Locus 5837

Sequence ID 2R_DroMel_CAF1
Location 18,491,882 – 18,492,034
Length 152
Max. P 0.719203
window9355 window9356 window9357

overview

Window 5

Location 18,491,882 – 18,491,995
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.30
Mean single sequence MFE -30.62
Consensus MFE -17.03
Energy contribution -19.09
Covariance contribution 2.06
Combinations/Pair 1.20
Mean z-score -2.14
Structure conservation index 0.56
SVM decision value 0.40
SVM RNA-class probability 0.719203
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18491882 113 + 20766785
--AACUGAUUUUUAGAGCUGCAUGUGCGACUCUUUUUAUAGGAAAAGUUAAGUCGUUUUC-AAGGCUAGAGCUCCUUAUCUGCAAAGUCAUACCUCAAAUUGAGUGAUGGCUUUAC----
--....(((.....(((((((.((.((((((((((((....))))))...))))))...)-)..))...)))))...)))...((((((((..(((.....)))..))))))))..---- ( -29.20)
>DroSec_CAF1 10489 117 + 1
--AACUGAGUUUUGGAGCUGCAUGUGCGACUCUUUUUAUAGGAAGAGUUAAGUUGUCUUC-AAGGCUAGAACUCCUUAUCUGCAAAGUCAUACCUCAAAUUGAAUGAUGGCUUUACUUCA
--..((.(((((((((((.((....))(((((((((....))))))))).....).))))-))))))))..............((((((((...((.....))...))))))))...... ( -28.50)
>DroEre_CAF1 15955 119 + 1
GGAACUGC-CUUUGGAGCUGCAUGUGCGACUCUUUUUAUGGGAAAUGUUAUUCAAUUUUUGGUGUGGAAUAUUUCUUAUCUGCAAAGCCAUACCUCAAAUUGAGUGAUAGCUUUGCUUCA
((.....)-)..((((((.((........(((.......)))...(((((((((((((..(((((((....((((......).))).)))))))..)))))))))))))))...)))))) ( -33.90)
>DroYak_CAF1 17765 116 + 1
--AACUGC-UUUUGCAGCGGCAAGUGCAACUCUUUUUAUAGGAAAUGUUACUCCGCUUUC-CUAACUAGCACUUCUUAUCUGCAAAGUCAUAGCUCACAUUGAGUGAUGGCUUUACUUCA
--......-....((((.((.((((((((......)).(((((((.((......))))))-)))....))))))))...))))((((((((.((((.....)))).))))))))...... ( -30.90)
>consensus
__AACUGA_UUUUGGAGCUGCAUGUGCGACUCUUUUUAUAGGAAAAGUUAAGCCGUUUUC_AAGGCUAGAACUCCUUAUCUGCAAAGUCAUACCUCAAAUUGAGUGAUGGCUUUACUUCA
.............((((..((....))..))))....(((((((((((((................)))))))))))))....((((((((..(((.....)))..))))))))...... (-17.03 = -19.09 +   2.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,491,882 – 18,491,995
Length 113
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 79.30
Mean single sequence MFE -26.74
Consensus MFE -17.01
Energy contribution -16.70
Covariance contribution -0.31
Combinations/Pair 1.17
Mean z-score -1.81
Structure conservation index 0.64
SVM decision value 0.32
SVM RNA-class probability 0.689040
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18491882 113 - 20766785
----GUAAAGCCAUCACUCAAUUUGAGGUAUGACUUUGCAGAUAAGGAGCUCUAGCCUU-GAAAACGACUUAACUUUUCCUAUAAAAAGAGUCGCACAUGCAGCUCUAAAAAUCAGUU--
----((((((.(((..(((.....)))..))).)))))).(((..((((((...((..(-(....(((((...(((((......))))))))))..)).))))))))....)))....-- ( -26.60)
>DroSec_CAF1 10489 117 - 1
UGAAGUAAAGCCAUCAUUCAAUUUGAGGUAUGACUUUGCAGAUAAGGAGUUCUAGCCUU-GAAGACAACUUAACUCUUCCUAUAAAAAGAGUCGCACAUGCAGCUCCAAAACUCAGUU--
