Locus 6889

Sequence ID 3L_DroMel_CAF1
Location 18,583,621 – 18,583,753
Length 132
Max. P 0.898282
window11168 window11169 window11170

overview

Window 8

Location 18,583,621 – 18,583,736
Length 115
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 83.42
Mean single sequence MFE -37.62
Consensus MFE -30.82
Energy contribution -30.82
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.82
SVM decision value 0.12
SVM RNA-class probability 0.594979
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18583621 115 - 23771897
--CAACCGACGUC--AACUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCUGCGGUACUGGGAGCGAUCAGAAUGAC
--........(((--((((((((((((((((((.......)))))((..((((((.......)))))).))..............))))))))).))).((((......))))..)))) ( -38.30)
>DroVir_CAF1 9159 111 - 1
--A--CAUUAACC--A-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCCCUAGACCAACGAGCCAGUUGAAGGUGGAUCG-CCAUAUUGUA
--.--......((--(-(((.((((((((((((.......)))))((..((((((.......)))))).))..............)))))))......))))))....-.......... ( -37.90)
>DroPse_CAF1 20371 115 - 1
--UAAUUCACUUCCAC-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCAGUUGAACAUGGAGAG-UCCUAUUGUG
--...........(((-...((((((((((.((........)).)))).((((((.......))))))........((((...((((......))))....)))))))-)))....))) ( -35.20)
>DroWil_CAF1 40632 115 - 1
UUCAUACUUCAAC--A-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCGGUUGAAGGUUGAGCG-CCGCAUUGUC
((((..(((((((--.-....((((((((((((.......)))))((..((((((.......)))))).))..............))))))).)))))))..))))..-.......... ( -41.20)
>DroAna_CAF1 17955 112 - 1
--AUUUCAAAUUA--G-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCAGUUGAAGGUGGAGCGC-CGGAUUGU-
--..(((...(((--(-((..((((((((((((.......)))))((..((((((.......)))))).))..............))))))))))))).((((...)))-))))....- ( -37.90)
>DroPer_CAF1 21027 115 - 1
--UAAUUCACUUCCAC-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCAGUUGAACAUGGAGAG-UCCUAUUGUG
--...........(((-...((((((((((.((........)).)))).((((((.......))))))........((((...((((......))))....)))))))-)))....))) ( -35.20)
>consensus
__AAAUCCACUUC__A_CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCUAGACCAACGAGCCAGUUGAACGUGGAGCG_UCAUAUUGUC
.....................((((((((((((.......)))))((..((((((.......)))))).))..............)))))))........................... (-30.82 = -30.82 +  -0.00)

alignment

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secondary structure

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Window 9

Location 18,583,661 – 18,583,753
Length 92
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 78.43
Mean single sequence MFE -27.25
Consensus MFE -23.50
Energy contribution -23.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -0.85
Structure conservation index 0.86
SVM decision value -0.02
SVM RNA-class probability 0.521936
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18583661 92 + 23771897
AGAGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAGUUGACG-UCGGUUG----UAAUUUUUUUU--UG---------UUUU----------
.((.((....(((((((.......)))))))((((.(((.......)))))))............)).-)).....----...........--..---------....---------- ( -23.90)
>DroGri_CAF1 9570 96 + 1
AGGGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG-UGGUA-UAAA--U----AAAUUUUUUGUAUU----------UUUUUUG--ACU--
..((((....(((((((.......)))))))((((.(((.......)))))))..))))(((-..(((-((((--.----......))))))).----------.)))...--...-- ( -29.90)
>DroEre_CAF1 19364 105 + 1
AGAGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG-UGAUG-UCGGUUG----UAAUUUUUUUU--UAAAAGCAAAUAUUU----UUAA-C
(((((((((((..((((((.((((.(....)((((.(((.......)))))))..)))))))-))).)-))..(((----(..((((....--.))))))))))))))----))..-. ( -28.40)
>DroWil_CAF1 40671 101 + 1
AGAGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG-UGUUG-AAGUAUGAAAUUAAUUUUUUUA--CG---------UUUU----AUAAAU
.(.(((....(((((((.......)))))))((((.(((.......)))))))..))))...-...((-(((..(((((.......)))))--..---------))))----)..... ( -26.80)
>DroYak_CAF1 21255 94 + 1
AGAGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG-UGAUG-UCGGUUG----UAAUUUUUUUU-------------CUUU----UUAA-U
.......((((..((((((.((((.(....)((((.(((.......)))))))..)))))))-))).)-)))....----...........-------------....----....-. ( -25.70)
>DroMoj_CAF1 10060 97 + 1
AGGGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG-UUGUUCAAAA--U----AAAUUUUUUGU--U----------GUGGUUUCUUCA--
..((((....(((((((.......)))))))((((.(((.......)))))))..))))(((-....(((.((--(----((.....))))--)----------.)))...)))..-- ( -28.80)
>consensus
AGAGGUAUGAUUCUCGCUUCGGGUGCGAGAGGUCCCGGGUUCAAUUCCCGGACGAGCCCAAG_UGAUG_UAGGUUG____UAAUUUUUUUU__U__________UUUU____UUAA__
.(.(((....(((((((.......)))))))((((.(((.......)))))))..))))........................................................... (-23.50 = -23.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,583,661 – 18,583,753
Length 92
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 78.43
Mean single sequence MFE -21.72
Consensus MFE -20.75
Energy contribution -20.53
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -1.54
Structure conservation index 0.96
SVM decision value 1.00
SVM RNA-class probability 0.898282
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18583661 92 - 23771897
----------AAAA---------CA--AAAAAAAAUUA----CAACCGA-CGUCAACUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCU
----------....---------..--...........----....(((-.(((......))))))((((((.......))))))...((((((.......))))))........... ( -22.20)
>DroGri_CAF1 9570 96 - 1
--AGU--CAAAAAA----------AAUACAAAAAAUUU----A--UUUA-UACCA-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCCCU
--...--.......----------..............----.--....-.....-...(((...((((.((........)).)))).((((((.......)))))).......))). ( -22.20)
>DroEre_CAF1 19364 105 - 1
G-UUAA----AAAUAUUUGCUUUUA--AAAAAAAAUUA----CAACCGA-CAUCA-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCU
.-((((----((........)))))--)..........----...((((-.....-.))))....((((.((........)).)))).((((((.......))))))........... ( -21.20)
>DroWil_CAF1 40671 101 - 1
AUUUAU----AAAA---------CG--UAAAAAAAUUAAUUUCAUACUU-CAACA-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCU
......----....---------.(--((....................-.....-...((.....((((((.......)))))).))((((((.......))))))....))).... ( -20.30)
>DroYak_CAF1 21255 94 - 1
A-UUAA----AAAG-------------AAAAAAAAUUA----CAACCGA-CAUCA-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCU
.-....----....-------------...........----...((((-.....-.))))....((((.((........)).)))).((((((.......))))))........... ( -20.90)
>DroMoj_CAF1 10060 97 - 1
--UGAAGAAACCAC----------A--ACAAAAAAUUU----A--UUUUGAACAA-CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCCCU
--............----------.--.(((((.....----.--))))).....-...(((...((((.((........)).)))).((((((.......)))))).......))). ( -23.50)
>consensus
__UUAA____AAAA__________A__AAAAAAAAUUA____CAACCGA_CAUCA_CUUGGGCUCGUCCGGGAAUUGAACCCGGGACCUCUCGCACCCGAAGCGAGAAUCAUACCUCU
...........................................................(((...((((.((........)).)))).((((((.......))))))......))).. (-20.75 = -20.53 +  -0.22)

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 12:32:15 2006