Locus 3442

Sequence ID 3R_DroMel_CAF1
Location 9,333,654 – 9,333,776
Length 122
Max. P 0.999913
window5522 window5523 window5524 window5525

overview

Window 2

Location 9,333,654 – 9,333,756
Length 102
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 71.48
Mean single sequence MFE -35.38
Consensus MFE -24.04
Energy contribution -24.24
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.68
SVM decision value 2.68
SVM RNA-class probability 0.996303
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9333654 102 + 27905053
------------AGGGGCACUGUGAGUGGAAGGAGGGGCAGGGGUAGGGAACCCUCACCUUAAGUAAUGAACCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
------------....(((...((((((((....((..((((((((((....))).)))))......))..)).((((((.((......)).))))))..))))))))...))) ( -32.40)
>DroPse_CAF1 102194 84 + 1
C-----------------------AGCGGGUAG--UGGG--CUGGAGGGG---CUCUCCUUAAGUAAUGAAGCAAGCGCUUGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
.-----------------------...(.(((.--((.(--((.(((((.---...))))).)))(((((((((.(((((..(......)..)))))))))))))))).))).) ( -33.20)
>DroSec_CAF1 105974 82 + 1
-----------------------AAG---------GGGGAGAGGUAGGGGACCCCCACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
-----------------------...---------.....(((((.(((....))))))))....(((((((((.(((((.((......)).))))))))))))))........ ( -35.30)
>DroEre_CAF1 105854 111 + 1
AGCGGGUGGAGCUGGAGCAGCGGGAGCAG---CGGGAGCAGCGGGAGGGUGCCCCAACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
.((((((...((((...))))(((.((((---(....))..(....)..)))))).))))((...(((((((((.(((((.((......)).))))))))))))))...)).)) ( -44.30)
>DroPer_CAF1 106930 91 + 1
C-------------GGG---UGUGAGCGGGUAG--UGGG--GUGGAGGGG---CUCUCCUUAAGUAAUGAAGCAAGCGCUUGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
.-------------...---.....(((.....--((((--(.((((...---)))))))))...(((((((((.(((((..(......)..)))))))))))))).....))) ( -31.70)
>consensus
______________G_G____G_GAGCGG___G__GGGGAGCGGGAGGGG_CCCUCACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGC
.............................................((((........))))....(((((((((.(((((.((......)).))))))))))))))........ (-24.04 = -24.24 +   0.20)

alignment

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secondary structure

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Window 3

Location 9,333,654 – 9,333,756
Length 102
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 71.48
Mean single sequence MFE -29.20
Consensus MFE -17.24
Energy contribution -17.00
Covariance contribution -0.24
Combinations/Pair 1.11
Mean z-score -3.66
Structure conservation index 0.59
SVM decision value 4.52
SVM RNA-class probability 0.999913
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9333654 102 - 27905053
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGGUUCAUUACUUAAGGUGAGGGUUCCCUACCCCUGCCCCUCCUUCCACUCACAGUGCCCCU------------
((((....((((((.((((((...((....))...)))).)).))))))......(((..((((.....))))..)))................))))....------------ ( -27.50)
>DroPse_CAF1 102194 84 - 1
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCAAGCGCUUGCUUCAUUACUUAAGGAGAG---CCCCUCCAG--CCCA--CUACCCGCU-----------------------G
((......(((((((((((((...((....))...)))).)))))))))......((((..---...))))..--....--......)).-----------------------. ( -25.60)
>DroSec_CAF1 105974 82 - 1
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUGGGGGUCCCCUACCUCUCCCC---------CUU-----------------------
........(((((((((((((...((....))...)))).))))))))).....((((((((...))))))))......---------...----------------------- ( -29.50)
>DroEre_CAF1 105854 111 - 1
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUUGGGGCACCCUCCCGCUGCUCCCG---CUGCUCCCGCUGCUCCAGCUCCACCCGCU
((......(((((((((((((...((....))...)))).)))))))))......((((((((((.......((.((....)---).))......))))))))))......)). ( -37.82)
>DroPer_CAF1 106930 91 - 1
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCAAGCGCUUGCUUCAUUACUUAAGGAGAG---CCCCUCCAC--CCCA--CUACCCGCUCACA---CCC-------------G
((......(((((((((((((...((....))...)))).)))))))))......((((..---...))))..--....--......)).....---...-------------. ( -25.60)
>consensus
GCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUGAGGG_CCCCUCCCCCUCCCC__C___CCGCUC_C____C_C______________
........(((((((((((((...((....))...)))).))))))))).....(((.(.....).)))............................................. (-17.24 = -17.00 +  -0.24)

