Locus 4696

Sequence ID 2L_DroMel_CAF1
Location 13,488,433 – 13,488,565
Length 132
Max. P 0.947478
window7429 window7430 window7431 window7432

overview

Window 9

Location 13,488,433 – 13,488,530
Length 97
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 85.06
Mean single sequence MFE -24.73
Consensus MFE -15.95
Energy contribution -15.23
Covariance contribution -0.72
Combinations/Pair 1.16
Mean z-score -2.95
Structure conservation index 0.65
SVM decision value -0.02
SVM RNA-class probability 0.522566
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13488433 97 + 22407834
UUACAAAAACGGCAAAAUGCAAAUAAAAAAA--AUUUUCCCUUUGACAAUGCCGAC-CGAUUCGCGUCGA-----GUCGACAGCCAAAGUGAAACUUUUGCCUUA
..........((((((((....)).......--..((((.(((((....((.((((-((((....)))).-----)))).))..))))).))))..))))))... ( -21.60)
>DroPse_CAF1 130476 103 + 1
UUACAAAAACGGCAAACUGAAAACGAAACAA--AUUUUCACUUUGACAAUACCAACCCGAUUCGAGUCGAGUCGCGUCGGCUGCCAAAGCGAAAACUUUGCCUCA
..........((((((.(....)........--.(((((.(((((.((...((.((.(((((((...))))))).)).)).)).))))).))))).))))))... ( -24.90)
>DroEre_CAF1 91933 97 + 1
UUACAAAAACGGCAAAAUGCAAAUAAAAAAA--UGUUUCCCUUUGACAAUGCCGAC-CGAUUCGCGUCGA-----GUCGACAGCCAAAGUGAAACUUUUGCCUUA
..........(((((((..............--.(((((.(((((....((.((((-((((....)))).-----)))).))..))))).))))))))))))... ( -25.36)
>DroYak_CAF1 89222 99 + 1
UUACAAAAACGGCAAAAUGCAAAUAAAAAAAAUUGUUUCCCUUUGACAAUGCCGAC-CGAUUCGCGUCGA-----GUCGACAGCCAAAGUGAAACUUUUGCCUUA
..........(((((((.................(((((.(((((....((.((((-((((....)))).-----)))).))..))))).))))))))))))... ( -25.22)
>DroAna_CAF1 151385 97 + 1
UUACAAAAACGGCAAAAUGAAAGUGAAACAA--AUUUUCCCUUUGACAAUGCCGAC-CGUUUCUAGUCGU-----GUCGGCUGCCAAAGUGAAAACUUUGCCUCA
..........((((((((....)).......--.(((((.(((((.((..((((((-((........)).-----)))))))).))))).))))).))))))... ( -27.80)
>DroPer_CAF1 106835 103 + 1
UUACAAAAACGGCAAACUGAAAACGAAACAA--AUUUUCACUUUGACAAUACCAACCCGAUUCCAGUCGAGUCGCGUCGGCUGCCAAAGCGAAAACUUUGCCUCA
..........((((((.(....)........--.(((((.(((((.((...((.((.((((((.....)))))).)).)).)).))))).))))).))))))... ( -23.50)
>consensus
UUACAAAAACGGCAAAAUGAAAAUAAAAAAA__AUUUUCCCUUUGACAAUGCCGAC_CGAUUCGAGUCGA_____GUCGACAGCCAAAGUGAAAACUUUGCCUCA
..........((((((.((....)).........(((((.(((((.(.....(.....)......(((((......))))).).))))).))))).))))))... (-15.95 = -15.23 +  -0.72)

