Locus 3240

Sequence ID 2L_DroMel_CAF1
Location 9,316,663 – 9,316,756
Length 93
Max. P 0.628045
window5148 window5149

overview

Window 8

Location 9,316,663 – 9,316,756
Length 93
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 85.20
Mean single sequence MFE -17.93
Consensus MFE -14.82
Energy contribution -15.37
Covariance contribution 0.54
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.83
SVM decision value 0.19
SVM RNA-class probability 0.628045
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9316663 93 + 22407834
--------CCACAUUUCCCCG---------CUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGUG
--------...........((---------(((..(((((.....((((.....)))).........((((((............)))))).)))))........))))) ( -17.80)
>DroVir_CAF1 217247 86 + 1
---AACUCACCCAGUUACC------------------C-AGUUUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCU--CGACUACAAUGAACG
---...(((...((((...------------------.-(((...((((.....))))...)))...((((((............))))))..--.))))....)))... ( -15.90)
>DroSec_CAF1 146022 93 + 1
--------CCCCAUUUCCCCG---------CUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGUG
--------...........((---------(((..(((((.....((((.....)))).........((((((............)))))).)))))........))))) ( -17.80)
>DroSim_CAF1 149312 93 + 1
--------CCCCAUUUCCCCG---------CUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGUG
--------...........((---------(((..(((((.....((((.....)))).........((((((............)))))).)))))........))))) ( -17.80)
>DroEre_CAF1 158435 110 + 1
CCCUGUUUCCCCAUUUCCCCGCUUUUCCCGCUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGCG
...................(((((...........(((((.....((((.....)))).........((((((............)))))).)))))........))))) ( -20.51)
>DroYak_CAF1 155234 101 + 1
CCCCAUUUCCCCAUUUCCCCG---------CUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGUG
...................((---------(((..(((((.....((((.....)))).........((((((............)))))).)))))........))))) ( -17.80)
>consensus
________CCCCAUUUCCCCG_________CUUUCCGCAACUCUUCACACCAAAUGUGUUUACUUCUGCGCCAUUUAUCUUGCUUUGGCGCCUUGCGACUACAAUGAGUG
...................................(((((.....((((.....)))).........((((((............)))))).)))))............. (-14.82 = -15.37 +   0.54)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,316,663 – 9,316,756
Length 93
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 85.20
Mean single sequence MFE -24.82
Consensus MFE -19.25
Energy contribution -19.78
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -1.74
Structure conservation index 0.78
SVM decision value -0.05
SVM RNA-class probability 0.510171
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9316663 93 - 22407834
CACUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAG---------CGGGGAAAUGUGG--------
(((((.((((..((((((.((((((............)))))).........(((((...))))).....))))))...)---------))).))...))).-------- ( -24.30)
>DroVir_CAF1 217247 86 - 1
CGUUCAUUGUAGUCG--AGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAAACU-G------------------GGUAACUGGGUGAGUU---
((..((..((..((.--((((((((............)))))).........(((((...)))))....))-.------------------))..))))..))....--- ( -20.20)
>DroSec_CAF1 146022 93 - 1
CACUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAG---------CGGGGAAAUGGGG--------
..((((((....((((...((((((............))))))....((((.(((((...))))).....)))).....)---------)))...)))))).-------- ( -25.30)
>DroSim_CAF1 149312 93 - 1
CACUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAG---------CGGGGAAAUGGGG--------
..((((((....((((...((((((............))))))....((((.(((((...))))).....)))).....)---------)))...)))))).-------- ( -25.30)
>DroEre_CAF1 158435 110 - 1
CGCUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAGCGGGAAAAGCGGGGAAAUGGGGAAACAGGG
((((..((((..((((((.((((((............)))))).........(((((...))))).....))))))...))))....)))).........(....).... ( -28.50)
>DroYak_CAF1 155234 101 - 1
CACUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAG---------CGGGGAAAUGGGGAAAUGGGG
..((((((....((((...((((((............))))))....((((.(((((...))))).....)))).....)---------)))...))))))......... ( -25.30)
>consensus
CACUCAUUGUAGUCGCAAGGCGCCAAAGCAAGAUAAAUGGCGCAGAAGUAAACACAUUUGGUGUGAAGAGUUGCGGAAAG_________CGGGGAAAUGGGG________
..((((((...(((....)))((((............))))((((......((((.....))))......)))).....................))))))......... (-19.25 = -19.78 +   0.53)

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 10:47:47 2006