Locus 1772

Sequence ID 3R_DroMel_CAF1
Location 5,101,185 – 5,101,338
Length 153
Max. P 0.981099
window2908 window2909 window2910

overview

Window 8

Location 5,101,185 – 5,101,298
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.11
Mean single sequence MFE -34.83
Consensus MFE -27.45
Energy contribution -28.05
Covariance contribution 0.60
Combinations/Pair 1.09
Mean z-score -2.49
Structure conservation index 0.79
SVM decision value 1.88
SVM RNA-class probability 0.981099
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101185 113 + 27905053
AACGACCGAACAUUUUGGUCAGUUCAUUCAGCUUCUUUGGCU-------UUCCAUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCC
...((((((.....)))))).((..((((((((...((((((-------(..(....)..))))))).)))..(((((..((((.(......).)))).)))))....)))))..))... ( -33.40)
>DroSec_CAF1 8142 105 + 1
AACGACCGAACAUUUUGGUCAGUUCAUUCAGCUUCUUUGGCU-------UUCCAGUCG--------AUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCC
...((((((.....)))))).((..((((((.((..((((((-------..(((((((--------(.((((((....))))))))))).))).)))...)))..))))))))..))... ( -33.30)
>DroSim_CAF1 8159 113 + 1
AACGACCGAACAUUUUGGUCAGUUCAUUCAGCUUCUUUGGCU-------UUCCAUUCGACGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCC
...((((((.....)))))).((..((((((((...((((((-------(((.....)).))))))).)))..(((((..((((.(......).)))).)))))....)))))..))... ( -33.00)
>DroEre_CAF1 8248 118 + 1
AAGGACCGAAAAU-UUGGUCAGUUCGUUCAGCUUCUUUGGCCAUCUUUGGUCCCAUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCGAUAAAUUGAAUUU-CGCC
..((((((((...-.(((((((..............)))))))..)))))))).......(((((...((((((....))))))..)))))(((((.((((((....)))))).)-)))) ( -40.64)
>DroYak_CAF1 9119 112 + 1
AACGACCGAAAAU-UUGGUCAGUUCGUUCAGCUUCUUUGGCU-------GUCCCUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGACUCGGUGGCAUUCGAUAAAUUGAAUUUACGCC
....(((((....-((((((...(((..(((((.....))))-------)......)))..)))))).((((((....)))))).....)))))(((((((((....))))))....))) ( -33.80)
>consensus
AACGACCGAACAUUUUGGUCAGUUCAUUCAGCUUCUUUGGCU_______UUCCAUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCC
...((((((.....)))))).((..((((((((...((((((...................)))))).)))..(((((..((((.(......).)))).)))))....)))))..))... (-27.45 = -28.05 +   0.60)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,101,225 – 5,101,338
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.04
Mean single sequence MFE -34.24
Consensus MFE -22.58
Energy contribution -22.38
Covariance contribution -0.20
Combinations/Pair 1.09
Mean z-score -2.24
Structure conservation index 0.66
SVM decision value 1.35
SVM RNA-class probability 0.945583
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101225 113 + 27905053
CU-------UUCCAUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCCGAUUUGGUGAAUUAUUGCAUUGCGCUGUCAUUGCGAGGGU
..-------.(((...(((((((((((((.(((..(((((..(((((((...((((.((((((....)))))))))))))))...))..))))))))))))).)))..)))))...))). ( -35.10)
>DroSec_CAF1 8182 105 + 1
CU-------UUCCAGUCG--------AUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCCGAUUUGGUGAAUUAUUGCAUUGCGCUGUCAUUGCGAGGGU
((-------(((((((.(--------(((((....(((((..(((((((...((((.((((((....)))))))))))))))...))..)))))..((...)))))))))))).))))). ( -33.60)
>DroSim_CAF1 8199 113 + 1
