Locus 175

Sequence ID 3L_DroMel_CAF1
Location 529,474 – 529,599
Length 125
Max. P 0.989246
window250 window251 window252

overview

Window 0

Location 529,474 – 529,564
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.99
Mean single sequence MFE -41.72
Consensus MFE -17.90
Energy contribution -19.73
Covariance contribution 1.84
Combinations/Pair 1.07
Mean z-score -1.97
Structure conservation index 0.43
SVM decision value 0.01
SVM RNA-class probability 0.538006
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 529474 90 + 23771897
-----GGAGACCGGGCU----UGCGCAGGCGCCUGGAAGAAUCCGAAGCCGAGA-AGAGCGG---CGAGUG----UCC---GCUCUCUUU---UUUCGG-------CUCUGUGGCAACAA
-----(((..((((((.----.((....)))))))).....)))((.(((((((-((((.((---((....----..)---)).).))))---))))))-------)))..((....)). ( -38.00)
>DroSec_CAF1 3703 91 + 1
-----GGAGACCGGGCU----UGCGCAGGCGCCUGGAAGAAUCCGAAGCGGAGA-AGAGCGG---CGAG---UGGCCC---GCUCUCUUU---UUUCGG-------CUCUGUGGCAACAA
-----((((.((((((.----.((....))))))))......((((((.(((((-.((((((---(...---..).))---)))))))))---))))))-------)))).((....)). ( -37.70)
>DroSim_CAF1 4527 93 + 1
-----GGAGACCGGGCU----UGCGCAGGCGCCUGGAAGAAUCCGAAGCGGAGA-AGAGCGG---CGAGUG-UGGCCC---GCUCUCUUU---UUUCGG-------CUCUGUGGCAACAA
-----((((.((((((.----.((....))))))))......((((((.(((((-.((((((---(.....-..).))---)))))))))---))))))-------)))).((....)). ( -37.40)
>DroEre_CAF1 3827 93 + 1
-----GGAGACCGGGCU----UGCGCAGGCGCCUGGAAGAAUCCGGAGCGGAGAAAGAGCGGCGGCGAAAG----GCC---GCUCUCUU----UUUCGG-------CUCUGUGGCAACAA
-----(((..((((((.----.((....)))))))).....)))(((((.(((((((((.((((((.....----)))---))))))))----)))).)-------)))).((....)). ( -49.00)
>DroYak_CAF1 3894 97 + 1
-----GGAGACCGGGCU----UGCGCAGGCGCCUGGAAGAAUCCAGAGCGGAGAAAGAGCGGCGGCGAGAG----GCC---GCUCUCUUUGGUUUUCGG-------CUCUGUGGCAACAA
-----(((..((((((.----.((....)))))))).....)))(((((.(((((((((.((((((.....----)))---)))))))....))))).)-------)))).((....)). ( -43.50)
>DroAna_CAF1 5786 109 + 1
UUGGAGGAGAGCGCGCUCAGCUGCGCAGGCUCCAAGGAGAGAGAGAGUGUGAG--AGAGCGA------AAGCCGGUCCGGGGCUCUCUUU---UGUGGGCGAGCUUCUCUGCUGGAAGCC
..(((((((..(((((......))))..((.(((....((((((((((.(((.--.(.((..------..)))..))..).)))))))))---).))))))..)))))))((.....)). ( -44.70)
>consensus
_____GGAGACCGGGCU____UGCGCAGGCGCCUGGAAGAAUCCGAAGCGGAGA_AGAGCGG___CGAGAG____CCC___GCUCUCUUU___UUUCGG_______CUCUGUGGCAACAA
.....((((.((((((......((....))))))))......((((((...(((.(((((.....................))))).)))...)))))).......)))).((....)). (-17.90 = -19.73 +   1.84) 

