Locus 458

Sequence ID 2R_DroMel_CAF1
Location 2,617,953 – 2,618,111
Length 158
Max. P 0.994880
window875 window876 window877

overview

Window 5

Location 2,617,953 – 2,618,052
Length 99
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 75.52
Mean single sequence MFE -29.18
Consensus MFE -23.00
Energy contribution -23.01
Covariance contribution 0.00
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.79
SVM decision value 2.52
SVM RNA-class probability 0.994880
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2617953 99 + 20766785
UUUGUUCCCUCGUCCACGUUCCAUCCGCCCGUCUUCAUUUCCAUU--------------CCGGGGCAAACGGAUGGAUUUCAUGAGAGGGGCCUUACCCGAUUACCACAUUUU
...(..(((((........((((((((((((..............--------------.)))).....))))))))........)))))..).................... ( -27.95)
>DroSim_CAF1 50116 113 + 1
UUUGUUCCCUCGUCCACGUUUCAUCCGCCCGUCUUCAUUUCCAUUGGCUGACCAUCAGCCCGGGGCACACGGAUGGAUUUCAUGAGAGGGGCCUUACCCGAUUACCACAUUUU
...(..(((((........((((((((((((....).........(((((.....)))))..))))....)))))))........)))))..).................... ( -33.19)
>DroYak_CAF1 50087 93 + 1
UUUAUUCCCUCGUCCACGUUCCAUCCGCC--------------------GACUAUCUGCCCGGGGAACGCGGAUGGAUUUCAUUAGAGGGUCUGCACCCGAUUACCACAUUUU
......(((((........(((((((((.--------------------.....(((....)))....)))))))))........)))))....................... ( -26.39)
>consensus
UUUGUUCCCUCGUCCACGUUCCAUCCGCCCGUCUUCAUUUCCAUU____GAC_AUC_GCCCGGGGCACACGGAUGGAUUUCAUGAGAGGGGCCUUACCCGAUUACCACAUUUU
...(..(((((........((((((((((((.............................)))).....))))))))........)))))..).................... (-23.00 = -23.01 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,617,953 – 2,618,052
Length 99
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 75.52
Mean single sequence MFE -32.63
Consensus MFE -22.53
Energy contribution -23.42
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 1.43
SVM RNA-class probability 0.952886
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2617953 99 - 20766785
AAAAUGUGGUAAUCGGGUAAGGCCCCUCUCAUGAAAUCCAUCCGUUUGCCCCGG--------------AAUGGAAAUGAAGACGGGCGGAUGGAACGUGGACGAGGGAACAAA
....................(..((((((((((...((((((((.....((((.--------------.((....)).....)))))))))))).)))))..)))))..)... ( -31.70)
>DroSim_CAF1 50116 113 - 1
AAAAUGUGGUAAUCGGGUAAGGCCCCUCUCAUGAAAUCCAUCCGUGUGCCCCGGGCUGAUGGUCAGCCAAUGGAAAUGAAGACGGGCGGAUGAAACGUGGACGAGGGAACAAA
....................(..((((((((((..((((..((((.(.((...(((((.....)))))...))......).))))..))))....)))))..)))))..)... ( -36.60)
>DroYak_CAF1 50087 93 - 1
AAAAUGUGGUAAUCGGGUGCAGACCCUCUAAUGAAAUCCAUCCGCGUUCCCCGGGCAGAUAGUC--------------------GGCGGAUGGAACGUGGACGAGGGAAUAAA
..............((((....))))..........(((.((((((((((((((((.....)))--------------------..)))..))))))))))....)))..... ( -29.60)
>consensus
AAAAUGUGGUAAUCGGGUAAGGCCCCUCUCAUGAAAUCCAUCCGUGUGCCCCGGGC_GAU_GUC____AAUGGAAAUGAAGACGGGCGGAUGGAACGUGGACGAGGGAACAAA
....................(..((((((((((...((((((((.....((((.............................)))))))))))).)))))..)))))..)... (-22.53 = -23.42 +   0.89)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,618,014 – 2,618,111
Length 97
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 79.03
Mean single sequence MFE -28.63
Consensus MFE -22.40
Energy contribution -21.15
Covariance contribution -1.25
Combinations/Pair 1.30
Mean z-score -1.31
Structure conservation index 0.78
SVM decision value 0.56
SVM RNA-class probability 0.780590
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2618014 97 - 20766785
CGUUGUGUUACCACAUUAGCA-GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCUUGGUGAAAAUGUGGUAAUCGGGUAA-GGCCCCUCUCAUGAAAUC
..(..((((((((((((..((-.((..(((....(..(((....)))..))))..)).))..))))))))))..(((...-..)))....))..).... ( -29.00)
>DroSec_CAF1 52753 81 - 1
CGUUGUGUUACCACAUUAGCA-GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCCAGGUGAAAAUGUGGUAAUCGGGUA-----------------AUC
..(((.(((((((((((..((-.(...(((....(..(((....)))..))))...).))..))))))))))))))...-----------------... ( -24.00)
>DroSim_CAF1 50191 97 - 1
CGUUGUGUUACCACAUUACCA-GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCCAGGUGAAAAUGUGGUAAUCGGGUAA-GGCCCCUCUCAUGAAAUC
..(..(((((((((((((((.-((.(.(.....)(..(((....)))..)).))..)))))...))))))))..(((...-..)))....))..).... ( -28.40)
>DroEre_CAF1 51901 83 - 1
CGUUCUGUUGCCACAUUAGCG-GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCCAGGUGAAAAUGUGGUAAU---------------CUAAUGAAAUC
((((..(((((((((((.(((-((.(.(.....)(..(((....)))..)).)))..))...)))))))))))---------------..))))..... ( -27.10)
>DroYak_CAF1 50142 97 - 1
CGUUCUGUUACCACAUUAGCG-GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCCAGGUGAAAAUGUGGUAAUCGGGUGC-AGACCCUCUAAUGAAAUC
.............((((((.(-(.((((((....(..(((....)))..)..((((.((....)).))))....))))))-....)).))))))..... ( -32.00)
>DroPer_CAF1 67846 87 - 1
CGGUUUGUUGCCACAUUAGCAGGCGGCCUCAUAGCCGGUCAUUAUGCUGGUGGCUAAGUGAAAAUGUGGCAAUCAGGUAGAGGCCC------------C
..((((((((......))))))))((((((...((((((......)))))).((((.((....)).)))).........)))))).------------. ( -31.30)
>consensus
CGUUGUGUUACCACAUUAGCA_GCGCACUCAUAGGUGGUCAUUAGACUGCGGGCCAGGUGAAAAUGUGGUAAUCGGGUA__GGCCC__CU_AUGAAAUC
......(((((((((((..((.((.(.(.....)((((((....))))))).))....))..))))))))))).......................... (-22.40 = -21.15 +  -1.25)

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 09:39:07 2006