Locus 6613

Sequence ID 2R_DroMel_CAF1
Location 20,705,184 – 20,705,322
Length 138
Max. P 0.833086
window10524 window10525 window10526

overview

Window 4

Location 20,705,184 – 20,705,284
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.49
Mean single sequence MFE -30.74
Consensus MFE -22.96
Energy contribution -23.40
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -1.98
Structure conservation index 0.75
SVM decision value 0.72
SVM RNA-class probability 0.833086
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20705184 100 + 20766785
ACGGGGUGGC-------UUGAUGCCCAAAAGGGGUGGACAUUAUGCAUAUAUGUAUA------------UGUCUAACAGAGAGGGCAAUAUGCAUAAUGCUAUUCGUAAGGGUUGACCA-
...(((((..-------....))))).....((((((.((((((((((((.(((...------------(.((.....)).)..)))))))))))))))))))))....((.....)).- ( -32.50)
>DroSec_CAF1 138813 97 + 1
ACGGGGUGGC-------UUGAUGCCGAAAAGGGGUGGACAUUAUGCA----UGUAUAC-----------UGUCUAAGAGGGAGGGCAAUAUGCAUAAAGCUAUCCGUAAGGGUUGACCA-
...(((((((-------((.((.((.....)).)).))..(((((((----(((...(-----------(.(((.....))).))..)))))))))).)))))))....((.....)).- ( -31.30)
>DroSim_CAF1 142528 101 + 1
ACGGGGUGGC-------UUGAUGCCGAAAAGGGGUGGACAUUAUGCAUAUAUGUAUAC-----------UGUCUAAGAGGGAGGGCAAUAUGCAUAAAGCUAUCCGUAAGGGUUGACCA-
...(((((((-------((.((.((.....)).)).))..((((((((((.(((...(-----------(.((.....)).)).))))))))))))).)))))))....((.....)).- ( -32.90)
>DroEre_CAF1 179542 117 + 1
ACGGGGUGGCUGAAUACUUGAUGCCGAAAAGGGGUGGACAUUAUGCAUAUACAUAUAUAUGA---UGGGUGUCUGAGAGGGAGGGUAAUAUGCAUAACGCUAUUCGUAAGGGUUGACCAG
...(((((((.......((.((.((.....)).)).))..((((((((((.(((....))).---......(((....)))......)))))))))).)))))))....((.....)).. ( -26.70)
>DroYak_CAF1 144723 116 + 1
ACGGGGUGGCUGA---CUUGAUGCCGAAAAGGGGUGGACAUUAUGCAUAUAUGUAUACUGGGUCCUUGAUAUCUAAGAGGGAGGGCAAUAUGCAUAACGCUAUUCGUAAGGGUUGACCA-
...(((((((...---.((.((.((.....)).)).))..((((((((((.(((...((...(((((.........))))))).))))))))))))).)))))))....((.....)).- ( -30.30)
>consensus
ACGGGGUGGC_______UUGAUGCCGAAAAGGGGUGGACAUUAUGCAUAUAUGUAUAC___________UGUCUAAGAGGGAGGGCAAUAUGCAUAAAGCUAUUCGUAAGGGUUGACCA_
...(((((((.......((.((.((.....)).)).))..((((((((((...................(((((........))))))))))))))).)))))))....((.....)).. (-22.96 = -23.40 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,705,184 – 20,705,284
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.49
Mean single sequence MFE -20.06
Consensus MFE -14.35
Energy contribution -15.27
Covariance contribution 0.92
Combinations/Pair 1.05
Mean z-score -1.72
Structure conservation index 0.72
SVM decision value 0.18
SVM RNA-class probability 0.623288
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20705184 100 - 20766785
-UGGUCAACCCUUACGAAUAGCAUUAUGCAUAUUGCCCUCUCUGUUAGACA------------UAUACAUAUAUGCAUAAUGUCCACCCCUUUUGGGCAUCAA-------GCCACCCCGU
-((((...............(((((((((((((((.....((.....))..------------....)).)))))))))))))....(((....)))......-------))))...... ( -20.80)
>DroSec_CAF1 138813 97 - 1
-UGGUCAACCCUUACGGAUAGCUUUAUGCAUAUUGCCCUCCCUCUUAGACA-----------GUAUACA----UGCAUAAUGUCCACCCCUUUUCGGCAUCAA-------GCCACCCCGU
-.(((..........(((((...((((((((..(((..((.......))..-----------)))...)----))))))))))))..........(((.....-------)))))).... ( -20.50)
>DroSim_CAF1 142528 101 - 1
