Locus 4915

Sequence ID 2L_DroMel_CAF1
Location 14,066,600 – 14,066,736
Length 136
Max. P 0.978982
window7797 window7798 window7799 window7800

overview

Window 7

Location 14,066,600 – 14,066,712
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.84
Mean single sequence MFE -26.20
Consensus MFE -16.12
Energy contribution -16.29
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.62
SVM decision value 0.38
SVM RNA-class probability 0.714066
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066600 112 + 22407834
UUCAUCUCACCCUGUCUGCCUGGCCAACGACUUGGUU--------UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCAACGG
...........((((..((..((((........(((.--------.(((...((((((.((......)).)))))))))..)))(((.((((((....))))))))))))).))..)))) ( -26.20)
>DroPse_CAF1 192910 102 + 1
----GCUGUCUCUGU----CUGGCCCAGGACUUGACU--------UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGAC--
----((.(((...((----((......))))..))).--------.((((.((((((((.((((((.........(((......)))....)))))).)))))))).)))).))....-- ( -25.12)
>DroGri_CAF1 186428 90 + 1
----------UUUGU----G-------CGACUUCG-G--------UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAA
----------.(((.----(-------((((....-)--------)((((.((((((((.((((((.........(((......)))....)))))).)))))))).))))...)))))) ( -24.12)
>DroWil_CAF1 218862 112 + 1
UUUAGCU---GCUG-----UUGGCCAUUGCCUUUGCUGCCUUCGCUCGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCAGUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAA
....((.---((..-----..((((.......((((((..(((((.......))))).))))))............((.....((((((...)))))).......)))))).)).))... ( -28.70)
>DroAna_CAF1 152946 100 + 1
UUCGGCACUCUGUGU----CUGGCCAACGACUUGGCA--------UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCC--------G
...(((((...))))----)..(((((....))))).--------.((((.((((((((.((((((.........(((......)))....)))))).)))))))).))))--------. ( -27.92)
>DroPer_CAF1 204970 102 + 1
----GCUGUCUCUGU----CUGGCCCAGGACUUGACU--------UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGAC--
----((.(((...((----((......))))..))).--------.((((.((((((((.((((((.........(((......)))....)))))).)))))))).)))).))....-- ( -25.12)
>consensus
____GCU_UCUCUGU____CUGGCCAACGACUUGGCU________UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGAC__
..............................................((((.((((((((.((((((.........(((......)))....)))))).)))))))).))))......... (-16.12 = -16.29 +   0.17)

