Locus 1431

Sequence ID 2L_DroMel_CAF1
Location 3,814,473 – 3,814,602
Length 129
Max. P 0.990755
window2332 window2333 window2334

overview

Window 2

Location 3,814,473 – 3,814,567
Length 94
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 77.35
Mean single sequence MFE -10.98
Consensus MFE -1.54
Energy contribution -3.18
Covariance contribution 1.64
Combinations/Pair 1.11
Mean z-score -2.20
Structure conservation index 0.14
SVM decision value 1.35
SVM RNA-class probability 0.945344
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3814473 94 - 22407834
GCUCCACA--AAC-CAACCAAUUGGUUGGAACAUAAAGUUCAACAACAAACAGAGCCAUAAACAUUCCCAU-UACAAAUUAACACUUC------AUAUAUAUUC
((((....--...-(((((....)))))((((.....))))...........))))...............-................------.......... ( -14.50)
>DroSim_CAF1 3478 94 - 1
GCUUCACA--AAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCAU-UACAAAUUAACACUUC------AUAUAUAUUC
((((....--(((-(((....))))))(((((.....)))))..........))))...............-................------.......... ( -13.70)
>DroEre_CAF1 7747 96 - 1
GCGCCACAAGAAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCAU-UACAAAUUAACACUUC------AUAUAUAUUC
((........(((-(((....))))))(((((.....)))))............))...............-................------.......... ( -12.40)
>DroWil_CAF1 13338 99 - 1
GCUUUUCA--UGCUGAACCAAUUUGUAGAGUCAUAAAAUUGAACAACAAACAU---CAUCAUCAUAAUCAUCAACAAAUUAACACUUCACAUUCAUAUAUGCUC
.......(--((.(((.....(((((....(((......)))...)))))...---..))).)))....................................... (  -6.50)
>DroAna_CAF1 4023 79 - 1
----------GA--GCACCAAUUGGCUGGAACAUAAAGUUC---AACAAACAGAGCCAUAAACAUUCCC-C-UACAAAUUAACACUUC------AUA--UAUUC
----------..--........(((((.((((.....))))---..(.....))))))...........-.-................------...--..... (  -7.80)
>consensus
GCUCCACA__AAC_CAACCAAUUGGUUGGAACAUAAAGUUCAACAACAAACAGAGCCAUAAACAUUCCCAU_UACAAAUUAACACUUC______AUAUAUAUUC
..............(((((....)))))((((.....))))............................................................... ( -1.54 =  -3.18 +   1.64)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,814,500 – 3,814,602
Length 102
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 77.27
Mean single sequence MFE -27.62
Consensus MFE -9.97
Energy contribution -12.63
Covariance contribution 2.67
Combinations/Pair 1.16
Mean z-score -2.41
Structure conservation index 0.36
SVM decision value 0.18
SVM RNA-class probability 0.619969
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3814500 102 + 22407834
UGGGAAUGUUUAUGGCUCUGUUUGUUGUUGAACUUUAUGUUCCAACCAAUUGGUUG-GUU--UGUGGAGCAA-UGGGGGAAAUUCCCAGAGGGAGACAUUAAUUUA
...((((....(((.((((.(((.(..(((..(((((((..((((((....)))))-)..--))))))))))-..)(((.....)))))).)))).)))..)))). ( -30.90)
>DroSec_CAF1 3515 101 + 1
UGGGAAUGUUUAUGGCUCUGUUUGUUGUGGAACUUUAUGUUCCAACCAAUUGGUUG-GUU--UGUGGAGCAA-UAGGGGA-AUUCCCAGAGGGAGACAAUAAUUUA
(((((((.(((((.((((..(.......(((((.....)))))((((((....)))-)))--.)..)))).)-))))...-)))))))...(....)......... ( -31.70)
>DroSim_CAF1 3505 101 + 1
UGGGAAUGUUUAUGGCUCUGUUUGUUGUGGAACUUUAUGUUCCAACCAAUUGGUUG-GUU--UGUGAAGCAA-UAGGGGA-AUUCCCAGACGGAGACCAUAAUUAA
.........((((((((((((((.........(((((((..((((((....)))))-)..--)))))))...-...(((.-...))))))))))).)))))).... ( -36.70)
>DroEre_CAF1 7774 94 + 1
