Locus 7137

Sequence ID 3R_DroMel_CAF1
Location 18,806,480 – 18,806,583
Length 103
Max. P 0.923069
window11547 window11548 window11549 window11550

overview

Window 7

Location 18,806,480 – 18,806,572
Length 92
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 79.53
Mean single sequence MFE -17.60
Consensus MFE -11.07
Energy contribution -11.27
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -2.30
Structure conservation index 0.63
SVM decision value 1.15
SVM RNA-class probability 0.923069
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18806480 92 + 27905053
---GGACAA--C-UCGAUGCUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUUUUUUGCUUU
---(((((.--.-..((...((((((......))))))....)).....(((((((............)))))))......)))))............ ( -15.40)
>DroSec_CAF1 31871 84 + 1
---GGACAA--CUCCGAUGCUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU---------
---(((...--.)))(((((((((((......))))))...........(((((((............))))))).....)))))....--------- ( -16.30)
>DroSim_CAF1 34406 78 + 1
---UG--------UCGAUGCUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU---------
---..--------..(((((((((((......))))))...........(((((((............))))))).....)))))....--------- ( -14.30)
>DroEre_CAF1 32407 84 + 1
UGGGGGCAA----------CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----GCUCU
(((((.(((----------....))).)))))(((..((....(((...(((((((............)))))))...))).))...))----).... ( -21.80)
>DroYak_CAF1 34170 94 + 1
AGGGGGCAGAAGCUCGAUGUUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----GCUCC
..(((((((((((.(((...((((((......))))))...........(((((((............)))))))...))).).)))))----))))) ( -26.20)
>DroAna_CAF1 33334 89 + 1
UCGGAAAAA---CUCGAUUCUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGCCAUUCUCUUUUGCUUUCUAUUAUAUCGUAUUUUUUUCC------
..(((((((---..((((..((((((......))))))..............((...........))..........))))....)))))))------ ( -11.60)
>consensus
___GGACAA____UCGAUGCUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU_________
....................((((((......))))))...........(((((((............)))))))....................... (-11.07 = -11.27 +   0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,806,480 – 18,806,572
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 79.53
Mean single sequence MFE -16.97
Consensus MFE -10.49
Energy contribution -10.72
Covariance contribution 0.22
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.62
SVM decision value 0.57
SVM RNA-class probability 0.786521
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18806480 92 - 27905053
AAAGCAAAAAAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAGCAUCGA-G--UUGUCC---
...((..........(((((...(((((((............)))))))..(((....)))..)))))((.....)).)).....-.--......--- ( -15.60)
>DroSec_CAF1 31871 84 - 1
---------AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAGCAUCGGAG--UUGUCC---
---------......(((((...(((((((............)))))))..(((....)))..)))))((((...((......))..--..))))--- ( -15.20)
>DroSim_CAF1 34406 78 - 1
---------AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAGCAUCGA--------CA---
---------........(((...(((((((............)))))))...)))....(((((.((.((.....)).))))).)--------).--- ( -14.10)
>DroEre_CAF1 32407 84 - 1
AGAGC----AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG----------UUGCCCCCA
...((----((...((.(((...(((((((............)))))))...)))....))..))))((((.(((....----------))).)))). ( -19.20)
>DroYak_CAF1 34170 94 - 1
GGAGC----AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAACAUCGAGCUUCUGCCCCCU
(((((----........(((...(((((((............)))))))...))).....((((..(((......)))..)))).)))))........ ( -20.50)
>DroAna_CAF1 33334 89 - 1
------GGAAAAAAAUACGAUAUAAUAGAAAGCAAAAGAGAAUGGCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAGAAUCGAG---UUUUUCCGA
------(((((((.........((((.(((.((...........)).))).)))).....(((((.(((......))).)))))..---))))))).. ( -17.20)
>consensus
