Locus 1435

Sequence ID 3R_DroMel_CAF1
Location 4,148,659 – 4,148,774
Length 115
Max. P 0.992262
window2392 window2393 window2394

overview

Window 2

Location 4,148,659 – 4,148,755
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 62.24
Mean single sequence MFE -22.88
Consensus MFE -15.36
Energy contribution -16.03
Covariance contribution 0.67
Combinations/Pair 1.32
Mean z-score -1.74
Structure conservation index 0.67
SVM decision value 1.19
SVM RNA-class probability 0.927831
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4148659 96 + 27905053
CAUACAAAA------------CCAUUACAU-U--------UUAUUGUAAACAAAAUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCC
.........------------...(((((.-.--------....))))).....(((---.....)))((((((((((((((...((((((...)))))).....))).))))))))))) ( -27.70)
>DroSec_CAF1 9618 96 + 1
CUUACAGAA------------CUAUUACAU-U--------UUAUUGUUAACAAACUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCC
.........------------.........-.--------.................---........((((((((((((((...((((((...)))))).....))).))))))))))) ( -24.80)
>DroEre_CAF1 9782 104 + 1
GCCACAGAAUAAAUGUAAAAAGUAUU-----A--------CUAUUGUUAAUGCCAUC---UUUUAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCC
(((....(((((..((((......))-----)--------)..)))))...((((((---.....)))))).((((((((((...((((((...)))))).....))).)))))))))). ( -28.50)
>DroWil_CAF1 18553 99 + 1
C---CAGAA------------GUUUUCCAUUCAAGUCCCUUAAUUGUC----CUUUC--UUUGCAGAUGGCCAAACUUGCUUUUUCAGUCGUCACAAUUGUCGAUCAGAUGAAUCUAGCC
.---...((------------((((.(((((((((.............----.....--))))..)))))..))))))(((..((((((((.((....)).))))....))))...))). ( -14.27)
>DroYak_CAF1 10072 108 + 1
UCCACAGAAUAUUUAUAAAAAAUAAUCAAU-U--------UUCUUGUCAAUGAAAUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCC
......((.(((((.....))))).))...-.--------.....(((..((((...---.)))))))((((((((((((((...((((((...)))))).....))).))))))))))) ( -27.50)
>DroAna_CAF1 11088 100 + 1
-----UUAACACUUUU-------AGUUCAUUU--------GUGUUCUACAUUAUUUUAUUCCACAAAUGGUCAAGUUUGCCUUUUCAGUCUUUACACUCGUUCAGGGAAUGGACCUAAUG
-----..(((((....-------.........--------)))))...(((((.((((((((...((((((.(((.(((......))).)))...)).))))...))))))))..))))) ( -14.52)
>consensus
C__ACAGAA____________CUAUUACAU_U________UUAUUGUAAAUAAAAUC___UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCC
....................................................................((((((((((((((...(((((.....))))).....))).))))))))))) (-15.36 = -16.03 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,148,678 – 4,148,774
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 68.00
Mean single sequence MFE -28.07
Consensus MFE -17.21
Energy contribution -17.88
Covariance contribution 0.67
Combinations/Pair 1.30
Mean z-score -2.32
Structure conservation index 0.61
SVM decision value 2.32
SVM RNA-class probability 0.992262
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4148678 96 + 27905053
UUAUUGUAAACAAAAUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCCGAGAAAUUG----AGAAG----GGAGU-------------
...............((---((((....((((((((((((((...((((((...)))))).....))).)))))))))))((....)).----.))))----))...------------- ( -31.20)
>DroSec_CAF1 9637 96 + 1
UUAUUGUUAACAAACUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCCGAGAAAUUG----AGAAG----GGAGU-------------
.............((((---((((....((((((((((((((...((((((...)))))).....))).)))))))))))((....)).----.))).----)))))------------- ( -31.80)
>DroEre_CAF1 9809 96 + 1
CUAUUGUUAAUGCCAUC---UUUUAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCCGAGAAAUUG----AGAAG----GGAGU-------------