alignment

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secondary structure

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Window 8

Location 14,066,600 – 14,066,712
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.84
Mean single sequence MFE -27.23
Consensus MFE -17.79
Energy contribution -18.40
Covariance contribution 0.61
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.65
SVM decision value 0.84
SVM RNA-class probability 0.863405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066600 112 - 22407834
CCGUUGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA--------AACCAAGUCGUUGGCCAGGCAGACAGGGUGAGAUGAA
(((((.((.((((((.....((((((((...))))))))((....(((((.(((....))).))))).....)).--------.........).)))))..)).))).)).......... ( -27.40)
>DroPse_CAF1 192910 102 - 1
--GUCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA--------AGUCAAGUCCUGGGCCAG----ACAGAGACAGC----
--((((((.....((.....((((((((...))))))))...)).(((((.(((....))).)))))....))).--------.(((..((.....))..)----))...)))...---- ( -25.80)
>DroGri_CAF1 186428 90 - 1
UUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA--------C-CGAAGUCG-------C----ACAAA----------
((((((((.((..((.......((((((...))))))((((((((............))))...))))...))..--------)-)...))))-------)----.))).---------- ( -24.00)
>DroWil_CAF1 218862 112 - 1
UUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCACUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCGAGCGAAGGCAGCAAAGGCAAUGGCCAA-----CAGC---AGCUAAA
(((((.((.(((((((......)))......(((((.((...((.(((((.(((....))).)))))........((....)).))..)))))))))))..-----..))---.))))). ( -34.20)
>DroAna_CAF1 152946 100 - 1
C--------GGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA--------UGCCAAGUCGUUGGCCAG----ACACAGAGUGCCGAA
(--------((((((((...((((((((...))))))))((....(((((.(((....))).))))).....)))--------)))...(((........)----)).....).)))).. ( -26.20)
>DroPer_CAF1 204970 102 - 1
--GUCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA--------AGUCAAGUCCUGGGCCAG----ACAGAGACAGC----
--((((((.....((.....((((((((...))))))))...)).(((((.(((....))).)))))....))).--------.(((..((.....))..)----))...)))...---- ( -25.80)
>consensus
__GUCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA________AGCCAAGUCGUUGGCCAG____ACAGAGA_AGC____
.........((((((.(...((((((((...)))))))).).)).(((((.(((....))).)))))............................))))..................... (-17.79 = -18.40 +   0.61)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,066,637 – 14,066,736
Length 99
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 78.78
Mean single sequence MFE -23.58
Consensus MFE -16.20
Energy contribution -16.37
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.69
SVM decision value 1.83
SVM RNA-class probability 0.978982
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066637 99 + 22407834
-----UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCAACGGACAAUAACAA------CAACAAC---GG--UGGCA
-----.((((.((((((((.((((((.........(((......)))....)))))).)))))))).)))).((((.((...........------......)---).--)))). ( -24.45)
>DroVir_CAF1 280227 94 + 1
-----UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAAACAAGCGAAG------C-----CUCCAA---A--A
-----.((((((((((((.((......)).))))))((((...((((((...)))))).......((((....)))).....))))))))------)-----).....---.--. ( -26.40)
>DroGri_CAF1 186443 100 + 1
-----UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAAACAAGCGAAG------CAAAAACACCAA--CA--A
-----(((....((((((.((......)).))))))(((((.(((((((...)))))........((((....))))......)).))))------).......))).--..--. ( -25.00)
>DroWil_CAF1 218894 112 + 1
UUCGCUCGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCAGUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAAACAACCAAAAAGUAAGAAACAAC---GAAACAACA
((((((..(((((((((((.((((((.........(((......)))....)))))).)))))))((((....))))...........))))..))......)---)))...... ( -21.42)
>DroMoj_CAF1 245599 94 + 1
-----UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCAGCCGCCAAACAAGCGAAG------C-----CUCCCA---A--A
-----.((((((((((((.((......)).))))))((((...((((((...)))))).......((((....)))).....))))))))------)-----).....---.--. ( -26.40)
>DroAna_CAF1 152979 89 + 1
-----UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUCCACUGCAAUAAAAUUGCAAUUUUAUGCGGCC--------GACA--AACAA------CAAAAAC---AC--UACCA
-----.((((.((((((((.((((((.........(((......)))....)))))).)))))))).))))--------....--.....------.......---..--..... ( -17.82)
>consensus
_____UGGCUUUGUGAAAUAGCAAUUACUUUUUCAUGCUUCACUGCAAUAAAAUUGCAAUUUUAUGCGGCCUGCCGCCAAACAAGCAAAA______CAA_AAC___AA___A__A
......((((.((((((((.((((((.........(((......)))....)))))).)))))))).))))............................................ (-16.20 = -16.37 +   0.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,066,637 – 14,066,736
Length 99
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 78.78
Mean single sequence MFE -26.64
Consensus MFE -15.74
Energy contribution -15.85
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -1.93
Structure conservation index 0.59
SVM decision value 0.67
SVM RNA-class probability 0.816499
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14066637 99 - 22407834
UGCCA--CC---GUUGUUG------UUGUUAUUGUCCGUUGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA-----
(((((--.(---(......------...........)).)))))(((.((.....((((((((...))))))))...)).(((((.(((....))).)))))....))).----- ( -23.73)
>DroVir_CAF1 280227 94 - 1
U--U---UUGGAG-----G------CUUCGCUUGUUUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA-----
.--.---.....(-----(------(((.((((.....((((....)))).....((((((((...)))))))).)))).(((((.(((....))).)))))..))))).----- ( -29.20)
>DroGri_CAF1 186443 100 - 1
U--UG--UUGGUGUUUUUG------CUUCGCUUGUUUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA-----
.--..--.((((.....((------((((((..((((.((((....))))...))))((((((...))))))))))))))(((((.(((....))).)))))....))))----- ( -31.40)
>DroWil_CAF1 218894 112 - 1
UGUUGUUUC---GUUGUUUCUUACUUUUUGGUUGUUUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCACUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCGAGCGAA
......(((---((......(((((((((.((.((((.((((....)))).......((((((...))))))...)))))).)))))))))(((((.........)))))))))) ( -27.70)
>DroMoj_CAF1 245599 94 - 1
U--U---UGGGAG-----G------CUUCGCUUGUUUGGCGGCUGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA-----
.--.---.....(-----(------(((.((((.....((((....)))).....((((((((...)))))))).)))).(((((.(((....))).)))))..))))).----- ( -29.20)
>DroAna_CAF1 152979 89 - 1
UGGUA--GU---GUUUUUG------UUGUU--UGUC--------GGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGGAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA-----
.(((.--((---(((((((------(.((.--....--------.)).)))....((((((((...)))))))))))))))((((.(((....))).)))).....))).----- ( -18.60)
>consensus
U__U___UU___GUU_UUG______CUUCGCUUGUUUGGCGGCAGGCCGCAUAAAAUUGCAAUUUUAUUGCAGUGAAGCAUGAAAAAGUAAUUGCUAUUUCACAAAGCCA_____
............................................(((.((.(...((((((((...)))))))).).)).(((((.(((....))).)))))....)))...... (-15.74 = -15.85 +   0.11)

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 11:30:57 2006