Locus 3411

Sequence ID 2L_DroMel_CAF1
Location 9,877,250 – 9,877,374
Length 124
Max. P 0.966921
window5397 window5398 window5399

overview

Window 7

Location 9,877,250 – 9,877,347
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 86.70
Mean single sequence MFE -26.92
Consensus MFE -18.88
Energy contribution -18.28
Covariance contribution -0.60
Combinations/Pair 1.26
Mean z-score -3.05
Structure conservation index 0.70
SVM decision value 1.60
SVM RNA-class probability 0.966921
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9877250 97 + 22407834
GUUGCUGCAGCUGCAAAGUAUCGGCGACCUUUUGGCUUUUACAAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAU
(((((((..(((....)))..)))))))...............((((((((..(((((((....))))).))..))))))))............... ( -25.50)
>DroGri_CAF1 95801 97 + 1
GUGGCUGCAGCUGCAAGCAAGCGGCGGCCUUAUCGUUUUGACAAUGGAACAAACACAACAAAAAUGUUGAGGAAUGUUCCAUAAUUAAUUAAGAAUU
..((((((.(((.......))).))))))...((...((((..((((((((..(.(((((....))))).)...))))))))..))))....))... ( -31.30)
>DroSim_CAF1 92189 97 + 1
GUUGCUGCAGCUGCAAAGUAUCGGCGACCUUUUGGCUUUUACAAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAU
(((((((..(((....)))..)))))))...............((((((((..(((((((....))))).))..))))))))............... ( -25.50)
>DroYak_CAF1 89589 97 + 1
GUUGCUGCAGCUGCAAACAAUCGGCGACCUUUUUGCUUUUACAAUGGAACAAACACAACGAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAU
(((((((.(..((....)).))))))))...............((((((((..(((((((....))))).))..))))))))............... ( -21.00)
>DroMoj_CAF1 135670 97 + 1
UUGGCUGCAGCUGGAAGCGGGCGACGGCCUUUUCGUUUUGGCAAUGGAACAAACACAACAAAUAUGUUGAUGAAUGUUCCAUAAUUAAUUGAGAAAU
..(((((..(((.(...).)))..)))))((((((..((((..((((((((..(((((((....))))).))..))))))))..)))).)))))).. ( -31.30)
>consensus
GUUGCUGCAGCUGCAAACAAUCGGCGACCUUUUCGCUUUUACAAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAU
(..((....))..)........(((((.....)))))......((((((((..(((((((....))))).))..))))))))............... (-18.88 = -18.28 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,877,250 – 9,877,347
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 86.70
Mean single sequence MFE -24.88
Consensus MFE -17.60
Energy contribution -17.60
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -2.87
Structure conservation index 0.71
SVM decision value 1.48
SVM RNA-class probability 0.957228
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9877250 97 - 22407834
AUUUUCAUAUUAAUUAUGGAACAUUCAUCAACAAUUUUGUUGUGUUUGUUCCAUUGUAAAAGCCAAAAGGUCGCCGAUACUUUGCAGCUGCAGCAAC
................(((((((..((.(((((....)))))))..)))))))((((...(((...(((((.......)))))...)))...)))). ( -23.20)
>DroGri_CAF1 95801 97 - 1
AAUUCUUAAUUAAUUAUGGAACAUUCCUCAACAUUUUUGUUGUGUUUGUUCCAUUGUCAAAACGAUAAGGCCGCCGCUUGCUUGCAGCUGCAGCCAC
................(((((((..(..(((((....))))).)..)))))))(((((.....)))))(((.((.(((.(....)))).)).))).. ( -29.00)
>DroSim_CAF1 92189 97 - 1
AUUUUCAUAUUAAUUAUGGAACAUUCAUCAACAAUUUUGUUGUGUUUGUUCCAUUGUAAAAGCCAAAAGGUCGCCGAUACUUUGCAGCUGCAGCAAC
................(((((((..((.(((((....)))))))..)))))))((((...(((...(((((.......)))))...)))...)))). ( -23.20)
>DroYak_CAF1 89589 97 - 1
