Locus 1992

Sequence ID X_DroMel_CAF1
Location 5,475,224 – 5,475,376
Length 152
Max. P 0.963584
window3245 window3246 window3247

overview

Window 5

Location 5,475,224 – 5,475,336
Length 112
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 73.79
Mean single sequence MFE -34.60
Consensus MFE -23.84
Energy contribution -24.32
Covariance contribution 0.47
Combinations/Pair 1.09
Mean z-score -1.68
Structure conservation index 0.69
SVM decision value 1.55
SVM RNA-class probability 0.963584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5475224 112 + 22224390
GUCCUGCUCCCGACAC--CCGUCACUCCUCGUCCAGACCUGAUGAAUCCCACAAUAAUGGCCAGAAUGGCGAACGCCAUCAGGAUGCAGUGGCUGGCGUCGGCGAGGUAAAUGG
......((((((((.(--(.((((((...(((((..............(((......)))...((.((((....)))))).))))).)))))).)).))))).)))........ ( -39.50)
>DroPse_CAF1 979 84 + 1
------------------------------AACCAGACCUGAUGAAGCCCACUAUGAUGGCCAGUAUGGCGAAGGCCAUGAGGAUGCAGUGGCUGGCAUCGGCCAGGUAAAUGG
------------------------------..(((.(((((.(((.(((..((((.....((..((((((....)))))).)).....))))..))).)))..)))))...))) ( -34.30)
>DroYak_CAF1 1022 113 + 1
GU-CUGCUCCCGACACUCCCCGCACUCCUCGUCCAGACCUGAUGAAUCCCACAAUAAUGGCCAGUAUGGCGAAGGCCAUCAGGAUGCAGUGGCUGGCGUCGGCGAGGUAAAUGG
..-...((((((((.((..((((.....((.....))((((((.....(((......))).......(((....))))))))).....))))..)).))))).)))........ ( -36.50)
>DroMoj_CAF1 1895 93 + 1
-------------------CG--CCUUCUGUUACGCACCUUAUGAAGCCCACUAUGAUGGCCAGUAUGGCAAAGGCCAUAAGAAUGCAGUGACUGGCAUCGGCCAGGUAAAUGG
-------------------.(--((....((((((((.((((((..(((..(......)(((.....)))...)))))))))..))).)))))((((....)))))))...... ( -27.80)
>DroAna_CAF1 1024 108 + 1
AU-CAGCUCCCAGU-C--CCAUC--CCAGUAUCCAGACCUGAUAAAGCCCACUAUUAUGGCCAGUAUGGCGAAGGCCAUCAGGAUGCAAUGACUGGCAUCGGCCAGGUAGAUGG
..-...........-.--(((((--...((((((.(.(((((((........))))).)).).(.(((((....)))))).)))))).....(((((....)))))...))))) ( -35.20)
>DroPer_CAF1 983 84 + 1
------------------------------AACCAGACCUGAUGAAGCCCACUAUGAUGGCCAGUAUGGCGAAGGCCAUGAGGAUGCAGUGGCUGGCAUCGGCCAGGUAAAUGG
------------------------------..(((.(((((.(((.(((..((((.....((..((((((....)))))).)).....))))..))).)))..)))))...))) ( -34.30)
>consensus
___________________C_____UCCU_AUCCAGACCUGAUGAAGCCCACUAUGAUGGCCAGUAUGGCGAAGGCCAUCAGGAUGCAGUGGCUGGCAUCGGCCAGGUAAAUGG
................................(((.((((..((.....)).......((((...(((((....)))))...(((((........)))))))))))))...))) (-23.84 = -24.32 +   0.47)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 5,475,224 – 5,475,336
Length 112
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 73.79
Mean single sequence MFE -34.90
Consensus MFE -20.95
Energy contribution -21.48
Covariance contribution 0.53
Combinations/Pair 1.05
Mean z-score -1.57
Structure conservation index 0.60
SVM decision value 0.74
SVM RNA-class probability 0.837930
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5475224 112 - 22224390
CCAUUUACCUCGCCGACGCCAGCCACUGCAUCCUGAUGGCGUUCGCCAUUCUGGCCAUUAUUGUGGGAUUCAUCAGGUCUGGACGAGGAGUGACGG--GUGUCGGGAGCAGGAC
.......((((.((((((((.(.((((.(..((((((((.(((((((.....)))(((....)))))))))))))))((.....))).)))).).)--)))))))..).))).. ( -42.50)
>DroPse_CAF1 979 84 - 1
CCAUUUACCUGGCCGAUGCCAGCCACUGCAUCCUCAUGGCCUUCGCCAUACUGGCCAUCAUAGUGGGCUUCAUCAGGUCUGGUU------------------------------
......(((.((((((((..((((((((.......((((((...........))))))..)))).)))).)))).)))).))).------------------------------ ( -28.10)
>DroYak_CAF1 1022 113 - 1
CCAUUUACCUCGCCGACGCCAGCCACUGCAUCCUGAUGGCCUUCGCCAUACUGGCCAUUAUUGUGGGAUUCAUCAGGUCUGGACGAGGAGUGCGGGGAGUGUCGGGAGCAG-AC
