Locus 1778

Sequence ID 2L_DroMel_CAF1
Location 4,860,892 – 4,861,054
Length 162
Max. P 0.931211
window2859 window2860 window2861

overview

Window 9

Location 4,860,892 – 4,860,991
Length 99
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.13
Mean single sequence MFE -39.40
Consensus MFE -25.05
Energy contribution -25.67
Covariance contribution 0.62
Combinations/Pair 1.19
Mean z-score -2.15
Structure conservation index 0.64
SVM decision value 0.08
SVM RNA-class probability 0.572613
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4860892 99 - 22407834
AGCGGUUCUU-GGGCCGUAAUCUACUUGGCCUACUUG-GACUAAGUGCGCUUUUAGAUAA-AGUCGCUGCCGAGUCGGCUU-GGCACGCACAAGCGGAAA--AGG------
.(((((((.(-((((((.........)))))))...)-))))..(((((((((.....))-))).(.(((((((....)))-)))))))))..)).....--...------ ( -35.80)
>DroVir_CAF1 12471 100 - 1
AGCAGCUCUU-UGGCCGUAAUCUACUUGGCCUACUUG-GGCUAAGUGCGCUUUUAGAUAAAAGUCGCUGGCGAGGCGGCAC-GGCACGCAUUACAGGCCA--AAG------
.......(((-((((((((((..(((((((((....)-))))))))((((((((....)))))).((((((......)).)-)))..))))))).)))))--)))------ ( -40.50)
>DroPse_CAF1 14367 103 - 1
AGCAGCUCUUUGGGUUGUAAUCUACUUGGCCUACUUGGGGCUAAGUGAGCUUUUAGAUAA-AGUCGCUGGCGGGGCGGCUU-GGCACGCACAAGCGGCCGAAGGG------
.((((((.....))))))....((((((((((.....))))))))))..(((((.....(-(((((((.....))))))))-(((.(((....))))))))))).------ ( -41.90)
>DroMoj_CAF1 12110 101 - 1
AGCAGCUCUU-UGGCUGUAAUCUACUUGGCCUACUUG-GGCUAAGUGCGCUUUUAGAUAAAAGUCGCUGGCUAGGCGGCACCGGCACGCAUUAGAGGCAG--CCG------
.((((((...-.))))))....((((((((((....)-))))))))).((((((....)))))).((((.((..(((((....)).))).....)).)))--)..------ ( -37.50)
>DroAna_CAF1 15648 105 - 1
AGCGGCUCUU-UGGCUAUAAUCUACUUGGCCUACUUG-GGCUAAGUGCGCUUUUAGAUAA-AGUCGCUGCCGAGUCGGCUU-GGCACGCACAAGCUAUGA--AGGGGGUUG
..((((((((-(((((......((((((((((....)-))))))))).(((((.....))-))).(((((((((....)))-)))).))...)))))...--.)))))))) ( -38.80)
>DroPer_CAF1 14214 103 - 1
AGCAGCUCUUUGGGUUGUAAUCUACUUGGCCUACUUGGGGCUAAGUGAGCUUUUAGAUAA-AGUCGCUGGCGGGGCGGCUU-GGCACGCACAAGCGGCCGAAGGG------
.((((((.....))))))....((((((((((.....))))))))))..(((((.....(-(((((((.....))))))))-(((.(((....))))))))))).------ ( -41.90)
>consensus
AGCAGCUCUU_GGGCUGUAAUCUACUUGGCCUACUUG_GGCUAAGUGCGCUUUUAGAUAA_AGUCGCUGGCGAGGCGGCUU_GGCACGCACAAGCGGCCA__AGG______
.((((((.....)))))).(((((...(((.((((((....)))))).)))..)))))....((((((......(((((....)).)))...))))))............. (-25.05 = -25.67 +   0.62)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,860,914 – 4,861,026
Length 112
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -33.02
Consensus MFE -25.72
Energy contribution -24.80
Covariance contribution -0.92
Combinations/Pair 1.19
Mean z-score -2.29
Structure conservation index 0.78
SVM decision value 1.21
SVM RNA-class probability 0.931211
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4860914 112 - 22407834
UGUAUCUUCUUCUAUGGAUGCCUCCUCCAAAGGCAAGCGGUUCUU-GGGCCGUAAUCUACUUGGCCUACUUG-GACUAAGUGCGCUUUUAGAUAAAGUCGCUGCCGAGUCGGCU
..............(((((((((.......))))..((((((...-.)))))).)))))...((((.(((((-(....((((.(((((.....))))))))).)))))).)))) ( -36.60)
>DroPse_CAF1 14391 96 - 1
---------------AUAUUUC---UUUAUAGACAAGCAGCUCUUUGGGUUGUAAUCUACUUGGCCUACUUGGGGCUAAGUGAGCUUUUAGAUAAAGUCGCUGGCGGGGCGGCU
---------------.....((---(....((.(..((((((.....))))))....((((((((((.....)))))))))).)))...)))...(((((((.....))))))) ( -29.50)
>DroEre_CAF1 11760 97 - 1
------------UAUACAUGCC---UCCAAAGGCAAGCGGCUCUC-UGGCCGUAAUCUACUUGGCCUACUUG-GACUAAGUGCGCUUUUAGAUAAAGUCGCUGCCGAGUCGGCU
