Locus 2371

Sequence ID X_DroMel_CAF1
Location 6,329,598 – 6,329,817
Length 219
Max. P 0.756618
window3857 window3858

overview

Window 7

Location 6,329,598 – 6,329,701
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.77
Mean single sequence MFE -18.78
Consensus MFE -12.21
Energy contribution -11.78
Covariance contribution -0.43
Combinations/Pair 1.23
Mean z-score -1.51
Structure conservation index 0.65
SVM decision value 0.49
SVM RNA-class probability 0.756618
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6329598 103 - 22224390
AAUACGGCAGUUGGCAUAGUUUUCAA-CUAU--CACAAAAAGUGAUUUAAUACAGCUGUUGAAAUUUUAGCUAAAUUGAAUUAUGACUGUUUUAUUC--------------GACACAAAA
((((..(((((((..(((((.....)-))))--..).....((((((((((..(((((.........)))))..))))))))))))))))..)))).--------------......... ( -21.20)
>DroSec_CAF1 14263 103 - 1
AAUACAGCAGUUGGCAUAGUUUUCAA-GCAU--CACAAAAAGUGAUUUAAUACAGCUGUUGAAAUUUUAUCUAAAUUGAAUUAUGAGUGUUUUACUC--------------UGCCAAAAA
....(((((((((((...........-))((--(((.....)))))......))))))))).......................(((((...)))))--------------......... ( -19.70)
>DroSim_CAF1 7675 103 - 1
AAUACAGCAGUUGGCAUAGUUUUCAA-CCAU--CACAAAAAGUGAUUUAAUACAGCUGUUGAAAUUUUAUCUAAAUUGAAUUAUGAGUGUUUUACUC--------------UGCCGAAAA
....(((((((((.....((.....)-).((--(((.....)))))......))))))))).......................(((((...)))))--------------......... ( -17.60)
>DroEre_CAF1 11844 78 - 1
AAUACGGCAGUUGGC-------------------ACAAAAAGUGAUUUAUCACAGCUGCUGAUAUGUUAGCUAAAUUGAAUUAUGACUGGCCU-----------------------AAAA
....(((((((((.(-------------------((.....)))........)))))))))....(((((((((......))).).)))))..-----------------------.... ( -16.80)
>DroYak_CAF1 10447 120 - 1
AAUACGCCAGUUGGCAUAGAUUUCAAACCAACACACAAAAAGUGAUUUAACACAGCUGGUGAUAUUUUAGAUAAAUUCAAUUUUGAACGUUAUAAUGCUAAAAAAAAAAAAAACAGAAAA
....(((((((((...((((((.....................))))))...)))))))))...((((((((((.((((....))))..))))....))))))................. ( -18.60)
>consensus
AAUACGGCAGUUGGCAUAGUUUUCAA_CCAU__CACAAAAAGUGAUUUAAUACAGCUGUUGAAAUUUUAGCUAAAUUGAAUUAUGACUGUUUUACUC______________UACAGAAAA
....(((((((((.....(....).........(((.....)))........)))))))))........................................................... (-12.21 = -11.78 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,329,701 – 6,329,817
Length 116
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 89.47
Mean single sequence MFE -25.02
Consensus MFE -16.59
Energy contribution -18.15
Covariance contribution 1.56
Combinations/Pair 1.15
Mean z-score -2.04
Structure conservation index 0.66
SVM decision value -0.01
SVM RNA-class probability 0.528950
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6329701 116 + 22224390
UAAAAAUAAUUGAACAGGGCAACAAGGCGUAUGAUGAAUACUAAUAUUUAUGCUGCGUACACACUUCGCUUGCAGCAUCAUACACAUGUUGUCAAUAAAUAUUUUUAAUGAAGCAA
((((((((.(((.....(((((((.(..((((((((((((....))))))(((((((..(.......)..))))))))))))).).)))))))..))).))))))))......... ( -29.20)
>DroSec_CAF1 14366 115 + 1
UCA-AAUAAUUGAACAGGGCAACACGGCGUAUGAUGAGUACUAAUAUUUAUGCUGCGUACACACUUCGCUUGCAGCAACAUGAACAUGUUGUCAAUAAAUAUUUUUAAUGAAGCAA
(((-(....))))....(((((((.(...(((((((((((....)))))))((((((..(.......)..))))))..))))..).)))))))....................... ( -23.40)
>DroSim_CAF1 7778 115 + 1
UCA-AAUAAUUGAACAGGGCAACACGGCGUAUGAUGAAUACUAAUAUUUAUGCUGCAUACACACUUCGCUUGCAGCAACAUACACAUGUUGUCAAUAAAUAUUUUUAAUGAAGCAA
(((-(....))))....(((((((.(..((((((((((((....)))))))((((((..(.......)..))))))..))))).).)))))))....................... ( -26.80)
>DroEre_CAF1 11922 115 + 1
UAA-AAUAAUUGAGCCGGACAACACGGCCUUUGAUGAAUACUAAUAUUUAUGCGGCGAACAUACUUCGUGUGCAGCAUAUUUCAUAUAUUGCCAAUAAAUAUUUUUAAUGAAGCAA
...-.........((((.......))))(((((.((((....(((((((((..(((((.(((((...))))).....(((.....)))))))).))))))))))))).)))))... ( -20.70)
>consensus
UAA_AAUAAUUGAACAGGGCAACACGGCGUAUGAUGAAUACUAAUAUUUAUGCUGCGUACACACUUCGCUUGCAGCAACAUACACAUGUUGUCAAUAAAUAUUUUUAAUGAAGCAA
.................(((((((..(.((((((((((((....)))))))((((((..(.......)..))))))..))))).).)))))))....................... (-16.59 = -18.15 +   1.56)

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 10:32:55 2006