UGGGAAUGUUUAUGGCUCUGUUUGUUGUGGAACUUUAUGUUCCAACCAAUUGGUUG-GUUCUUGUGGCGCAA-UGGGU----------GAGGGUGACAUUAAUUUA
....((((((....((((((..(((((((..((.....(..((((((....)))))-)..)..))..)))))-))..)----------.)))))))))))...... ( -25.80)
>DroWil_CAF1 13372 85 + 1
UGAUUAUGAUGAUG---AUGUUUGUUGUUCAAUUUUAUGACUCUACAAAUUGGUUCAGCA--UGAAAAGCAAAUAUAGGA-AUUACCU--------------UUA-
......((((....---(((((((((.((((......(((..(........)..)))...--)))).)))))))))....-))))...--------------...- ( -13.00)
>DroYak_CAF1 3448 102 + 1
UGGAAAUGUUUAUGGCACUGUUUGUUGUGGAACUUUAUGUUCCAACCAAUUGGUUG-GUU-UGGUGGAGCAA-UGGGGCA-AUUCCCAGAGGGUGACAUUAAUUUA
...((((....(((.((((.((((....((((((((((((((((.((((.......-..)-))))))))).)-)))))..-.)))))))).)))).)))..)))). ( -27.60)
>consensus
UGGGAAUGUUUAUGGCUCUGUUUGUUGUGGAACUUUAUGUUCCAACCAAUUGGUUG_GUU__UGUGGAGCAA_UAGGGGA_AUUCCCAGAGGGAGACAUUAAUUUA
.((((((........(((((.(((((..(((((.....)))))((((....))))............))))).)))))...))))))................... ( -9.97 = -12.63 +   2.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,814,500 – 3,814,602
Length 102
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 77.27
Mean single sequence MFE -19.14
Consensus MFE -7.75
Energy contribution -9.37
Covariance contribution 1.61
Combinations/Pair 1.27
Mean z-score -3.41
Structure conservation index 0.41
SVM decision value 2.23
SVM RNA-class probability 0.990755
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3814500 102 - 22407834
UAAAUUAAUGUCUCCCUCUGGGAAUUUCCCCCA-UUGCUCCACA--AAC-CAACCAAUUGGUUGGAACAUAAAGUUCAACAACAAACAGAGCCAUAAACAUUCCCA
...................((((((........-..((((....--...-(((((....)))))((((.....))))...........)))).......)))))). ( -21.13)
>DroSec_CAF1 3515 101 - 1
UAAAUUAUUGUCUCCCUCUGGGAAU-UCCCCUA-UUGCUCCACA--AAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCA
...................((((((-.....((-(.((((....--(((-(((....))))))(((((.....)))))..........)))).)))...)))))). ( -24.40)
>DroSim_CAF1 3505 101 - 1
UUAAUUAUGGUCUCCGUCUGGGAAU-UCCCCUA-UUGCUUCACA--AAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCA
....((((((.(((.((..(((...-.)))...-(((.......--(((-(((....))))))(((((.....)))))....))))).)))))))))......... ( -25.10)
>DroEre_CAF1 7774 94 - 1
UAAAUUAAUGUCACCCUC----------ACCCA-UUGCGCCACAAGAAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCA
......(((((....(((----------.....-............(((-(((....))))))(((((.....)))))..........)))......))))).... ( -14.60)
>DroWil_CAF1 13372 85 - 1
-UAA--------------AGGUAAU-UCCUAUAUUUGCUUUUCA--UGCUGAACCAAUUUGUAGAGUCAUAAAAUUGAACAACAAACAU---CAUCAUCAUAAUCA
-.((--------------((((((.-........)))))))).(--((.(((.....(((((....(((......)))...)))))...---..))).)))..... (  -9.90)
>DroYak_CAF1 3448 102 - 1
UAAAUUAAUGUCACCCUCUGGGAAU-UGCCCCA-UUGCUCCACCA-AAC-CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGUGCCAUAAACAUUUCCA
.......(((.(((....((((...-...))))-(((........-(((-(((....))))))(((((.....)))))....)))...))).)))........... ( -19.70)
>consensus
UAAAUUAAUGUCUCCCUCUGGGAAU_UCCCCCA_UUGCUCCACA__AAC_CAACCAAUUGGUUGGAACAUAAAGUUCCACAACAAACAGAGCCAUAAACAUUCCCA
...................((((((.........................(((((....)))))((((.....))))......................)))))). ( -7.75 =  -9.37 +   1.61)

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 10:02:31 2006