Locus 3412

Sequence ID	3L_DroMel_CAF1
Location	10,003,938 – 10,004,107
Length	169
Max. P	0.958656

overview

Window 2

Location	10,003,938 – 10,004,034
Length	96
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	85.08
Mean single sequence MFE	-27.46
Consensus MFE	-19.46
Energy contribution	-20.38
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-2.68
Structure conservation index	0.71
SVM decision value	1.49
SVM RNA-class probability	0.958656
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10003938 96 + 23771897
UGAGUGGUGCGAUAAAGCAGUCAACAGACAGAAAGGCGCGG--AAGAUGCUACAGAGCGGGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAUUA-
((((((.(((......((.(((....))).....(((((..--..).)))).....)).(((((((........))))))).)))..)))))).....- ( -30.70)
>DroSec_CAF1 56621 93 + 1
UGAGUGGUGCGAUAAAGCAGUCAACAGGCAGAAAGGCGCGGGGGGGAUGCU-----GCGGGGUAUCGACUAUUAGAUACCCAGUAUGCAUUAAAAAUA-
....(((((((....((((..(..(..((........))..)..)..))))-----((.(((((((........))))))).)).)))))))......- ( -28.10)
>DroSim_CAF1 66291 96 + 1
UGAGUGGUGCGAUAAAGCAGUCAACAGACAGAAAGGCGCGG--AAGAUGCUACAGAGCGGGGUAUCGACUAUUAGAUACCCAGUAAGCAAUCAAAAUA-
(((....(((......((.(((....))).....(((((..--..).)))).....)).(((((((........))))))).....))).))).....- ( -27.70)
>DroEre_CAF1 58840 96 + 1
UGAGUGGUGCGAUAAAGCAGUCAGCAGACAGAAAGGCGCAG--AAGAUGCUGCAGUGCCAGGCAACGACUAUAAGAUACCCAGUCAGCACUCAAAAUU-
((((((.((((((......))).)))(((.....(((((((--......))))...))).(....)................)))..)))))).....- ( -25.50)
>DroYak_CAF1 58092 92 + 1
UGAGUGGUGCGAUAGAGCAGUCGACAGACAGAAAG-----G--AAGAUGCUACAGAGCGGGGUAUCGACUACAAGAUACCCAAUAGGCAUUCAAAAUAU
((((((.(((......)))(((....)))......-----.--....((((....))))(((((((........)))))))......))))))...... ( -25.30)
>consensus
UGAGUGGUGCGAUAAAGCAGUCAACAGACAGAAAGGCGCGG__AAGAUGCUACAGAGCGGGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAAUA_
((((((..((.....(((((((....))).........(......).)))).....)).(((((((........)))))))......))))))...... (-19.46 = -20.38 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	10,003,965 – 10,004,067
Length	102
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	76.23
Mean single sequence MFE	-23.87
Consensus MFE	-11.54
Energy contribution	-12.82
Covariance contribution	1.28
Combinations/Pair	1.07
Mean z-score	-2.24
Structure conservation index	0.48
SVM decision value	1.46
SVM RNA-class probability	0.956281
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10003965 102 + 23771897
ACAGAAAGGCGCGG--AAGAUGCUACAGAGCGGGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAUUA-----AGUAAGCAGCUUACCAAAAUAGUACACUUAA---AG
.......(((((..--..).))))...(((.((((((((........))))))).((((((..........-----........))))))..........).)))..---.. ( -24.37)
>DroSec_CAF1 56648 99 + 1
GCAGAAAGGCGCGGGGGGGAUGCU-----GCGGGGUAUCGACUAUUAGAUACCCAGUAUGCAUUAAAAAUA-----UGUAAGCCGCUUACCAAAAUAGUACAUUUAA---AG
.......((((((.....((((((-----((.(((((((........))))))).))).))))).......-----)))..))).......................---.. ( -25.80)
>DroSim_CAF1 66318 102 + 1
ACAGAAAGGCGCGG--AAGAUGCUACAGAGCGGGGUAUCGACUAUUAGAUACCCAGUAAGCAAUCAAAAUA-----AGUUAGCAGCUUACCAAAAUAGUACAUUUAA---AA
.......(((((..--..).))))...(.((.(((((((........))))))).((((((..........-----........)))))).......)).)......---.. ( -23.47)
>DroEre_CAF1 58867 105 + 1
ACAGAAAGGCGCAG--AAGAUGCUGCAGUGCCAGGCAACGACUAUAAGAUACCCAGUCAGCACUCAAAAUU-----AGUAAGCCUCCUACCAAAAAAGUACACGCCAUGUAC
......((((((((--......))))(((((..(....)((((...........)))).))))).......-----.....))))............(((((.....))))) ( -23.70)
>DroYak_CAF1 58119 100 + 1
ACAGAAAG-----G--AAGAUGCUACAGAGCGGGGUAUCGACUACAAGAUACCCAAUAGGCAUUCAAAAUAUAUCAAAUAAAACUA--GACAAAAUAGUAUAUUUGA---AG
........-----.--..((((((........(((((((........)))))))....)))))).........(((((((..((((--.......)))).)))))))---.. ( -22.00)
>consensus
ACAGAAAGGCGCGG__AAGAUGCUACAGAGCGGGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAAUA_____AGUAAGCCGCUUACCAAAAUAGUACAUUUAA___AG
..................((((((.....((.(((((((........))))))).)).))))))................................................ (-11.54 = -12.82 +   1.28)

