Locus 3880

Sequence ID	X_DroMel_CAF1
Location	10,339,269 – 10,339,378
Length	109
Max. P	0.952894

overview

Window 7

Location	10,339,269 – 10,339,378
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.72
Mean single sequence MFE	-35.92
Consensus MFE	-20.52
Energy contribution	-21.15
Covariance contribution	0.63
Combinations/Pair	1.07
Mean z-score	-2.35
Structure conservation index	0.57
SVM decision value	0.28
SVM RNA-class probability	0.664605
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10339269 109 + 22224390
-CCCACAGGUAGCCCAAUCCCAGCGUAAUGUAAUUGGACAUUGGUCCAUCCAAGCCACUAC---------CU-GUAGGAAUCGCUCGCAAGUUAUCGCCUUCGCGAGCUGAUUCAUUGUG
-...((((((((.(((((..((......))..)))))...((((.....))))....))))---------))-))..((((((((((((((.......))).)))))).)))))...... ( -38.30)
>DroSec_CAF1 3245 105 + 1
-C---CAGGUAGCCCAAUCCCAGCGUAAUGUU-UUGGACAUUGGUCCAUCCAAGCCACUAC---------CU-GUAUGAAUCGCUCGCAAGCUAUCGCCUUCGCGAGCUGAUUCAUUGUG
-.---(((((((.((((...((......))..-))))...((((.....))))....))))---------))-).(((((((((((((((((....).))).)))))).))))))).... ( -35.10)
>DroEre_CAF1 2973 105 + 1
----UCAGGUAGUCCAAUCCCAGUUUGAUUUU-UUGGACAUUGGCCCAUCCCAGCCACUAC---------CU-GUAGGAAUCGCUGGCAAGCUAUCGCCAUCGCGAGCUGAUUCAUUGUG
----.((((((((.........(((..(....-)..)))...(((........))))))))---------))-)...((((((((.((..((....))....)).))).)))))...... ( -32.10)
>DroYak_CAF1 3494 119 + 1
CCGCCCAGGUAGCCCAAUCCCCGUUUAGUGUC-UUGGACAUUGGUCCAUCGAAGCCACUACUACUACUACCUGGUAGGAAUCGCUGGCAAGCUAUCGCCAGCGCAAGCUGAUUCAUUGUG
.(..((((((((..........((.(((((.(-((((((....)))))....)).)))))..))..))))))))..)(((((((((((........))))))(....).)))))...... ( -38.20)
>consensus
_C___CAGGUAGCCCAAUCCCAGCGUAAUGUU_UUGGACAUUGGUCCAUCCAAGCCACUAC_________CU_GUAGGAAUCGCUCGCAAGCUAUCGCCAUCGCGAGCUGAUUCAUUGUG
........((((.((((...((......))...))))....((((........))))))))................(((((((((((..((....))....)))))).)))))...... (-20.52 = -21.15 +   0.63)

alignment

secondary structure

dotplot

Window 8

Location	10,339,269 – 10,339,378
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.72
Mean single sequence MFE	-41.58
Consensus MFE	-26.19
Energy contribution	-26.62
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-2.83
Structure conservation index	0.63
SVM decision value	1.43
SVM RNA-class probability	0.952894
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10339269 109 - 22224390
CACAAUGAAUCAGCUCGCGAAGGCGAUAACUUGCGAGCGAUUCCUAC-AG---------GUAGUGGCUUGGAUGGACCAAUGUCCAAUUACAUUACGCUGGGAUUGGGCUACCUGUGGG-
......(((((.((((((.(((.......))))))))))))))((((-((---------(((((.((((((.....)))).))(((((..((......))..)))))))))))))))).- ( -45.50)
>DroSec_CAF1 3245 105 - 1
CACAAUGAAUCAGCUCGCGAAGGCGAUAGCUUGCGAGCGAUUCAUAC-AG---------GUAGUGGCUUGGAUGGACCAAUGUCCAA-AACAUUACGCUGGGAUUGGGCUACCUG---G-
....(((((((.(((((((..(((....))))))))))))))))).(-((---------((((((..(((((((......)))))))-..)))))).))).....((....))..---.- ( -42.20)
>DroEre_CAF1 2973 105 - 1
CACAAUGAAUCAGCUCGCGAUGGCGAUAGCUUGCCAGCGAUUCCUAC-AG---------GUAGUGGCUGGGAUGGGCCAAUGUCCAA-AAAAUCAAACUGGGAUUGGACUACCUGA----
......(((((.(((.(((..(((....)))))).))))))))...(-((---------(((.(((((......)))))..((((((-....((.....))..)))))))))))).---- ( -34.90)
>DroYak_CAF1 3494 119 - 1
CACAAUGAAUCAGCUUGCGCUGGCGAUAGCUUGCCAGCGAUUCCUACCAGGUAGUAGUAGUAGUGGCUUCGAUGGACCAAUGUCCAA-GACACUAAACGGGGAUUGGGCUACCUGGGCGG
......(((((.(....)((((((((....)))))))))))))...(((((((((.(.(((....))).)......(((((.(((..-..........))).)))))))))))))).... ( -43.70)
>consensus
CACAAUGAAUCAGCUCGCGAAGGCGAUAGCUUGCCAGCGAUUCCUAC_AG_________GUAGUGGCUUGGAUGGACCAAUGUCCAA_AACAUUAAACUGGGAUUGGGCUACCUG___G_
......(((((.(((((((..(((....)))))))))))))))...................((((((..(.(((((....)))))......((......)).)..))))))........ (-26.19 = -26.62 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:55 2006