Locus 7659

Sequence ID	3R_DroMel_CAF1
Location	20,526,802 – 20,526,893
Length	91
Max. P	0.983396

overview

Window 2

Location	20,526,802 – 20,526,893
Length	91
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.38
Mean single sequence MFE	-21.51
Consensus MFE	-10.78
Energy contribution	-11.95
Covariance contribution	1.17
Combinations/Pair	1.00
Mean z-score	-1.75
Structure conservation index	0.50
SVM decision value	-0.02
SVM RNA-class probability	0.523234
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20526802 91 + 27905053
AAC----AUAAAAAGCA-----AGCAG----CUCCUCCUCAUCCCCCCGAACACUG--CACCAAUCCCAAUCGUCCGGGGAACAGGAGAU----UCCAAUUAGAGAGCUA-
...----..........-----...((----((((((((..(((((.(((......--............)))...)))))..)))))..----((......))))))).- ( -20.87)
>DroPse_CAF1 9019 94 + 1
UAAGUAUGCGGCAAUCA-----AGCAGCUAGCUCCUCC-CAUCCCC--------AG--CACCAGCCACAAAAAGGAAGGGAAAGGGAGG-AAGUAUCCAUUGCAAACUCAA
..(((.((((((.....-----.)).....((((((((-(.((((.--------..--..((...........))..))))..))))))-.)))......)))).)))... ( -24.90)
>DroSec_CAF1 13455 91 + 1
AAC----AUAAAAAGCA-----AGCAU----CUCCUCCUCAUCCCCCCGAGCACUG--CACCAAUCACAAUCCUCCGGGGAACAGGAGAU----UCCAAUUAGAGAGCGA-
...----..........-----.((.(----((((((((..(((((..(((...((--.........))...))).)))))..)))))..----........))))))..- ( -20.50)
>DroSim_CAF1 11696 91 + 1
AAC----AUGAAAAGCA-----AGCAG----CUCCUCGUCAUCCCCCCGAGCACUG--CACCAAUCCCAAUCCUCCGGGGAACAGGAGAU----UCCAAUUAGAGAGCGA-
...----..........-----....(----(((.((......((((.(((...((--.........))...))).))))....((....----.)).....))))))..- ( -18.60)
>DroEre_CAF1 9284 91 + 1
AAC----AUAAAAAGCA-----AGCAG----CUCCUCCUCAUCCCCCCGAGCACUG--CACCAAACCCAAUCCUCCGGGGAACAGGAGAU----UCCAAUUAGAGAGCGA-
...----..........-----....(----((((((((..(((((..(((...((--.........))...))).)))))..)))))..----((......))))))..- ( -20.60)
>DroYak_CAF1 9630 98 + 1
AAC----AUAAAAAGCAUGAGGAGCAG----CUCCUCCUCAUCCCCCAGAGCACUGCGCACCAAUCCCAAUCCUCCGGGGCACAGGAGAU----UCCAAUUAGAGAGCGA-
...----.......((..((((((...----))))))(((...((((.(((...((.(........)))...))).))))....((....----.)).....))).))..- ( -23.60)
>consensus
AAC____AUAAAAAGCA_____AGCAG____CUCCUCCUCAUCCCCCCGAGCACUG__CACCAAUCCCAAUCCUCCGGGGAACAGGAGAU____UCCAAUUAGAGAGCGA_
..................................(((((....((((.(((.....................))).))))...)))))....................... (-10.78 = -11.95 +   1.17)

alignment

secondary structure

dotplot

Window 3

Location	20,526,802 – 20,526,893
Length	91
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	76.38
Mean single sequence MFE	-33.95
Consensus MFE	-20.87
Energy contribution	-22.73
Covariance contribution	1.86
Combinations/Pair	1.05
Mean z-score	-2.41
Structure conservation index	0.61
SVM decision value	1.94
SVM RNA-class probability	0.983396
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20526802 91 - 27905053
-UAGCUCUCUAAUUGGA----AUCUCCUGUUCCCCGGACGAUUGGGAUUGGUG--CAGUGUUCGGGGGGAUGAGGAGGAG----CUGCU-----UGCUUUUUAU----GUU
-(((((((((....)))----..(((((.((((((((((.((((.(.....).--))))))))))))))...))))))))----)))..-----..........----... ( -33.10)
>DroPse_CAF1 9019 94 - 1
UUGAGUUUGCAAUGGAUACUU-CCUCCCUUUCCCUUCCUUUUUGUGGCUGGUG--CU--------GGGGAUG-GGAGGAGCUAGCUGCU-----UGAUUGCCGCAUACUUA
.(((((.(((...((.((.((-((((((.(((((..((...........))..--..--------))))).)-))))))).)).))((.-----.....)).))).))))) ( -32.30)
>DroSec_CAF1 13455 91 - 1
-UCGCUCUCUAAUUGGA----AUCUCCUGUUCCCCGGAGGAUUGUGAUUGGUG--CAGUGCUCGGGGGGAUGAGGAGGAG----AUGCU-----UGCUUUUUAU----GUU
-..((((((........----..((((((((((((.(((.(((((.......)--)))).))).))))))).))))))))----).)).-----..........----... ( -34.70)
>DroSim_CAF1 11696 91 - 1
-UCGCUCUCUAAUUGGA----AUCUCCUGUUCCCCGGAGGAUUGGGAUUGGUG--CAGUGCUCGGGGGGAUGACGAGGAG----CUGCU-----UGCUUUUCAU----GUU
-.............((.----....)).(((((((.(((.((((.(.....).--)))).))).)))))))...((((((----(....-----.)))))))..----... ( -30.90)
>DroEre_CAF1 9284 91 - 1
-UCGCUCUCUAAUUGGA----AUCUCCUGUUCCCCGGAGGAUUGGGUUUGGUG--CAGUGCUCGGGGGGAUGAGGAGGAG----CUGCU-----UGCUUUUUAU----GUU
-..(((((((....)))----..((((((((((((.(((.((((.(.....).--)))).))).))))))).))))))))----)....-----..........----... ( -35.20)
>DroYak_CAF1 9630 98 - 1
-UCGCUCUCUAAUUGGA----AUCUCCUGUGCCCCGGAGGAUUGGGAUUGGUGCGCAGUGCUCUGGGGGAUGAGGAGGAG----CUGCUCCUCAUGCUUUUUAU----GUU
-..(((((((....)))----..(((((((.((((((((.((((.(.......).)))).)))))))).)).))))))))----).((.......)).......----... ( -37.50)
>consensus
_UCGCUCUCUAAUUGGA____AUCUCCUGUUCCCCGGAGGAUUGGGAUUGGUG__CAGUGCUCGGGGGGAUGAGGAGGAG____CUGCU_____UGCUUUUUAU____GUU
......................(((((((((((((.(((.((((...........)))).))).))))))).))))))................................. (-20.87 = -22.73 +   1.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:25 2006