Locus 5500

Sequence ID 2L_DroMel_CAF1
Location 15,732,420 – 15,732,546
Length 126
Max. P 0.872020
window8725 window8726 window8727

overview

Window 5

Location 15,732,420 – 15,732,516
Length 96
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -22.24
Consensus MFE -15.57
Energy contribution -16.58
Covariance contribution 1.01
Combinations/Pair 1.13
Mean z-score -1.89
Structure conservation index 0.70
SVM decision value 0.29
SVM RNA-class probability 0.669481
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15732420 96 - 22407834
UCUAGAUGGGUAUCUUUAUCUUUGCAAGAUUAUGAAUAUCUAUAAGUUUUCAUAUAUUAAAUCUUAGGCAUGUUAAAAGGACUGUUUUAGAAC-UCA------
((((((..(((.(((((.....(((.((((((((((.((......)).))))))......))))...))).....))))))))..))))))..-...------ ( -15.90)
>DroSec_CAF1 51931 103 - 1
UCUAAAUGGGUAUCUUUAUCUAUGCAAGAGUUUGAAUAUCUAGAAGUUUUCUUAAAUUAAAUGUAAGGCAUGUUAGGAGGACCUUUCUGGAACAUCAGAUUUU
.....(((((((....)))))))...(((((((((...(((((((((((((((((.....(((.....))).))))))))))..)))))))...))))))))) ( -27.20)
>DroSim_CAF1 44650 103 - 1
UCUAAAUAGGUAUCUUUAUCUAUGCCAGAGUUUGAAUAUCUAGAAGUUUUCUUAUAUUAAAUAUAAGGCAUGUUAAGAGGACUGUUCUGGAGCAUCAACUUUU
.....(((((((....)))))))...((((((.((...((((((((((((((((...................))))))))))..))))))...)))))))). ( -23.61)
>consensus
UCUAAAUGGGUAUCUUUAUCUAUGCAAGAGUUUGAAUAUCUAGAAGUUUUCUUAUAUUAAAUAUAAGGCAUGUUAAGAGGACUGUUCUGGAACAUCA__UUUU
(((..(((((((....)))))))...)))..((((...((((((((((((((((...................)))))))))..)))))))...))))..... (-15.57 = -16.58 +   1.01)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,732,453 – 15,732,546
Length 93
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 71.74
Mean single sequence MFE -15.00
Consensus MFE -6.30
Energy contribution -6.14
Covariance contribution -0.16
Combinations/Pair 1.17
Mean z-score -1.84
Structure conservation index 0.42
SVM decision value 0.54
SVM RNA-class probability 0.774539
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15732453 93 + 22407834
GAUUUAAUAU-----AUGAAAACUUAUAG---AUAUUCAUAAUCUUGCAAAGAUAAAGAUACCCAUCUAGAGGGUACCAAACUAUCAAACAAGAAAACAAU
.........(-----(((((.........---...)))))).(((((....((((..(.(((((.......))))).)....))))...)))))....... ( -13.10)
>DroSec_CAF1 51971 93 + 1
CAUUUAAUUU-----AAGAAAACUUCUAG---AUAUUCAAACUCUUGCAUAGAUAAAGAUACCCAUUUAGAGGGUAGCAAACUAUCAAACAAGAAAACAAU
......((((-----(.((.....)))))---))........(((((....((((....(((((.......)))))......))))...)))))....... ( -12.10)
>DroSim_CAF1 44690 93 + 1
UAUUUAAUAU-----AAGAAAACUUCUAG---AUAUUCAAACUCUGGCAUAGAUAAAGAUACCUAUUUAGAGGGUACCAAACUAUCAAACAAGAAAACAAU
..........-----.......(((((((---(((.((....((((...))))....))....))))))))))............................ (  -9.30)
>DroEre_CAF1 50953 97 + 1
----CACGAGCAAAACUAAAAAGUUGUAGUUUGUAUUUAUACUCUGGUAUAAAUGAAGAUACCCUUCCAUAGGGUACCAAACUAACCAGCGGGCAAACCAU
----..................((((((((((((((((((((....)))))))))....((((((.....)))))).)))))))..))))((.....)).. ( -25.90)
>DroYak_CAF1 56699 89 + 1
----UAAGACCAGAACUGAAAAGCCG--------AUCUAUACUCUGGUAUAAUUCAAGAUACCCUUCCAGAGGGUACCAAACCAACAAACAAGAAAACCAU
----....((((((...((.......--------.)).....)))))).........(.(((((((...))))))).)....................... ( -14.60)
>consensus
_AUUUAAUAU_____AUGAAAACUUCUAG___AUAUUCAUACUCUGGCAUAGAUAAAGAUACCCAUCUAGAGGGUACCAAACUAUCAAACAAGAAAACAAU
.........................................................(.(((((.......))))).)....................... ( -6.30 =  -6.14 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,732,453 – 15,732,546
Length 93
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 71.74
Mean single sequence MFE -20.16
Consensus MFE -10.72
Energy contribution -11.92
Covariance contribution 1.20
Combinations/Pair 1.17
Mean z-score -1.84
Structure conservation index 0.53
SVM decision value 0.87
SVM RNA-class probability 0.872020
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15732453 93 - 22407834
AUUGUUUUCUUGUUUGAUAGUUUGGUACCCUCUAGAUGGGUAUCUUUAUCUUUGCAAGAUUAUGAAUAU---CUAUAAGUUUUCAU-----AUAUUAAAUC
.......((((((..(((((...(((((((.......))))))).)))))...)))))).((((((.((---......)).)))))-----)......... ( -24.00)
>DroSec_CAF1 51971 93 - 1
AUUGUUUUCUUGUUUGAUAGUUUGCUACCCUCUAAAUGGGUAUCUUUAUCUAUGCAAGAGUUUGAAUAU---CUAGAAGUUUUCUU-----AAAUUAAAUG
.(((..(((((((..(((((...(.(((((.......))))).).)))))...)))))))..)))....---..............-----.......... ( -18.50)
>DroSim_CAF1 44690 93 - 1
AUUGUUUUCUUGUUUGAUAGUUUGGUACCCUCUAAAUAGGUAUCUUUAUCUAUGCCAGAGUUUGAAUAU---CUAGAAGUUUUCUU-----AUAUUAAAUA
..........((((((((((((..(....((((..(((((((....)))))))...)))).)..)))..---....(((....)))-----.))))))))) ( -14.70)
>DroEre_CAF1 50953 97 - 1
AUGGUUUGCCCGCUGGUUAGUUUGGUACCCUAUGGAAGGGUAUCUUCAUUUAUACCAGAGUAUAAAUACAAACUACAACUUUUUAGUUUUGCUCGUG----
..((....))(((.(((((((((((((((((.....)))))))....((((((((....)))))))).))))))).((((....))))..))).)))---- ( -24.00)
>DroYak_CAF1 56699 89 - 1
AUGGUUUUCUUGUUUGUUGGUUUGGUACCCUCUGGAAGGGUAUCUUGAAUUAUACCAGAGUAUAGAU--------CGGCUUUUCAGUUCUGGUCUUA----
......((((.((....((((((((((((((.....))))))))..)))))).)).))))...((((--------(((..(....)..)))))))..---- ( -19.60)
>consensus
AUUGUUUUCUUGUUUGAUAGUUUGGUACCCUCUAGAUGGGUAUCUUUAUCUAUGCCAGAGUAUGAAUAU___CUACAAGUUUUCAU_____AUAUUAAAU_
......((((.((..(((((...(((((((.......))))))).)))))...)).))))......................................... (-10.72 = -11.92 +   1.20)

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 11:45:40 2006