Locus 3182

Sequence ID 2R_DroMel_CAF1
Location 10,869,745 – 10,869,889
Length 144
Max. P 0.989810
window5235 window5236 window5237 window5238

overview

Window 5

Location 10,869,745 – 10,869,855
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.09
Mean single sequence MFE -31.88
Consensus MFE -20.61
Energy contribution -21.80
Covariance contribution 1.19
Combinations/Pair 1.09
Mean z-score -2.68
Structure conservation index 0.65
SVM decision value 2.18
SVM RNA-class probability 0.989810
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10869745 110 + 20766785
AGUAAUAAAUAAGCCAUGUUUGUAAG---------AGCUGAAAAUUUGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUUAGU-UUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAAC
.................((((((..(---------.(((..........(((((..((((.....)))).)))))....((-(((((((((......)))))))))))))))..)))))) ( -33.40)
>DroSim_CAF1 10645 110 + 1
AGUAAUAAAUAAGCCAUGUUUAUAAG---------AGCUGAAAAUCAGUUCGAUUUUCGCUGAUGGCGCUAUCGAUUUAGU-UUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAAC
............(((..........(---------(((((.....))))))(((...(((.....)))..)))......((-(((((((((......))))))))))).....))).... ( -33.40)
>DroEre_CAF1 11595 107 + 1
AGUAAUAAAUAAGUCAUGUGUAUAGG---------AGCCGA--AUCAGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUU-GC-UUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAAC
..........................---------.((((.--......(((((..((((.....)))).))))).((-((-(((((((((......)))))))))))))..)))).... ( -36.00)
>DroAna_CAF1 23077 108 + 1
AGUAAUAAAUAAAGUUUGCCUAUAUGGAGGAUGGAGGCUAA--AACAGUUCGAUUCUCGCUGAUGGCUAUAUCGAUUCAGUUUUAGCCGAAAUGUAAUUUGGCUUAGCAG----------
.............(((.(((...((...(.((...((((((--(((...(((((....((.....))...)))))....)))))))))...)).).))..)))..)))..---------- ( -24.70)
>consensus
AGUAAUAAAUAAGCCAUGUUUAUAAG_________AGCUGA__AUCAGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUUAGU_UUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAAC
....................................((((.........(((((...(((.....)))..)))))....((.(((((((((......)))))))))))....)))).... (-20.61 = -21.80 +   1.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,869,745 – 10,869,855
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.09
Mean single sequence MFE -26.55
Consensus MFE -15.45
Energy contribution -16.07
Covariance contribution 0.63
Combinations/Pair 1.10
Mean z-score -2.75
Structure conservation index 0.58
SVM decision value 1.75
SVM RNA-class probability 0.975324
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10869745 110 - 20766785
GUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAA-ACUAAAUCGAUAUCGCCAUCAGCGAAAAUCGAACAAAUUUUCAGCU---------CUUACAAACAUGGCUUAUUUAUUACU
(((((..((((((.((((((.((......)).))))))-......(((((.((((.....))))..))))).........)))))---------)...)))))................. ( -28.10)
>DroSim_CAF1 10645 110 - 1
GUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAA-ACUAAAUCGAUAGCGCCAUCAGCGAAAAUCGAACUGAUUUUCAGCU---------CUUAUAAACAUGGCUUAUUUAUUACU
(((((..((((((.((((((.((......)).))))))-......(((((..(((.....)))...))))).........)))))---------)...)))))................. ( -25.90)
>DroEre_CAF1 11595 107 - 1
GUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAA-GC-AAAUCGAUAUCGCCAUCAGCGAAAAUCGAACUGAU--UCGGCU---------CCUAUACACAUGACUUAUUUAUUACU
....((((((.(((((((((.((......)).))))))-))-)..(((((.((((.....))))..))))).....)--))))).---------.......................... ( -31.10)
>DroAna_CAF1 23077 108 - 1
----------CUGCUAAGCCAAAUUACAUUUCGGCUAAAACUGAAUCGAUAUAGCCAUCAGCGAGAAUCGAACUGUU--UUAGCCUCCAUCCUCCAUAUAGGCAAACUUUAUUUAUUACU
