Locus 4173

Sequence ID X_DroMel_CAF1
Location 10,953,561 – 10,953,682
Length 121
Max. P 0.966245
window6847 window6848 window6849 window6850

overview

Window 7

Location 10,953,561 – 10,953,660
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 83.28
Mean single sequence MFE -25.86
Consensus MFE -19.12
Energy contribution -20.28
Covariance contribution 1.16
Combinations/Pair 1.12
Mean z-score -2.46
Structure conservation index 0.74
SVM decision value 1.58
SVM RNA-class probability 0.965593
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10953561 99 + 22224390
AUCGGCGAAAGCUCAAUUUAUUAUAAAUAUUACUUG-AAUGCGAGUCCCCCAUAUGGCUGCCGAUAAUAUUCGAUUGCCCGACGCAAGCAAUCGAUAAGC
(((((((...((((.(((((..............))-)))..))))...((....)).))))))).....((((((((.........))))))))..... ( -23.84)
>DroSec_CAF1 4199 100 + 1
AUCGGUAAAAUAUCAAGUUAUUCCAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCCUACGCAGGCAAUCGAUAUUC
(((((((.......((((((.........))))))(((((.............))))))))))))(((((.((((((((.......))))))))))))). ( -30.52)
>DroSim_CAF1 1798 100 + 1
AUCGGUAAAAUAUGAAGUUAUUCCAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCUUACGCAGGCAAUCGAUAUUC
(((((((.......((((((.........))))))(((((.............))))))))))))(((((.(((((((((.....)))))))))))))). ( -32.12)
>DroEre_CAF1 6756 99 + 1
AUCGGUAAAAGAUCAAGUGAUUAUAAAGUUAACUUGCUAUGCGAGUCCCCCAAAUGAAUGGUGAUAACAUGCGAUUGCCC-AGAAAGACAAUCGAUAACC
((((((....((((....)))).....(((.((((((...)))))).............((..((........))..)).-.....))).)))))).... ( -16.40)
>DroYak_CAF1 3520 98 + 1
AUCGGUAAAAGAUCAAGCUAUUAUUAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGG-GCCUAUAAUAUUCGAUUGCCC-AGAAAGGCAAUCGAUAAUA
.(..((((.((......)).))))..)((((((((((...)))))).((((....)))-)....))))..(((((((((.-.....)))))))))..... ( -26.40)
>consensus
AUCGGUAAAAGAUCAAGUUAUUAUAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCC_ACGCAGGCAAUCGAUAAUC
(((((((........................((((((...))))))...((....)).))))))).....(((((((((.......)))))))))..... (-19.12 = -20.28 +   1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,953,561 – 10,953,660
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 83.28
Mean single sequence MFE -29.41
Consensus MFE -21.10
Energy contribution -22.54
Covariance contribution 1.44
Combinations/Pair 1.17
Mean z-score -2.54
Structure conservation index 0.72
SVM decision value 1.59
SVM RNA-class probability 0.966245
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10953561 99 - 22224390
GCUUAUCGAUUGCUUGCGUCGGGCAAUCGAAUAUUAUCGGCAGCCAUAUGGGGGACUCGCAUU-CAAGUAAUAUUUAUAAUAAAUUGAGCUUUCGCCGAU
.....(((((((((((...))))))))))).....((((((..((....))(..(((((....-...(((.....))).......)))).)..))))))) ( -26.94)
>DroSec_CAF1 4199 100 - 1
GAAUAUCGAUUGCCUGCGUAGGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUGGAAUAACUUGAUAUUUUACCGAU
.((((((((((((((.....))))))))).)))))(((((..(((((.(((....).)).)))))((((((.........)))))).........))))) ( -34.30)
>DroSim_CAF1 1798 100 - 1
GAAUAUCGAUUGCCUGCGUAAGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUGGAAUAACUUCAUAUUUUACCGAU
.((((((((((((((.....))))))))).)))))(((((..(((((.(((....).)).)))))((((((.........)))))).........))))) ( -34.30)
>DroEre_CAF1 6756 99 - 1
GGUUAUCGAUUGUCUUUCU-GGGCAAUCGCAUGUUAUCACCAUUCAUUUGGGGGACUCGCAUAGCAAGUUAACUUUAUAAUCACUUGAUCUUUUACCGAU
((((((.((((((((....-))))))))((((((..((.(((......)))..))...)))).))...........)))))).................. ( -21.70)
>DroYak_CAF1 3520 98 - 1
UAUUAUCGAUUGCCUUUCU-GGGCAAUCGAAUAUUAUAGGC-CCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUAAUAAUAGCUUGAUCUUUUACCGAU
.....((((((((((....-))))))))))........(((-(((....)))).........(((((((((.........))))))).)).....))... ( -29.80)
>consensus
GAUUAUCGAUUGCCUGCGU_GGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUAUAAUAACUUGAUCUUUUACCGAU
.....((((((((((.....)))))))))).....(((((...((((.(((....).)).))))(((((((.........)))))))........))))) (-21.10 = -22.54 +   1.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,953,581 – 10,953,682
