Locus 3326

Sequence ID X_DroMel_CAF1
Location 8,880,691 – 8,880,853
Length 162
Max. P 0.953552
window5442 window5443 window5444 window5445 window5446

overview

Window 2

Location 8,880,691 – 8,880,784
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.73
Mean single sequence MFE -25.50
Consensus MFE -17.75
Energy contribution -18.64
Covariance contribution 0.89
Combinations/Pair 1.14
Mean z-score -1.30
Structure conservation index 0.70
SVM decision value 0.22
SVM RNA-class probability 0.639033
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8880691 93 + 22224390
----------G-GAACGGGCGAAGAACUGUUCUCAUUUC-------UCAUUUCGCGACGGUUGGAAAGUAUUCAAAUGCCUCA-AUGGAAACA----UUCCCUUUCUCCGCCA----ACU
----------(-(..(((((((((((.((....)).)))-------)....))))((.(((..(((....)))....)))))(-(((....))----))........))))).----... ( -19.70)
>DroSec_CAF1 11201 94 + 1
----------G-GAACGGGCGAAGAACUGUUCUCAUUUC-------UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCAAAUGGAGACA----UUCCCUUUCUCCGCCA----UUU
----------(-((((((........)))))))......-------.........(((((..((((((......((((.(((.....))).))----))..))))))))))).----... ( -26.00)
>DroSim_CAF1 11338 94 + 1
----------G-GAACGGGCGAAGAACUGUUCUCAUUUC-------UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCAAAUGGAGACA----UUCCCUUUCUCCGCCA----UCU
----------(-((((((........)))))))......-------.........(((((..((((((......((((.(((.....))).))----))..))))))))))).----... ( -26.00)
>DroEre_CAF1 10088 94 + 1
----------GCGAACGGACGGAGAACUGUUCUCAUUUC-------GCAUUUCACGGCGGUUGGAAAGUAUUCAAAUGCCUCA-ACGGAGACA----UUCCCUUUCUCCGCCA----UCU
----------(((((.((((((....))))))....)))-------)).......(((((..((((((......((((.(((.-...))).))----))..))))))))))).----... ( -29.30)
>DroYak_CAF1 11087 100 + 1
----------G-GAACGCGCGGAGAACUGUUCUCAUUUCUCAUUUCUCAUUUCUCGACGGUUGGAAAGUAUUCAAAUGCCUCA-AUGGAGACA----UUCCCUUUCUCCGUCA----UCU
----------(-(((.(.(..(((((.((....)).)))))....).).))))..(((((..((((((......((((.(((.-...))).))----))..))))))))))).----... ( -22.40)
>DroAna_CAF1 14779 102 + 1
CCGAUCUCGGG-GAAAAGGC--AGAAACGUUCUCGUUUC--------------UCGCCAGUUGGAAAGUAUUCAAAUGCCUCA-AUGGAGUCGCUGUUUUCCUUUCUCCGCUCCACAAUU
.......((((-((((.(((--(((((((....))))))--------------).)))....(((((((((....))))(((.-...))).......))))))))))))).......... ( -29.60)
>consensus
__________G_GAACGGGCGAAGAACUGUUCUCAUUUC_______UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCA_AUGGAGACA____UUCCCUUUCUCCGCCA____UCU
............((((((........)))))).......................(((((..((((((........((.(((.....))).))........)))))))))))........ (-17.75 = -18.64 +   0.89)