alignment

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secondary structure

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dotplot

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Window 1

Location 529,505 – 529,599
Length 94
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 90.41
Mean single sequence MFE -34.22
Consensus MFE -28.44
Energy contribution -28.60
Covariance contribution 0.16
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.83
SVM decision value 0.76
SVM RNA-class probability 0.844106
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 529505 94 + 23771897
AUCCGAAGCCGAGA-AGAGCGG---CGAGUG---UCCGCUCUCUUU---UUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
...(((((((((((-((((.((---((....---..))).).))))---)))))))..((.((((.(........).)))).))....))))............ ( -30.40)
>DroSec_CAF1 3734 95 + 1
AUCCGAAGCGGAGA-AGAGCGG---CGAG--UGGCCCGCUCUCUUU---UUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
.((.(((.((((((-(((((((---(...--..).)))))).....---....(((.(((..((......))..))).)))....))))))).))).))..... ( -32.50)
>DroSim_CAF1 4558 97 + 1
AUCCGAAGCGGAGA-AGAGCGG---CGAGUGUGGCCCGCUCUCUUU---UUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
.((.(((.((((((-(((((((---(.......).)))))).....---....(((.(((..((......))..))).)))....))))))).))).))..... ( -32.20)
>DroEre_CAF1 3858 97 + 1
AUCCGGAGCGGAGAAAGAGCGGCGGCGAAAG---GCCGCUCUCUU----UUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
...((((((.(((((((((.((((((.....---)))))))))))----)))).)))))).((((.(........).))))...(((((.......)))))... ( -40.10)
>DroYak_CAF1 3925 101 + 1
AUCCAGAGCGGAGAAAGAGCGGCGGCGAGAG---GCCGCUCUCUUUGGUUUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
.....((((((((((((((((((........---))))))))....(((..((((..((.((....)).))..)))).)))....))))))).)))........ ( -35.90)
>consensus
AUCCGAAGCGGAGA_AGAGCGG___CGAGAG___CCCGCUCUCUUU___UUUCGGCUCUGUGGCAACAAAGUUUCGGUGCCUCAAUUCUUCGAUUCAGAGUCUC
.((.(((.((((((.(((((((.............)))))))...........(((.(((..((......))..))).))).....)))))).))).))..... (-28.44 = -28.60 +   0.16) 

alignment

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secondary structure

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dotplot

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Window 2

Location 529,505 – 529,599
Length 94
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 90.41
Mean single sequence MFE -32.78
Consensus MFE -28.85
Energy contribution -29.09
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.88
SVM decision value 2.16
SVM RNA-class probability 0.989246
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 529505 94 - 23771897
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAA---AAAGAGAGCGGA---CACUCG---CCGCUCU-UCUCGGCUUCGGAU
.....(((((.........(((.((((.(((....))).)))).)))((((((..---...((((((((.---(....)---)))))))-).))))))))))). ( -33.10)
>DroSec_CAF1 3734 95 - 1
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAA---AAAGAGAGCGGGCCA--CUCG---CCGCUCU-UCUCCGCUUCGGAU
....(((((..((((....))))((((.(((....))).)))).)))))(((((.---..(((((((((....--....---)))))).-)))....))))).. ( -32.40)
>DroSim_CAF1 4558 97 - 1
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAA---AAAGAGAGCGGGCCACACUCG---CCGCUCU-UCUCCGCUUCGGAU
....(((((..((((....))))((((.(((....))).)))).)))))(((((.---..(((((((((..........---)))))).-)))....))))).. ( -31.50)
>DroEre_CAF1 3858 97 - 1
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAA----AAGAGAGCGGC---CUUUCGCCGCCGCUCUUUCUCCGCUCCGGAU
.....((((...........((.((((.(((....))).)))).))((((.((.(----(((((.(((((---.....)))))..)))))).)).)))))))). ( -34.00)
>DroYak_CAF1 3925 101 - 1
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAAACCAAAGAGAGCGGC---CUCUCGCCGCCGCUCUUUCUCCGCUCUGGAU
(((((((((..((((....))))((((.(((....))).)))).)))))............(((((((((---........))))))))))))).......... ( -32.90)
>consensus
GAGACUCUGAAUCGAAGAAUUGAGGCACCGAAACUUUGUUGCCACAGAGCCGAAA___AAAGAGAGCGGC___CACUCG___CCGCUCU_UCUCCGCUUCGGAU
....(((((..((((....))))((((.(((....))).)))).)))))(((((........(((((((.............)))))))........))))).. (-28.85 = -29.09 +   0.24) 

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 09:34:36 2006