Length 101
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 84.40
Mean single sequence MFE -30.17
Consensus MFE -21.08
Energy contribution -22.80
Covariance contribution 1.72
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.70
SVM decision value 0.95
SVM RNA-class probability 0.888783
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10953581 101 + 22224390
UUAUAAAUAUUACUUG-AAUGCGAGUCCCCCAUAUGGCUGCCGAUAAUAUUCGAUUGCCCGACGCAAGCAAUCGAUAAGCGCCGGCUAUUUUCGAUGGCCAA
...........(((((-....)))))........(((((..(((.(((..((((((((.........))))))))..(((....)))))).)))..))))). ( -26.40)
>DroSec_CAF1 4219 102 + 1
UUCCAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCCUACGCAGGCAAUCGAUAUUCGCCGGCUAUUUUCGAUGGUCGA
...............(((((.(((.......(((((((((.(((......(((((((((.......)))))))))...))).)))))))))))))))))... ( -33.11)
>DroSim_CAF1 1818 102 + 1
UUCCAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCUUACGCAGGCAAUCGAUAUUCGCCGGCUAUUUUCGAUGGCCGA
...............(((((.(((.......(((((((((.(((......((((((((((.....))))))))))...))).)))))))))))))))))... ( -36.51)
>DroEre_CAF1 6776 101 + 1
UUAUAAAGUUAACUUGCUAUGCGAGUCCCCCAAAUGAAUGGUGAUAACAUGCGAUUGCCC-AGAAAGACAAUCGAUAACCGCCGGCUAUUUUCAAUGGCCCG
...........((((((...)))))).............((((........((((((.(.-.....).)))))).....))))((((((.....)))))).. ( -21.12)
>DroYak_CAF1 3540 100 + 1
UUAUUAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGG-GCCUAUAAUAUUCGAUUGCCC-AGAAAGGCAAUCGAUAAUAGCCGGCUAUUUCCGAUGGCCCG
((((((.((((((((((...)))))).((((....)))-)....))))..(((((((((.-.....)))))))))))))))..(((((((...))))))).. ( -33.70)
>consensus
UUAUAAAGUUAACUUGCCAUGCGAGUCCCCCAAAUGGCUGCCGAUAAUAUUCGAUUGCCC_ACGCAGGCAAUCGAUAAUCGCCGGCUAUUUUCGAUGGCCCA
...........((((((...))))))...(((((((((((.(((......(((((((((.......)))))))))...))).)))))))).....))).... (-21.08 = -22.80 +   1.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,953,581 – 10,953,682
Length 101
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 84.40
Mean single sequence MFE -33.40
Consensus MFE -25.46
Energy contribution -26.26
Covariance contribution 0.80
Combinations/Pair 1.21
Mean z-score -2.34
Structure conservation index 0.76
SVM decision value 1.42
SVM RNA-class probability 0.951882
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10953581 101 - 22224390
UUGGCCAUCGAAAAUAGCCGGCGCUUAUCGAUUGCUUGCGUCGGGCAAUCGAAUAUUAUCGGCAGCCAUAUGGGGGACUCGCAUU-CAAGUAAUAUUUAUAA
.((((..((((.((((((....))...(((((((((((...))))))))))).)))).))))..))))...((....))......-................ ( -26.70)
>DroSec_CAF1 4219 102 - 1
UCGACCAUCGAAAAUAGCCGGCGAAUAUCGAUUGCCUGCGUAGGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUGGAA
....(((..(......(((((..((((((((((((((.....))))))))).))))).))))).(((((.(((....).)).))))).......)..))).. ( -39.10)
>DroSim_CAF1 1818 102 - 1
UCGGCCAUCGAAAAUAGCCGGCGAAUAUCGAUUGCCUGCGUAAGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUGGAA
....(((..(......(((((..((((((((((((((.....))))))))).))))).))))).(((((.(((....).)).))))).......)..))).. ( -39.40)
>DroEre_CAF1 6776 101 - 1
CGGGCCAUUGAAAAUAGCCGGCGGUUAUCGAUUGUCUUUCU-GGGCAAUCGCAUGUUAUCACCAUUCAUUUGGGGGACUCGCAUAGCAAGUUAACUUUAUAA
(.(((...(....)..))).).(((((.(((((((((....-))))))))((((((..((.(((......)))..))...)))).))..).)))))...... ( -24.80)
>DroYak_CAF1 3540 100 - 1
CGGGCCAUCGGAAAUAGCCGGCUAUUAUCGAUUGCCUUUCU-GGGCAAUCGAAUAUUAUAGGC-CCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUAAUAA
.(((((.((((......))))......((((((((((....-))))))))))........)))-)).(((.((..((((.((...)).))))..)).))).. ( -37.00)
>consensus
UCGGCCAUCGAAAAUAGCCGGCGAUUAUCGAUUGCCUGCGU_GGGCAAUCGAAUAUUAUCGGCAGCCAUUUGGGGGACUCGCAUGGCAAGUUAACUUUAUAA
...((((((((.....(((((......((((((((((.....))))))))))......))))).........(....)))).)))))............... (-25.46 = -26.26 +   0.80)

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 11:18:09 2006