Locus 3574

Sequence ID	3L_DroMel_CAF1
Location	10,515,256 – 10,515,391
Length	135
Max. P	0.999960

overview

Window 0

Location	10,515,256 – 10,515,372
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	65.35
Mean single sequence MFE	-22.50
Consensus MFE	-13.52
Energy contribution	-14.56
Covariance contribution	1.04
Combinations/Pair	1.15
Mean z-score	-1.75
Structure conservation index	0.60
SVM decision value	1.34
SVM RNA-class probability	0.943663
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10515256 116 - 23771897
UCACACUUUGCUUCUACUAGGCGGAGUGUGACCAUGCAAGUAAUUUU--UUCGUUCGGUUUCCAAUGUUAAUUAAAAUACUUUAAUUUAAAAUCAGUU--CUCUAAACACCAGGAAAAGA
(((((((((((((.....)))))))))))))((..(((((......)--)).))..))(((((......(((((((....)))))))........(((--.....)))....)))))... ( -23.30)
>DroSec_CAF1 394755 93 - 1
UCACACUUUGCUUCUACUAG---AAGUGUGACCAUGCCAGUAAUUUU--UUCG---GGUUUUCU-----------------CUAAUUUAAAAUCAGUU--CUCUGAACACAAGGAAAAAA
(((((((((..........)---))))))))............((((--((((---((....))-----------------)..........((((..--..))))......))))))). ( -18.00)
>DroSim_CAF1 403140 102 - 1
UCACACUUUGCUUCUACUAGGCAGAGUGUGACCAUGCAAUGAAUUUU--UUCGUUCGGUUUCCAAUG--------------UUAAUUUAAAAUCAGUU--CUCUGAACACAAGGAAAAGA
(((((((((((((.....)))))))))))))...((.((((((....--)))))))).((((((((.--------------...))).....((((..--..))))......)))))... ( -26.80)
>DroEre_CAF1 401765 93 - 1
UCACACUUUGCUUUAGGUAGGC-UAGUGUGACCAUGCCACCCAUUUU--UUCGUUUGGCUUCUCAUGCGAAUUGAAAA-------UCGAAA--AAGUUUACUUGG---------------
(((((((..((((.....))))-.)))))))(((........(((((--((((((..(.(((......))))..))..-------.)))))--)))).....)))--------------- ( -20.72)
>DroYak_CAF1 403487 103 - 1
UCACACUUUGCUUCAGGUAGGCGUAGUGUGACCAAACCAUUCAUUUUUCUUUGUUUGGUUACCCAUGUGAAUUGAAAUCCUUUAAUUUAAAAUAAGUU--CUUUG---------------
(((((((.(((((.....))))).)))))))...(((((..((........))..))))).......(((((((((....))))))))).........--.....--------------- ( -23.70)
>consensus
UCACACUUUGCUUCUACUAGGC_GAGUGUGACCAUGCCAGUAAUUUU__UUCGUUCGGUUUCCAAUG__AAUU_AAA____UUAAUUUAAAAUCAGUU__CUCUGAACAC_AGGAAAA_A
(((((((((((((.....)))))))))))))......................................................................................... (-13.52 = -14.56 +   1.04)