alignment

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secondary structure

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Window 0

Location 13,488,433 – 13,488,530
Length 97
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 85.06
Mean single sequence MFE -35.27
Consensus MFE -26.41
Energy contribution -25.97
Covariance contribution -0.44
Combinations/Pair 1.19
Mean z-score -4.10
Structure conservation index 0.75
SVM decision value 1.37
SVM RNA-class probability 0.947478
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13488433 97 - 22407834
UAAGGCAAAAGUUUCACUUUGGCUGUCGAC-----UCGACGCGAAUCG-GUCGGCAUUGUCAAAGGGAAAAU--UUUUUUUAUUUGCAUUUUGCCGUUUUUGUAA
...(((((((.((((.((((((((((((((-----.(((......)))-)))))))..))))))).))))..--..............))))))).......... ( -30.73)
>DroPse_CAF1 130476 103 - 1
UGAGGCAAAGUUUUCGCUUUGGCAGCCGACGCGACUCGACUCGAAUCGGGUUGGUAUUGUCAAAGUGAAAAU--UUGUUUCGUUUUCAGUUUGCCGUUUUUGUAA
.((((((((.((((((((((((((((((((.(((.(((...))).))).))))))..)))))))))))))))--)))))))........................ ( -40.80)
>DroEre_CAF1 91933 97 - 1
UAAGGCAAAAGUUUCACUUUGGCUGUCGAC-----UCGACGCGAAUCG-GUCGGCAUUGUCAAAGGGAAACA--UUUUUUUAUUUGCAUUUUGCCGUUUUUGUAA
...((((((((((((.((((((((((((((-----.(((......)))-)))))))..))))))).)))))(--(......)).....))))))).......... ( -32.50)
>DroYak_CAF1 89222 99 - 1
UAAGGCAAAAGUUUCACUUUGGCUGUCGAC-----UCGACGCGAAUCG-GUCGGCAUUGUCAAAGGGAAACAAUUUUUUUUAUUUGCAUUUUGCCGUUUUUGUAA
...((((((((((((.((((((((((((((-----.(((......)))-)))))))..))))))).)))))((......)).......))))))).......... ( -33.20)
>DroAna_CAF1 151385 97 - 1
UGAGGCAAAGUUUUCACUUUGGCAGCCGAC-----ACGACUAGAAACG-GUCGGCAUUGUCAAAGGGAAAAU--UUGUUUCACUUUCAUUUUGCCGUUUUUGUAA
(((((((((.(((((.((((((((((((((-----.((........))-))))))..))))))))))))).)--))))))))....................... ( -34.30)
>DroPer_CAF1 106835 103 - 1
UGAGGCAAAGUUUUCGCUUUGGCAGCCGACGCGACUCGACUGGAAUCGGGUUGGUAUUGUCAAAGUGAAAAU--UUGUUUCGUUUUCAGUUUGCCGUUUUUGUAA
.((((((((.((((((((((((((((((((.(((.((.....)).))).))))))..)))))))))))))))--)))))))........................ ( -40.10)
>consensus
UAAGGCAAAAGUUUCACUUUGGCAGCCGAC_____UCGACGCGAAUCG_GUCGGCAUUGUCAAAGGGAAAAU__UUGUUUCAUUUGCAUUUUGCCGUUUUUGUAA
...((((((((((((.(((((((.((((((.....((.....)).....))))))...))))))).))))).................))))))).......... (-26.41 = -25.97 +  -0.44)

