Locus 2556

Sequence ID 2R_DroMel_CAF1
Location 9,073,628 – 9,073,780
Length 152
Max. P 0.997762
window4207 window4208 window4209

overview

Window 7

Location 9,073,628 – 9,073,748
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.00
Mean single sequence MFE -30.98
Consensus MFE -25.94
Energy contribution -26.62
Covariance contribution 0.68
Combinations/Pair 1.04
Mean z-score -2.63
Structure conservation index 0.84
SVM decision value 2.93
SVM RNA-class probability 0.997762
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073628 120 - 20766785
CAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUGAAGGACAUAUAGAAAUCAUGUGAACAAUCUUACCGAAACGUUUUGCUAAUUUUUUGGCACUGCUUUUCAUU
......((((((.((((((........)))))).))))))...........(..((((((....).)))))..).........((((.((..((((((....))))))..)).))))... ( -33.20)
>DroSec_CAF1 38609 120 - 1
UAUGCACGCCCAUUCGCCCAUUUUCUAGGGUAUAUGGGUGCUAUUUUUAAAGGACAUAUAGAAAUUAUGUGAACAAUCUUACCGAAACGUUUUGCUAACAUCUUGGCACAGCUUUUCAUU
......(((((((..((((........))))..)))))))...........(..(((((((...)))))))..).........((((.(((.((((((....)))))).))).))))... ( -32.00)
>DroSim_CAF1 40366 120 - 1
UAUGCACGCCCAUUCCCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUGAAGGGCAUAUAGAAAUUAUGUGAACAAUCUUACCGAAACGUUUUGCUAACUUCUUGGCACUGCUUUUCAUU
......((((((.(..(((........)))..).))))))...........(..(((((((...)))))))..).........((((.((..((((((....))))))..)).))))... ( -29.60)
>DroEre_CAF1 44292 120 - 1
UAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCUUGUGAACAAUCUUACCGAAACGUUUUGCUAACUUCCUGGCACUGCUUUUCAUU
......((((((.((((((........)))))).))))))...........(..((((.((....))))))..).........((((.((..(((((......)))))..)).))))... ( -31.50)
>DroYak_CAF1 40734 117 - 1
UAUGCACGCCCAUUUGCCCAUUUUACAGGGUAAUAGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCUU---AACAAUCUUACCGAAACGUUGUGCUUAUUUUCAGGCACUGCUUUUCAUU
......(((((..((((((........))))))..)))))..........((((.....((....)).---.....))))...((((.((.((((((......)))))).)).))))... ( -28.60)
>consensus
UAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCAUGUGAACAAUCUUACCGAAACGUUUUGCUAACUUCUUGGCACUGCUUUUCAUU
......((((((.((((((........)))))).))))))...........................................((((.((..(((((......)))))..)).))))... (-25.94 = -26.62 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,073,668 – 9,073,780
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.08
Mean single sequence MFE -23.64
Consensus MFE -18.88
Energy contribution -19.08
Covariance contribution 0.20
Combinations/Pair 1.12
Mean z-score -1.47
Structure conservation index 0.80
SVM decision value -0.05
SVM RNA-class probability 0.507204
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073668 112 + 20766785
AAGAUUGUUCACAUGAUUUCUAUAUGUCCUUCAAAAAUAGCACCCAAUUACCCUGGAAAAUGGGCAAAUGGGCGUGCAUGGGACAACGCACAUUUAAUU----AACCAAU----UUAUAU
.((((((.((....))........((((((.........((.((((.((.(((........))).)).)))).))....))))))..............----...))))----)).... ( -22.22)
>DroSec_CAF1 38649 111 + 1
AAGAUUGUUCACAUAAUUUCUAUAUGUCCUUUAAAAAUAGCACCCAUAUACCCUAGAAAAUGGGCGAAUGGGCGUGCAUAGGACAACGCAGAUGUACUU----AACUUAU----U-AUAU
.(((((((....))))))).....((((((.........((.(((((...(((........)))...))))).))....))))))..............----.......----.-.... ( -21.52)
>DroSim_CAF1 40406 111 + 1