----------.......(((((((...)))).(((((((((....(((((...((.....))....)))))...)))--))))))...............)))................. ( -21.10)
>consensus
GUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAA_ACUAAAUCGAUAUCGCCAUCAGCGAAAAUCGAACUGAU__UCAGCU_________CUUAUAAACAUGGCUUAUUUAUUACU
........(((((.((((((.((......)).)))))).......(((((..(((.....)))...))))).........)))))................................... (-15.45 = -16.07 +   0.63)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,869,776 – 10,869,889
Length 113
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 95.28
Mean single sequence MFE -35.00
Consensus MFE -33.45
Energy contribution -33.23
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.41
Structure conservation index 0.96
SVM decision value 1.47
SVM RNA-class probability 0.956863
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10869776 113 + 20766785
AAAAUUUGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUUAGUUUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAACAAUGUGGCCCAAUAUCGGCCUCGUCAAACAAAGG
....((((((.(((....((((..((((....)......(((((((((((......))))))))))).))))))).......(.((((.......)))).)))).)))))).. ( -35.70)
>DroSim_CAF1 10676 113 + 1
AAAAUCAGUUCGAUUUUCGCUGAUGGCGCUAUCGAUUUAGUUUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAACAAUGUGGCCCAAUAUCGGCCUCGUCAAACAAAGG
.......(((.(((....((((..(((..((......))(((((((((((......))))))))))).))))))).......(.((((.......)))).)))).)))..... ( -32.00)
>DroEre_CAF1 11626 110 + 1
A--AUCAGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUU-GCUUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAACAAUGUGGCCCAAUCUCGGCCUCGUCAAACAAAGG
.--......(((((..((((.....)))).))))).((-(((((((((((......))))))))))))).((........(((.((((.......)))).)))........)) ( -37.29)
>consensus
AAAAUCAGUUCGAUUUUCGCUGAUGGCGAUAUCGAUUUAGUUUAGCCGAAAUGUAAUUUGGCUAAGCAGCCCGGCAAACAAUGUGGCCCAAUAUCGGCCUCGUCAAACAAAGG
.......(((.(((....((((..((((....)......(((((((((((......))))))))))).))))))).......(.((((.......)))).)))).)))..... (-33.45 = -33.23 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,869,776 – 10,869,889
Length 113
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -32.30
Consensus MFE -28.89
Energy contribution -29.00
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.78
Structure conservation index 0.89
SVM decision value 0.06
SVM RNA-class probability 0.563425
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10869776 113 - 20766785
CCUUUGUUUGACGAGGCCGAUAUUGGGCCACAUUGUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAAACUAAAUCGAUAUCGCCAUCAGCGAAAAUCGAACAAAUUUU
..((((((((((((((((.......)))).....((((((((((((....))))((((...)))))))).))))....)))...((((.....))))...))))))))).... ( -33.30)
>DroSim_CAF1 10676 113 - 1
CCUUUGUUUGACGAGGCCGAUAUUGGGCCACAUUGUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAAACUAAAUCGAUAGCGCCAUCAGCGAAAAUCGAACUGAUUUU
.....(((((((((((((.......)))).....((((((((((((....))))((((...)))))))).))))....)))....(((.....)))....))))))....... ( -28.70)
>DroEre_CAF1 11626 110 - 1
CCUUUGUUUGACGAGGCCGAGAUUGGGCCACAUUGUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAAGC-AAAUCGAUAUCGCCAUCAGCGAAAAUCGAACUGAU--U
.....((((((...((((.......))))......(((((..((((((((((((.((......)).))))))))-)....(....))))....)))))..))))))....--. ( -34.90)
>consensus
CCUUUGUUUGACGAGGCCGAUAUUGGGCCACAUUGUUUGCCGGGCUGCUUAGCCAAAUUACAUUUCGGCUAAACUAAAUCGAUAUCGCCAUCAGCGAAAAUCGAACUGAUUUU
.....(((((((((((((.......)))).....((((((((((((....))))((((...)))))))).))))....)))...((((.....))))...))))))....... (-28.89 = -29.00 +   0.11)

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 10:49:27 2006