alignment

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secondary structure

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Window 1

Location 13,488,465 – 13,488,565
Length 100
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 81.70
Mean single sequence MFE -25.42
Consensus MFE -15.23
Energy contribution -16.30
Covariance contribution 1.07
Combinations/Pair 1.07
Mean z-score -2.69
Structure conservation index 0.60
SVM decision value 0.75
SVM RNA-class probability 0.839964
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13488465 100 + 22407834
UUUUCCCUUUGACAAUGCCGAC-CGAUUCGCGUCGA-----GUCGACAGCCAAAGUGAAACUUUUGCCUUAAAUUGAAAUGCACAUUUUAAUUUCGGCCCGAAACC----
.((((.(((((....((.((((-((((....)))).-----)))).))..))))).)))).....(((..((((((((((....)))))))))).)))........---- ( -25.30)
>DroPse_CAF1 130508 106 + 1
UUUUCACUUUGACAAUACCAACCCGAUUCGAGUCGAGUCGCGUCGGCUGCCAAAGCGAAAACUUUGCCUCAAAUUUAAAUGCACAUUUUAAUUUCGGCCCGAAACC----
(((((.(((((.((...((.((.(((((((...))))))).)).)).)).))))).)))))....(((..(((((.((((....)))).))))).)))........---- ( -24.90)
>DroSec_CAF1 87221 100 + 1
UUUUCCCUUUGACAAUGCCGAC-CGAUUCGCGUCGA-----GUCGACAGCCAAAGUGAAACUUUUGCCUUAAAUUGAAAUGCACAUUUUAAUUUCGGCCCAAAACC----
.((((.(((((....((.((((-((((....)))).-----)))).))..))))).)))).....(((..((((((((((....)))))))))).)))........---- ( -25.30)
>DroWil_CAF1 138682 91 + 1
UGUUCACUUUGACAAUGCCCCC-CGAC------------------AAUGCCAAAGUGAAAACUUUGCCUCGAAUUGAAAUGAAAAUUUUAAUUUCGGCUCAAAACCGUUU
..(((((((((.((.((.....-...)------------------).)).)))))))))......(((..((((((((((....)))))))))).)))............ ( -23.60)
>DroAna_CAF1 151417 100 + 1
UUUUCCCUUUGACAAUGCCGAC-CGUUUCUAGUCGU-----GUCGGCUGCCAAAGUGAAAACUUUGCCUCAAAUUGAAAUGCACAUUUUAAUUUCGGCCCGAAACC----
(((((.(((((.((..((((((-((........)).-----)))))))).))))).)))))....(((..((((((((((....)))))))))).)))........---- ( -29.90)
>DroPer_CAF1 106867 106 + 1
UUUUCACUUUGACAAUACCAACCCGAUUCCAGUCGAGUCGCGUCGGCUGCCAAAGCGAAAACUUUGCCUCAAAUUUAAAUGCACAUUUUAAUUUCGGCCCGAAACC----
(((((.(((((.((...((.((.((((((.....)))))).)).)).)).))))).)))))....(((..(((((.((((....)))).))))).)))........---- ( -23.50)
>consensus
UUUUCACUUUGACAAUGCCGAC_CGAUUCGAGUCGA_____GUCGACUGCCAAAGUGAAAACUUUGCCUCAAAUUGAAAUGCACAUUUUAAUUUCGGCCCGAAACC____
.((((.(((((.......(.....)......(((((......)))))...))))).)))).....(((..((((((((((....)))))))))).)))............ (-15.23 = -16.30 +   1.07)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,488,465 – 13,488,565
Length 100
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 81.70
Mean single sequence MFE -33.03
Consensus MFE -20.85
Energy contribution -21.85
Covariance contribution 1.00
Combinations/Pair 1.10
Mean z-score -3.06
Structure conservation index 0.63
SVM decision value 1.09
SVM RNA-class probability 0.914081
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13488465 100 - 22407834
----GGUUUCGGGCCGAAAUUAAAAUGUGCAUUUCAAUUUAAGGCAAAAGUUUCACUUUGGCUGUCGAC-----UCGACGCGAAUCG-GUCGGCAUUGUCAAAGGGAAAA
----........(((.(((((.((((....)))).)))))..))).....((((.((((((((((((((-----.(((......)))-)))))))..))))))).)))). ( -29.60)
>DroPse_CAF1 130508 106 - 1
----GGUUUCGGGCCGAAAUUAAAAUGUGCAUUUAAAUUUGAGGCAAAGUUUUCGCUUUGGCAGCCGACGCGACUCGACUCGAAUCGGGUUGGUAUUGUCAAAGUGAAAA
----........(((.(((((.((((....)))).)))))..)))....((((((((((((((((((((.(((.(((...))).))).))))))..)))))))))))))) ( -39.00)
>DroSec_CAF1 87221 100 - 1
----GGUUUUGGGCCGAAAUUAAAAUGUGCAUUUCAAUUUAAGGCAAAAGUUUCACUUUGGCUGUCGAC-----UCGACGCGAAUCG-GUCGGCAUUGUCAAAGGGAAAA
----...(((..(((.(((((.((((....)))).)))))..)))..)))((((.((((((((((((((-----.(((......)))-)))))))..))))))).)))). ( -29.70)
>DroWil_CAF1 138682 91 - 1
AAACGGUUUUGAGCCGAAAUUAAAAUUUUCAUUUCAAUUCGAGGCAAAGUUUUCACUUUGGCAUU------------------GUCG-GGGGGCAUUGUCAAAGUGAACA
((((.((((((((..(((((.((....)).)))))..))))))))...))))(((((((((((.(------------------(((.-...)))).)))))))))))... ( -29.70)
>DroAna_CAF1 151417 100 - 1
----GGUUUCGGGCCGAAAUUAAAAUGUGCAUUUCAAUUUGAGGCAAAGUUUUCACUUUGGCAGCCGAC-----ACGACUAGAAACG-GUCGGCAUUGUCAAAGGGAAAA
----........(((.(((((.((((....)))).)))))..)))....(((((.((((((((((((((-----.((........))-))))))..))))))))))))). ( -31.90)
>DroPer_CAF1 106867 106 - 1
----GGUUUCGGGCCGAAAUUAAAAUGUGCAUUUAAAUUUGAGGCAAAGUUUUCGCUUUGGCAGCCGACGCGACUCGACUGGAAUCGGGUUGGUAUUGUCAAAGUGAAAA
----........(((.(((((.((((....)))).)))))..)))....((((((((((((((((((((.(((.((.....)).))).))))))..)))))))))))))) ( -38.30)
>consensus
____GGUUUCGGGCCGAAAUUAAAAUGUGCAUUUCAAUUUGAGGCAAAGUUUUCACUUUGGCAGCCGAC_____UCGACUCGAAUCG_GUCGGCAUUGUCAAAGGGAAAA
............(((..((((.((((....)))).))))...))).....((((.((((((((((((((.....((.....)).....))))))..)))))))).)))). (-20.85 = -21.85 +   1.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:57 2006