alignment

secondary structure

dotplot

Window 1

Location	10,515,294 – 10,515,391
Length	97
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	66.47
Mean single sequence MFE	-25.85
Consensus MFE	-17.19
Energy contribution	-17.25
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-2.98
Structure conservation index	0.66
SVM decision value	4.90
SVM RNA-class probability	0.999960
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10515294 97 + 23771897
GUAUUUUAAUUAACAUUGGAAACCGAACGAA--AAAAUUACUUGCAUGGUCACACUCCGCCUAGUAGAAGCAAAGUGUGACCAUA-------------------AUAGUAUCAGAAAG
...............((((...)))).....--.....((((...(((((((((((..((.........))..))))))))))).-------------------..))))........ ( -22.00)
>DroSim_CAF1 403177 92 + 1
-------------CAUUGGAAACCGAACGAA--AAAAUUCAUUGCAUGGUCACACUCUGCCUAGUAGAAGCAAAGUGUGACCGUAAACUCAAA-----------AUAGUAUCAGAAAU
-------------....(....).(((((((--....))).....(((((((((((.(((.........))).))))))))))).........-----------...)).))...... ( -21.90)
>DroEre_CAF1 401783 112 + 1
--UUUUCAAUUCGCAUGAGAAGCCAAACGAA--AAAAUGGGUGGCAUGGUCACACUA-GCCUACCUAAAGCAAAGUGUGACCAUAAAGUAUAAUUUUUGGCAAA-AAUUAUACGAUAG
--((((((.......))))))((((..((..--....))..))))(((((((((((.-((.........))..)))))))))))...((((((((((.....))-))))))))..... ( -33.90)
>DroYak_CAF1 403510 118 + 1
GGAUUUCAAUUCACAUGGGUAACCAAACAAAGAAAAAUGAAUGGUUUGGUCACACUACGCCUACCUGAAGCAAAGUGUGACCAUCAAGUAUAAUUUUUGGUAAAAAAGUAUAAGAAUG
........((((...(((....)))..((((((...(((..(((..((((((((((..((.........))..)))))))))))))..)))..))))))..............)))). ( -25.60)
>consensus
__AUUUCAAUUCACAUGGGAAACCAAACGAA__AAAAUGAAUGGCAUGGUCACACUACGCCUACCAGAAGCAAAGUGUGACCAUAAAGUAUAA___________AAAGUAUAAGAAAG
.............................................(((((((((((..((.........))..))))))))))).................................. (-17.19 = -17.25 +   0.06)

alignment

secondary structure

dotplot

Window 2

Location	10,515,294 – 10,515,391
Length	97
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	66.47
Mean single sequence MFE	-31.23
Consensus MFE	-22.92
Energy contribution	-24.30
Covariance contribution	1.38
Combinations/Pair	1.06
Mean z-score	-4.42
Structure conservation index	0.73
SVM decision value	4.83
SVM RNA-class probability	0.999954
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10515294 97 - 23771897
CUUUCUGAUACUAU-------------------UAUGGUCACACUUUGCUUCUACUAGGCGGAGUGUGACCAUGCAAGUAAUUUU--UUCGUUCGGUUUCCAAUGUUAAUUAAAAUAC
........((((..-------------------((((((((((((((((((.....))))))))))))))))))..))))...((--..((((.((...))))))..))......... ( -30.10)
>DroSim_CAF1 403177 92 - 1
AUUUCUGAUACUAU-----------UUUGAGUUUACGGUCACACUUUGCUUCUACUAGGCAGAGUGUGACCAUGCAAUGAAUUUU--UUCGUUCGGUUUCCAAUG-------------
......((.(((..-----------...........(((((((((((((((.....)))))))))))))))..(.((((((....--)))))))))).)).....------------- ( -29.80)
>DroEre_CAF1 401783 112 - 1
CUAUCGUAUAAUU-UUUGCCAAAAAUUAUACUUUAUGGUCACACUUUGCUUUAGGUAGGC-UAGUGUGACCAUGCCACCCAUUUU--UUCGUUUGGCUUCUCAUGCGAAUUGAAAA--
.....((((((((-((.....))))))))))..((((((((((((..((((.....))))-.)))))))))))).........((--((((.((.((.......)).)).))))))-- ( -35.00)
>DroYak_CAF1 403510 118 - 1
CAUUCUUAUACUUUUUUACCAAAAAUUAUACUUGAUGGUCACACUUUGCUUCAGGUAGGCGUAGUGUGACCAAACCAUUCAUUUUUCUUUGUUUGGUUACCCAUGUGAAUUGAAAUCC
..............(((((................((((((((((.(((((.....))))).))))))))))(((((..((........))..)))))......)))))......... ( -30.00)
>consensus
CUUUCUGAUACUAU___________UUAUACUUUAUGGUCACACUUUGCUUCAACUAGGCGGAGUGUGACCAUGCAAUUAAUUUU__UUCGUUCGGUUUCCAAUGUGAAUUGAAAU__
.................................((((((((((((((((((.....))))))))))))))))))............................................ (-22.92 = -24.30 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:18 2006