alignment

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secondary structure

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Window 4

Location 9,333,682 – 9,333,776
Length 94
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.08
Mean single sequence MFE -37.73
Consensus MFE -23.20
Energy contribution -23.32
Covariance contribution 0.11
Combinations/Pair 1.17
Mean z-score -3.10
Structure conservation index 0.61
SVM decision value 1.60
SVM RNA-class probability 0.966939
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9333682 94 + 27905053
GGGGUAGG-GAACCCUCACCUUAAGUAAUGAACCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCA--------------GG--CAACAUAGCCCC----AUCU
((((((((-....)))..(((((...((((((...((((((.((......)).))))))..))))))...))....)--------------))--.......)))))----.... ( -31.40)
>DroPse_CAF1 102208 106 + 1
-CUGGAGG-GG---CUCUCCUUAAGUAAUGAAGCAAGCGCUUGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCACAAACUGAGUUUCAGGUACAAUAUAUCCCU----CUCU
-..(((((-((---(....((.....(((((((((.(((((..(......)..)))))))))))))).))...))).....(((.....)))............)))----)).. ( -38.60)
>DroSim_CAF1 115261 94 + 1
GGGGUAGG-GGACCCCCACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCA--------------GG--CAACAUAGCCCC----AUCU
(((((.((-(....))).(((((...(((((((((.(((((.((......)).))))))))))))))...))....)--------------))--.......)))))----.... ( -41.10)
>DroEre_CAF1 105891 94 + 1
GCGGGAGG-GUGCCCCAACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCG--------------GG--UAACAUAGCCCC----AUCU
((((..((-(...)))..)).((...(((((((((.(((((.((......)).))))))))))))))...)).)).(--------------((--(......)))).----.... ( -36.50)
>DroYak_CAF1 106175 95 + 1
GGGGGAGGUGGAUCCCCACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCA--------------GG--UAACAUAGCCCC----AUCU
(((((((((((....)))))))....(((((((((.(((((.((......)).))))))))))))))...((((...--------------..--...)))).))))----.... ( -43.10)
>DroAna_CAF1 102077 89 + 1
------GG-GG---CUCUCCUUAAGUAAUGAAGCAGGCGCUUGCAGUUUUGCGGGCGCUGCUUCAUUUAGUAUGCCA--------------GG--UUACCCAGCUCCCCUGGUCC
------((-((---((..(((((...((((((((((.(((((((......)))))))))))))))))...))....)--------------))--......))))))........ ( -35.70)
>consensus
GGGGGAGG_GGACCCCCACCUUAAGUAAUGAAGCAAGCGCUGGCAGUUUUGUGGGCGCUGCUUCAUUUAGUAUGCCA______________GG__CAACAUAGCCCC____AUCU
.....(((.((....)).)))((...((((((((.((((((.((......)).))))))))))))))...))........................................... (-23.20 = -23.32 +   0.11)

alignment

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secondary structure

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Window 5

Location 9,333,682 – 9,333,776
Length 94
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.08
Mean single sequence MFE -32.67
Consensus MFE -17.28
Energy contribution -18.00
Covariance contribution 0.72
Combinations/Pair 1.07
Mean z-score -2.36
Structure conservation index 0.53
SVM decision value 0.58
SVM RNA-class probability 0.788552
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9333682 94 - 27905053
AGAU----GGGGCUAUGUUG--CC--------------UGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGGUUCAUUACUUAAGGUGAGGGUUC-CCUACCCC
....----((((.((.(..(--((--------------(..(((....((((((.((((((...((....))...)))).)).)))))).......))).))))..-).)))))) ( -27.30)
>DroPse_CAF1 102208 106 - 1
AGAG----AGGGAUAUAUUGUACCUGAAACUCAGUUUGUGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCAAGCGCUUGCUUCAUUACUUAAGGAGAG---CC-CCUCCAG-
.(.(----((((.(((.(..((.(((.....)))..))..).)))...(((((((((((((...((....))...)))).)))))))))............---.)-)))))..- ( -29.50)
>DroSim_CAF1 115261 94 - 1
AGAU----GGGGCUAUGUUG--CC--------------UGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUGGGGGUCC-CCUACCCC
.(.(----.((((......)--))--------------).))......(((((((((((((...((....))...)))).)))))))))......(((((((...)-)))))).. ( -34.90)
>DroEre_CAF1 105891 94 - 1
AGAU----GGGGCUAUGUUA--CC--------------CGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUUGGGGCAC-CCUCCCGC
....----((((...(((..--((--------------((((......(((((((((((((...((....))...)))).))))))))).......))))))))).-..)))).. ( -33.32)
>DroYak_CAF1 106175 95 - 1
AGAU----GGGGCUAUGUUA--CC--------------UGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUGGGGAUCCACCUCCCCC
....----((((.((((((.--..--------------.))))))...(((((((((((((...((....))...)))).))))))))).....((((((....)))))))))). ( -35.20)
>DroAna_CAF1 102077 89 - 1
GGACCAGGGGAGCUGGGUAA--CC--------------UGGCAUACUAAAUGAAGCAGCGCCCGCAAAACUGCAAGCGCCUGCUUCAUUACUUAAGGAGAG---CC-CC------
......((((.((..((...--))--------------..))......(((((((((((((..(((....)))..))).))))))))))............---))-))------ ( -35.80)
>consensus
AGAU____GGGGCUAUGUUA__CC______________UGGCAUACUAAAUGAAGCAGCGCCCACAAAACUGCCAGCGCUUGCUUCAUUACUUAAGGUGAGGGUCC_CCUCCCCC
..........((.((((((....................)))))))).(((((((((((((...((....))...)))).))))))))).....(((.(......).)))..... (-17.28 = -18.00 +   0.72)

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 11:01:07 2006