Locus 6675

Sequence ID X_DroMel_CAF1
Location 16,665,398 – 16,665,547
Length 149
Max. P 0.981874
window10898 window10899 window10900

overview

Window 8

Location 16,665,398 – 16,665,507
Length 109
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 78.76
Mean single sequence MFE -24.24
Consensus MFE -19.21
Energy contribution -19.78
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.12
Structure conservation index 0.79
SVM decision value 1.74
SVM RNA-class probability 0.975011
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16665398 109 + 22224390
AAUUUGGAAUAUAAGUAGUUCCACACACU-UCCAUUCACAAAUUGCAUCAGCAUCGGGUCGAAAAUCG-AUUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUC
((((((((((..((((.((.....)))))-)..)))).))))))((.((((((((.((((((...(((-...)))....)))))).))))))))...))............ ( -28.90)
>DroSec_CAF1 4339 85 + 1
AAUU--------------------------UCCAUUCACAAAUUGCAUCAGCAUCGGGUCGAAAAUCGGGUUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUC
....--------------------------.............(((.((((((((.((((((...(((....)))....)))))).))))))))...)))........... ( -23.10)
>DroEre_CAF1 5611 104 + 1
AAUUUUGAAUACAAUU-----CGCAUGCU-UCCAUUCACAAAUUGCACCAGCUUUGGGUCGAGGAUCG-GAUCGAGUCAUUGACCCGAUGUUGAAGAGCAAAUUAUAUUUC
......(((((.((((-----.((.(((.-..............))).((((.(((((((((.(((((-...))).)).))))))))).))))....)).)))).))))). ( -25.86)
>DroYak_CAF1 4123 105 + 1
AAUUUUGAAUACAAUU-----CGCAUGCUUUCCAUUCACAAAUUGCAUCAGCAACGGGUCGAAAAUCG-GAUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUCACAUUUC
................-----.((.(((................)))((((((.(.((((((...(((-...)))....)))))).).))))))...))............ ( -19.09)
>consensus
AAUUUUGAAUACAAUU_____CGCAUGCU_UCCAUUCACAAAUUGCAUCAGCAUCGGGUCGAAAAUCG_GAUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUC
...........................................(((.((((((((.((((((...(((....)))....)))))).))))))))...)))........... (-19.21 = -19.78 +   0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,665,437 – 16,665,547
Length 110
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -28.15
Consensus MFE -20.69
Energy contribution -20.62
Covariance contribution -0.06
Combinations/Pair 1.25
Mean z-score -2.18
Structure conservation index 0.73
SVM decision value 1.90
SVM RNA-class probability 0.981874
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16665437 110 + 22224390
AAUUGCAUCAGCAUCGGGUCGAAAAUCG-AUUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUCCAGAGGUUAAGUGUGUGUGUGUGUGUGUGAUAUGGUCAUA
.((..(.((((((((.((((((...(((-...)))....)))))).))))))))...((((((.(((((..((.........))..))))))))))))..))......... ( -31.90)
>DroSec_CAF1 4353 101 + 1
AAUUGCAUCAGCAUCGGGUCGAAAAUCGGGUUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUCCAGAGGUUAAGUAUAUAUAUA----UACAAU------AUA
...(((.((((((((.((((((...(((....)))....)))))).))))))))...))).....................(((((....))----)))...------... ( -25.60)
>DroEre_CAF1 5645 102 + 1
AAUUGCACCAGCUUUGGGUCGAGGAUCG-GAUCGAGUCAUUGACCCGAUGUUGAAGAGCAAAUUAUAUUUCCAAACGUUAAGUAUGUGUG---GUAUGA--UAUAUU---A
..((((..((((.(((((((((.(((((-...))).)).))))))))).))))....))))..((((((.(((.((((.....)))).))---)...))--))))..---. ( -30.70)
>DroYak_CAF1 4158 107 + 1
AAUUGCAUCAGCAACGGGUCGAAAAUCG-GAUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUCACAUUUCCAGACGUUAAGUAUGUGUG---AUAUGGGAUAUACUUUAG
...(((.((((((.(.((((((...(((-...)))....)))))).).))))))...))).(((.(((...((.((((.....)))).))---..))).)))......... ( -24.40)
>consensus
AAUUGCAUCAGCAUCGGGUCGAAAAUCG_GAUCGAGUCAUUGACCAGAUGUUGAAAAGCACAUUAUAUAUCCAGACGUUAAGUAUGUGUG___GUAUGAGAUAUA_U_AUA
...(((.((((((((.((((((...(((....)))....)))))).))))))))...)))...(((((((.(.........).)))))))..................... (-20.69 = -20.62 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,665,437 – 16,665,547
Length 110
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -20.80
Consensus MFE -14.45
Energy contribution -15.08
Covariance contribution 0.63
Combinations/Pair 1.11
Mean z-score -1.63
Structure conservation index 0.69
SVM decision value 0.30
SVM RNA-class probability 0.676580
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16665437 110 - 22224390
UAUGACCAUAUCACACACACACACACACACUUAACCUCUGGAUAUAUAAUGUGCUUUUCAACAUCUGGUCAAUGACUCGAAU-CGAUUUUCGACCCGAUGCUGAUGCAAUU
.......(((((.((.......................)))))))......(((...(((.((((.((((...((.(((...-))).))..)))).)))).))).)))... ( -17.70)
>DroSec_CAF1 4353 101 - 1
UAU------AUUGUA----UAUAUAUAUACUUAACCUCUGGAUAUAUAAUGUGCUUUUCAACAUCUGGUCAAUGACUCGAACCCGAUUUUCGACCCGAUGCUGAUGCAAUU
.((------((((((----(((...................)))))))))))((...(((.((((.((((...((.(((....))).))..)))).)))).))).)).... ( -23.01)
>DroEre_CAF1 5645 102 - 1
U---AAUAUA--UCAUAC---CACACAUACUUAACGUUUGGAAAUAUAAUUUGCUCUUCAACAUCGGGUCAAUGACUCGAUC-CGAUCCUCGACCCAAAGCUGGUGCAAUU
.---..((((--(....(---((.((.........)).)))..)))))..((((........((((((((........))))-)))).......(((....))).)))).. ( -17.50)
>DroYak_CAF1 4158 107 - 1
CUAAAGUAUAUCCCAUAU---CACACAUACUUAACGUCUGGAAAUGUGAUGUGCUUUUCAACAUCUGGUCAAUGACUCGAUC-CGAUUUUCGACCCGUUGCUGAUGCAAUU
..((((((((((.(((.(---(.((.((.......)).)))).))).))))))))))....((((.((.(((((..((((..-......))))..)))))))))))..... ( -25.00)
>consensus
UAU_A_UAUAUCACAUAC___CACACAUACUUAACCUCUGGAAAUAUAAUGUGCUUUUCAACAUCUGGUCAAUGACUCGAAC_CGAUUUUCGACCCGAUGCUGAUGCAAUU
...................................................(((...(((.((((.((((...((.(((....))).))..)))).)))).))).)))... (-14.45 = -15.08 +   0.63)

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 12:19:45 2006