Locus 4629

Sequence ID	3R_DroMel_CAF1
Location	12,177,323 – 12,177,543
Length	220
Max. P	0.903603

overview

Window 8

Location	12,177,323 – 12,177,428
Length	105
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	71.41
Mean single sequence MFE	-27.26
Consensus MFE	-13.86
Energy contribution	-14.78
Covariance contribution	0.92
Combinations/Pair	1.12
Mean z-score	-1.86
Structure conservation index	0.51
SVM decision value	1.03
SVM RNA-class probability	0.903603
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12177323 105 + 27905053
UCUGCAGCUGACAUUUCUA----CAAAUGGCCUCAACAAGCCACUUUGCGCCUCAUUUGCUUGCACCACCCGGCAAGUUACCUCCAAAAUCCUCUAGUCUGCGGCGCCG
.(((((((((.........----((((((((........)))).))))..........((((((........))))))................))).))))))..... ( -23.00)
>DroSec_CAF1 2094 80 + 1
GCUGCAGCAGACAUUUCUA----CAAAUGGCUUCAACAAGCCACUUUGCGCUUCAUUUGCUUGCACCACCCGGCAAGU-------------------------GCGCCG
(.(((((((((........----((((((((((....)))))).)))).......))))).)))).)...((((....-------------------------..)))) ( -22.76)
>DroSim_CAF1 2100 105 + 1
GCUGCAGCGGACAUUUUUA----CAAAUGGCAUCAACAAGCCACUUUGCGCCUCAUUAGCUUGCACCACCCGGCAAGUUCCCUCCAAAAACCUCUAGUCUGCGGCGCCG
(((((((((((..(((((.----((((((((........)))).)))).........(((((((........)))))))......)))))..))).).))))))).... ( -29.20)
>DroEre_CAF1 1939 106 + 1
GUUU--GUGGAAAUGUCAGUUCACAAAUGGCCUCAACAAGCCACUUUGCGCCUCAUUUGCUUGCACCACCCGGCAAG-CCCCUCCAAAAACUUCUAGCCUGCGGCGCCG
((((--(((((........)))))))))(((........))).....(((((......((((((........)))))-).................(....)))))).. ( -28.50)
>DroWil_CAF1 5503 90 + 1
-UUUCUGUUGGCAUUCAAA----CAAAUUGCUU-GGCCAACCACCUAGCACCUCAUUUGUUUGCUC------GCACG-CCUCUCA------UUGGGGCCUGAGGUGCCG
-.....((((((...(((.----....)))...-.))))))......((((((((..(((......------))).(-((((...------..))))).)))))))).. ( -30.30)
>DroYak_CAF1 2025 105 + 1
GCUGCCGCUGUAAUUUCAG----CAAAUGGCCUCAACAAGCCACUUUGCGCCUCAUUUGCUUGCACCACCCGGCAAGUCCCCUCCAAAAACUUCUAGCUUGCGGCGCCG
((.(((((.((.......(----((((((((........)))).))))).........((((((........))))))..................))..))))))).. ( -29.80)
>consensus
GCUGCAGCUGACAUUUCAA____CAAAUGGCCUCAACAAGCCACUUUGCGCCUCAUUUGCUUGCACCACCCGGCAAGUCCCCUCCAAAAACUUCUAGCCUGCGGCGCCG
...........................((((........))))....(((((.((...((((((........)))))).....................)).))))).. (-13.86 = -14.78 +   0.92)

alignment

secondary structure

dotplot

Window 9

Location	12,177,428 – 12,177,543
Length	115
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.30
Mean single sequence MFE	-35.89
Consensus MFE	-19.22
Energy contribution	-21.47
Covariance contribution	2.25
Combinations/Pair	1.21
Mean z-score	-1.72
Structure conservation index	0.54
SVM decision value	0.10
SVM RNA-class probability	0.583946
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12177428 115 - 27905053
GCUACUUCUCCAUGUGCGGUUUUUAGCACCGGAUGACGGUUA-UUGCGAGCCGUUUUUAAUUUAUAGACGCAUUUAUCAUGCCAUGAUUGCC-CGUGUGCUGAAAACAGAAGUG-CCC-
((.((((((.........((((((((((((((..(((((((.-.....)))))))..............(((.((((......)))).))))-)).))))))))))))))))))-)..- ( -36.70)
>DroPse_CAF1 3535 117 - 1
GUAACUUCUCCAUGUGCGGGUUUUAGCACCGGAUGGCGUUUU-AUGCGAGCCGUUUUUACUUUAUUGACGCAUUUAUCAUGCGUUGAUUGCCCCGUGUGCUGAAAGCAAAAAAGGCGG-
.......(.((...(((...(((((((((((((((((.....-......))))).........((..((((((.....))))))..))....))).)))))))))))).....)).).- ( -34.10)
>DroGri_CAF1 15475 117 - 1
GUGGCUUCUACUUGUGUGGUUUUUAGCACCGGAUGGCGUUUU-AUGCCACUGGUGAAUAGUUUAUUGACGCAUUUAUCAUGCGUCGAUUACC-UGCAUGCUGAAAGCAAAGGGGGCAGC
...((((((((....)).((((((((((((((.((((((...-)))))))))))...(((...((((((((((.....))))))))))...)-))...)))))))))...))))))... ( -44.30)
>DroMoj_CAF1 2091 116 - 1
GUGGCUACUCCUUGUGCGGUUUUUAGCACCGGAUGGCGUUUAUAUGCCAGCCAUUUUCACUUUAUUGACGCAUUUAUCAUGCGUCGAUCACC-UUCGUACCGAGAGCAAAAU--GCGGC
((((((..(((..((((........)))).))).(((((....))))))))))).........((((((((((.....))))))))))..((-((((...)))).((.....--)))). ( -36.60)
>DroAna_CAF1 2448 113 - 1
GCGACUUCUCCUUAAGUGGUUUUUAGCACCGGAAGGCGGUUU-AUGCGAGUCUCUUUUUCUUUAUUGACGCAUUUAUCAUGCGUUGAUGGGC-CAUUCCGCCAAUACAAAA-UA-AG--
((.......((......))......)).......(((((...-..(((((.......))).((((..((((((.....))))))..))))))-....))))).........-..-..-- ( -27.52)
>DroPer_CAF1 3817 117 - 1
GUAACUUCUCCAUGUGCGGUUUUUAGCACCGGAUGGCGUUUU-AUGCGAGCCGUUUUUACUUUAUUGACGCAUUUAUCAUGCGUUGAUUGCCCCGUGUGCUGAAAGCAAAAAAGGCGG-
.......(.((.......(((((((((((((((((((.....-......))))).........((..((((((.....))))))..))....))).)))))))))))......)).).- ( -36.12)
>consensus
GUGACUUCUCCAUGUGCGGUUUUUAGCACCGGAUGGCGUUUU_AUGCGAGCCGUUUUUACUUUAUUGACGCAUUUAUCAUGCGUUGAUUGCC_CGUGUGCUGAAAGCAAAAAAGGCGG_
..................(((((((((((.(((((((............))))))).......((((((((((.....))))))))))........)))))))))))............ (-19.22 = -21.47 +   2.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:04 2006