Locus 231

Sequence ID 3R_DroMel_CAF1
Location 924,437 – 924,546
Length 109
Max. P 0.983110
window414 window415

overview

Window 4

Location 924,437 – 924,546
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.16
Mean single sequence MFE -28.48
Consensus MFE -17.71
Energy contribution -18.77
Covariance contribution 1.06
Combinations/Pair 1.23
Mean z-score -2.24
Structure conservation index 0.62
SVM decision value 1.77
SVM RNA-class probability 0.976652
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 924437 109 + 27905053
AUAAAUAGAGGCUGAAAGAGAA---AAGUUUGGGGCACUGU--------GAACAAGCAAAAAGUGAAAAGUUGCUGGGCUGCGUGCAACUAAAUUAAAUACAUCACACAGUGCCCCCAUU
........(((((.........---.)))))((((((((((--------(.....((.....))....((((((..........))))))...............))))))))))).... ( -30.70)
>DroSec_CAF1 13422 108 + 1
AUAAAUAGAGGCUGAAAGAGAA---AAGUCUGGGGCGCUGC--------GAACAAACAA-AAGUGAAAAGUUGCUGGGCUGGGCGCAACUAAAUUAAAUACAUCAGACAGUGCCCCCAUU
........(((((.........---.)))))((((((((((--------(..((..(..-.((..(....)..)).)..))..)))..............(....)..)))))))).... ( -28.20)
>DroSim_CAF1 19325 108 + 1
AUAAAUAGAGGCUGAAAGAGAA---AAGUCUGGGGCGCUGC--------GAACAAACAA-AAGUGAAAAGUUGCUGGGCUGGGCGCAACUAAAUUAAAUACAUCACACAGUGCCCCCAUU
........(((((.........---.)))))(((((((((.--------(.....((..-..))....((((((..........))))))...............).))))))))).... ( -28.00)
>DroEre_CAF1 14522 102 + 1
AUAAAUAGGGGCUGAAAGGGAG---AAGUCUGGUGCGCUGA--------GAACAUAGAG-AAGUGAAAAGUUGCUGG-----GCGCAACUAA-UGAAAUACAUCACACAGUGCCCCCAUU
.......(((((.......((.---...(((((((((((.(--------((((......-.........))).)).)-----)))).)))).-.))......)).......))))).... ( -25.70)
>DroYak_CAF1 34120 109 + 1
AUAAAUAGAGGCUGAAAAAAAG--UGAGUCUGGGGCGCUGC--------GAACAAACAA-AAGUGAAAAGUUUCUGGGCUGAGCGCAACUAAGUGAAAUACAUCACACAGUGCCCCCAUU
........(((((.(.......--).)))))(((((((((.--------..........-..(((...((((....))))...)))......((((......)))).))))))))).... ( -31.00)
>DroAna_CAF1 12121 109 + 1
ACAAAUGCAGGCUGAAGGUACAUAUGGGAGGGGGACACUGUCAAGGGAUGCACAAAUAA-AAGUGAAAAGUUGCAAUUC-CCUUGCAAGA---------ACCUUCAACAGAGCACUCAUA
.....(((..(.(((((((.(.........(....)..((.(((((((((((.......-...........))))..))-))))))).).---------))))))).)...)))...... ( -27.27)
>consensus
AUAAAUAGAGGCUGAAAGAGAA___AAGUCUGGGGCGCUGC________GAACAAACAA_AAGUGAAAAGUUGCUGGGCUGCGCGCAACUAAAUUAAAUACAUCACACAGUGCCCCCAUU
........(((((.............)))))(((((((((...........((.........))....((((((..........)))))).................))))))))).... (-17.71 = -18.77 +   1.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 924,437 – 924,546
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.16
Mean single sequence MFE -27.99
Consensus MFE -14.79
Energy contribution -15.65
Covariance contribution 0.86
Combinations/Pair 1.12
Mean z-score -2.56
Structure conservation index 0.53
SVM decision value 1.93
SVM RNA-class probability 0.983110
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 924437 109 - 27905053
AAUGGGGGCACUGUGUGAUGUAUUUAAUUUAGUUGCACGCAGCCCAGCAACUUUUCACUUUUUGCUUGUUC--------ACAGUGCCCCAAACUU---UUCUCUUUCAGCCUCUAUUUAU
....(((((((((((....(((........((((((..........))))))..........))).....)--------))))))))))......---...................... ( -31.37)
>DroSec_CAF1 13422 108 - 1
AAUGGGGGCACUGUCUGAUGUAUUUAAUUUAGUUGCGCCCAGCCCAGCAACUUUUCACUU-UUGUUUGUUC--------GCAGCGCCCCAGACUU---UUCUCUUUCAGCCUCUAUUUAU
(((((((((...(((((..((..........((((((..(((....((((..........-)))))))..)--------)))))))..)))))..---..........)))))))))... ( -22.86)
>DroSim_CAF1 19325 108 - 1
AAUGGGGGCACUGUGUGAUGUAUUUAAUUUAGUUGCGCCCAGCCCAGCAACUUUUCACUU-UUGUUUGUUC--------GCAGCGCCCCAGACUU---UUCUCUUUCAGCCUCUAUUUAU
....(((((.(((((.((((..........((((((..........))))))........-.))))....)--------)))).)))))......---...................... ( -26.01)
>DroEre_CAF1 14522 102 - 1
AAUGGGGGCACUGUGUGAUGUAUUUCA-UUAGUUGCGC-----CCAGCAACUUUUCACUU-CUCUAUGUUC--------UCAGCGCACCAGACUU---CUCCCUUUCAGCCCCUAUUUAU
(((((((((((((.((((......)))-)))))(((((-----..((.(((.........-......))))--------)..)))))........---..........)))))))))... ( -27.26)
>DroYak_CAF1 34120 109 - 1
AAUGGGGGCACUGUGUGAUGUAUUUCACUUAGUUGCGCUCAGCCCAGAAACUUUUCACUU-UUGUUUGUUC--------GCAGCGCCCCAGACUCA--CUUUUUUUCAGCCUCUAUUUAU
(((((((((((((.((((......)))).)))).(((((..((..(.((((.........-..)))).)..--------)))))))..........--..........)))))))))... ( -28.60)
>DroAna_CAF1 12121 109 - 1
UAUGAGUGCUCUGUUGAAGGU---------UCUUGCAAGG-GAAUUGCAACUUUUCACUU-UUAUUUGUGCAUCCCUUGACAGUGUCCCCCUCCCAUAUGUACCUUCAGCCUGCAUUUGU
.(..(((((...(((((((((---------.(.(((((((-((..((((.(.........-......)))))))))))).))(((.........)))..).)))))))))..)))))..) ( -31.86)
>consensus
AAUGGGGGCACUGUGUGAUGUAUUUAAUUUAGUUGCGCCCAGCCCAGCAACUUUUCACUU_UUGUUUGUUC________GCAGCGCCCCAGACUU___UUCUCUUUCAGCCUCUAUUUAU
....(((((.((((................((((((..........))))))....((.........))..........)))).)))))............................... (-14.79 = -15.65 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:17 2006