AUUUUCAUAUUAAUUAUGGAACAUUCAUCAACAAUUUCGUUGUGUUUGUUCCAUUGUAAAAGCAAAAAGGUCGCCGAUUGUUUGCAGCUGCAGCAAC
.........(((...((((((((..((.((((......))))))..))))))))..)))..(((((...(((...)))..))))).((....))... ( -22.90)
>DroMoj_CAF1 135670 97 - 1
AUUUCUCAAUUAAUUAUGGAACAUUCAUCAACAUAUUUGUUGUGUUUGUUCCAUUGCCAAAACGAAAAGGCCGUCGCCCGCUUCCAGCUGCAGCCAA
.((((..........((((((((..((.(((((....)))))))..)))))))).........)))).(((.((.((.........)).)).))).. ( -26.11)
>consensus
AUUUUCAUAUUAAUUAUGGAACAUUCAUCAACAAUUUUGUUGUGUUUGUUCCAUUGUAAAAGCCAAAAGGUCGCCGAUAGUUUGCAGCUGCAGCAAC
...............((((((((..((.(((((....)))))))..))))))))...............((.((.(........).)).))...... (-17.60 = -17.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,877,270 – 9,877,374
Length 104
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 86.73
Mean single sequence MFE -24.10
Consensus MFE -18.14
Energy contribution -18.45
Covariance contribution 0.31
Combinations/Pair 1.10
Mean z-score -2.37
Structure conservation index 0.75
SVM decision value -0.01
SVM RNA-class probability 0.526942
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9877270 104 + 22407834
UCGGCGACCUUUUGGCUUUUA--C-AAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUGAAUUCGUUCUCU--UUUCGUUC--------
..(((((((....))......--.-.((((((((..(((((((....))))).))..))))))))..((((((..(...)..))))))..)))))....--........-------- ( -21.00)
>DroSec_CAF1 85320 102 + 1
UCGGCGACCUUUUGGCUUUUA--C-AAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUGAACUCG--CCCU--UUUCGUUC--------
..(((((((....))......--.-.((((((((..(((((((....))))).))..))))))))..((((((..(...)..))))))..)))--))..--........-------- ( -25.80)
>DroSim_CAF1 92209 102 + 1
UCGGCGACCUUUUGGCUUUUA--C-AAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUGAACUCG--CUCU--UUUCGUUC--------
..(((((((....))......--.-.((((((((..(((((((....))))).))..))))))))..((((((..(...)..))))))..)))--))..--........-------- ( -23.40)
>DroEre_CAF1 90211 102 + 1
UCGGCGACCUUUUUGCUUUUA--C-AAUGGAACAGACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUGAACUCG--CUCU--CUUCGUUC--------
..(((((..............--.-.((((((((..(((((((....))))).))..))))))))..((((((..(...)..))))))..)))--))..--........-------- ( -24.40)
>DroYak_CAF1 89609 102 + 1
UCGGCGACCUUUUUGCUUUUA--C-AAUGGAACAAACACAACGAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUUAACUCG--CUCG--CUUCGUUC--------
.((((((......(((.....--.-.((((((((..(((((((....))))).))..)))))))).......((....)).)))......)))--).))--........-------- ( -19.80)
>DroAna_CAF1 93852 115 + 1
UCGGCAACCUUUUCGUUUUGGAACAAAUGGAACAAACUCAACAAAAAUGUUGAUGAAUGUUCCAUAAUUAACAGGAAGAUUUAAUAUAGUUAG--CUCUCUGUUUGUUGCCUUCCCC
..((((((..................((((((((..(((((((....)))))).)..))))))))....(((((..((...((((...)))).--))..))))).))))))...... ( -30.20)
>consensus
UCGGCGACCUUUUGGCUUUUA__C_AAUGGAACAAACACAACAAAAUUGUUGAUGAAUGUUCCAUAAUUAAUAUGAAAAUUGUAUUGAACUCG__CUCU__UUUCGUUC________
..(((((...................((((((((..(((((((....))))).))..))))))))..(((((((((...)))))))))...............)))))......... (-18.14 = -18.45 +   0.31)

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 10:51:50 2006