Locus 5718

Sequence ID 3R_DroMel_CAF1
Location 14,936,710 – 14,936,856
Length 146
Max. P 0.619135
window9356 window9357

overview

Window 6

Location 14,936,710 – 14,936,816
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.08
Mean single sequence MFE -27.50
Consensus MFE -20.38
Energy contribution -22.18
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.74
SVM decision value 0.17
SVM RNA-class probability 0.619135
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14936710 106 + 27905053
UUCAUCA--------CUUCAUACCGUCAUCUCC-----UCAUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAUCCAGUAGUUGUCGUCGCAGCGU-UGAAUGACAAUUUGCAAAUGGCUC
.......--------.........(((((....-----.....((((.((((.((....)))))).))))......(((((((((((((......-)).))))))).))))..))))).. ( -28.20)
>DroSec_CAF1 72420 111 + 1
UUCAUCA--------CUUCAUAACGUCAUCUCCUCCUCUCAUCGGCGUCAUCUGCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGU-UGAAUGACAAUUUGCAAAUGGCUC
.......--------............................((((.(((((.(....)))))).)))).(((((..(((((((((..(.....-.).)))))))))......))))). ( -28.60)
>DroSim_CAF1 65211 112 + 1
UUCAUCA--------CUUCAUACCGUCAUCUCCUCCUCUCAUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGUUUGAAUGACAAUUUGCAAAUGGCUC
.......--------............................((((.((((.((....)))))).)))).(((((..(((((((((.(........).)))))))))......))))). ( -28.80)
>DroEre_CAF1 63085 103 + 1
UUCAUCU--------CUUCAUGCCAUCAUCUCC-----UCUUUGGCGUCAUCAUCCACGGCGAUGUCGCCACGCCAGUAGUUG---UCCCAACGA-UGAAUGACAAUUUGCAAAUGGCUC
.......--------......(((((.....((-----.....)).(((((((((...((((....)))).........((((---...))))))-)).))))).........))))).. ( -26.10)
>DroYak_CAF1 69932 111 + 1
UUCAUCACUUUAUCACUUCAUACCGUCACCUCC-----UCUUUGGCGUCAUCGUCCACGGAGAUGUCGCCACGCCAGUAGUUG---UCCCAACGA-UGAAUGACAAUUUGCAAAUGGCUC
.................................-----....(((((.((((.((....)))))).))))).((((..(((((---((.......-.....)))))))......)))).. ( -25.80)
>consensus
UUCAUCA________CUUCAUACCGUCAUCUCC_____UCAUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGU_UGAAUGACAAUUUGCAAAUGGCUC
...........................................((((.((((.((....)))))).))))..((((..(((((((((..((.....)).)))))))))......)))).. (-20.38 = -22.18 +   1.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 14,936,737 – 14,936,856
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.69
Mean single sequence MFE -38.82
Consensus MFE -28.88
Energy contribution -30.32
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.74
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14936737 119 + 27905053
AUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAUCCAGUAGUUGUCGUCGCAGCGU-UGAAUGACAAUUUGCAAAUGGCUCUGGGUGCAUAAUUUAUGCAGAUGCAACUGCAGCAGCUCCG
...((((.((((.((....)))))).))))......(((((((.((((((((.((-((.....)))))))).............((((((...))))))))))))))))).......... ( -39.20)
>DroSec_CAF1 72452 119 + 1
AUCGGCGUCAUCUGCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGU-UGAAUGACAAUUUGCAAAUGGCUCUGGGUGCAUAAUUUAUGCAGAUGCAACUGCAGCAGCUACG
...((((.(((((.(....)))))).))))......((((((((.(((((((.((-((..((.(.....)))..)))).))))).))........(((((......))))))))))))). ( -42.70)
>DroSim_CAF1 65243 120 + 1
AUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGUUUGAAUGACAAUUUGCAAAUGGCUCUGGGUGCAUAAUUUAUGCAGAUGCAACUGCAGCAGCUACG
...((((.((((.((....)))))).))))......((((((((.(((((((((((((((.......)).))))))...))))).))........(((((......))))))))))))). ( -43.10)
>DroEre_CAF1 63112 116 + 1
UUUGGCGUCAUCAUCCACGGCGAUGUCGCCACGCCAGUAGUUG---UCCCAACGA-UGAAUGACAAUUUGCAAAUGGCUCUGGGUGCAUAAUUUAUGCAGAUGCAACUGCAGCAGCUUCG
...((((((((((((...((((....)))).........((((---...))))))-)).)))))...(((((....((((((.(((.......))).)))).))...)))))..)))... ( -34.20)
>DroYak_CAF1 69967 116 + 1
UUUGGCGUCAUCGUCCACGGAGAUGUCGCCACGCCAGUAGUUG---UCCCAACGA-UGAAUGACAAUUUGCAAAUGGCUCUAGGUGCAUAAUUUAUGUAGAUGCAACUGCAGCAGCACAG
..(((((.((((.((....)))))).))))).((..(((((((---(..(.((.(-(((((.......((((..((....))..))))..)))))))).)..)))))))).))....... ( -34.90)
>consensus
AUCGGCGUCAUCAUCCACGGAGAUGUCGCCAAGCCAGUAGUUGUCGUCCCAGCGU_UGAAUGACAAUUUGCAAAUGGCUCUGGGUGCAUAAUUUAUGCAGAUGCAACUGCAGCAGCUACG
...((((.((((.((....)))))).))))......((((((((...(((((.....((((....))))((.....)).)))))((((((...))))))...)))))))).......... (-28.88 = -30.32 +   1.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:44 2006