Locus 901

Sequence ID 3L_DroMel_CAF1
Location 2,726,398 – 2,726,539
Length 141
Max. P 0.691211
window1385 window1386

overview

Window 5

Location 2,726,398 – 2,726,501
Length 103
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 82.99
Mean single sequence MFE -26.42
Consensus MFE -18.18
Energy contribution -18.47
Covariance contribution 0.28
Combinations/Pair 1.23
Mean z-score -1.75
Structure conservation index 0.69
SVM decision value 0.07
SVM RNA-class probability 0.570444
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2726398 103 + 23771897
AUCGUAGAUAUAU---UUGGCACAGCGAA-----AGCUGGCGCU-UUUGGAUCUGCAGUUUGUGCUGUUGUUCAGUUUUUG-GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
.............---......((((...-----.))))((((.-..(((((..(((((....))))).)))))(((...(-((((((.....))))))).)))..))))... ( -30.20)
>DroSec_CAF1 86546 103 + 1
AUCGUAGAUAUAU---UUGGCACACCGAA-----AGCUGGCGCU-UUUGAAUCUGCAGUUUGUGCUGUUGUUCAGUUUUUG-GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
............(---((((....)))))-----...((((((.-..(((((..(((((....))))).)))))(((...(-((((((.....))))))).)))..)))))). ( -27.00)
>DroSim_CAF1 84759 103 + 1
AUCGUAGAUAUAU---UUGGCACCGCGAA-----AGCUGGCGCU-UUUGAAUCUGCAGUUUGUGCUGUUGUUCAGUUUUUG-GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
...((((((.((.---..(((.((((...-----.)).)).)))-..)).)))))).....((((........((((...(-((((((.....))))))).)))).))))... ( -28.50)
>DroEre_CAF1 94845 101 + 1
AUCGUAGGUAUAU---UUGGCACAUU--U-----CGCUGGCGCU-UUUGGAUCUGCAGUUUGUGCUGUUGCUCAGUUUUUG-GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
.............---..(((.....--.-----.)))(((((.-....((.(.(((((....))))).).))((((...(-((((((.....))))))).)))).))))).. ( -22.50)
>DroYak_CAF1 88245 101 + 1
AUCGUUGGUAUAU---UUGGCACUUU--U-----CGCUGGCGCU-UUUGGAUCUGCAGUUUGUGCUGUUGCUCAGUUUUUG-GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
...((..(.....---)..)).....--.-----...((((((.-....((.(.(((((....))))).).))((((...(-((((((.....))))))).)))).)))))). ( -24.90)
>DroAna_CAF1 84813 109 + 1
UACGUAUCUAUAUACUUUCGGGCAGCGGACUAUGCGCUUUUGCUUUUUGGAUUUUUAGUUUCUGG----GUCCAACGUAUGCAUAAUCUGUCUGAUUAUUUAUCUUGCGCUAA
..((((...(((.....((((((((.....(((((((....))...((((((((.........))----)))))).....)))))..)))))))).....)))..)))).... ( -25.40)
>consensus
AUCGUAGAUAUAU___UUGGCACAGCGAA_____AGCUGGCGCU_UUUGGAUCUGCAGUUUGUGCUGUUGUUCAGUUUUUG_GUAAUCUGUCUGAUUAUUUAACUUGCGCUAA
.....................................((((((...((((((..(((((....))))).))))))...(((.((((((.....)))))).)))...)))))). (-18.18 = -18.47 +   0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,726,430 – 2,726,539
Length 109
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 75.86
Mean single sequence MFE -15.78
Consensus MFE -8.05
Energy contribution -8.38
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.51
SVM decision value 0.33
SVM RNA-class probability 0.691211
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2726430 109 - 23771897
AUAAAAAUUGCCGCAAAAUAUUUUCUAAAUAUUUGUAUUUAGCGCAAGUUAAAUAAUCAGACAGAUUAC-CAAAAACUGAACAACAGCACAAA-CUGCAGA---UCCAAA-AGCG
...........(((.(((((((.....))))))).((((((((....))))))))(((...(((.((..-...)).))).......(((....-.))).))---).....-.))) ( -16.30)
>DroVir_CAF1 103639 107 - 1
AUAAAAAUCGCCACAAAAUA-UUUCUAAAUAUUUGUAUUUAGCGCAAGUUAAAUAAUCAGACAGAUUAU-GCAUACGUUAUAAAAAUAACAAAAAGCCAAA---CCGAAA-AA--
.......(((.....(((((-((....)))))))(((((((((....)))))((((((.....))))))-..))))(((((....)))))...........---.)))..-..-- ( -15.10)
>DroSec_CAF1 86578 91 - 1
------------------UUUUUUCUAAAUAUUUGUAUUUAGCGCAAGUUAAAUAAUCAGACAGAUUAC-CAAAAACUGAACAACAGCACAAA-CUGCAGA---UUCAAA-AGCG
------------------.....(((......(((((((((((....)))))))..((((.........-......))))))))..(((....-.))))))---......-.... ( -12.66)
>DroSim_CAF1 84791 109 - 1
AUAAAAAUUGCCGCAGAAUAUUUUCUAAAUAUUUGUAUUUAGCGCAAGUUAAAUAAUCAGACAGAUUAC-CAAAAACUGAACAACAGCACAAA-CUGCAGA---UUCAAA-AGCG
...........(((((((....)))).....((((((((((((....))))))))(((...(((.((..-...)).))).......(((....-.))).))---).))))-.))) ( -17.30)
>DroMoj_CAF1 94208 109 - 1
AUAAAAAUUGCCUGAAAAUA-UUUCUAAAUAUUUGUAUAUAGCGCAAGUUAAAUAAUCAGACAGAUUAU-GCAUACGUUAUAAAAAUAACAAA-AGCCAAAGCAGCGAAA-AA--
.......(((.(((((((((-((....))))))).(((.((((....)))).))).)))).)))....(-((....(((((....)))))...-.((....)).)))...-..-- ( -17.90)
>DroAna_CAF1 84853 106 - 1
AUAAAAAUUGCCGCA-AAUAUUUUCUAAAUAUUUGUAUUUAGCGCAAGAUAAAUAAUCAGACAGAUUAUGCAUACGUUGGAC----CCAGAAA-CUAAAAA---UCCAAAAAGCA
........(((.(((-((((((.....))))))))).(((((((....((..((((((.....))))))..)).))))))).----.......-.......---........))) ( -15.40)
>consensus
AUAAAAAUUGCCGCAAAAUAUUUUCUAAAUAUUUGUAUUUAGCGCAAGUUAAAUAAUCAGACAGAUUAC_CAAAAACUGAACAACAGCACAAA_CUGCAAA___UCCAAA_AGCG
...............................((((((((((((....))))))))..))))...................................................... ( -8.05 =  -8.38 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:58 2006