..........(.((.((---((.....(((((((((((((((...((((((...)))))).....))).)))))))))))).......)----))).)----).)..------------- ( -31.40)
>DroWil_CAF1 18578 110 + 1
UAAUUGUC----CUUUC--UUUGCAGAUGGCCAAACUUGCUUUUUCAGUCGUCACAAUUGUCGAUCAGAUGAAUCUAGCCGACAAAAUGUCUUAAAAUGAUUUUAGCGAGAAUC----AA
...(((.(----(..((--(....))).)).))).((((((...(((......(((.((((((...(((....)))...))))))..))).......)))....))))))....----.. ( -20.52)
>DroYak_CAF1 10103 96 + 1
UUCUUGUCAAUGAAAUC---UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCCGAGAAAUUG----AGAAG----GGAGU-------------
(((((.(((((...(((---.....)))((((((((((((((...((((((...)))))).....))).))))))))))).....))))----).)))----))...------------- ( -34.70)
>DroAna_CAF1 11108 112 + 1
GUGUUCUACAUUAUUUUAUUCCACAAAUGGUCAAGUUUGCCUUUUCAGUCUUUACACUCGUUCAGGGAAUGGACCUAAUGGAAAAAUUU----AAAAA----CUAGAGAGCUCCCGAAAA
..(((((...(((..((.(((((.....((((....((.(((...((((......))).)...))).))..))))...))))).))..)----))...----....)))))......... ( -18.80)
>consensus
UUAUUGUAAAUAAAAUC___UUUCAGAUGGCCAAGUUCGCUUUCUCAGUGGUGACCAUUGUAAAUGAGAUGGACUUGGCCGAGAAAUUG____AGAAG____GGAGU_____________
...........................(((((((((((((((...(((((.....))))).....))).))))))))))))....................................... (-17.21 = -17.88 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,148,678 – 4,148,774
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 68.00
Mean single sequence MFE -20.25
Consensus MFE -11.76
Energy contribution -11.32
Covariance contribution -0.44
Combinations/Pair 1.44
Mean z-score -1.34
Structure conservation index 0.58
SVM decision value 0.42
SVM RNA-class probability 0.730749
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4148678 96 - 27905053
-------------ACUCC----CUUCU----CAAUUUCUCGGCCAAGUCCAUCUCAUUUACAAUGGUCACCACUGAGAAAGCGAACUUGGCCAUCUGAAA---GAUUUUGUUUACAAUAA
-------------.....----.....----...((((..((((((((...((.(.(((.((.(((...))).)).))).).))))))))))....))))---................. ( -18.10)
>DroSec_CAF1 9637 96 - 1
-------------ACUCC----CUUCU----CAAUUUCUCGGCCAAGUCCAUCUCAUUUACAAUGGUCACCACUGAGAAAGCGAACUUGGCCAUCUGAAA---GAGUUUGUUAACAAUAA
-------------.....----...((----(..((((..((((((((...((.(.(((.((.(((...))).)).))).).))))))))))....))))---))).............. ( -19.40)
>DroEre_CAF1 9809 96 - 1
-------------ACUCC----CUUCU----CAAUUUCUCGGCCAAGUCCAUCUCAUUUACAAUGGUCACCACUGAGAAAGCGAACUUGGCCAUCUAAAA---GAUGGCAUUAACAAUAG
-------------.....----....(----(..((((((((....(.((((..........)))).)....))))))))..)).....((((((.....---))))))........... ( -22.60)
>DroWil_CAF1 18578 110 - 1
UU----GAUUCUCGCUAAAAUCAUUUUAAGACAUUUUGUCGGCUAGAUUCAUCUGAUCGACAAUUGUGACGACUGAAAAAGCAAGUUUGGCCAUCUGCAAA--GAAAG----GACAAUUA
.(----((((.((((((((............(((.((((((..((((....))))..))))))..)))..(.((.....)))...))))))..(((....)--))...----)).))))) ( -20.90)
>DroYak_CAF1 10103 96 - 1
-------------ACUCC----CUUCU----CAAUUUCUCGGCCAAGUCCAUCUCAUUUACAAUGGUCACCACUGAGAAAGCGAACUUGGCCAUCUGAAA---GAUUUCAUUGACAAGAA
-------------.....----(((.(----((((.....((((((((...((.(.(((.((.(((...))).)).))).).))))))))))....(((.---...)))))))).))).. ( -21.80)
>DroAna_CAF1 11108 112 - 1
UUUUCGGGAGCUCUCUAG----UUUUU----AAAUUUUUCCAUUAGGUCCAUUCCCUGAACGAGUGUAAAGACUGAAAAGGCAAACUUGACCAUUUGUGGAAUAAAAUAAUGUAGAACAC
.....(((....)))..(----((((.----..(((.((((((..(((((((((.......)))))......((....))........))))....))))))......)))..))))).. ( -18.70)
>consensus
_____________ACUCC____CUUCU____CAAUUUCUCGGCCAAGUCCAUCUCAUUUACAAUGGUCACCACUGAGAAAGCGAACUUGGCCAUCUGAAA___GAUUUCAUUAACAAUAA
........................................((((((((...((.(.(((.((.((.....)).)).))).).))))))))))............................ (-11.76 = -11.32 +  -0.44)

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 10:10:32 2006