-UGGUCAACCCUUACGGAUAGCUUUAUGCAUAUUGCCCUCCCUCUUAGACA-----------GUAUACAUAUAUGCAUAAUGUCCACCCCUUUUCGGCAUCAA-------GCCACCCCGU
-.(((..........(((((...(((((((((((((..((.......))..-----------))).....)))))))))))))))..........(((.....-------)))))).... ( -20.90)
>DroEre_CAF1 179542 117 - 1
CUGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUACCCUCCCUCUCAGACACCCA---UCAUAUAUAUGUAUAUGCAUAAUGUCCACCCCUUUUCGGCAUCAAGUAUUCAGCCACCCCGU
..(((...............(((((((((((((......................---............)))))))))))))............(((............)))))).... ( -17.68)
>DroYak_CAF1 144723 116 - 1
-UGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUGCCCUCCCUCUUAGAUAUCAAGGACCCAGUAUACAUAUAUGCAUAAUGUCCACCCCUUUUCGGCAUCAAG---UCAGCCACCCCGU
-.(((...............(((((((((((((((..((...((((.(....).))))...))....)).)))))))))))))............(((......---...)))))).... ( -20.40)
>consensus
_UGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUGCCCUCCCUCUUAGACA___________GUAUACAUAUAUGCAUAAUGUCCACCCCUUUUCGGCAUCAA_______GCCACCCCGU
..(((...............(((((((((((((.....................................)))))))))))))............(((............)))))).... (-14.35 = -15.27 +   0.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,705,217 – 20,705,322
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.53
Mean single sequence MFE -20.56
Consensus MFE -6.15
Energy contribution -6.75
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.30
SVM decision value 0.03
SVM RNA-class probability 0.550597
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20705217 105 - 20766785
UGUAUAUGUACGUGUGUCAACGGUCUUCCAUUUCCAAA---UGGUCAACCCUUACGAAUAGCAUUAUGCAUAUUGCCCUCUCUGUUAGACA------------UAUACAUAUAUGCAUAA
(((((((((..(((((((((((((...(((((....))---)))...)))......((((((.....)).)))).........))).))))------------)))..)))))))))... ( -26.30)
>DroSec_CAF1 138846 98 - 1
UGUAU----ACGUGCGUAAACGGUCUUCCUUUUCCAAG---UGGUCAACCCUUACGGAUAGCUUUAUGCAUAUUGCCCUCCCUCUUAGACA-----------GUAUACA----UGCAUAA
(((((----((((((((((..(((..(((......(((---.((....)))))..)))..)))))))))))......((.......))...-----------)))))))----....... ( -20.00)
>DroSim_CAF1 142561 102 - 1
UGUAU----ACGUGUGUAAACGGUCUUUCUUUUCCAAG---UGGUCAACCCUUACGGAUAGCUUUAUGCAUAUUGCCCUCCCUCUUAGACA-----------GUAUACAUAUAUGCAUAA
(((((----(..((((((....((((.........(((---.((....)))))..(((..((..((....))..))..))).....)))).-----------.))))))..))))))... ( -23.50)
>DroEre_CAF1 179582 102 - 1
UGUAU----AUG-----------UCGUCCUUUUCCAAACCCUGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUACCCUCCCUCUCAGACACCCA---UCAUAUAUAUGUAUAUGCAUAA
.(((.----..(-----------(.(.((.............)).).))...))).....((((.((((((((......................---......)))))))))))).... ( -12.51)
>DroYak_CAF1 144760 109 - 1
UAUUU----AUGU----AUGCUCUCGUCCUUUUCCAAA---UGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUGCCCUCCCUCUUAGAUAUCAAGGACCCAGUAUACAUAUAUGCAUAA
(((.(----((((----(((((...((((((.((.((.---.((.........(((.....)))...((.....))....))..)).))....))))))..)))))))))).)))..... ( -20.50)
>consensus
UGUAU____ACGUG_GUAAACGGUCUUCCUUUUCCAAA___UGGUCAACCCUUACGAAUAGCGUUAUGCAUAUUGCCCUCCCUCUUAGACA___________GUAUACAUAUAUGCAUAA
.................................(((.....)))...................((((((((((.....................................)))))))))) ( -6.15 =  -6.75 +   0.60)

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 12:15:07 2006