_________AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAGCAUCGA____UUGUCC___
...............(((((...(((((((............)))))))..(((....)))..)))))((.....))..................... (-10.49 = -10.72 +   0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,806,493 – 18,806,583
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 83.05
Mean single sequence MFE -14.28
Consensus MFE -11.07
Energy contribution -11.27
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -2.50
Structure conservation index 0.78
SVM decision value 0.87
SVM RNA-class probability 0.870576
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18806493 90 + 27905053
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUUUUUUGCUUUAGCCAUGGCUC
.((((((......)))))).....(((...(((((((............)))))))...))).................(((....))). ( -16.00)
>DroSec_CAF1 31885 74 + 1
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----------------GCUC
.((((((......)))))).....(((...(((((((............)))))))...)))........----------------.... ( -13.40)
>DroSim_CAF1 34414 74 + 1
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----------------GCUC
.((((((......)))))).....(((...(((((((............)))))))...)))........----------------.... ( -13.40)
>DroEre_CAF1 32416 86 + 1
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----GCUCUAUGCAGCGCUC
.((((((......))))))...........(((((((............))))))).....((((....(----((.....))))))).. ( -17.80)
>DroYak_CAF1 34189 86 + 1
UUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU----GCUCCAUGCAACGCUC
.((((((......))))))...........(((((((............))))))).....((((....(----((.....))))))).. ( -17.60)
>DroAna_CAF1 33350 83 + 1
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGCCAUUCUCUUUUGCUUUCUAUUAUAUCGUAUUUUUUUCC-------UGCCUGGAUC
.((((((......))))))...................................................(((-------.....))).. (  -7.50)
>consensus
CUGGUUGGCCCCACAAUCACUUUUCAAUUAAAUGGCAUUCUUUCCUCUUUGCCAUUAUUUUGUGUUUUUU__________UGCA__GCUC
.((((((......))))))...........(((((((............))))))).................................. (-11.07 = -11.27 +   0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,806,493 – 18,806,583
Length 90
Sequences 6
Columns 90
Reading direction reverse
Mean pairwise identity 83.05
Mean single sequence MFE -14.12
Consensus MFE -10.49
Energy contribution -10.72
Covariance contribution 0.22
Combinations/Pair 1.12
Mean z-score -1.63
Structure conservation index 0.74
SVM decision value 0.14
SVM RNA-class probability 0.600765
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18806493 90 - 27905053
GAGCCAUGGCUAAAGCAAAAAAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
......(((((...((((................(((((((............)))))))..(((....)))..))))..)))))..... ( -17.60)
>DroSec_CAF1 31885 74 - 1
GAGC----------------AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
....----------------......(((((...(((((((............)))))))..(((....)))..)))))((.....)).. ( -13.00)
>DroSim_CAF1 34414 74 - 1
GAGC----------------AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
....----------------......(((((...(((((((............)))))))..(((....)))..)))))((.....)).. ( -13.00)
>DroEre_CAF1 32416 86 - 1
GAGCGCUGCAUAGAGC----AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
..(.(((.(((((..(----(.......(((...(((((((............)))))))...))).....)).))))).))))...... ( -16.20)
>DroYak_CAF1 34189 86 - 1
GAGCGUUGCAUGGAGC----AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAA
.....((((.....))----))....(((((...(((((((............)))))))..(((....)))..)))))((.....)).. ( -15.80)
>DroAna_CAF1 33350 83 - 1
GAUCCAGGCA-------GGAAAAAAAUACGAUAUAAUAGAAAGCAAAAGAGAAUGGCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
..(((.....-------))).................................((((...(((((.......)))))....))))..... (  -9.10)
>consensus
GAGC__UGCA__________AAAAAACACAAAAUAAUGGCAAAGAGGAAAGAAUGCCAUUUAAUUGAAAAGUGAUUGUGGGGCCAACCAG
..........................(((((...(((((((............)))))))..(((....)))..)))))((.....)).. (-10.49 = -10.72 +   0.22)

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 12:38:23 2006