...((((((...........)))))). ( -34.30)
>DroSim_CAF1 11991 112 - 1
AGACAUGUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCACUGGGGGCAAUGUCAAUUUGCGUCGGCCAAGGGAACAG----UCAUCAGUGGACAUCAUCGUCAUCCACUA
.(((.(((.....((((((((.(((.(((.(((.....))))))..))).))).)))))..((((.(....)))))...))))----))...((((((...........)))))). ( -34.40)
>DroEre_CAF1 13258 108 - 1
AGACAU----AUUGACGUGCCGCCACGAGCUGCAAGUUGCACUCACUGGGGGCAAUGUCAAUUUGCCUCGGCCAAGGGAACAG----UCAUCACUGGACACCAUCGUCAUCCAAUA
.(((..----(((((((((((.(((.(((.(((.....))))))..))).))).))))))))..((....))...(((..(((----(....))))..).))...)))........ ( -36.10)
>DroYak_CAF1 12388 108 - 1
AGACAU----AUUGACGUGCCGCCACGAGCUGCAUGUUGCACUCACUGGGGGCAAUGUCAAUUUGCGUCGGCCAAGGGAACAC----UCAUCAGUGGACAUCAUCGUCAUCCACUA
.(((..----(((((((((((.(((.(((.(((.....))))))..))).))).))))))))....))).....(((((.(((----(....))))(((......))).))).)). ( -37.60)
>consensus
AGACAU__GUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCACUGGGGGCAAUGUCAAUUUGCGUCGGCCAAGGGAACAG____UCAUCAGUGGACAUCAUCGUCAUCCACUA
.(((.........((((((((.(((.(((.(((.....))))))..))).))).))))).......(((.((.....((........))....)).)))......)))........ (-29.86 = -30.26 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,326,780 – 4,326,896
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.19
Mean single sequence MFE -39.90
Consensus MFE -29.14
Energy contribution -30.75
Covariance contribution 1.61
Combinations/Pair 1.07
Mean z-score -1.28
Structure conservation index 0.73
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4326780 116 - 23771897
CGAACUGAAGGCGGUAAAAGGGGGCGUGGCGGAAACCAAUAGACUUACGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCAC-UGGGGGCAAUGUCAAUUUGCGUCGGCC---AAG
...((((....)))).......(((.(((((.(((.......((....))...((((((((.(((.(((.(((.....))))))..-))).))).)))))..))).))))))))---... ( -36.50)
>DroSec_CAF1 13433 116 - 1
CAAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUAUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCAC-UGGGGGCAAUGUCAAUUUGCGUCGGCC---AAG
....((((.....)))).....(((.((((....))))...(((.((...((.((((((((.(((.(((.(((.....))))))..-))).))).))))).)).)).))).)))---... ( -40.00)
>DroSim_CAF1 12027 116 - 1
CGAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUGUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCAC-UGGGGGCAAUGUCAAUUUGCGUCGGCC---AAG
....((((.....)))).....(((.((((....))))...(((..(((.((.((((((((.(((.(((.(((.....))))))..-))).))).))))).)).)))))).)))---... ( -40.50)
>DroEre_CAF1 13294 112 - 1
UGCAGGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACAU----AUUGACGUGCCGCCACGAGCUGCAAGUUGCACUCAC-UGGGGGCAAUGUCAAUUUGCCUCGGCC---AAG
.((.......))(((.....((((((((((....))))........----(((((((((((.(((.(((.(((.....))))))..-))).))).)))))))).)))))).)))---... ( -47.20)
>DroYak_CAF1 12424 112 - 1
UGCAUGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACAU----AUUGACGUGCCGCCACGAGCUGCAUGUUGCACUCAC-UGGGGGCAAUGUCAAUUUGCGUCGGCC---AAG
....(((..((((.............((((....)))).....((.----(((((((((((.(((.(((.(((.....))))))..-))).))).)))))))).))))))..))---).. ( -45.40)
>DroAna_CAF1 13081 101 - 1
---UCUGGGGGCAUCGAAAAGGGGCGUGGCGGAAGCCAAUAGACAUAC----------------AUUUGUUGCAUGUUGCAGUCACCCGGGGGCAAUGUCGAUUUGAGUCAGCUCUUGAG
---.((((((((.((.....)).((.((((....))))...(((((.(----------------(.....)).))))))).))).)))))((((..((.(.......).))))))..... ( -29.80)
>consensus
CGAAUUGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACAUA___AUAGACGUGCCGCCACGAGCUGCAUGUUGCACUCAC_UGGGGGCAAUGUCAAUUUGCGUCGGCC___AAG
.........(((.(...(((..((((((((....)))....................((((.(((.(((.(((.....))))))...))).)))))))))..)))....).)))...... (-29.14 = -30.75 +   1.61)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,326,816 – 4,326,934
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.39
Mean single sequence MFE -30.26
Consensus MFE -20.69
Energy contribution -21.09
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.68
SVM decision value 0.39
SVM RNA-class probability 0.717212
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4326816 118 - 23771897
CAUGCUAAACUGAAAAAACA--GAAGAAAAAAAAUUCCAUCGAACUGAAGGCGGUAAAAGGGGGCGUGGCGGAAACCAAUAGACUUACGUAUAGACGUGCCGCCACGAGCUGCAUGUUGC
(((((....(((......))--)...........((((.....((((....)))).....))))((((((((.............(((((....)))))))))))))....))))).... ( -29.41)
>DroSec_CAF1 13469 116 - 1
CAUGCUAAACUGAAAAAA----ACAGAAAAAAAAGUCCAUCAAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUAUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGC
(((((....(((......----.))).......((..(......((((.....))))..((.(((.((((....))))........((((....))))))).))..)..))))))).... ( -29.70)
>DroSim_CAF1 12063 105 - 1
CAUGCUAAACUGAAAA---------------AAAUUCCAUCGAAUUGCAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAUGUGUAUAGACGUGCCGCCACGAGCUGCAUGUUGC
(((((...((((....---------------.(((((....))))).....))))....((.(((.((((....))))......((((......))))))).)).......))))).... ( -32.10)
>DroEre_CAF1 13330 112 - 1
CAUGCUAAACUAAAAAA----AAACAGAAAAAAAUACCAUUGCAGGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACAU----AUUGACGUGCCGCCACGAGCUGCAAGUUGC
.................----..................((((((....(((((((..((...((.((((....))))...).)..----.))....))))))).....))))))..... ( -29.20)
>DroYak_CAF1 12460 116 - 1
CAUGCUAAACUAAUAAAACGAAAAAAAAAAAAAAUAACAUUGCAUGGAAGGCGGUAAAAAGGGGCGUGGCGGAAGCCAAUAGACAU----AUUGACGUGCCGCCACGAGCUGCAUGUUGC
(((((.................................(((((.......))))).....((..((((((((..(.(((((....)----)))).)...))))))))..))))))).... ( -30.90)
>consensus
CAUGCUAAACUGAAAAAA____AAAAAAAAAAAAUUCCAUCGAAUUGAAGGCGGUAAAAGGGGGCGUGGCGGAAGCCAAUAGACAU__GUAUAGACGUGCCGCCACGAGCUGCAUGUUGC
(((((................................(........)..(((((((..........((((....))))...................))))))).......))))).... (-20.69 = -21.09 +   0.40)

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 10:08:54 2006