Locus 1726

Sequence ID 2L_DroMel_CAF1
Location 4,748,603 – 4,748,714
Length 111
Max. P 0.997513
window2770 window2771

overview

Window 0

Location 4,748,603 – 4,748,714
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -29.96
Consensus MFE -24.16
Energy contribution -26.46
Covariance contribution 2.30
Combinations/Pair 1.06
Mean z-score -2.26
Structure conservation index 0.81
SVM decision value 1.79
SVM RNA-class probability 0.977254
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4748603 111 + 22407834
CUCGAGCCACAAGGAAAACGUUUUAUUUACUUAGAUUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUGGAGAGUGC-------AAAAGGGAUUAUCUUGUGUUGCUG--U
....((((((((((((..(.((((........((.(((..(((((....)))))..))).))(((((((.((.....)))))))))-------)))).)..)).)))))))..))).--. ( -28.30)
>DroSec_CAF1 177210 111 + 1
CUGGAGCCACAAGGAAAUCGUUUUAUUUACUUAGAUUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUGGAGAGUGC-------AAAGGGGAUUAUCUUGUGUUGCUG--U
....((((((((((.((((.((((...........(((..(((((....)))))..)))..((((((((.((.....)))))))))-------))))).)))).)))))))..))).--. ( -32.00)
>DroSim_CAF1 172965 111 + 1
CUGGAGCCACAAGGAAAUCGUUUUAUUUACUUAGAUUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUGGAGAGUGC-------AAAGGGGAUUAUCUUGUGUUGCUG--U
....((((((((((.((((.((((...........(((..(((((....)))))..)))..((((((((.((.....)))))))))-------))))).)))).)))))))..))).--. ( -32.00)
>DroEre_CAF1 185557 112 + 1
CUAGAGCCACAAGGAAAUCGUUUUAUUUACUUAGACUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUAGGGAAUGCA--------AGGGGAUUAUCUUGUGUUGCUGUGU
.((.((((((((((.((((.((((................(((((....)))))........((((((((......)))))..))))--------))).)))).)))))))..))).)). ( -26.90)
>DroYak_CAF1 183612 118 + 1
CUAGAGCCACAAGGAAAUCGUUUUAUUUACUUAGAUUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUGCAGAAUGCAGAAUGCAAAAGGGAUUAUCUUGUAUUGCUG--U
....(((.((((((.((((............(((.(((..(((((....)))))..))).)))..((((..((((((((.....))))))))..)))).)))).))))))...))).--. ( -30.60)
>consensus
CUAGAGCCACAAGGAAAUCGUUUUAUUUACUUAGAUUAAGCUGUAGUGAUACAGAAUAAACUGCACUUUAUCAUUUUGGAGAGUGC_______AAAGGGGAUUAUCUUGUGUUGCUG__U
....((((((((((.((((.((((........((.(((..(((((....)))))..))).))(((((((..........)))))))........)))).)))).)))))))..))).... (-24.16 = -26.46 +   2.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,748,603 – 4,748,714
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -21.41
Consensus MFE -20.48
Energy contribution -20.12
Covariance contribution -0.36
Combinations/Pair 1.11
Mean z-score -1.83
Structure conservation index 0.96
SVM decision value 2.87
SVM RNA-class probability 0.997513
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4748603 111 - 22407834
A--CAGCAACACAAGAUAAUCCCUUUU-------GCACUCUCCAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAAUCUAAGUAAAUAAAACGUUUUCCUUGUGGCUCGAG
.--.(((..((((((............-------(((((.((......))...)))))((.(((..(((((....)))))..))).))...................))))))))).... ( -19.40)
>DroSec_CAF1 177210 111 - 1
A--CAGCAACACAAGAUAAUCCCCUUU-------GCACUCUCCAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAAUCUAAGUAAAUAAAACGAUUUCCUUGUGGCUCCAG
.--.(((..((((((..((((......-------(((((.((......))...)))))((.(((..(((((....)))))..))).)).............))))..))))))))).... ( -22.50)
>DroSim_CAF1 172965 111 - 1
A--CAGCAACACAAGAUAAUCCCCUUU-------GCACUCUCCAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAAUCUAAGUAAAUAAAACGAUUUCCUUGUGGCUCCAG
.--.(((..((((((..((((......-------(((((.((......))...)))))((.(((..(((((....)))))..))).)).............))))..))))))))).... ( -22.50)
>DroEre_CAF1 185557 112 - 1
ACACAGCAACACAAGAUAAUCCCCU--------UGCAUUCCCUAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAGUCUAAGUAAAUAAAACGAUUUCCUUGUGGCUCUAG
....(((..((((((..((((....--------.(((((..............)))))((.(((..(((((....)))))..))).)).............))))..))))))))).... ( -19.44)
>DroYak_CAF1 183612 118 - 1
A--CAGCAAUACAAGAUAAUCCCUUUUGCAUUCUGCAUUCUGCAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAAUCUAAGUAAAUAAAACGAUUUCCUUGUGGCUCUAG
.--.(((..((((((..((((...(((((...(((((((.(((.....).)).))))))).(((..(((((....)))))..))).....)))))......))))..))))))))).... ( -23.20)
>consensus
A__CAGCAACACAAGAUAAUCCCCUUU_______GCACUCUCCAAAAUGAUAAAGUGCAGUUUAUUCUGUAUCACUACAGCUUAAUCUAAGUAAAUAAAACGAUUUCCUUGUGGCUCCAG
....(((..((((((..((((.............(((((..............)))))((.(((..(((((....)))))..))).)).............))))..))))))))).... (-20.48 = -20.12 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:34 2006