alignment

secondary structure

dotplot

Window 4

Location	10,003,995 – 10,004,107
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	68.19
Mean single sequence MFE	-22.77
Consensus MFE	-8.80
Energy contribution	-9.40
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.39
SVM decision value	1.19
SVM RNA-class probability	0.928520
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10003995 112 + 23771897
GGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAUUA-----AGUAAGCAGCUUACCAAAAUAGUACACUUAA---AGUAUGGUUAGUUACACAAUUUCUAUAGGUUCCUAUGGUGGA
(((((((........)))))))..(((((..........-----........)))))(((..((((...(((((.---((..((((.....)).))....)).)))))..))))..))). ( -24.77)
>DroSec_CAF1 56675 112 + 1
GGGUAUCGACUAUUAGAUACCCAGUAUGCAUUAAAAAUA-----UGUAAGCCGCUUACCAAAAUAGUACAUUUAA---AGUAUGGUUAGUUACACAAUUUGUAUAGGUUCCUACCGUGGA
(((((((........)))))))....(((((.......)-----))))..((((...........(((((.....---.(((........)))......))))).(((....))))))). ( -25.90)
>DroSim_CAF1 66348 112 + 1
GGGUAUCGACUAUUAGAUACCCAGUAAGCAAUCAAAAUA-----AGUUAGCAGCUUACCAAAAUAGUACAUUUAA---AAUAUGGUUAGUUAUACAAUUUGUAUAGGUUUCUACCGUGGA
(((((((........))))))).((((((..........-----........)))))).................---..((((((.(.((((((.....)))))).)....)))))).. ( -26.87)
>DroEre_CAF1 58897 92 + 1
AGGCAACGACUAUAAGAUACCCAGUCAGCACUCAAAAUU-----AGUAAGCCUCCUACCAAAAAAGUACACGCCAUGUACUAAU--------------UUGUAUAAGUUUA---------
((((...((((...........))))...(((.......-----)))..)))).....((((..((((((.....))))))..)--------------)))..........--------- ( -13.40)
>DroYak_CAF1 58144 101 + 1
GGGUAUCGACUACAAGAUACCCAAUAGGCAUUCAAAAUAUAUCAAAUAAAACUA--GACAAAAUAGUAUAUUUGA---AGUAUG--------------GCGCAUAAGUUCAAGUCAAGGA
(((((((........)))))))....(((.......((((.(((((((..((((--.......)))).)))))))---.))))(--------------((......)))...)))..... ( -22.90)
>consensus
GGGUAUCGACUAUAAGAUACCCAGUAAGCAUUCAAAAUA_____AGUAAGCCGCUUACCAAAAUAGUACAUUUAA___AGUAUGGUUAGUUA_ACAAUUUGUAUAGGUUCCUACCGUGGA
(((((((........))))))).................................................................................................. ( -8.80 =  -9.40 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:32 2006