Locus 4072

Sequence ID	3L_DroMel_CAF1
Location	11,859,676 – 11,859,816
Length	140
Max. P	0.891336

overview

Window 9

Location	11,859,676 – 11,859,786
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	74.81
Mean single sequence MFE	-20.58
Consensus MFE	-11.33
Energy contribution	-11.57
Covariance contribution	0.24
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	0.55
SVM decision value	0.97
SVM RNA-class probability	0.891336
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11859676 110 + 23771897
UUCUCAGGCUCUUGCCGUAUUUUUUUUUUCCACCCAUUUCCCAUGCUCUGCGGCGGAAAAAGUUUUUUCAGCUUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAA
.....((((((..((.(......((((((((.((((............)).)).))))))))......).))....)))))).(((((.......))))).......... ( -24.50)
>DroSec_CAF1 35575 87 + 1
UUCUCUGCCUCUUGCUGUAAU-----------------------GCUCUGCGGCGGAAAAAGUUUUUCCAGCUUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAA
...((((((.(..((......-----------------------))...).))))))..(((((.....)))))..((((...(((((.......)))))....)))).. ( -22.50)
>DroSim_CAF1 36038 108 + 1
UUCUCAGCCUCUUGCUGUAAUUU--UUUCCCUCCCAUUUCCCGCGCUCUGCGGCGGAAAAAGUUUUUCCAGCCUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAA
......((.....((((.(((((--(((((..........((((.....)))).))))))))))....))))..))((((...(((((.......)))))....)))).. ( -26.40)
>DroEre_CAF1 38049 94 + 1
UGCUCAGCCUCUUGCACUCAUUU--UG-UCCACAAUUUCGCCAUGCUCUGCGGCGGAAAAAGUUUUUCCA-------------GGCAACUUUCUUUUGCCAUUCACUCAA
......(((.(..(((......(--((-....)))........)))...).)))(((((.....))))).-------------(((((.......))))).......... ( -18.04)
>DroYak_CAF1 36841 94 + 1
UUCUCAGCCUCUUGCACUCAUUU--UU-UUCACAAUUUUCCCAUGCUUUGCGGCGGAAAAAGUUUUUCCC-------------AGCAACUUUCUUUUGCCAUUCAUUCGA
......((.....(((.......--..-...............)))...))(((((((((((((......-------------...)))))).))))))).......... ( -11.46)
>consensus
UUCUCAGCCUCUUGCAGUAAUUU__UU_UCCACAAAUUUCCCAUGCUCUGCGGCGGAAAAAGUUUUUCCAGC_UGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAA
......(((.(..((.............................))...).)))(((((.....)))))..............(((((.......))))).......... (-11.33 = -11.57 +   0.24)

alignment

secondary structure

dotplot

Window 0

Location	11,859,715 – 11,859,816
Length	101
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	81.94
Mean single sequence MFE	-26.40
Consensus MFE	-18.86
Energy contribution	-18.62
Covariance contribution	-0.24
Combinations/Pair	1.20
Mean z-score	-1.51
Structure conservation index	0.71
SVM decision value	-0.05
SVM RNA-class probability	0.508201
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11859715 101 + 23771897
CCCAUGCUCUGCGGCGGAAAAAGUUUUUUCAGCUUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAAUGCUUUC--UCUCCAGUAGGGCA--CAAAGCCGA
....((((((((((.(((.(((((.......(....)((((...(((((.......)))))....))))...))))).--))))).))))))))--......... ( -27.00)
>DroSec_CAF1 35596 98 + 1
-----GCUCUGCGGCGGAAAAAGUUUUUCCAGCUUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAAUGCUUUC--UCUGUAGUAGGGCACACAAAGCCGA
-----(((((((.(((((.(((((.......(....)((((...(((((.......)))))....))))...))))).--))))).)))))))............ ( -29.50)
>DroSim_CAF1 36075 103 + 1
CCCGCGCUCUGCGGCGGAAAAAGUUUUUCCAGCCUGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAAUGCUUUC--UCUCCAGUGGGGCACACAAAGCCGA
.((((((((.((((((((((.....))))).))).))))))...(((((.......))))).................--......))))(((.......))).. ( -31.00)
>DroEre_CAF1 38085 88 + 1
GCCAUGCUCUGCGGCGGAAAAAGUUUUUCCA-------------GGCAACUUUCUUUUGCCAUUCACUCAAUGCCUUC--UCCUCAGUGGGGCA--CAAAGCCGA
...........(((((((((.....))))).-------------(((((.......)))))..........(((((((--(....)).))))))--....)))). ( -23.40)
>DroYak_CAF1 36877 90 + 1
CCCAUGCUUUGCGGCGGAAAAAGUUUUUCCC-------------AGCAACUUUCUUUUGCCAUUCAUUCGAUGCUUUCACUCCACAGUUGGGCA--CAAAGCCGA
.....((((((.(((((((((((((......-------------...)))))).)))))))..........(((((..(((....))).)))))--))))))... ( -21.10)
>consensus
CCCAUGCUCUGCGGCGGAAAAAGUUUUUCCAGC_UGCGAGUCUAGGCAACUUUCUUUUGCCAUUCACUCAAUGCUUUC__UCUCCAGUAGGGCA__CAAAGCCGA
.....(((((((((((((((.....)))))..............(((((.......)))))...........)))...........)))))))............ (-18.86 = -18.62 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:50 2006