alignment

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secondary structure

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Window 3

Location 8,880,691 – 8,880,784
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.73
Mean single sequence MFE -27.97
Consensus MFE -18.10
Energy contribution -17.94
Covariance contribution -0.16
Combinations/Pair 1.24
Mean z-score -1.43
Structure conservation index 0.65
SVM decision value 0.15
SVM RNA-class probability 0.608680
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8880691 93 - 22224390
AGU----UGGCGGAGAAAGGGAA----UGUUUCCAU-UGAGGCAUUUGAAUACUUUCCAACCGUCGCGAAAUGA-------GAAAUGAGAACAGUUCUUCGCCCGUUC-C----------
...----.(((((.(((((.(((----((((((...-.))))))))).....)))))...)))))((((....(-------(((.((....)).))))))))......-.---------- ( -24.00)
>DroSec_CAF1 11201 94 - 1
AAA----UGGCGGAGAAAGGGAA----UGUCUCCAUUUGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA-------GAAAUGAGAACAGUUCUUCGCCCGUUC-C----------
...----.(((((.(((((.(((----((((((.....))))))))).....)))))...)))))((((....(-------(((.((....)).))))))))......-.---------- ( -29.20)
>DroSim_CAF1 11338 94 - 1
AGA----UGGCGGAGAAAGGGAA----UGUCUCCAUUUGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA-------GAAAUGAGAACAGUUCUUCGCCCGUUC-C----------
...----.(((((.(((((.(((----((((((.....))))))))).....)))))...)))))((((....(-------(((.((....)).))))))))......-.---------- ( -29.20)
>DroEre_CAF1 10088 94 - 1
AGA----UGGCGGAGAAAGGGAA----UGUCUCCGU-UGAGGCAUUUGAAUACUUUCCAACCGCCGUGAAAUGC-------GAAAUGAGAACAGUUCUCCGUCCGUUCGC----------
..(----((((((.(((((.(((----((((((...-.))))))))).....)))))...))))))).....((-------(((..((((.....))))......)))))---------- ( -31.70)
>DroYak_CAF1 11087 100 - 1
AGA----UGACGGAGAAAGGGAA----UGUCUCCAU-UGAGGCAUUUGAAUACUUUCCAACCGUCGAGAAAUGAGAAAUGAGAAAUGAGAACAGUUCUCCGCGCGUUC-C----------
...----((((((.(((((.(((----((((((...-.))))))))).....)))))...))))))...((((.(....(((((.((....)).)))))..).)))).-.---------- ( -26.90)
>DroAna_CAF1 14779 102 - 1
AAUUGUGGAGCGGAGAAAGGAAAACAGCGACUCCAU-UGAGGCAUUUGAAUACUUUCCAACUGGCGA--------------GAAACGAGAACGUUUCU--GCCUUUUC-CCCGAGAUCGG
.......((.(((.(((((((((....(((..((..-...))...))).....)))))....(((.(--------------((((((....)))))))--))).))))-.)))...)).. ( -26.80)
>consensus
AGA____UGGCGGAGAAAGGGAA____UGUCUCCAU_UGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA_______GAAAUGAGAACAGUUCUUCGCCCGUUC_C__________
........(((((.(((((........((((((.....))))))........)))))...)))))................(((.((....)).)))....................... (-18.10 = -17.94 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,880,719 – 8,880,822
Length 103
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 84.29
Mean single sequence MFE -23.46
Consensus MFE -16.02
Energy contribution -16.18
Covariance contribution 0.16
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.68
SVM decision value 0.15
SVM RNA-class probability 0.609124
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8880719 103 + 22224390
------UCAUUUCGCGACGGUUGGAAAGUAUUCAAAUGCCUCA-AUGGAAACAUUCCCUUUCUCCGCCAACUCGAAUUCUAAAAUGUGUCCGUUUUUUUUCAUACCCUCU--
------.........((.(((((((((((((....))))...(-(((((.(((((....(((...........)))......))))).))))))..)))))).))).)).-- ( -16.10)
>DroSec_CAF1 11229 102 + 1
------UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCAAAUGGAGACAUUCCCUUUCUCCGCCAUUUCACAUGCG-AAAUGAUUCCGUUU-UUUUCAUACCCUCG--
------((((((((((((((..((((((......((((.(((.....))).))))..))))))))))).........)))-))))))........-..............-- ( -27.40)
>DroSim_CAF1 11366 102 + 1
------UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCAAAUGGAGACAUUCCCUUUCUCCGCCAUCUCGAAUUCG-AAAUGAUUCCGUUU-CUUUCAUACCCUCU--
------(((((((..(((((..((((((......((((.(((.....))).))))..))))))))))).....(....))-))))))........-..............-- ( -24.30)
>DroEre_CAF1 10117 102 + 1
------GCAUUUCACGGCGGUUGGAAAGUAUUCAAAUGCCUCA-ACGGAGACAUUCCCUUUCUCCGCCAUCUCGAACUCG-AAAUGAUUCGG-UU-UUGUCUUACCCUCGAU
------.((((((..(((((..((((((......((((.(((.-...))).))))..))))))))))).....(....))-)))))....((-(.-.......)))...... ( -24.90)
>DroYak_CAF1 11116 109 + 1
CAUUUCUCAUUUCUCGACGGUUGGAAAGUAUUCAAAUGCCUCA-AUGGAGACAUUCCCUUUCUCCGUCAUCUCGAGUUCG-AAAUGAAUCGACUU-UCGUCAUAUCCUCGAU
...............(((((..((((((......((((.(((.-...))).))))..)))))))))))...(((((...(-(.((((..((....-.)))))).))))))). ( -24.60)
>consensus
