Locus 3632

Sequence ID 3L_DroMel_CAF1
Location 10,682,580 – 10,682,735
Length 155
Max. P 0.848181
window5664 window5665 window5666

overview

Window 4

Location 10,682,580 – 10,682,695
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 88.06
Mean single sequence MFE -23.52
Consensus MFE -20.70
Energy contribution -20.73
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.88
SVM decision value 0.24
SVM RNA-class probability 0.650646
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10682580 115 + 23771897
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAA-----AAACUGGUUACCC
.((((((((.((((........((((.((...............)))))).......((.(((......)))...))..))))...))))))))..((((..-----....))))..... ( -23.16)
>DroSec_CAF1 16922 115 + 1
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAA-----AAACUGGUUUUCC
.((((((((.((((........((((.((...............)))))).......((.(((......)))...))..))))...))))))))..((((..-----....))))..... ( -23.16)
>DroSim_CAF1 18152 115 + 1
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAA-----AAACUGGUUUCCC
.((((((((.((((........((((.((...............)))))).......((.(((......)))...))..))))...))))))))..((((..-----....))))..... ( -23.16)
>DroEre_CAF1 17547 115 + 1
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUGCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAA-----AAACUGGUUUUCC
.((((((((.((((........((((.((...(......)....)))))).......((.(((......)))...))..))))...))))))))..((((..-----....))))..... ( -23.20)
>DroYak_CAF1 28946 120 + 1
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAAAAAAAAAACUGGUUUUCC
.((((((((.((((........((((.((...............)))))).......((.(((......)))...))..))))...)))))))).......................... ( -22.96)
>DroAna_CAF1 17306 96 + 1
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCCCC---------------CCCUCGAUGGCUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGGGCCUUCG-----AAACAGGUU----
.((((((((.((((((((((.......(((.((...---------------.....)).)))..))))))(.....)..))))...))))))))(((((...-----....)))))---- ( -25.50)
>consensus
UUAGGCGCCCGUGCUAAUUGUCACAGUGUCUUCUCUUUUUCUCCACCUGUUCUCCCAGUUACUUCAAUUAGUUUUACAUGCACUUUGGCGCCUGCUACUAAA_____AAACUGGUUUUCC
.((((((((.((((((((((....((((...............................)))).))))))(.....)..))))...)))))))).......................... (-20.70 = -20.73 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,682,580 – 10,682,695
Length 115
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -29.70
Consensus MFE -24.18
Energy contribution -25.18
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.81
SVM decision value 0.27
SVM RNA-class probability 0.660412
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10682580 115 - 23771897
GGGUAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
((....)).....-----.........(((((((...((((..(.....)((((((......(((......)))(((...............))).....)))))))))).))))))).. ( -29.86)
>DroSec_CAF1 16922 115 - 1
GGAAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
((((((....)))-----)))......(((((((...((((..(.....)((((((......(((......)))(((...............))).....)))))))))).))))))).. ( -28.66)
>DroSim_CAF1 18152 115 - 1
GGGAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
((....)).....-----.........(((((((...((((..(.....)((((((......(((......)))(((...............))).....)))))))))).))))))).. ( -32.86)
>DroEre_CAF1 17547 115 - 1
GGAAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGCAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
((((((....)))-----)))......(((((((...((((..(.....)((((((......(((......)))(((...(......)....))).....)))))))))).))))))).. ( -28.80)
>DroYak_CAF1 28946 120 - 1
GGAAAACCAGUUUUUUUUUUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
......((((((.((((..(((((.(((.((((....)))).)))...)))))..)))).))))))......(((((........(......).(((((........))))).))))).. ( -30.90)
>DroAna_CAF1 17306 96 - 1
----AACCUGUUU-----CGAAGGCCCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGCCAUCGAGGG---------------GGGGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
----..(((....-----...)))...(((((((...((((........((..((((.....))))..)---------------)((.......))..........)))).))))))).. ( -27.10)
>consensus
GGAAAACCAGUUU_____UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAGAAAAAGAGAAGACACUGUGACAAUUAGCACGGGCGCCUAA
...........................(((((((...((((..(.....)((((((......(((......)))(((...............))).....)))))))))).))))))).. (-24.18 = -25.18 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,682,620 – 10,682,735
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.44
Mean single sequence MFE -27.34
Consensus MFE -24.88
Energy contribution -24.72
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.36
Structure conservation index 0.91
SVM decision value 0.78
SVM RNA-class probability 0.848181
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10682620 115 - 23771897
CUCAUUUCUUCGACAAGAAAGAAAGAGAGAAGCGGCGAUUGGGUAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
(((.(((((((.....).))))))))).....(.((..(((..(..((((((.-----.(((((.(((.((((....)))).)))...))))).......))))))..)..))))).).. ( -25.80)
>DroSec_CAF1 16962 115 - 1
CUCAUUUCUCCGACAAGAUAGAAAGAGAGAGAAGGCGAUUGGAAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
(((.(((((((.............).))))))...((.(((.....((((((.-----.(((((.(((.((((....)))).)))...))))).......)))))).....))).))))) ( -23.82)
>DroSim_CAF1 18192 115 - 1
CUCAUUUCUCCAACAAGAAAGAAAGAGAGAGAAGGCGAUUGGGAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
.((((((((((....((...................((((((....)))))).-----.(((((.(((.((((....)))).)))...))))).........)).))))))...)))).. ( -26.90)
>DroEre_CAF1 17587 113 - 1
CUCAUUUCUCCGUCAAGAAAAA--GAGAGAGAUGGCGAUUGGAAAACCAGUUU-----UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
.((((((((((...........--).)))))))))((.(((.....((((((.-----.(((((.(((.((((....)))).)))...))))).......)))))).....))).))... ( -26.60)
>DroYak_CAF1 28986 118 - 1
CUCAUUUCUCGAUCAAGAAAGA--GAGAGAGCAAACGUUUGGAAAACCAGUUUUUUUUUUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
(((..(((((..((......))--..)))))....((..((.....((((((.((((..(((((.(((.((((....)))).)))...)))))..)))).)))))).....))..))))) ( -33.60)
>consensus
CUCAUUUCUCCGACAAGAAAGAAAGAGAGAGAAGGCGAUUGGAAAACCAGUUU_____UUUAGUAGCAGGCGCCAAAGUGCAUGUAAAACUAAUUGAAGUAACUGGGAGAACAGGUGGAG
(((.((((((..............)))))).....((.(((.....((((((.......(((((.(((.((((....)))).)))...))))).......)))))).....))).))))) (-24.88 = -24.72 +  -0.16)

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 11:02:47 2006