Locus 1388

Sequence ID 3R_DroMel_CAF1
Location 4,053,992 – 4,054,123
Length 131
Max. P 0.968645
window2287 window2288 window2289

overview

Window 7

Location 4,053,992 – 4,054,098
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.63
Mean single sequence MFE -26.14
Consensus MFE -24.48
Energy contribution -25.14
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.94
SVM decision value 1.63
SVM RNA-class probability 0.968645
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4053992 106 + 27905053
-----AGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAG---------
-----.........(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))..--------- ( -24.96)
>DroVir_CAF1 39861 115 + 1
GAUGCAGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC---AACG--
..(((....)))..(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))..---....-- ( -27.26)
>DroGri_CAF1 23294 116 + 1
GAUGCAGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC---AACG-G
..(((....)))..(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))..---....-. ( -27.26)
>DroWil_CAF1 70476 111 + 1
GAUGCAGAUGCAACGAGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC---------
..(((....)))....(.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)....--------- ( -22.86)
>DroMoj_CAF1 45874 117 + 1
GAUGCAGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC-AGAACG--
..(((....)))..(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))..-......-- ( -27.26)
>DroAna_CAF1 44939 120 + 1
GAUGCAGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAGCCAAGCCAG
..(((....)))..(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))........... ( -27.26)
>consensus
GAUGCAGAUGCAACGUGAUGCUUGUUGGUAAUAAAAUUGGUGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC___AACG__
..(((....)))..(((.(((((((((((......(((.((......)).)))......((((((((...............))))))))...))))))).)))).)))........... (-24.48 = -25.14 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,053,992 – 4,054,098
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.63
Mean single sequence MFE -26.79
Consensus MFE -24.43
Energy contribution -25.09
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.05
Structure conservation index 0.91
SVM decision value 0.05
SVM RNA-class probability 0.561032
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4053992 106 - 27905053
---------CUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCU-----
---------..(((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).))).........----- ( -25.16)
>DroVir_CAF1 39861 115 - 1
--CGUU---GUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCUGCAUC
--.((.---.((((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).))))..))......... ( -28.06)
>DroGri_CAF1 23294 116 - 1
C-CGUU---GUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCUGCAUC
.-.((.---.((((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).))))..))......... ( -28.06)
>DroWil_CAF1 70476 111 - 1
---------GUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCUCGUUGCAUCUGCAUC
---------..(.(.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).).)..(((....))).. ( -23.16)
>DroMoj_CAF1 45874 117 - 1
--CGUUCU-GUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCUGCAUC
--......-..(((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).)))..(((....))).. ( -27.16)
>DroAna_CAF1 44939 120 - 1
CUGGCUUGGCUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCUGCAUC
...((...((((((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).))))..))....))... ( -29.16)
>consensus
__CGUU___GUGUGUUGCUCUGUUAAUUUUACAGCCAUGUCUGAUAUUGCUAAAUGGCUGUGAGUGGAUUCGUUUAAGCACCAAUUUUAUUACCAACAAGCAUCACGUUGCAUCUGCAUC
...........(((.((((.((((...(((((((((((...............)))))))))))(((...(......)..)))...........)))))))).)))..(((....))).. (-24.43 = -25.09 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,054,027 – 4,054,123
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.26
Mean single sequence MFE -18.89
Consensus MFE -14.56
Energy contribution -14.56
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.31
Structure conservation index 0.77
SVM decision value 1.02
SVM RNA-class probability 0.900710
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4054027 96 + 27905053
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAG---------CGAUCCG-------C-GA-----UGGAGCAACUGGCAA--
((((........((((.((((((((((...............))))))))....................(---------((...))-------)-))-----))))......)))).-- ( -21.30)
>DroVir_CAF1 39901 92 + 1
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC---AACG--------------AAC-GA-----UGCUCCAA---ACAA--
...................((((((((...............))))))))..........(((((.(....---....--------------...-).-----)))))...---....-- ( -14.76)
>DroGri_CAF1 23334 99 + 1
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC---AACG-GCGACCCGGCCGAAAC-GA-----UGGACC-----------
............((((.((((((((((...............)))))))).....................---..((-((......))))....-))-----))))..----------- ( -22.06)
>DroMoj_CAF1 45914 92 + 1
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC-AGAACG--------------AGC-GA-----UGGACCCA---A--A--
.........(..((((.((((((((((...............))))))))............((.......-......--------------.))-))-----))))..).---.--.-- ( -15.20)
>DroAna_CAF1 44979 93 + 1
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAGCCAAGCCAGCGAUCCA-------G-CA-------------------ACC
(((((....((......))((((((((...............))))))))..........)))))..............((......-------)-).-------------------... ( -16.66)
>DroPer_CAF1 40425 100 + 1
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAG---------CGAUGCG-------GCCAGAGCGUGGCGC----GGCAAUC
(((((....((......))((((((((...............))))))))..........))))).....(---------(.((((.-------......)))).))..----....... ( -23.36)
>consensus
UGCUUAAACGAAUCCACUCACAGCCAUUUAGCAAUAUCAGACAUGGCUGUAAAAUUAACAGAGCAACACAC___AACG__CGAUCCG_______C_GA_____UGGACC________A__
(((((....((......))((((((((...............))))))))..........)))))....................................................... (-14.56 = -14.56 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:50 2006