Locus 5684

Sequence ID X_DroMel_CAF1
Location 14,704,299 – 14,704,421
Length 122
Max. P 0.999939
window9228 window9229 window9230 window9231

overview

Window 8

Location 14,704,299 – 14,704,389
Length 90
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 75.16
Mean single sequence MFE -25.83
Consensus MFE -17.52
Energy contribution -17.63
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.68
SVM decision value 2.54
SVM RNA-class probability 0.995039
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14704299 90 + 22224390
AAGAUGUUGCUGCU--------------CUGCGCUGAAGUUAUGCGAAAUGGACGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUAGCCAUCGUUUUUUUUCU--
..((((..((....--------------..))(((((((.....)((((((((.((((.((....)).)))).)).)))))).))))))))))...........-- ( -25.50)
>DroEre_CAF1 23610 98 + 1
AAGAUGUUGUUGAUGCGCAUUGCUGCUGCUGCGCUGAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUUUCCUUUUUUUU--------
..............(((((..((....))))))).((((..(((.(((.((((((((.....)).)))))).))).)))..)))).............-------- ( -29.00)
>DroYak_CAF1 21404 90 + 1
AAGAUGUU----------------GCUACUGCGCUAAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUCUUCCAUUUUUUUUUUUGUUU
((((((..----------------((....))...((((..(((.(((.((((((((.....)).)))))).))).)))..))))....))))))........... ( -23.00)
>consensus
AAGAUGUUG_UG_U__________GCU_CUGCGCUGAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUUUCCAUUUUUUUUUUU_U__
...................................((((..(((.(((.((((((((.....)).)))))).))).)))..))))..................... (-17.52 = -17.63 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,704,299 – 14,704,389
Length 90
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 75.16
Mean single sequence MFE -25.87
Consensus MFE -17.82
Energy contribution -17.60
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -3.06
Structure conservation index 0.69
SVM decision value 4.69
SVM RNA-class probability 0.999939
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14704299 90 - 22224390
--AGAAAAAAAACGAUGGCUAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGUCCAUUUCGCAUAACUUCAGCGCAG--------------AGCAGCAACAUCUU
--...........(((((((....((((((.((.((((.((....)).)))).))))))))...........((....--------------.)))))..)))).. ( -26.30)
>DroEre_CAF1 23610 98 - 1
--------AAAAAAAAGGAAAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUCAGCGCAGCAGCAGCAAUGCGCAUCAACAACAUCUU
--------.......((((.....((((((.((((((((((..........)))))))))).)))...))).(((((((....))..)))))..........)))) ( -28.80)
>DroYak_CAF1 21404 90 - 1
AAACAAAAAAAAAAAUGGAAGAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUUAGCGCAGUAGC----------------AACAUCUU
..............(((....((((..(((.((((((((((..........)))))))))).)))..)))).((......))----------------..)))... ( -22.50)
>consensus
__A_AAAAAAAAAAAUGGAAAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUCAGCGCAG_AGC__________A_CA_CAACAUCUU
......................(((..(((.((((((((((..........)))))))))).)))..))).................................... (-17.82 = -17.60 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,704,313 – 14,704,421
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.00
Mean single sequence MFE -25.37
Consensus MFE -20.46
Energy contribution -21.47
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.77
Structure conservation index 0.81
SVM decision value 1.44
SVM RNA-class probability 0.953804
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14704313 108 + 22224390
--CUGCGCUGAAGUUAUGCGAAAUGGACGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUAGCCAUCGUUUUUUUUCU----------UCCAUUUUGUUUGAUGUAAAUGCAAAUUUCUU
--.((((((((((.....)((((((((.((((.((....)).)))).)).)))))).))))))(((((..........----------...........))))).....)))........ ( -24.70)
>DroSec_CAF1 23272 93 + 1
UGCUGCGCUAAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUAGCC---------------------------AUUUUGGUUGAUGUAAAUGCAAAUUUCUU
...((((((((((..(((.(((.((((((((.....)).)))))).))).)))..).))))))(---------------------------(((......)))).....)))........ ( -27.70)
>DroYak_CAF1 21414 120 + 1
UACUGCGCUAAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUCUUCCAUUUUUUUUUUUGUUUUGUUGUUGUCUAUUUUGGUUGAUGUUAAUGCAAAUUUCUU
...(((...((((..(((.(((.((((((((.....)).)))))).))).)))..))))......................((((..(((..........)))..)))))))........ ( -23.70)
>consensus
U_CUGCGCUAAAGUUAUGCGAAAUGGGCGUGGCCGACGUCGCCCACUUCUCAUUUCUUUUAGCCAU__UUUUUUUU_U__________UC_AUUUUGGUUGAUGUAAAUGCAAAUUUCUU
...((((((((((..(((.(((.((((((((.....)).)))))).))).)))..)))).)))...........................((((......)))).....)))........ (-20.46 = -21.47 +   1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,704,313 – 14,704,421
Length 108
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.00
Mean single sequence MFE -25.30
Consensus MFE -20.37
Energy contribution -20.37
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.69
Structure conservation index 0.80
SVM decision value 3.22
SVM RNA-class probability 0.998775
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14704313 108 - 22224390
AAGAAAUUUGCAUUUACAUCAAACAAAAUGGA----------AGAAAAAAAACGAUGGCUAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGUCCAUUUCGCAUAACUUCAGCGCAG--
..(((...(((.....((((............----------...........)))).......((((((.((.((((.((....)).)))).)))))))))))....))).......-- ( -24.90)
>DroSec_CAF1 23272 93 - 1
AAGAAAUUUGCAUUUACAUCAACCAAAAU---------------------------GGCUAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUUAGCGCAGCA
.......((((.....(((........))---------------------------)((((((.(..(((.((((((((((..........)))))))))).)))..))))))))))).. ( -27.50)
>DroYak_CAF1 21414 120 - 1
AAGAAAUUUGCAUUAACAUCAACCAAAAUAGACAACAACAAAACAAAAAAAAAAAUGGAAGAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUUAGCGCAGUA
.......((((...........(((..............................)))...((((..(((.((((((((((..........)))))))))).)))..))))...)))).. ( -23.51)
>consensus
AAGAAAUUUGCAUUUACAUCAACCAAAAU_GA__________A_AAAAAAAA__AUGGCUAAAAGAAAUGAGAAGUGGGCGACGUCGGCCACGCCCAUUUCGCAUAACUUUAGCGCAG_A
.......((((.....................................................((((((....((((.((....)).))))...))))))((.........)))))).. (-20.37 = -20.37 +  -0.00)

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 11:53:59 2006