Locus 6860

Sequence ID	2L_DroMel_CAF1
Location	19,187,783 – 19,187,875
Length	92
Max. P	0.972184

overview

Window 6

Location	19,187,783 – 19,187,875
Length	92
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	71.50
Mean single sequence MFE	-27.30
Consensus MFE	-11.57
Energy contribution	-11.77
Covariance contribution	0.19
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.42
SVM decision value	0.69
SVM RNA-class probability	0.824130
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19187783 92 + 22407834
AAAGGAAAGGGUGAAGCGGCCCAAGUUGUGCCACAUCCAU-GUGGCAUCAUAAAACACAUGCAAAGUGUUUGUUUUG---------------UAGGCAGUGUGUUCUG
...((((.((((......))))..((.((((((((....)-))))))).))...((((.(((((((......)))))---------------))....)))).)))). ( -25.90)
>DroSec_CAF1 7818 75 + 1
AAGGGAAAGGGUGAAGCGGCCCAAGUUGUGCCACAUCCAU-GUGGCAUCAUAAAACACAUGCAAAGUGUUUGUUU--------------------------------G
........((((......))))..((.((((((((....)-))))))).)).((((((.......))))))....--------------------------------. ( -21.80)
>DroSim_CAF1 9080 75 + 1
AAGGGAAAGGGUGAAGCGGCCCAAGUUGUGCCACAUCCAU-GUGGCAUCAUAAAACACAUGCAAAGUGUUUGCUU--------------------------------G
........((((......))))((((.((((((((....)-)))))))....((((((.......))))))))))--------------------------------. ( -22.60)
>DroEre_CAF1 7960 107 + 1
AAAGGAAAGGGUGAAGCGGCCCAAGUUGGGCCACAUCCAU-GUGGGAUCAUAAAACACAUGCAAAGUGUUUGUUCGGUGAGCGGCAGAGGGGUGGGCAGUGUUUUCUG
..((((((.(.((....(((((.....))))).(((((.(-((.(..((((.((((((.......)))))).....)))).).)))...)))))..)).).)))))). ( -37.80)
>DroYak_CAF1 8888 105 + 1
G-AGAAAAGGGUGAAGCGGCCCAAGUUGGGCCACAUCCAU-GUGGAAUCAUAAAACGCAUGCAAAGUGUUUGCUUGG-GAGUGGCAAAGGGGUGGGCAGUGGGUUCUU
.-....(((..(...((.(((((..((..(((((.(((((-(((...........)))))((((.....))))...)-)))))))...))..))))).))..)..))) ( -34.20)
>DroAna_CAF1 58151 86 + 1
AAGGGAAAGGGU-----GGCCAAGGUGGGGACAAAUCCACCGAGGAAUCGUAAAACACAUGCAAAGUGUUUGUUUGUUU-------------UGGG---U-GAUUGUC
.........(((-----.(((..((((((......))))))..(((((....((((((.......))))))....))))-------------).))---)-.)))... ( -21.50)
>consensus
AAAGGAAAGGGUGAAGCGGCCCAAGUUGGGCCACAUCCAU_GUGGCAUCAUAAAACACAUGCAAAGUGUUUGUUUGG_______________UGGG___U___UUCUG
........(((((....(((.........))).)))))..............((((((.......))))))..................................... (-11.57 = -11.77 +   0.19)

alignment

secondary structure

dotplot

Window 7

Location	19,187,783 – 19,187,875
Length	92
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	71.50
Mean single sequence MFE	-21.09
Consensus MFE	-9.32
Energy contribution	-10.48
Covariance contribution	1.17
Combinations/Pair	1.00
Mean z-score	-2.26
Structure conservation index	0.44
SVM decision value	1.69
SVM RNA-class probability	0.972184
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19187783 92 - 22407834
CAGAACACACUGCCUA---------------CAAAACAAACACUUUGCAUGUGUUUUAUGAUGCCAC-AUGGAUGUGGCACAACUUGGGCCGCUUCACCCUUUCCUUU
.((((((((.(((...---------------...............))))))))))).((.((((((-(....)))))))))....(((........)))........ ( -22.67)
>DroSec_CAF1 7818 75 - 1
C--------------------------------AAACAAACACUUUGCAUGUGUUUUAUGAUGCCAC-AUGGAUGUGGCACAACUUGGGCCGCUUCACCCUUUCCCUU
.--------------------------------....((((((.......))))))..((.((((((-(....)))))))))....(((........)))........ ( -18.60)
>DroSim_CAF1 9080 75 - 1
C--------------------------------AAGCAAACACUUUGCAUGUGUUUUAUGAUGCCAC-AUGGAUGUGGCACAACUUGGGCCGCUUCACCCUUUCCCUU
.--------------------------------((((((((((.......))))))..((.((((((-(....))))))))).........))))............. ( -19.00)
>DroEre_CAF1 7960 107 - 1
CAGAAAACACUGCCCACCCCUCUGCCGCUCACCGAACAAACACUUUGCAUGUGUUUUAUGAUCCCAC-AUGGAUGUGGCCCAACUUGGGCCGCUUCACCCUUUCCUUU
((.((((((((((............((.....))............))).))))))).))((((...-..))))(((((((.....)))))))............... ( -25.75)
>DroYak_CAF1 8888 105 - 1
AAGAACCCACUGCCCACCCCUUUGCCACUC-CCAAGCAAACACUUUGCAUGCGUUUUAUGAUUCCAC-AUGGAUGUGGCCCAACUUGGGCCGCUUCACCCUUUUCU-C
.(((((.((.(((.......(((((.....-....)))))......))))).))))).(((.(((..-..))).(((((((.....))))))).))).........-. ( -25.12)
>DroAna_CAF1 58151 86 - 1
GACAAUC-A---CCCA-------------AAACAAACAAACACUUUGCAUGUGUUUUACGAUUCCUCGGUGGAUUUGUCCCCACCUUGGCC-----ACCCUUUCCCUU
.......-.---.(((-------------(.......((((((.......))))))...........(((((........)))))))))..-----............ ( -15.40)
>consensus
CAGAA___A___CCCA_______________CCAAACAAACACUUUGCAUGUGUUUUAUGAUGCCAC_AUGGAUGUGGCACAACUUGGGCCGCUUCACCCUUUCCCUU
.....................................((((((.......)))))).............((((.(((((.........)))))))))........... ( -9.32 = -10.48 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:30 2006