Locus 1725

Sequence ID 2L_DroMel_CAF1
Location 4,746,718 – 4,746,846
Length 128
Max. P 0.859672
window2767 window2768 window2769

overview

Window 7

Location 4,746,718 – 4,746,822
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.98
Mean single sequence MFE -26.03
Consensus MFE -19.13
Energy contribution -19.63
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.29
Structure conservation index 0.73
SVM decision value 0.59
SVM RNA-class probability 0.791291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4746718 104 - 22407834
AAAGGAAAGCG-----UGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCAAC-----CAACAAGACAUAUGCCC------CCCAUUCCGA
...((((.(.(-----.((((...((((((....))))))((((.((((((....)))))).))))....((.....))...-----............)))).------).).)))).. ( -25.40)
>DroPse_CAF1 212125 106 - 1
-AAAGAAAGCG-----UGGCAAACAUGCAUGACAAUGCAUGACAAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCACA---CACAACAAGACAUAUGGCC-----CCCGAUCCGGG
-.......(((-----((((...(((((((....)))))))....((((((....)))))).........).)))).))...---...................-----((((...)))) ( -24.00)
>DroEre_CAF1 183678 105 - 1
AAAGGAAAGCG-----UGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCAAC-----CAACAGCACAUAUGUCC-----CCCAAUUCCGA
...((((.(((-----.((.....((((((....))))))((((.((((((....)))))).)))))).)))....(((...-----.....))).........-----.....)))).. ( -26.50)
>DroYak_CAF1 181704 106 - 1
AAAGGAAAGCGUGGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCAGC-----CCCC----CAUUCCGAA-----ACCGAAUCCGA
...(((..((((((((.((.....((((((....))))))((((.((((((....)))))).)))))).)).)))).))...-----....----.....((..-----..))..))).. ( -30.50)
>DroAna_CAF1 194502 114 - 1
AUACCAAAGCG-----UGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAG-CCCUCGCCCACUGCACUGAACACAGCAAGACAUAUGGCCAAAGAACCGGAUCAGA
...(((..(((-----.(((...(((((((....)))))))....((((((....))))))..)-))..)))...((...(((....)))..)).....)))((........))...... ( -25.80)
>DroPer_CAF1 219827 106 - 1
-AAAGAAAGCG-----UGGCAAACAUGCAUGACAAUGCAUGACAAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCACA---CACAACAAGACAUAUGGCC-----CCCGAUCCGGG
-.......(((-----((((...(((((((....)))))))....((((((....)))))).........).)))).))...---...................-----((((...)))) ( -24.00)
>consensus
AAAGGAAAGCG_____UGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCACC_____CAACAAGACAUAUGGCC_____CCCGAUUCCGA
........(((......(((...(((((((....)))))))(((.((((((....)))))).))).....)))...)))......................................... (-19.13 = -19.63 +   0.50)

alignment

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secondary structure

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Window 8

Location 4,746,747 – 4,746,846
Length 99
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 84.94
Mean single sequence MFE -27.03
Consensus MFE -22.87
Energy contribution -23.37
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.13
Structure conservation index 0.85
SVM decision value 0.82
SVM RNA-class probability 0.859672
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4746747 99 + 22407834
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUAGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCCUUUCCGUGCCUUUGCGAUCCUUUCCGU----------
.((((.(((((.((((((.((((((....)))))).))))((((((....))))))...................)).)))))))))............---------- ( -27.20)
>DroPse_CAF1 212157 99 + 1
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUUGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCUUU--CAUUCCUUCCCUCUUUUUUUCGU--------GU
...((((((((((.(((..((((((....))))))..)))((((((....)))))).)))))).))))......--.......................--------.. ( -24.20)
>DroSec_CAF1 175442 99 + 1
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUAGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCCUUUCCGUGCCUUUGCAAUUUUUUCCGC----------
(((((.(((((.((((((.((((((....)))))).))))((((((....))))))...................)).))))))))))...........---------- ( -27.90)
>DroSim_CAF1 171140 99 + 1
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUAGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCCUUUCCGUGCCUUUGCCAUCCUUUCCGC----------
.......(((((((((((.((((((....)))))).)))(((((((....))))))).....((((..........))))))))))))...........---------- ( -26.70)
>DroAna_CAF1 194542 108 + 1
UGCAGUGGGCGAGGG-CUUAAGUAAUUCAUUACUUUAGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUGGUAUCCUUGCCGCUUCCCUCCAGUUCCAGGCUCUGACU
..(((.(((((((((-((.((((((....)))))).)))(((((((....)))))))..(((((.....))))).))))))).....(((........)))).)))... ( -32.00)
>DroPer_CAF1 219859 99 + 1
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUUGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCUUU--CAUUCCUUCCCUCUUUUUUUCGU--------GU
...((((((((((.(((..((((((....))))))..)))((((((....)))))).)))))).))))......--.......................--------.. ( -24.20)
>consensus
UGCAGUGGGCGAGGGACUUAAGUAAUUCAUUACUUUAGUCAUGCAUUGUCAUGCAUGUUUGCCACGCUUUCCUUUCCGUGCCUUUGCCAUCCUUUCCGU__________
...((((((((((.((((.((((((....)))))).))))((((((....)))))).)))))).))))......................................... (-22.87 = -23.37 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,746,747 – 4,746,846
Length 99
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 84.94
Mean single sequence MFE -26.30
Consensus MFE -20.85
Energy contribution -21.35
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.79
SVM decision value 0.63
SVM RNA-class probability 0.803934
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4746747 99 - 22407834
----------ACGGAAAGGAUCGCAAAGGCACGGAAAGGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
----------..((..(((........(.((((..........)))).)...(((((((....)))))))(((.((((((....)))))).))).)))..))....... ( -25.50)
>DroPse_CAF1 212157 99 - 1
AC--------ACGAAAAAAAGAGGGAAGGAAUG--AAAGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACAAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
..--------..........((((((.......--.................(((((((....)))))))....((((((....))))))...))))))((.....)). ( -23.80)
>DroSec_CAF1 175442 99 - 1
----------GCGGAAAAAAUUGCAAAGGCACGGAAAGGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
----------((((.......(((....)))......((...(((.((.....((((((....))))))((((.((((((....)))))).)))))).))))).)))). ( -28.60)
>DroSim_CAF1 171140 99 - 1
----------GCGGAAAGGAUGGCAAAGGCACGGAAAGGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
----------((((........((....)).......((...(((.((.....((((((....))))))((((.((((((....)))))).)))))).))))).)))). ( -28.00)
>DroAna_CAF1 194542 108 - 1
AGUCAGAGCCUGGAACUGGAGGGAAGCGGCAAGGAUACCAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAG-CCCUCGCCCACUGCA
........(((........)))...((((...((...))...(((.(((...(((((((....)))))))....((((((....))))))..)-))..)))...)))). ( -28.10)
>DroPer_CAF1 219859 99 - 1
AC--------ACGAAAAAAAGAGGGAAGGAAUG--AAAGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACAAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
..--------..........((((((.......--.................(((((((....)))))))....((((((....))))))...))))))((.....)). ( -23.80)
>consensus
__________ACGAAAAAAAGAGCAAAGGCACGGAAAGGAAAGCGUGGCAAACAUGCAUGACAAUGCAUGACUAAAGUAAUGAAUUACUUAAGUCCCUCGCCCACUGCA
..........................................(((((((...(((((((....)))))))(((.((((((....)))))).))).....).)))).)). (-20.85 = -21.35 +   0.50)

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 10:09:32 2006