Locus 10332

Sequence ID 3R_DroMel_CAF1
Location 27,766,020 – 27,766,160
Length 140
Max. P 0.873712
window16445 window16446

overview

Window 5

Location 27,766,020 – 27,766,134
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.72
Mean single sequence MFE -26.78
Consensus MFE -21.16
Energy contribution -22.12
Covariance contribution 0.96
Combinations/Pair 1.06
Mean z-score -1.89
Structure conservation index 0.79
SVM decision value 0.88
SVM RNA-class probability 0.873712
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27766020 114 - 27905053
CUCGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGUAGCCGAGUCUAA----AAAAAAACAGU--ACUUAAUUUUUAAUUAGCAACAUGUAAGUUAUAACAUAACUGU
(((((..(((((...(((.(((((((.....)).)))))))).)))))..))))).....----......(((((--..........(((((.((.....)).))))).......))))) ( -24.23)
>DroSec_CAF1 80415 115 - 1
CUUGGAAACAAGAGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGAAGCCGAGUUUUA----AA-AAAGCAGUAUACUUAAUUUGUAAUUAGCAACAUGUAAGUUAUAACAUAACUGU
((((....)))).....((((((((((((((((((..((((((((((....)))))))..----..-.)))..)).(((.......)))....)))))))))..((....)).))))))) ( -31.20)
>DroSim_CAF1 80717 115 - 1
CUUGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAGCUUGAAGCCGAGUUUUA----AA-AAAGCAGUAUACUUAAUUUUUAUUUAGCAACAUGUAAGUUAUAACAUAACUGU
((((....)))).....((((((((((((((((.......(((((((....)))))))((----((-((...((....))...))))))....)))))))))..((....)).))))))) ( -30.10)
>DroEre_CAF1 86336 118 - 1
CUUGGAAACAAGGGGUUGCAGUUGGCGUGUUGCACGACUUAAAUUUAAAGGCGAAUUUAAAAUGAA-AAAACAGAGUACUUAAUUUUUAAUUUGCAACAUGUAAGUUAUAACAUAACUG-
((((....))))......((((((((((((((((....((((((((......))))))))..((((-((...((....))...))))))...))))))))))..((....)).))))))- ( -26.20)
>DroYak_CAF1 82947 115 - 1
CUUGGAAACAAUGGCUUGCAGUUGGCGUGUUGCACGACUUAAAUUUAAAGGCGAAUUUUA----AA-AAAGCAAAGUACUUAAUUUUUAAUUUGCAACAUAUAAGUUACAACAUAACUGU
.(((....)))......((((((...((((((...((((((..(((((((.....)))))----))-...(((((...............)))))......)))))).)))))))))))) ( -22.16)
>consensus
CUUGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGAAGCCGAGUUUUA____AA_AAAGCAGUAUACUUAAUUUUUAAUUAGCAACAUGUAAGUUAUAACAUAACUGU
((((....)))).....((((((((((((((((.......(((((((....)))))))..............((....)).............)))))))))..((....)).))))))) (-21.16 = -22.12 +   0.96)

alignment

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secondary structure

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dotplot

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Window 6

Location 27,766,060 – 27,766,160
Length 100
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 86.52
Mean single sequence MFE -28.42
Consensus MFE -18.02
Energy contribution -18.02
Covariance contribution -0.00
Combinations/Pair 1.19
Mean z-score -2.03
Structure conservation index 0.63
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27766060 100 - 27905053
AGCCUCAUGGUUGUUUUAGUUUAUACCUCGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGUAGCCGAGUCUAA----AAAAAAACAGU--ACU
((((....))))(((((..((((...(((((..(((((...(((.(((((((.....)).)))))))).)))))..)))))..)))----)..)))))...--... ( -27.50)
>DroSec_CAF1 80455 100 - 1
AGC-UGUUGGUUGUUUCAGUUUAUACCUUGGAAACAAGAGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGAAGCCGAGUUUUA----AA-AAAGCAGUAUACU
.((-((((((((((....((..((((((((....)))).(((.......))))))).)))))))).(((((((....)))))))..----..-..))))))..... ( -25.10)
>DroSim_CAF1 80757 100 - 1
AGC-UGUUGGUUGUUUCGGUUUAUACCUUGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAGCUUGAAGCCGAGUUUUA----AA-AAAGCAGUAUACU
.((-((((..(((.((((((((...(((((....)))))(((((.(((((((.....)).))))))))))...))))))))...))----).-..))))))..... ( -38.20)
>DroEre_CAF1 86375 104 - 1
AGC-UCUUGGUUGUUUCGGCUUAUACCUUGGAAACAAGGGGUUGCAGUUGGCGUGUUGCACGACUUAAAUUUAAAGGCGAAUUUAAAAUGAA-AAAACAGAGUACU
.((-(((..(((.(((((((.....(((((....)))))....)).((((((.....)).))))((((((((......))))))))..))))-).))))))))... ( -28.40)
>DroYak_CAF1 82987 100 - 1
AGC-UCUUCGUUGUUUCGGUUUAUACCUUGGAAACAAUGGCUUGCAGUUGGCGUGUUGCACGACUUAAAUUUAAAGGCGAAUUUUA----AA-AAAGCAAAGUACU
...-....((((((((((((....)))...)))))))))(((((((((((((.....)).)))))....(((((((.....)))))----))-...)).))))... ( -22.90)
>consensus
AGC_UCUUGGUUGUUUCGGUUUAUACCUUGGAAACAAGGGCUUGCAGUUGGCGUGUUGCACGACUUAAACUUGAAGCCGAGUUUUA____AA_AAAGCAGUAUACU
..........((((((..((.....(((((....)))))....))(((((((.....)).))))).(((((((....)))))))..........))))))...... (-18.02 = -18.02 +  -0.00)

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 13:54:16 2006