Locus 7308

Sequence ID 3R_DroMel_CAF1
Location 19,291,538 – 19,291,663
Length 125
Max. P 0.717965
window11819 window11820

overview

Window 9

Location 19,291,538 – 19,291,636
Length 98
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 72.56
Mean single sequence MFE -26.23
Consensus MFE -7.22
Energy contribution -8.20
Covariance contribution 0.98
Combinations/Pair 1.29
Mean z-score -2.17
Structure conservation index 0.28
SVM decision value 0.05
SVM RNA-class probability 0.559275
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19291538 98 + 27905053
AAGUGCGUAACAAGAAUUGAGGCAG--------UUGCGGUCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGACAGCUAGAU
.(((.((((((.............)--------)))))(((((((((.(((((((.((((.(((......))))))).))))))...).))))))))).))).... ( -32.62)
>DroGri_CAF1 100818 94 + 1
AAGUGCGUAGCAAGAAUUGAGCAAAGCGAAACUUUGCUUAUAAAAAUAAGUUUAUGAGGUUACACUGAAGGUUGCA-GCUAAAGUG-----------CAUUUAAAU
(((((((((((.......((((((((.....))))))))(((((......)))))...)))))(((...(((....-)))..))))-----------))))).... ( -21.40)
>DroSec_CAF1 87355 98 + 1
AAGUGCGUAACAAGAAUUGAGGCAG--------UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGACAGCUAGAU
.(((.((((((.............)--------)))))..(((((((.(((((((.((((.(((......))))))).))))))...).)))))))...))).... ( -27.62)
>DroSim_CAF1 89273 98 + 1
AAGUGCGUAACAAGAAUUGAGGCAG--------UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGACAGCUAGAU
.(((.((((((.............)--------)))))..(((((((.(((((((.((((.(((......))))))).))))))...).)))))))...))).... ( -27.62)
>DroEre_CAF1 88527 98 + 1
AAGUGCGUAACAAGAAUUGAGGCAG--------UUGCGGGCUAUAAUGGAUUUAUGGGGUUACCGCGAAGGCUGCCCGGUAGAUAGACGCUUAUAGACAGAUAGAU
....((((.......((((.(((((--------((((((.((((((.....)))))).....)))))...))))))))))......))))................ ( -27.12)
>DroMoj_CAF1 104792 76 + 1
AAGUGCGUAGCAAGAGCUGAGCU------------------AAAAGUUAGCUUAUGAGGUUAGCCCGAAGGCCGCA-GCUAAAUUG-----------CGUUUAAAU
.........((((.(((((.(((------------------....(((((((.....))))))).....)))..))-)))...)))-----------)........ ( -21.00)
>consensus
AAGUGCGUAACAAGAAUUGAGGCAG________UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGACAGCUAGAU
..((.....))......................................((((((.((((....((....)).)))).))))))...................... ( -7.22 =  -8.20 +   0.98)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,291,563 – 19,291,663
Length 100
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 75.23
Mean single sequence MFE -25.73
Consensus MFE -12.64
Energy contribution -11.08
Covariance contribution -1.55
Combinations/Pair 1.50
Mean z-score -1.87
Structure conservation index 0.49
SVM decision value 0.39
SVM RNA-class probability 0.717965
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19291563 100 + 27905053
UUGCGGUCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGAC--AGCUAGAUGGAUAUGUAUAUAGAUAAAUGUCUAUG
..((.(((((((((.(((((((.((((.(((......))))))).))))))...).)))))))))--.))...((((((((.(((....))).)))))))). ( -35.30)
>DroPse_CAF1 103956 90 + 1
AU------AAUAAUAAAUUUAUGGGGUUAGCACGAAGGUUGUUCGAUGAAUGGUCU---AUGCCUGGAGCU--CUGGGCACACAUAUAG-CAUAUGCUCAUA
..------...........((((((..((((....(((..((((...))))..)))---.((((..(....--)..))))........)-).))..)))))) ( -20.50)
>DroSec_CAF1 87380 100 + 1
UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGAC--AGCUAGAUGGAUAUGUAUAUAGAUAAAUGGCUAUG
....(..(((((((.(((((((.((((.(((......))))))).))))))...).))))))).)--(((((..((..(((....)))..))..)))))... ( -27.00)
>DroSim_CAF1 89298 100 + 1
UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGAC--AGCUAGAUGGAUAUGUAUAUAGAUAAAUGGCUAUG
....(..(((((((.(((((((.((((.(((......))))))).))))))...).))))))).)--(((((..((..(((....)))..))..)))))... ( -27.00)
>DroEre_CAF1 88552 100 + 1
UUGCGGGCUAUAAUGGAUUUAUGGGGUUACCGCGAAGGCUGCCCGGUAGAUAGACGCUUAUAGAC--AGAUAGAUGGAUAUGUAUAUAGAUAAAUGGCUAUG
.....((((((.....((((((.((((..((.....))..)))).)))))).......((((..(--(......))..))))...........))))))... ( -24.10)
>DroPer_CAF1 104073 90 + 1
AU------AAUAAUAAAUUUAUGGGGUUAGCACGAAGGUUGUUCUAUGAAUGGUCU---AUGCCUGGAGCU--CUGGGCACAUAUAUAG-CAUAUGCUCAUA
..------...........((((((..((((....(((..((((...))))..)))---.((((..(....--)..))))........)-).))..)))))) ( -20.50)
>consensus
UUGCGGGCUAUAAUGGAUUUAUGGGGUUAGCGCGAAGGCUGCCCGGUAGAUAGACGGUUAUAGAC__AGCUAGAUGGAUAUGUAUAUAGAUAAAUGGCUAUG
................((((((.((((....((....)).)))).))))))................................................... (-12.64 = -11.08 +  -1.55)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:41 2006