AAGAUUGUUCACAUAAUUUCUAUAUGCCCUUCAAAAAUAGCACCCAAUUACCCUGGAAAAUGGGGGAAUGGGCGUGCAUAGGACAACGCAGAUGUACUU----AACUAAA----U-AUAU
.(((((((....))))))).((((((((((((..........((((.((.(....).)).)))).))).))))((((((..(......)..))))))..----......)----)-))). ( -21.90)
>DroEre_CAF1 44332 111 + 1
AAGAUUGUUCACAAGAUUUCUAUAUGUCCUUGAAAAAUAGCACCCAAUUACCCUGGAAAAUGGGCAAAUGGGCGUGCAUAGGACAACCCGGAAUUACUU----UAUUAAU----U-AUAU
..(((((.......((((((....((((((((.......((.((((.((.(((........))).)).)))).)).)).))))))....))))))....----...))))----)-.... ( -24.54)
>DroYak_CAF1 40774 116 + 1
AAGAUUGUU---AAGAUUUCUAUAUGUCCUUGAAAAAUAGCACCCUAUUACCCUGUAAAAUGGGCAAAUGGGCGUGCAUAGGACAACACGCAAUAACUUAUUUCAAUAAUCAUGU-AUAU
..(((((((---.((....))...(((((((....))..((((((((((.(((........)))..)))))).))))...)))))...................)))))))....-.... ( -28.00)
>consensus
AAGAUUGUUCACAUGAUUUCUAUAUGUCCUUCAAAAAUAGCACCCAAUUACCCUGGAAAAUGGGCAAAUGGGCGUGCAUAGGACAACGCAGAUUUACUU____AACUAAU____U_AUAU
........................((((((.........((.((((.((.(((........))).)).)))).))....))))))................................... (-18.88 = -19.08 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,073,668 – 9,073,780
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.08
Mean single sequence MFE -26.73
Consensus MFE -21.06
Energy contribution -22.10
Covariance contribution 1.04
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.79
SVM decision value 0.55
SVM RNA-class probability 0.777158
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9073668 112 - 20766785
AUAUAA----AUUGGUU----AAUUAAAUGUGCGUUGUCCCAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUGAAGGACAUAUAGAAAUCAUGUGAACAAUCUU
...(((----(.((((.----........((((((......))))))(((((.((((((........)))))).)))))))))..))))..(..((((((....).)))))..)...... ( -28.80)
>DroSec_CAF1 38649 111 - 1
AUAU-A----AUAAGUU----AAGUACAUCUGCGUUGUCCUAUGCACGCCCAUUCGCCCAUUUUCUAGGGUAUAUGGGUGCUAUUUUUAAAGGACAUAUAGAAAUUAUGUGAACAAUCUU
((((-(----((..((.----....)).((((...((((((.....(((((((..((((........))))..))))))).((....)).))))))..)))).))))))).......... ( -28.20)
>DroSim_CAF1 40406 111 - 1
AUAU-A----UUUAGUU----AAGUACAUCUGCGUUGUCCUAUGCACGCCCAUUCCCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUGAAGGGCAUAUAGAAAUUAUGUGAACAAUCUU
....-.----....(((----..(((..((((...((((((...((((((((.(..(((........)))..).)))))).......)).))))))..))))...)))...)))...... ( -24.71)
>DroEre_CAF1 44332 111 - 1
AUAU-A----AUUAAUA----AAGUAAUUCCGGGUUGUCCUAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCUUGUGAACAAUCUU
....-.----.......----......(((((((.((((((.....((((((.((((((........)))))).))))))..........)))))).........)))).)))....... ( -26.56)
>DroYak_CAF1 40774 116 - 1
AUAU-ACAUGAUUAUUGAAAUAAGUUAUUGCGUGUUGUCCUAUGCACGCCCAUUUGCCCAUUUUACAGGGUAAUAGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCUU---AACAAUCUU
....-..(((.((.((((((........((((((......))))))(((((..((((((........))))))..))))).....)))))).)))))...........---......... ( -25.40)
>consensus
AUAU_A____AUUAGUU____AAGUAAAUCUGCGUUGUCCUAUGCACGCCCAUUUGCCCAUUUUCCAGGGUAAUUGGGUGCUAUUUUUCAAGGACAUAUAGAAAUCAUGUGAACAAUCUU
...................................((((((.....((((((.((((((........)))))).))))))..........))))))........................ (-21.06 = -22.10 +   1.04)

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 10:32:58 2006