Locus 1257

Sequence ID 2R_DroMel_CAF1
Location 4,910,410 – 4,910,561
Length 151
Max. P 0.949451
window2178 window2179 window2180

overview

Window 8

Location 4,910,410 – 4,910,524
Length 114
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.76
Mean single sequence MFE -22.60
Consensus MFE -13.52
Energy contribution -13.54
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -1.64
Structure conservation index 0.60
SVM decision value -0.04
SVM RNA-class probability 0.514270
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4910410 114 + 20766785
CCACCAUGAUCUUUUUGAAGUUGUACAGACUCAUCUUGGCAGG-AUUUGUUUAUUUUCCACGCGU--C-G-AAAGGAAAAUAAAUGCGGAAUCGAAAGCAAAAACACCACGCGGUGUCA
...(((.(((...((((........))))...))).)))...(-(((((((((((((((......--.-.-...)))))))))))...)))))..........(((((....))))).. ( -22.50)
>DroVir_CAF1 75493 116 + 1
CCACCAUUAUCUUUUUAAAGUUGUACAAACUCAUUUUUGUACUUAUUUAUUUAUUUUCCACGGCAA-A-UUAAAGGAAAAUAAAUG-GGAAUCGCUUGCAAAAACACCACGCGGUGUCU
............((((.((((.(((((((......)))))))...((((((((((((((.......-.-.....))))))))))))-))....))))..))))(((((....))))).. ( -24.12)
>DroGri_CAF1 69581 115 + 1
CCACCAUUAUCUUUUUAAAGUUGUACAAACUCAUUUUCGCAGUUAUUUAUUUAUUUUCCAAGUUAA-U-C-UAAGGAAAAUAAAGG-GAAAUCGCUAACAAAUACACCACGCGGUGCCU
.((((.............((((.....)))).........(((.((((.((((((((((.......-.-.-...))))))))))..-.)))).)))................))))... ( -18.40)
>DroWil_CAF1 60186 117 + 1
CCACCAUUAUCUUUUUAAAAUUGUACAAACUCAUUUUUGUAGAAAUUUAUUUAUUUUCCAAGCCAAUU-A-AACGGAAAAUAAAUGAAAUGUGCAAAGCAAUAACACCACGCGGUGCUA
.((((...............(((((((..((((....)).))...((((((((((((((.........-.-...)))))))))))))).))))))).((...........))))))... ( -25.42)
>DroMoj_CAF1 93477 116 + 1
CCACCAUGAUCUUUUUAAAGUUGUACAAACUCAUUUUUGUGGCUAUUUAUUUAUUUUCCACGGCAA-A-A-AAAGGAAAAUAAAAGAGGAAUCGCUAGCAUAAACACCACGCGGUGUUC
.......(((((((((..(((..((((((......)))))))))......(((((((((.......-.-.-...))))))))))))))).))).........((((((....)))))). ( -21.90)
>DroPer_CAF1 37331 114 + 1
CCACCAUUAUCUUCUUAAAGUUGUACAAACUCAUUUUGUAUGG-UUUUAUUUAUUUUCCACGCGU--AAA-AAAGGAAAAUAAACGC-GAAUCUCAAGCAAAAACACCACGCGGUGCCU
.((((..........(((((..(((((((.....)))))))..-)))))((((((((((......--...-...)))))))))).((-(....................)))))))... ( -23.25)
>consensus
CCACCAUUAUCUUUUUAAAGUUGUACAAACUCAUUUUUGUAGGUAUUUAUUUAUUUUCCACGCCAA_A_A_AAAGGAAAAUAAAUG_GGAAUCGCAAGCAAAAACACCACGCGGUGCCU
.((((.............((((.....))))..................((((((((((...............))))))))))............................))))... (-13.52 = -13.54 +   0.03)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,910,450 – 4,910,561
Length 111
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 80.13
Mean single sequence MFE -28.95
Consensus MFE -20.30
Energy contribution -20.60
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -2.31
Structure conservation index 0.70
SVM decision value 1.19
SVM RNA-class probability 0.928173
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4910450 111 + 20766785
AGG-AUUUGUUUAUUUUCCACGCGU-CG-AAAGGAAAAUAAAUGCGGAA-UCGAAAGCAAAAACACCACGCGGUGUCAGCUUCGUAUUCCAAAAAGAACCGGUUCUCGGGCGGAA
...-....(((((((((((......-..-...)))))))))))((((((-(((((.((....(((((....)))))..)))))).)))))........(((.....))))).... ( -32.30)
>DroVir_CAF1 75533 106 + 1
ACUUAUUUAUUUAUUUUCCACGGCAAAUUAAAGGAAAAUAAAUG-GGAA-UCGCUUGCAAAAACACCACGCGGUGUCUGCAACAAAUUCCAAAAAGAGCUGAUAU------AGA-
.(((...((((((((((((.............))))))))))))-((((-(...(((((...(((((....))))).)))))...)))))...))).........------...- ( -26.52)
>DroSim_CAF1 62290 111 + 1
AGG-AUUUGUUUAUUUUCCACGCGU-CA-AAAGGAAAAUAAAUGCGGAA-UCGAAAGCAAAAACACCACGCGGUGUCAGCUUCGUAUUCCAAAAAGAACUGGUUCACGGGUGGAA