______UCAUUUCGCGGCGGUUGGAAAGUAUUCAAAUGCCUCA_AUGGAGACAUUCCCUUUCUCCGCCAUCUCGAAUUCG_AAAUGAUUCCGUUU_UUUUCAUACCCUCG__
...............(((((..((((((......((((.(((.....))).))))..)))))))))))............................................ (-16.02 = -16.18 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,880,719 – 8,880,822
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 84.29
Mean single sequence MFE -30.14
Consensus MFE -22.66
Energy contribution -22.14
Covariance contribution -0.52
Combinations/Pair 1.15
Mean z-score -2.38
Structure conservation index 0.75
SVM decision value 1.43
SVM RNA-class probability 0.953552
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8880719 103 - 22224390
--AGAGGGUAUGAAAAAAAACGGACACAUUUUAGAAUUCGAGUUGGCGGAGAAAGGGAAUGUUUCCAU-UGAGGCAUUUGAAUACUUUCCAACCGUCGCGAAAUGA------
--........................((((((.((...((.(((((.((((.....(((((((((...-.))))))))).....)))))))))))))..)))))).------ ( -20.60)
>DroSec_CAF1 11229 102 - 1
--CGAGGGUAUGAAAA-AAACGGAAUCAUUU-CGCAUGUGAAAUGGCGGAGAAAGGGAAUGUCUCCAUUUGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA------
--..............-........((((((-(((((.....))(((((.(((((.(((((((((.....))))))))).....)))))...))))))))))))))------ ( -33.40)
>DroSim_CAF1 11366 102 - 1
--AGAGGGUAUGAAAG-AAACGGAAUCAUUU-CGAAUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCAUUUGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA------
--..............-........((((((-((.........((((((.(((((.(((((((((.....))))))))).....)))))...))))))))))))))------ ( -29.60)
>DroEre_CAF1 10117 102 - 1
AUCGAGGGUAAGACAA-AA-CCGAAUCAUUU-CGAGUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCGU-UGAGGCAUUUGAAUACUUUCCAACCGCCGUGAAAUGC------
.((((((((.......-.)-))(((....))-)...))))).(((((((.(((((.(((((((((...-.))))))))).....)))))...))))))).......------ ( -32.10)
>DroYak_CAF1 11116 109 - 1
AUCGAGGAUAUGACGA-AAGUCGAUUCAUUU-CGAACUCGAGAUGACGGAGAAAGGGAAUGUCUCCAU-UGAGGCAUUUGAAUACUUUCCAACCGUCGAGAAAUGAGAAAUG
.((((((...((((..-..))))..((((((-((....)))))))).(((((....(((((((((...-.)))))))))......)))))..)).))))............. ( -35.00)
>consensus
__CGAGGGUAUGAAAA_AAACGGAAUCAUUU_CGAAUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCAU_UGAGGCAUUUGAAUACUUUCCAACCGCCGCGAAAUGA______
..........................(((((.((....))...((((((.(((((.(((((((((.....))))))))).....)))))...))))))..)))))....... (-22.66 = -22.14 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,880,753 – 8,880,853
Length 100
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 72.98
Mean single sequence MFE -22.92
Consensus MFE -7.92
Energy contribution -7.84
Covariance contribution -0.08
Combinations/Pair 1.25
Mean z-score -1.94
Structure conservation index 0.35
SVM decision value 0.85
SVM RNA-class probability 0.866337
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8880753 100 - 22224390
AAAGUGGAUAAAACUUUAGGGUAGCAACAAU-----------AGAGGGUAUGAAAAAAAACGGACACAUUUUAGAAUUCGAGUUGGCGGAGAAAGGGAAUGUUUCCAU-UGA
.......(((...(((((..((....))..)-----------))))..)))..........(((.(((((((....((((......)))).....))))))).)))..-... ( -17.90)
>DroSec_CAF1 11263 89 - 1
AAAA----------UAUAGGGUAGCAACUAU-----------CGAGGGUAUGAAAA-AAACGGAAUCAUUU-CGCAUGUGAAAUGGCGGAGAAAGGGAAUGUCUCCAUUUGA
....----------.....(((((...))))-----------).............-...((((.((((((-((....)))))))).(((((.........))))).)))). ( -15.70)
>DroSim_CAF1 11400 89 - 1
AAAA----------UAUAGGGUAGCAACUAU-----------AGAGGGUAUGAAAG-AAACGGAAUCAUUU-CGAAUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCAUUUGA
....----------(((((........))))-----------).............-...((((.((((((-((....)))))))).(((((.........))))).)))). ( -18.30)
>DroEre_CAF1 10151 108 - 1
GAAAUGGAUAAGGCUGCAGGGUAUUAACAGUAGUUUAUCCAUCGAGGGUAAGACAA-AA-CCGAAUCAUUU-CGAGUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCGU-UGA
....((((((((.((((.(........).))))))))))))((((.((..(((((.-..-((...((((((-((....))))))))........))...))))))).)-))) ( -31.70)
>DroYak_CAF1 11156 109 - 1
AAAAUGCUUAAAGCUAUAGGGUAGCAACUAUAGUUUACACAUCGAGGAUAUGACGA-AAGUCGAUUCAUUU-CGAACUCGAGAUGACGGAGAAAGGGAAUGUCUCCAU-UGA
..........(((((((((........))))))))).....((((.....((((..-..))))..((((((-((....)))))))).(((((.........))))).)-))) ( -31.00)
>consensus
AAAAUG__UAA__CUAUAGGGUAGCAACUAU___________CGAGGGUAUGAAAA_AAACGGAAUCAUUU_CGAAUUCGAGAUGGCGGAGAAAGGGAAUGUCUCCAU_UGA
..................................................................(((((.((....)))))))..(((((.........)))))...... ( -7.92 =  -7.84 +  -0.08)

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 10:56:33 2006