Locus 5305

Sequence ID 3L_DroMel_CAF1
Location 14,664,866 – 14,665,042
Length 176
Max. P 0.993126
window8383 window8384 window8385

overview

Window 3

Location 14,664,866 – 14,664,974
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 69.80
Mean single sequence MFE -21.37
Consensus MFE -10.73
Energy contribution -11.07
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.50
SVM decision value 0.57
SVM RNA-class probability 0.784502
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14664866 108 - 23771897
UCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAGAUAAUUCGUAAAUACAAAUUAAACAAAAAAAUGUUAAUGUUAAAUUAAACAAAUGUUGUAUUUGAAAAUC
((.((((((((..((.......))..)))))))).))....(((..(((((((((....((((......))))..((((......))))....)))))))))..))). ( -23.30)
>DroSec_CAF1 14659 81 - 1
UCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUGUAUUUCGUGGAUA-------------------------GUAUAUUAAA--AAUGUUGUAUUCGAAAAAC
((.((((((((..((.......))..)))))))).))....(((((...(((-------------------------((((......--.)))))))...)))))... ( -19.20)
>DroSim_CAF1 15473 82 - 1
UCCUGGUUGGGGGCAUCGAUUUUGACCGCAAUCGGGAUGUACUUAAUGGGAA-------------------------GUAUAUUAAAU-AAUGUUGUAUUCGGAAAAC
(((((((((.((.((.......)).)).)))))))))(((((((......))-------------------------)))))......-................... ( -21.60)
>consensus
UCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUGUAAUUCGUGGAUA_________________________GUAUAUUAAA__AAUGUUGUAUUCGAAAAAC
((.((((((((..((.......))..)))))))).))....................................................................... (-10.73 = -11.07 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,664,894 – 14,665,008
Length 114
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 67.48
Mean single sequence MFE -28.22
Consensus MFE -16.02
Energy contribution -15.90
Covariance contribution -0.12
Combinations/Pair 1.21
Mean z-score -1.54
Structure conservation index 0.57
SVM decision value 0.78
SVM RNA-class probability 0.848688
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14664894 114 - 23771897
-CCCAAGCCGAAGCCAACACGAGAAUGGUCUGGUGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAGAUAAUUCGUAAAUACAAAUUAAACAAAAAAAUGUUAAUGUUA
-(((............((((.(((....))).))))...(((((((..((.......))..))))))))))...(((((.((....)).)))))((((......))))....... ( -26.50)
>DroSec_CAF1 14685 89 - 1
-CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUGUAUUUCGUGGAUA-------------------------GUA
-((((..(((...(......)....)))..))))(((.((((((((..((.......))..)))))))).)))..............-------------------------... ( -25.50)
>DroSim_CAF1 15500 89 - 1
-CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCCUGGUUGGGGGCAUCGAUUUUGACCGCAAUCGGGAUGUACUUAAUGGGAA-------------------------GUA
-((((..((.(..(((.........)))..).))((((((((((.((.((.......)).)).))))))))))........))))..-------------------------... ( -31.10)
>DroEre_CAF1 15157 90 - 1
CCGCAAGGAAAAGCCAAAAAGAAAGUGGAGUGGGGUUUUGGUUGGGGGUAUCCAUUUUGAACCCGAACGCCUAAAGCUUCCUUUAUG-------------------------GUC
((....))....((((.((((.((((....((((((((.((((.(((((....))))).)))).)))).))))..)))).)))).))-------------------------)). ( -29.80)
>consensus
_CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUAUACUUCGUGGAUA_________________________GUA
.(((.....((..(((.((......))...)))..))..(((((((..((.......))..))))))))))............................................ (-16.02 = -15.90 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,664,934 – 14,665,042
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.61
Mean single sequence MFE -27.93
Consensus MFE -12.03
Energy contribution -12.11
Covariance contribution 0.08
Combinations/Pair 1.33
Mean z-score -2.41
Structure conservation index 0.43
SVM decision value 2.38
SVM RNA-class probability 0.993126
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14664934 108 - 23771897
AAAGAAGAAACAAAAAAAUAAAUCUAAGCGUAAG------------CCCAAGCCGAAGCCAACACGAGAAUGGUCUGGUGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAGAU
.....................((((..((....)------------).....(((((((((((((.(((....))).))))..)))))(((..((.......))..)))..)))).)))) ( -29.40)
>DroSec_CAF1 14700 96 - 1
AAAGAAAAAAAAGAAAAAUAAA------------------------CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUGU
......................------------------------((((..(((...(......)....)))..))))(((.((((((((..((.......))..)))))))).))).. ( -26.00)
>DroSim_CAF1 15515 96 - 1
AAAGAAGAAAAAAAAAAAUAAA------------------------CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCCUGGUUGGGGGCAUCGAUUUUGACCGCAAUCGGGAUGU
......................------------------------((((..(((...(......)....)))..))))((((((((((.((.((.......)).)).)))))))))).. ( -28.60)
>DroEre_CAF1 15172 114 - 1
AAAGGUAGUACCAAAAUAUAAACCCACACGUAAGGUUAG------CCGCAAGGAAAAGCCAAAAAGAAAGUGGAGUGGGGUUUUGGUUGGGGGUAUCCAUUUUGAACCCGAACGCCUAAA
..((((....(((((((....((((((......((((..------((....))...)))).........)))).))...)))))))(((((..((.......))..)))))..))))... ( -32.36)
>DroYak_CAF1 15483 120 - 1
AAAGAAAAAACCUGUAAAGAAACCUAAGCGUAAGCCCAAGCCCAAACCCAAGCCCAAGCCAACACGAAAACGUUAUAAGGCUAUCGUUGGGGGCAUCGAUUUUGAACCCGAUGGCCACAA
............(((............((....))................(((..((((...(((....))).....))))...((((((..((.......))..))))))))).))). ( -23.30)
>consensus
AAAGAAAAAACAAAAAAAUAAA_C_A__CGUAAG____________CCCAAGCCGAAGCCAACACGAAAAUGGUCUGGGGUCAUGGUUGGGGGCAUCGAUUUUGAACCCAAUCGGGAUAU
..............................................(((........(((..................)))...(((((((..((.......))..)))))))))).... (-12.03 = -12.11 +   0.08)

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 11:46:49 2006