...-...........((((((.(((-..-................((((-(((((.((....(((((....)))))..)))))).))))).....(((....)))))).)))))) ( -31.00)
>DroEre_CAF1 58273 111 + 1
AGG-AUCUGUUUAUUUUCCACGCGA-CG-AAAGGAAAAUAAAUGCGGAA-UCGACAGCAAAAACACCACGCGGUGUCAGCUUCGUAUUCCAAAAAGAACCGGUUCUUAGGUGGAA
.((-.((((((((((((((......-..-...)))))))))))..((((-((((.(((....(((((....)))))..)))))).)))))....))).))..((((.....)))) ( -31.80)
>DroMoj_CAF1 93517 106 + 1
GGCUAUUUAUUUAUUUUCCACGGCAAAA-AAAGGAAAAUAAAAGAGGAA-UCGCUAGCAUAAACACCACGCGGUGUUCGCAACAAAUUCCAAAAAGAGCUGAUGU------AGA-
((((.(((.((((((((((.........-...))))))))))...((((-(.....((...((((((....)))))).)).....)))))..))).)))).....------...- ( -24.80)
>DroAna_CAF1 38501 112 + 1
AGG-AUUUGUUUAUUUUCCACGCGA-CA-AAAGGAAAAUAAAACGGGAAUUCGACAGCAUAAACACCACGCGGUGUUCGCUCCGUAUUCCAAAAAGAGCCGGUUCAAGGGUGGAA
...-...........((((((.(..-.(-(..((...........(((((.((..(((...((((((....)))))).))).)).)))))........))..))...).)))))) ( -27.31)
>consensus
AGG_AUUUGUUUAUUUUCCACGCGA_CA_AAAGGAAAAUAAAUGCGGAA_UCGAAAGCAAAAACACCACGCGGUGUCAGCUUCGUAUUCCAAAAAGAACCGGUUC__GGGUGGAA
........(((((((((((.............)))))))))))..((((.....((((....(((((....)))))..))))....))))......................... (-20.30 = -20.60 +   0.31)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,910,450 – 4,910,561
Length 111
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 80.13
Mean single sequence MFE -29.79
Consensus MFE -24.00
Energy contribution -22.97
Covariance contribution -1.03
Combinations/Pair 1.19
Mean z-score -2.42
Structure conservation index 0.81
SVM decision value 1.39
SVM RNA-class probability 0.949451
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4910450 111 - 20766785
UUCCGCCCGAGAACCGGUUCUUUUUGGAAUACGAAGCUGACACCGCGUGGUGUUUUUGCUUUCGA-UUCCGCAUUUAUUUUCCUUU-CG-ACGCGUGGAAAAUAAACAAAU-CCU
....(((((.....)))........(((((.((((((.((((((....))))))...)).)))))-)))))).((((((((((...-..-......)))))))))).....-... ( -32.70)
>DroVir_CAF1 75533 106 - 1
-UCU------AUAUCAGCUCUUUUUGGAAUUUGUUGCAGACACCGCGUGGUGUUUUUGCAAGCGA-UUCC-CAUUUAUUUUCCUUUAAUUUGCCGUGGAAAAUAAAUAAAUAAGU
-...------......(((..(((.((((((..(((((((((((....))))))..)))))..))-))))-.(((((((((((.............))))))))))))))..))) ( -28.02)
>DroSim_CAF1 62290 111 - 1
UUCCACCCGUGAACCAGUUCUUUUUGGAAUACGAAGCUGACACCGCGUGGUGUUUUUGCUUUCGA-UUCCGCAUUUAUUUUCCUUU-UG-ACGCGUGGAAAAUAAACAAAU-CCU
((((((.((((((....))).....(((((.((((((.((((((....))))))...)).)))))-))))................-..-))).))))))...........-... ( -31.70)
>DroEre_CAF1 58273 111 - 1
UUCCACCUAAGAACCGGUUCUUUUUGGAAUACGAAGCUGACACCGCGUGGUGUUUUUGCUGUCGA-UUCCGCAUUUAUUUUCCUUU-CG-UCGCGUGGAAAAUAAACAGAU-CCU
...............((.(((....(((((.((((((.((((((....))))))...))).))))-))))...((((((((((...-..-......)))))))))).))).-)). ( -31.90)
>DroMoj_CAF1 93517 106 - 1
-UCU------ACAUCAGCUCUUUUUGGAAUUUGUUGCGAACACCGCGUGGUGUUUAUGCUAGCGA-UUCCUCUUUUAUUUUCCUUU-UUUUGCCGUGGAAAAUAAAUAAAUAGCC
-...------......(((.(((..((((((.((((((((((((....)))))))..)).)))))-))))...((((((((((...-.........)))))))))).))).))). ( -26.80)
>DroAna_CAF1 38501 112 - 1
UUCCACCCUUGAACCGGCUCUUUUUGGAAUACGGAGCGAACACCGCGUGGUGUUUAUGCUGUCGAAUUCCCGUUUUAUUUUCCUUU-UG-UCGCGUGGAAAAUAAACAAAU-CCU
...............((........(((((.(((((((((((((....)))))))..))).))).))))).((((.(((((((...-..-......)))))))))))....-)). ( -27.60)
>consensus
UUCCACCC__GAACCAGCUCUUUUUGGAAUACGAAGCUGACACCGCGUGGUGUUUUUGCUAUCGA_UUCCGCAUUUAUUUUCCUUU_UG_UCGCGUGGAAAAUAAACAAAU_CCU
.........................((((..((((((.((((((....))))))...))).)))..))))...((((((((((.............))))))))))......... (-24.00 = -22.97 +  -1.03)

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 10:00:15 2006