Locus 4282

Sequence ID X_DroMel_CAF1
Location 11,270,415 – 11,270,594
Length 179
Max. P 0.999616
window7039 window7040 window7041

overview

Window 9

Location 11,270,415 – 11,270,517
Length 102
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 75.15
Mean single sequence MFE -15.85
Consensus MFE -10.26
Energy contribution -10.26
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.76
Structure conservation index 0.65
SVM decision value 3.79
SVM RNA-class probability 0.999616
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11270415 102 + 22224390
U-UCA-CAUA--CAUGU----------ACAUAUGUAUAUUAAUCCCAUAAGGUCUAUGCUUCUCACUAUCAGCUUAGCAUAGAUAAUAAUCUUUUCCUAAUUAGAAACUAUAUAAA
(-((.-.(((--((((.----------...)))))))..............(((((((((...............)))))))))...................))).......... ( -15.26)
>DroSec_CAF1 923 98 + 1
UAUAA-CAUA-----------------ACAUAUAUUUAUUAUUCCCAUAUGGUCUAUGCUUCGCACUAUCAGCUUAGCAUAGAUAAUAAUCUCUUCCUAAUUAGAAACUAUAUAAA
.....-....-----------------...................((((((((((((((..((.......))..))))))))........(((........)))..))))))... ( -16.30)
>DroEre_CAF1 990 115 + 1
U-CUCUUAUUAUCUACUAUGAAUAUAUAUAUAUAUAUAUUGUUUCCAUAAGGUCUAUGCUUCCUACUAUCAGCUGAGCAUAGAUAAUACCCAUUUCCUAAUUAAAAACUAUAUAAA
.-..(((((.....((.(((.(((((....))))).))).))....)))))((((((((((.((......))..))))))))))................................ ( -16.00)
>consensus
U_UAA_CAUA__C___U__________ACAUAUAUAUAUUAUUCCCAUAAGGUCUAUGCUUCCCACUAUCAGCUUAGCAUAGAUAAUAAUCUUUUCCUAAUUAGAAACUAUAUAAA
...................................................(((((((((...............)))))))))................................ (-10.26 = -10.26 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,270,415 – 11,270,517
Length 102
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 75.15
Mean single sequence MFE -20.47
Consensus MFE -14.86
Energy contribution -15.20
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -1.56
Structure conservation index 0.73
SVM decision value 1.11
SVM RNA-class probability 0.917482
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11270415 102 - 22224390
UUUAUAUAGUUUCUAAUUAGGAAAAGAUUAUUAUCUAUGCUAAGCUGAUAGUGAGAAGCAUAGACCUUAUGGGAUUAAUAUACAUAUGU----------ACAUG--UAUG-UGA-A
......((((..(.....(((............((((((((..((.....))....)))))))))))...)..))))((((((((....----------..)))--))))-)..-. ( -20.00)
>DroSec_CAF1 923 98 - 1
UUUAUAUAGUUUCUAAUUAGGAAGAGAUUAUUAUCUAUGCUAAGCUGAUAGUGCGAAGCAUAGACCAUAUGGGAAUAAUAAAUAUAUGU-----------------UAUG-UUAUA
.....(((((((((........)))))))))..((((((((..((.......))..))))))))((....))..((((((......)))-----------------))).-..... ( -21.20)
>DroEre_CAF1 990 115 - 1
UUUAUAUAGUUUUUAAUUAGGAAAUGGGUAUUAUCUAUGCUCAGCUGAUAGUAGGAAGCAUAGACCUUAUGGAAACAAUAUAUAUAUAUAUAUAUUCAUAGUAGAUAAUAAGAG-A
........(((((..((((.....(((((((.....))))))).....))))..)))))......((((((....)((((((((....))))))))...........)))))..-. ( -20.20)
>consensus
UUUAUAUAGUUUCUAAUUAGGAAAAGAUUAUUAUCUAUGCUAAGCUGAUAGUGAGAAGCAUAGACCUUAUGGGAAUAAUAUAUAUAUGU__________A___G__UAUG_UAA_A
..(((((.(((((((...(((............((((((((..((.....))....)))))))))))..))))))).))))).................................. (-14.86 = -15.20 +   0.34)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,270,481 – 11,270,594
Length 113
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 90.67
Mean single sequence MFE -26.12
Consensus MFE -21.16
Energy contribution -20.98
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -1.51
Structure conservation index 0.81
SVM decision value 0.13
SVM RNA-class probability 0.595639
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11270481 113 - 22224390
UUGCUGCCAAAUGCGAAUUUAAAGCGAUUUA-AAGACUGACAAUUUGCAGGCGGAAGAUAGUGGAUGGGACAUGUACGUUUAUAUAGUUUCUAAUUAGGAAAAGAUUAUUAUCU
...(((((...((((((((...(((......-..).))...))))))))))))).(((((((((...((((......))))......(((((.....)))))...))))))))) ( -23.50)
>DroSec_CAF1 985 112 - 1
UUGCUGCCAAAUGCGAAUUUAAAGCGAUUUAAAAGACUGGCAAUUUGCAGGCGGCAGAUAGUGGAUG--ACAUGUACUUUUAUAUAGUUUCUAAUUAGGAAGAGAUUAUUAUCU
.(((((((...((((((((...(((.........).))...)))))))))))))))(((((((....--.)))..........(((((((((........))))))))))))). ( -27.20)
>DroEre_CAF1 1069 111 - 1
UUGCUGCCAAAUGCGAAUUUAAAGCGAUUUG-AAGACUGGGAAUUCGCAGGCGGAAGAUAGUGGAUG--ACAUGUACAUUUAUAUAGUUUUUAAUUAGGAAAUGGGUAUUAUCU
...(((((...(((((((((..(((......-..).))..))))))))))))))........(((((--(..((..(((((...((((.....))))..)))))..)))))))) ( -26.70)
>DroYak_CAF1 1060 111 - 1
UUGCCGCCAAAUGCGAAUUUAAGGCGAUUUA-AAGACUGAGAAUUUGCAGGCGGAAGAUUGUGGAUG--ACACGUACAUUUAUAUAGUCUUUAAUUAGGAAAUGAUUAUUAUCU
...(((((...(((((((((..(((......-..).))..))))))))))))))(((((((((((((--.......))))..)))))))))((((((.....))))))...... ( -27.10)
>consensus
UUGCUGCCAAAUGCGAAUUUAAAGCGAUUUA_AAGACUGACAAUUUGCAGGCGGAAGAUAGUGGAUG__ACAUGUACAUUUAUAUAGUUUCUAAUUAGGAAAAGAUUAUUAUCU
...(((((...(((((((((..(((.........).))..)))))))))))))).((((((((.......)))...(((((...((((.....))))..))))).....))))) (-21.16 = -20.98 +  -0.19)

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 11:21:10 2006