Locus 4172

Sequence ID	3R_DroMel_CAF1
Location	11,331,326 – 11,331,509
Length	183
Max. P	0.999872

overview

Window 3

Location	11,331,326 – 11,331,438
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.19
Mean single sequence MFE	-32.10
Consensus MFE	-25.98
Energy contribution	-26.14
Covariance contribution	0.16
Combinations/Pair	1.04
Mean z-score	-2.51
Structure conservation index	0.81
SVM decision value	2.23
SVM RNA-class probability	0.990796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331326 112 + 27905053
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUACGCAAAAGGGCUGGGGU--------UGGGAAUGGGGUUCCAGUGACUUUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....)))))))..............((((...(--------(((((((...))))).((((((....))))))..)))..)))) ( -30.20)
>DroSec_CAF1 70503 112 + 1
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUACGCAAAAGGGCUGGGGU--------UGGGAAUGGGGUUCCAGUGACUUUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....)))))))..............((((...(--------(((((((...))))).((((((....))))))..)))..)))) ( -30.20)
>DroSim_CAF1 68722 112 + 1
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUACGCAAAAGGGCUGGGGU--------UGGGAAUGGGGUUCCAGUGACUUUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....)))))))..............((((...(--------(((((((...))))).((((((....))))))..)))..)))) ( -30.20)
>DroEre_CAF1 66074 105 + 1
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUACGGAAAAGGGCUGG---------------GAUGGGGUUCCAGUGACUCUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....))))))).((..(......)..)).(---------------((......))).((((((....))))))........... ( -27.90)
>DroYak_CAF1 67785 120 + 1
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUGCGGCAAAGGGCUGGGAAUGCAUCCAUGGGGAUGGGGUUCCAGUGACUUUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....)))))))..((((..(((((.(((((((.(.(((((....))))).).)))))))..)))))..).)))........... ( -42.00)
>consensus
UUUUAAAUUUGCACAAAAUUGCAAAUAACUUGCAAUCAAGGUGCAAGAAGUACGCAAAAGGGCUGGGGU________UGGGAAUGGGGUUCCAGUGACUUUGGAGUCACAACAAAAUGGC
.......(((((((...(((((((.....)))))))....)))))))..............(((...............(((((...))))).((((((....))))))........))) (-25.98 = -26.14 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	11,331,326 – 11,331,438
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.19
Mean single sequence MFE	-26.42
Consensus MFE	-24.10
Energy contribution	-24.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.66
Structure conservation index	0.91
SVM decision value	4.33
SVM RNA-class probability	0.999872
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331326 112 - 27905053
GCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUCCCA--------ACCCCAGCCCUUUUGCGUACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((......(((((((((....)))))).((((.....))))..--------.....)))......)).......((((((...(((((((((...)))))))))..))))))........ ( -25.10)
>DroSec_CAF1 70503 112 - 1
GCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUCCCA--------ACCCCAGCCCUUUUGCGUACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((......(((((((((....)))))).((((.....))))..--------.....)))......)).......((((((...(((((((((...)))))))))..))))))........ ( -25.10)
>DroSim_CAF1 68722 112 - 1
GCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUCCCA--------ACCCCAGCCCUUUUGCGUACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((......(((((((((....)))))).((((.....))))..--------.....)))......)).......((((((...(((((((((...)))))))))..))))))........ ( -25.10)
>DroEre_CAF1 66074 105 - 1
GCCAUUUUGUUGUGACUCCAGAGUCACUGGAACCCCAUC---------------CCAGCCCUUUUCCGUACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((.........((((((....))))))(((....)))..---------------...))...............((((((...(((((((((...)))))))))..))))))........ ( -24.90)
>DroYak_CAF1 67785 120 - 1
GCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUCCCCAUGGAUGCAUUCCCAGCCCUUUGCCGCACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((.........((((((....)))))).((((...(((((....)))))..))))............)).....((((((...(((((((((...)))))))))..))))))........ ( -31.90)
>consensus
GCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUCCCA________ACCCCAGCCCUUUUGCGUACUUCUUGCACCUUGAUUGCAAGUUAUUUGCAAUUUUGUGCAAAUUUAAAA
((.........((((((....))))))(((....)))....................))...............((((((...(((((((((...)))))))))..))))))........ (-24.10 = -24.10 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	11,331,398 – 11,331,509
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.29
Mean single sequence MFE	-26.97
Consensus MFE	-22.72
Energy contribution	-22.68
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.84
SVM decision value	1.76
SVM RNA-class probability	0.975971
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11331398 111 - 27905053
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCC-----GGCGAAAUGAAACCCAACUCAACUCAACGCUCG----AGCUUCGCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUC
(((((((......)))))))......(((((.-----((((((.(((........))).(((.......)----)).))))))........((((((....)))))).)))))....... ( -27.20)
>DroSec_CAF1 70575 106 - 1
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCC-----GGCAAAAUGAAACCCAACUCAACU-----CUCG----AGCUUCGCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUC
(((((((......)))))))......(((((.-----(((((((((........(((....-----...)----))......)))))))))((((((....)))))).)))))....... ( -23.74)
>DroSim_CAF1 68794 106 - 1
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCC-----GGCGAAAUGAAACCCAACUCAACU-----CUCG----AGCUUCGCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUC
(((((((......)))))))......(((((.-----((((((.((.....)).(((....-----...)----)).))))))........((((((....)))))).)))))....... ( -25.80)
>DroEre_CAF1 66140 108 - 1
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCC-----GGCGAAAUGAAACCCAACUCAA-U-----CUCGGGCGGGCUUCGCCAUUUUGUUGUGACUCCAGAGUCACUGGAACCCCAUC-
(((((((......)))))))......(((((.-----((((((......(((..(((..-.-----...))).))).))))))........((((((....)))))).)))))......- ( -30.00)
>DroYak_CAF1 67865 110 - 1
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCCGGCCCGGCGAAAUGAAACCCAACUCAA-U-----CUCG----GGCUUCGCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUCC
(((((((......)))))))......(((((.(((((((.((..(((........))).-)-----))))----)))).............((((((....)))))).)))))....... ( -28.10)
>consensus
GAGUUAACUUAAAUUGAUUCCCAGACGUUCCC_____GGCGAAAUGAAACCCAACUCAACU_____CUCG____AGCUUCGCCAUUUUGUUGUGACUCCAAAGUCACUGGAACCCCAUUC
(((((((......)))))))......(((((......((((((.(((........)))........((......)).))))))........((((((....)))))).)))))....... (-22.72 = -22.68 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:13 2006