........(((.(((((((...((.((((((((((((((((...........))))))))((((.(((((.....))))).).)))))).))))))).))))))))))...-.. ( -43.40)
>DroMoj_CAF1 1895 93 - 1
CCAUUUACCUGGCCGAUGCCAGUCACUGCAUUCUUAUGGCCUUUGCCAUACUGGCCAUCAUAGUGGGCUUCAUAAGGUGCGUAACAGAAGG--CG-------------------
(((((....((((((((((........)))))..((((((....))))))..)))))....)))))((((......((.....))...)))--).------------------- ( -26.80)
>DroAna_CAF1 1024 108 - 1
CCAUCUACCUGGCCGAUGCCAGUCAUUGCAUCCUGAUGGCCUUCGCCAUACUGGCCAUAAUAGUGGGCUUUAUCAGGUCUGGAUACUGG--GAUGG--G-ACUGGGAGCUG-AU
.((.((.((..(((.((.(((((.(((....((((((((((...(((.....)))(((....)))))))..))))))....))))))))--.)).)--)-.)..)))).))-.. ( -40.50)
>DroPer_CAF1 983 84 - 1
CCAUUUACCUGGCCGAUGCCAGCCACUGCAUCCUCAUGGCCUUCGCCAUACUGGCCAUCAUAGUGGGCUUCAUCAGGUCUGGUU------------------------------
......(((.((((((((..((((((((.......((((((...........))))))..)))).)))).)))).)))).))).------------------------------ ( -28.10)
>consensus
CCAUUUACCUGGCCGAUGCCAGCCACUGCAUCCUGAUGGCCUUCGCCAUACUGGCCAUCAUAGUGGGCUUCAUCAGGUCUGGAU_AGGA_____G___________________
((((.....((((((((((........)))))...(((((....)))))...))))).....))))................................................ (-20.95 = -21.48 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 5,475,256 – 5,475,376
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 87.83
Mean single sequence MFE -38.42
Consensus MFE -31.90
Energy contribution -31.68
Covariance contribution -0.22
Combinations/Pair 1.25
Mean z-score -2.30
Structure conservation index 0.83
SVM decision value 0.75
SVM RNA-class probability 0.841135
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5475256 120 - 22224390
UUCUUCGUCUUGGUGCGCCAUCAGCAGUUCUCGCUGUUGGCCAUUUACCUCGCCGACGCCAGCCACUGCAUCCUGAUGGCGUUCGCCAUUCUGGCCAUUAUUGUGGGAUUCAUCAGGUCU
......(.((((((((((((((((((((.((.((.((((((..........)))))))).))..)))))....))))))))((((((.....)))(((....))))))..))))))).). ( -41.70)
>DroVir_CAF1 8569 120 - 1
UUCUUCGUCUUGGUGCGUCAUCAGCAGUUCUCGCUGUUGGCCAUUUACCUGGCCGAUGCCAGUCACUGCAUUCUAAUGGCCUUUGCCAUACUCGCUAUCAUUAUCGGUUUUAUCAGGUGC
....(((...(((((((......(((((.((.((.((((((((......)))))))))).))..)))))......(((((....)))))...))).))))....)))............. ( -35.30)
>DroGri_CAF1 1382 120 - 1
UUCUUCGUCUUGGUGCGUCAUCAGCAGUUCUCGCUGUUGGCCAUUUACCUCGCCGAUGCCAGUCACUGUAUUCUAAUGGCCUUUGCCAUACUAGCCAUCAUUAUUGGCUUCAUCAGGUGC
...........((((.((..((((((((....))))))))..)).)))).((((((((.................(((((....)))))...(((((.......))))).)))).)))). ( -32.10)
>DroWil_CAF1 23008 120 - 1
UUCUUCGUCUUGGUGCGUCAUCAGAAGUUCUCGCUAUUGGCCGUUUAUCUGGCCGAUGCCAGCCAUUGUAUACUGAUGGCAUUUGCCAUUUUGGCCAUCAUAGUGGGCUUUAUAAGGUAA
..((((....(((((...)))))))))..((((((((((((((......((((.(((((((..((........)).))))))).))))...))))))..))))))))............. ( -37.40)
>DroMoj_CAF1 1908 120 - 1
UUCUUCGUCUUGGUGCGUCAUCAGCAGUUCUCGCUGUUGGCCAUUUACCUGGCCGAUGCCAGUCACUGCAUUCUUAUGGCCUUUGCCAUACUGGCCAUCAUAGUGGGCUUCAUAAGGUGC
......(((((((((.((((...(((((.((.((.((((((((......)))))))))).))..))))).....((((((....)))))).)))))))))....))))............ ( -40.20)
>DroAna_CAF1 1052 120 - 1
UUCUUCGUCUUGGUGCGCCAUCAGCAGUUCUCGCUGUUGGCCAUCUACCUGGCCGAUGCCAGUCAUUGCAUCCUGAUGGCCUUCGCCAUACUGGCCAUAAUAGUGGGCUUUAUCAGGUCU
......(.(((((((.((((((((((((.((.((.((((((((......)))))))))).))..)))))....)))))))....(((.(((((.......))))))))..))))))).). ( -43.80)
>consensus
UUCUUCGUCUUGGUGCGUCAUCAGCAGUUCUCGCUGUUGGCCAUUUACCUGGCCGAUGCCAGUCACUGCAUUCUGAUGGCCUUUGCCAUACUGGCCAUCAUAGUGGGCUUCAUCAGGUGC
...(((((..(((((.((((...(((((.((.((.((((((((......)))))))))).))..)))))......(((((....)))))..)))))))))..)))))............. (-31.90 = -31.68 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:44 2006