------------......((((---(....))))).((((((...-.)))))).........((((.(((((-(....((((.(((((.....))))))))).)))))).)))) ( -35.90)
>DroYak_CAF1 11557 97 - 1
------------UAUACAUGCC---UCCAAAGGCAAGCGGCUCUU-CGGCCGUAAUCUACUUGGCCUACUUG-GACUAAGUGCGCUUUUAGAUAAAGUCGCUGCCGAGUCGGCU
------------......((((---(....))))).((((((...-.)))))).........((((.(((((-(....((((.(((((.....))))))))).)))))).)))) ( -36.00)
>DroAna_CAF1 15676 95 - 1
--UAUU------------UUCC---UUUAUAGACAAGCGGCUCUU-UGGCUAUAAUCUACUUGGCCUACUUG-GGCUAAGUGCGCUUUUAGAUAAAGUCGCUGCCGAGUCGGCU
--....------------....---............((((((..-.(((........(((((((((....)-))))))))(((((((.....)))).))).)))))))))... ( -30.60)
>DroPer_CAF1 14238 96 - 1
---------------AUAUUUC---UUUAUAGACAAGCAGCUCUUUGGGUUGUAAUCUACUUGGCCUACUUGGGGCUAAGUGAGCUUUUAGAUAAAGUCGCUGGCGGGGCGGCU
---------------.....((---(....((.(..((((((.....))))))....((((((((((.....)))))))))).)))...)))...(((((((.....))))))) ( -29.50)
>consensus
_______________ACAUGCC___UCCAAAGACAAGCGGCUCUU_GGGCCGUAAUCUACUUGGCCUACUUG_GACUAAGUGCGCUUUUAGAUAAAGUCGCUGCCGAGUCGGCU
...............................(((..((((((.....)))))).(((((...(((.((((((....)))))).)))..)))))...)))((((......)))). (-25.72 = -24.80 +  -0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,860,953 – 4,861,054
Length 101
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 77.60
Mean single sequence MFE -19.97
Consensus MFE -14.11
Energy contribution -13.92
Covariance contribution -0.19
Combinations/Pair 1.31
Mean z-score -1.08
Structure conservation index 0.71
SVM decision value 0.17
SVM RNA-class probability 0.619244
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4860953 101 - 22407834
AUGU------AU---UUAUAAU-CUAUCUAUGUAUCUGUGUAUCUUCUUCUAUGGAUGCCUCCUCCAAAGGCAAGCGGUUCUUGGGCCGUAAUCUACUUGGCCUACUUGGA
....------..---.......-........(((((((((.(......).)))))))))....(((((((((..((((((....))))))...(.....)))))..))))) ( -22.00)
>DroSec_CAF1 11171 96 - 1
AUGU------AU---UUAUAAU-CUAUCUAUGUAUCUG--UAUCUCCGUCUAUACAUGCC---UCCAAAGGCAAGCGGCUCUCGGGCCGUAAUCUACUUGGCCUACUUGGA
....------..---.......-........((((.((--((........)))).)))).---(((((((((..((((((....))))))...(.....)))))..))))) ( -20.60)
>DroSim_CAF1 12039 96 - 1
AUGU------AU---UUAUAAU-CUAUCUAUGUAUCUG--UAUCUCCGUCUAUACAUGCC---UCCAAAGGCAAGCGGCUCUUGGGCCGUAAUCUACUUGGCCUACUUGGA
....------..---.......-........((((.((--((........)))).)))).---(((((((((..((((((....))))))...(.....)))))..))))) ( -20.60)
>DroEre_CAF1 11799 84 - 1
AUGU------AU---UUAUAAG-CUAUCUUUGUAUC--------------UAUACAUGCC---UCCAAAGGCAAGCGGCUCUCUGGCCGUAAUCUACUUGGCCUACUUGGA
((((------((---.((((((-.....))))))..--------------.))))))...---(((((((((..((((((....))))))...(.....)))))..))))) ( -21.90)
>DroYak_CAF1 11596 90 - 1
AUGUACUCGUAU---UUAUAAU-CUAUCUAUGUAUC--------------UAUACAUGCC---UCCAAAGGCAAGCGGCUCUUCGGCCGUAAUCUACUUGGCCUACUUGGA
............---.......-.....((((((..--------------..))))))..---(((((((((..((((((....))))))...(.....)))))..))))) ( -19.40)
>DroAna_CAF1 15715 88 - 1
AUGU------AUAUUUUAUAAGACUAAAUACAAGUAUG--UAUU------------UUCC---UUUAUAGACAAGCGGCUCUUUGGCUAUAAUCUACUUGGCCUACUUGGG
....------....((((((((...(((((((....))--))))------------)...---))))))))((((.((((...(((.......)))...))))..)))).. ( -15.30)
>consensus
AUGU______AU___UUAUAAU_CUAUCUAUGUAUCUG__UAUC______UAUACAUGCC___UCCAAAGGCAAGCGGCUCUUGGGCCGUAAUCUACUUGGCCUACUUGGA
...............................................................(((((((((..((((((....))))))...(.....)))))..))))) (-14.11 = -13.92 +  -0.19)

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 10:11:00 2006