Locus 1877

Sequence ID	3L_DroMel_CAF1
Location	5,242,496 – 5,242,588
Length	92
Max. P	0.781338

overview

Window 4

Location	5,242,496 – 5,242,588
Length	92
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.36
Mean single sequence MFE	-24.20
Consensus MFE	-13.38
Energy contribution	-13.88
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.43
Structure conservation index	0.55
SVM decision value	0.42
SVM RNA-class probability	0.728117
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5242496 92 + 23771897
-----GGAGGGUCAAAA--GCAAAUUGCAAAUGAUGA--AACUUUGCCCAUCAUAAACGCCAUUUU----AUGUUAUCCAAUAUGGCGUC----GC-------UUUCUGCC----CUUUU
-----(((((((..(((--((.........((((((.--.........))))))..(((((((...----............))))))).----))-------)))..)))----)))). ( -27.86)
>DroGri_CAF1 130769 105 + 1
UUCUUUGGGGGUCA-CU--GUAAAUUGCAAAUGAUGA--AACUUUGCCCAUCAUAAACGCCAUUUU----AUGUUAGCCAAUAUGGCGUC----GU-CCACA-UUUCCGUAUCACUCCUC
......((((((..-..--...........((((((.--.........))))))..(((((((...----............))))))).----..-.....-..........)))))). ( -18.86)
>DroSec_CAF1 106806 92 + 1
-----GGAGGGUCAAAA--GCAAAUUGCAAAUGAUGA--AACUUUGCCCAUCAUAAACGCCAUUUU----AUGUUAUCCAAUAUGGCGUA----GC-------UUUCUGCC----CUUUU
-----(((((((..(((--((.........((((((.--.........))))))..(((((((...----............))))))).----))-------)))..)))----)))). ( -28.36)
>DroWil_CAF1 144426 105 + 1
-----CUUGGGUCAACAUUUCAAAUUGCAAAUGAUCAAAAACUUUGCCCAUCAUAAACGCCAUUUUGUAUAUGUUAGCCAAUAUGGCGUC----CCUGUACUUUUUCUGCC----UUU--
-----...(((.((((((..((((..((..((((((((.....)))...)))))....))...))))...))))).(((.....)))).)----))...............----...-- ( -17.90)
>DroYak_CAF1 109254 92 + 1
-----GGAGGGUCAAAA--GCAAAUUGCAAAUGAUGA--AACUUUGCCCAUCAUAAACGCCAUUUU----AUGUUAUCCAAUAUGGCGUC----GC-------UUUCUGUC----CUUUU
-----.(((((.(((((--((.........((((((.--.........))))))..(((((((...----............))))))).----))-------))).)).)----)))). ( -24.46)
>DroAna_CAF1 104318 96 + 1
-----GGAGGGUCAAAA--GCAAAUUGCAAAUGAUGA--AACUUUGCCCAUCAUAAACGCCAUUUU----AUGUUAUCCAAUAUGGCGUCCGUAGC-------UUUCUGCC----CUUUU
-----(((((((..(((--((.........((((((.--.........))))))..(((((((...----............))))))).....))-------)))..)))----)))). ( -27.76)
>consensus
_____GGAGGGUCAAAA__GCAAAUUGCAAAUGAUGA__AACUUUGCCCAUCAUAAACGCCAUUUU____AUGUUAUCCAAUAUGGCGUC____GC_______UUUCUGCC____CUUUU
........(((.((((.......(((......))).......))))))).......(((((((...................)))))))............................... (-13.38 = -13.88 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	5,242,496 – 5,242,588
Length	92
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.36
Mean single sequence MFE	-28.05
Consensus MFE	-13.61
Energy contribution	-14.14
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-2.92
Structure conservation index	0.49
SVM decision value	0.56
SVM RNA-class probability	0.781338
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5242496 92 - 23771897
AAAAG----GGCAGAAA-------GC----GACGCCAUAUUGGAUAACAU----AAAAUGGCGUUUAUGAUGGGCAAAGUU--UCAUCAUUUGCAAUUUGC--UUUUGACCCUCC-----
...((----((..((((-------((----((.(((((.(((.......)----)).)))))((..((((((((......)--)))))))..))...))))--))))..))))..----- ( -30.80)
>DroGri_CAF1 130769 105 - 1
GAGGAGUGAUACGGAAA-UGUGG-AC----GACGCCAUAUUGGCUAACAU----AAAAUGGCGUUUAUGAUGGGCAAAGUU--UCAUCAUUUGCAAUUUAC--AG-UGACCCCCAAAGAA
(.((.((.((...(((.-((..(-(.----((((((((.(((.......)----)).))))))))..(((((((......)--))))))))..)).)))..--.)-).)).)))...... ( -25.20)
>DroSec_CAF1 106806 92 - 1
AAAAG----GGCAGAAA-------GC----UACGCCAUAUUGGAUAACAU----AAAAUGGCGUUUAUGAUGGGCAAAGUU--UCAUCAUUUGCAAUUUGC--UUUUGACCCUCC-----
...((----((..((((-------((----...(((((.(((.......)----)).)))))((..((((((((......)--)))))))..)).....))--))))..))))..----- ( -29.10)
>DroWil_CAF1 144426 105 - 1
--AAA----GGCAGAAAAAGUACAGG----GACGCCAUAUUGGCUAACAUAUACAAAAUGGCGUUUAUGAUGGGCAAAGUUUUUGAUCAUUUGCAAUUUGAAAUGUUGACCCAAG-----
--...----.............((..----((((((((.(((...........))).))))))))..)).(((((((.(((((.(((........))).))))).))).))))..----- ( -26.10)
>DroYak_CAF1 109254 92 - 1
AAAAG----GACAGAAA-------GC----GACGCCAUAUUGGAUAACAU----AAAAUGGCGUUUAUGAUGGGCAAAGUU--UCAUCAUUUGCAAUUUGC--UUUUGACCCUCC-----
...((----(...((((-------((----((.(((((.(((.......)----)).)))))((..((((((((......)--)))))))..))...))))--))))...)))..----- ( -26.70)
>DroAna_CAF1 104318 96 - 1
AAAAG----GGCAGAAA-------GCUACGGACGCCAUAUUGGAUAACAU----AAAAUGGCGUUUAUGAUGGGCAAAGUU--UCAUCAUUUGCAAUUUGC--UUUUGACCCUCC-----
...((----((..((((-------((...(((((((((.(((.......)----)).)))))))))((((((((......)--))))))).........))--))))..))))..----- ( -30.40)
>consensus
AAAAG____GGCAGAAA_______GC____GACGCCAUAUUGGAUAACAU____AAAAUGGCGUUUAUGAUGGGCAAAGUU__UCAUCAUUUGCAAUUUGC__UUUUGACCCUCC_____
..........(((((...............((((((((...................))))))))..((((((..........))))))))))).......................... (-13.61 = -14.14 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:54 2006