(((.((((((.(((..(((.....)))..))).))))))......((((((........-............((((((........)))))).((....)))))))).....)))...-- ( -23.60)
>DroEre_CAF1 15955 119 - 1
UGAAGCAAAGCUAUCACUCAAUUUGAGGUAUGGCUUUGCAGAUAAGAAAUAUUCCACACCAAAAAUUGAAUAACAUUUCCCAUAAAAAGAGUCGCACAUGCAGCUCCAAAG-GCAGUUCC
....((((((((((..(((.....)))..))))))))))......(((.....((............(((......))).........((((.((....)).))))....)-)...))). ( -27.10)
>DroYak_CAF1 17765 116 - 1
UGAAGUAAAGCCAUCACUCAAUGUGAGCUAUGACUUUGCAGAUAAGAAGUGCUAGUUAG-GAAAGCGGAGUAACAUUUCCUAUAAAAAGAGUUGCACUUGCCGCUGCAAAA-GCAGUU--
....((((((.(((..(((.....)))..))).)))))).......((((((....(((-((((..(......).)))))))...........))))))...(((((....-))))).-- ( -29.66)
>consensus
UGAAGUAAAGCCAUCACUCAAUUUGAGGUAUGACUUUGCAGAUAAGAAGUUCUAGCCAU_GAAAACGAAUUAACAUUUCCUAUAAAAAGAGUCGCACAUGCAGCUCCAAAA_GCAGUU__
....((((((.(((..(((.....)))..))).)))))).................................................((((.((....)).)))).............. (-17.01 = -16.70 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,491,920 – 18,492,034
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.59
Mean single sequence MFE -27.02
Consensus MFE -17.69
Energy contribution -17.82
Covariance contribution 0.12
Combinations/Pair 1.29
Mean z-score -1.67
Structure conservation index 0.65
SVM decision value 0.07
SVM RNA-class probability 0.570143
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18491920 114 - 20766785
AGUAAUACGCAAUACUUCCUAUUUUGAUAGAGCUUCGAA-----GUAAAGCCAUCACUCAAUUUGAGGUAUGACUUUGCAGAUAAGGAGCUCUAGCCUU-GAAAACGACUUAACUUUUCC
.....................(((..((((((((((...-----((((((.(((..(((.....)))..))).))))))......)))))))))...).-.)))................ ( -24.60)
>DroSec_CAF1 10527 119 - 1
AGUAAUACGCAAUACUUCCUGUUUUGAUAGAGCUUCGAAGUGAAGUAAAGCCAUCAUUCAAUUUGAGGUAUGACUUUGCAGAUAAGGAGUUCUAGCCUU-GAAGACAACUUAACUCUUCC
.........(((.((.....)).))).(((((((((...(..((((...(((.(((.......))))))...))))..)......))))))))).....-(((((.........))))). ( -26.00)
>DroEre_CAF1 15994 120 - 1
AGUAAUAGGCAAUACUUCCUAUUUUGAUAGACCUUCGAAGUGAAGCAAAGCUAUCACUCAAUUUGAGGUAUGGCUUUGCAGAUAAGAAAUAUUCCACACCAAAAAUUGAAUAACAUUUCC
.......((.((((.(((.((((((((.......))))))))..((((((((((..(((.....)))..))))))))))......))).))))))......................... ( -28.50)
>DroYak_CAF1 17802 119 - 1
AGUAAUACGCAACACUUCCUACUUUGAUAGAGCUUCAAAGUGAAGUAAAGCCAUCACUCAAUGUGAGCUAUGACUUUGCAGAUAAGAAGUGCUAGUUAG-GAAAGCGGAGUAACAUUUCC
.((.((.(((..((((((.((((((((.......))))))))..((((((.(((..(((.....)))..))).))))))......))))))((....))-....)))..)).))...... ( -29.00)
>consensus
AGUAAUACGCAAUACUUCCUAUUUUGAUAGAGCUUCGAAGUGAAGUAAAGCCAUCACUCAAUUUGAGGUAUGACUUUGCAGAUAAGAAGUUCUAGCCAU_GAAAACGAAUUAACAUUUCC
...........................(((((((((........((((((.(((..(((.....)))..))).))))))......))))))))).......................... (-17.69 = -17.82 +   0.12)

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 11:55:48 2006