Locus 4406

Sequence ID X_DroMel_CAF1
Location 11,626,343 – 11,626,543
Length 200
Max. P 0.875727
window7237 window7238 window7239 window7240

overview

Window 7

Location 11,626,343 – 11,626,463
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 74.26
Mean single sequence MFE -29.97
Consensus MFE -15.20
Energy contribution -17.45
Covariance contribution 2.25
Combinations/Pair 1.35
Mean z-score -1.90
Structure conservation index 0.51
SVM decision value -0.03
SVM RNA-class probability 0.518911
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11626343 120 - 22224390
GCCGUGUCAUCGCUAAGCGAUGUAUCGGCUAAUCGGGAUUGCGCGUUUCGCAACACUGGUUCGGAAAAGCAAUUAACCAAACAAAACGCGGAAUUAUUUGUUAAAUAAGCAAAUCAAGCC
((((...((((((...))))))...)))).....((((((((...(((((.(((....))))))))..))))))..))...........((....(((((((.....)))))))....)) ( -33.70)
>DroSim_CAF1 56249 117 - 1
GCCGUGUCAUCGCUAAGCGAUGUAUCGGCUAAUCAGGGUUGCGCGUUUCGCAACACUGGUUCGGGAAAGUAAUUAACCAAACAAAACGCGGAAUUAUUUCUUAAAUAA---AAGCAAGCC
((((...((((((...))))))...))))......((.((((((((((..((....))(((.((..((....))..)).))).))))))((((....)))).......---..)))).)) ( -34.80)
>DroEre_CAF1 57106 97 - 1
GCCGUGUCAUCGCUAAGCGAUAUAUCGGCAAAU-------------CUGGAAACACUGUUUCGGGAACG---UUAUACUAAUAUAAGUAGGAAUGAUUUGUCAAAUAA---AUGAA----
(((((((.(((((...)))))))).))))...(-------------((.(((((...))))).))).((---((.((((......))))..)))).............---.....---- ( -23.60)
>DroYak_CAF1 58524 113 - 1
GCCGUGUCAUCGCUAAGCGAUAUAUCGGUUUGUAUGGCUUGCGCGCUUGAAAACACUGUUUCAGGAAAGCAAUUAACCUAAUAUAACGUGGCAUUAUUUGUUAAAAAA---AUGCA----
(((((((....((.((((.(((((......))))).))))))((.(((((((......)))))))...))...............)))))))................---.....---- ( -27.80)
>consensus
GCCGUGUCAUCGCUAAGCGAUAUAUCGGCUAAUC_GG_UUGCGCGUUUCGAAACACUGGUUCGGGAAAGCAAUUAACCAAACAAAACGCGGAAUUAUUUGUUAAAUAA___AAGCA____
((((...((((((...))))))...)))).......((((((...(((((((......)))))))...)))))).............................................. (-15.20 = -17.45 +   2.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,626,383 – 11,626,503
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.67
Mean single sequence MFE -38.41
Consensus MFE -28.77
Energy contribution -28.65
Covariance contribution -0.12
Combinations/Pair 1.25
Mean z-score -1.54
Structure conservation index 0.75
SVM decision value 0.09
SVM RNA-class probability 0.579633
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11626383 120 + 22224390
UUGGUUAAUUGCUUUUCCGAACCAGUGUUGCGAAACGCGCAAUCCCGAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACA
.(((((.............)))))(..(((((.....)))))..)(((((.((((...((((((...))))))...))))((((.......)))))))))((((((.....))))))... ( -42.42)
>DroSim_CAF1 56286 120 + 1
UUGGUUAAUUACUUUCCCGAACCAGUGUUGCGAAACGCGCAACCCUGAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUUGCCUGCGGACAGCGCAGGACA
((((..((....))..))))..(((.((((((.....)))))).)))....((((...((((((...))))))...))))((((.......))))...((((((((.....)))))).)) ( -44.00)
>DroEre_CAF1 57139 104 + 1
UAGUAUAA---CGUUCCCGAAACAGUGUUUCCAG-------------AUUUGCCGAUAUAUCGCUUAGCGAUGACACGGCGUCACAUCGAUUGACAAUCGCCUGCGGACAGCGCAGGACG
........---.......(((((...)))))..(-------------(((.((((...((((((...))))))...))))((((.......))))))))(((((((.....)))))).). ( -29.80)
>DroYak_CAF1 58557 120 + 1
UAGGUUAAUUGCUUUCCUGAAACAGUGUUUUCAAGCGCGCAAGCCAUACAAACCGAUAUAUCGCUUAGCGAUGACACGGCGUCACGGCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACA
...((((((((((....(((....(((((.((((((((....))..........((....))))))...)).)))))....))).))))))))))....(((((((.....)))))).). ( -37.40)
>consensus
UAGGUUAAUUGCUUUCCCGAAACAGUGUUGCCAAACGCGCAA_CC_GAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACA
.................(((....(((((....))))).............((((...((((((...))))))...))))((((.......))))..)))((((((.....))))))... (-28.77 = -28.65 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,626,383 – 11,626,503
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.67
Mean single sequence MFE -42.38
Consensus MFE -28.90
Energy contribution -30.77
Covariance contribution 1.88
Combinations/Pair 1.31
Mean z-score -2.05
Structure conservation index 0.68
SVM decision value 0.89
SVM RNA-class probability 0.875727
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11626383 120 - 22224390
UGUCCUGCGCUGUCCGCAGGCGAUUGCCAAUCGAUGUGGCGCCGUGUCAUCGCUAAGCGAUGUAUCGGCUAAUCGGGAUUGCGCGUUUCGCAACACUGGUUCGGAAAAGCAAUUAACCAA
.(.((((((.....)))))))((((((((.......))))((((...((((((...))))))...)))).))))((((((((...(((((.(((....))))))))..))))))..)).. ( -46.10)
>DroSim_CAF1 56286 120 - 1
UGUCCUGCGCUGUCCGCAGGCAAUUGCCAAUCGAUGUGGCGCCGUGUCAUCGCUAAGCGAUGUAUCGGCUAAUCAGGGUUGCGCGUUUCGCAACACUGGUUCGGGAAAGUAAUUAACCAA
((.((((((.....))))))))...((((.......))))((((...((((((...))))))...)))).((((((.((((((.....)))))).)))))).((..((....))..)).. ( -47.40)
>DroEre_CAF1 57139 104 - 1
CGUCCUGCGCUGUCCGCAGGCGAUUGUCAAUCGAUGUGACGCCGUGUCAUCGCUAAGCGAUAUAUCGGCAAAU-------------CUGGAAACACUGUUUCGGGAACG---UUAUACUA
((.((((((.....))))))))............(((((((((((((.(((((...)))))))).))))...(-------------((.(((((...))))).)))..)---)))))... ( -35.90)
>DroYak_CAF1 58557 120 - 1
UGUCCUGCGCUGUCCGCAGGCGAUUGCCAAUCGCCGUGACGCCGUGUCAUCGCUAAGCGAUAUAUCGGUUUGUAUGGCUUGCGCGCUUGAAAACACUGUUUCAGGAAAGCAAUUAACCUA
.(.((((((.....)))))))(((.....)))((((((..(((((((.(((((...)))))))).))))...))))))((((...(((((((......)))))))...))))........ ( -40.10)
>consensus
UGUCCUGCGCUGUCCGCAGGCGAUUGCCAAUCGAUGUGACGCCGUGUCAUCGCUAAGCGAUAUAUCGGCUAAUC_GG_UUGCGCGUUUCGAAACACUGGUUCGGGAAAGCAAUUAACCAA
((.((((((.....))))))))...((((.......))))((((...((((((...))))))...)))).......((((((...(((((((......)))))))...))))))...... (-28.90 = -30.77 +   1.88)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,626,423 – 11,626,543
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -40.47
Consensus MFE -32.92
Energy contribution -32.80
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.66
Structure conservation index 0.81
SVM decision value 0.43
SVM RNA-class probability 0.735316
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11626423 120 + 22224390
AAUCCCGAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACAGCGGUAAUCGAUAGUCGAGAUUGCAUACCUGAUAUCAUCG
((((.((((((((((...((((((...))))))...))))......(((((((.(.....((((((.....)))))).....).))))))))))))).)))).................. ( -42.40)
>DroSim_CAF1 56326 120 + 1
AACCCUGAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUUGCCUGCGGACAGCGCAGGACAGCGGUAAUCGAUAGUCGAGAUUGCAUACCUGAUAUCAUCG
......(((((((((...((((((...))))))...))))......(((((((.(..(((((((((.....)))))).)))..)))))))))))))(((((..((....))..))).)). ( -39.30)
>DroEre_CAF1 57170 113 + 1
-------AUUUGCCGAUAUAUCGCUUAGCGAUGACACGGCGUCACAUCGAUUGACAAUCGCCUGCGGACAGCGCAGGACGGCAGUUAUCGAUAGUGCCGAUUGCAUACCUGGUAUCAUCG
-------....((((...((((((...))))))...))))(.(((((((((.(((..(((((((((.....)))))).)))..))))))))).))).)(((.(.((((...)))))))). ( -39.10)
>DroYak_CAF1 58597 120 + 1
AAGCCAUACAAACCGAUAUAUCGCUUAGCGAUGACACGGCGUCACGGCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACAGCGGUUAUCGAUAGUCGCGAUUGCAUACCUGGUACCAUCG
..((((..(((.(((...((((((...))))))...)))(((....))).)))(((((((((((((.....)))))).).(((..((....))..))))))))).....))))....... ( -41.10)
>consensus
AA_CC_GAUUAGCCGAUACAUCGCUUAGCGAUGACACGGCGCCACAUCGAUUGGCAAUCGCCUGCGGACAGCGCAGGACAGCGGUAAUCGAUAGUCGAGAUUGCAUACCUGAUAUCAUCG
...........((((...((((((...))))))...))))((((.......)))).....((((((.....)))))).(((..((((((.........))))))....)))......... (-32.92 = -32.80 +  -0.12)

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 11:24:15 2006