CU-------UUCCAUUCGACGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCCGAUUUGGUGAAUUAUUGCAUUGCGCUGUCAUUGCGAGGGU
((-------(((((...(((((((.((((.(((..(((((..(((((((...((((.((((((....)))))))))))))))...))..)))))))))))))).)))))..)).))))). ( -37.10)
>DroEre_CAF1 8287 103 + 1
CCAUCUUUGGUCCCAUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCGAUAAAUUGAAUUU-CGCCGUUUUGGUGAAUUAUUGCGC----------------AGGA
((....((((.((((....))))))))((((((..(((((..((..(((..(((((.((((((....)))))).)-)))))))..))..))))))))).)----------------))). ( -35.40)
>DroYak_CAF1 9158 97 + 1
CU-------GUCCCUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGACUCGGUGGCAUUCGAUAAAUUGAAUUUACGCCGAUUUGGUGAAUUAUUGCAA----------------AGGC
((-------(((.....)))))(((....((((..(((((..((.....((((((..((((((....))))))...))))))...))..)))))))))..----------------.))) ( -30.00)
>consensus
CU_______UUCCAUUCGAUGGGCCAAUGGCAAAUUGAUUUGCCUCGGCUUGGUGGCAUUCAAUAAAUUGAAUUUACGCCGAUUUGGUGAAUUAUUGCAUUGCGCUGUCAUUGCGAGGGU
.............................((((..(((((..((.....((((((..((((((....))))))...))))))...))..)))))))))...................... (-22.58 = -22.38 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,101,225 – 5,101,338
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.04
Mean single sequence MFE -27.50
Consensus MFE -17.70
Energy contribution -18.78
Covariance contribution 1.08
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.64
SVM decision value 1.28
SVM RNA-class probability 0.939443
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5101225 113 - 27905053
ACCCUCGCAAUGACAGCGCAAUGCAAUAAUUCACCAAAUCGGCGUAAAUUCAAUUUAUUGAAUGCCACCAAGCCGAGGCAAAUCAAUUUGCCAUUGGCCCAUCGAAUGGAA-------AG
..((..(((.((......)).)))....((((........(((((....((((....))))))))).....(((((((((((....)))))).))))).....))))))..-------.. ( -28.40)
>DroSec_CAF1 8182 105 - 1
ACCCUCGCAAUGACAGCGCAAUGCAAUAAUUCACCAAAUCGGCGUAAAUUCAAUUUAUUGAAUGCCACCAAGCCGAGGCAAAUCAAUUUGCCAU--------CGACUGGAA-------AG
......(((.((......)).))).........(((..(((((....((((((....))))))........)))))((((((....))))))..--------....)))..-------.. ( -24.80)
>DroSim_CAF1 8199 113 - 1
ACCCUCGCAAUGACAGCGCAAUGCAAUAAUUCACCAAAUCGGCGUAAAUUCAAUUUAUUGAAUGCCACCAAGCCGAGGCAAAUCAAUUUGCCAUUGGCCCGUCGAAUGGAA-------AG
......(((.((......)).))).........(((..((((((...((((((....))))))........(((((((((((....)))))).))))).)))))).)))..-------.. ( -31.00)
>DroEre_CAF1 8287 103 - 1
UCCU----------------GCGCAAUAAUUCACCAAAACGGCG-AAAUUCAAUUUAUCGAAUGCCACCAAGCCGAGGCAAAUCAAUUUGCCAUUGGCCCAUCGAUGGGACCAAAGAUGG
...(----------------(.((.....(((.((.....)).)-))((((........))))))))....(((((((((((....)))))).)))))(((((..((....))..))))) ( -28.10)
>DroYak_CAF1 9158 97 - 1
GCCU----------------UUGCAAUAAUUCACCAAAUCGGCGUAAAUUCAAUUUAUCGAAUGCCACCGAGUCGAGGCAAAUCAAUUUGCCAUUGGCCCAUCGAAGGGAC-------AG
.(((----------------(((...............((((.(...((((........))))..).))))(((((((((((....)))))).)))))....))))))...-------.. ( -25.20)
>consensus
ACCCUCGCAAUGACAGCGCAAUGCAAUAAUUCACCAAAUCGGCGUAAAUUCAAUUUAUUGAAUGCCACCAAGCCGAGGCAAAUCAAUUUGCCAUUGGCCCAUCGAAUGGAA_______AG
.................................((.....(((....((((((....))))))))).....(((((((((((....)))))).))))).........))........... (-17.70 = -18.78 +   1.08)

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 10:18:57 2006