Locus 2198

Sequence ID	3R_DroMel_CAF1
Location	6,275,661 – 6,275,756
Length	95
Max. P	0.996328

overview

Window 3

Location	6,275,661 – 6,275,756
Length	95
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	70.89
Mean single sequence MFE	-22.40
Consensus MFE	-9.78
Energy contribution	-9.78
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.44
SVM decision value	2.68
SVM RNA-class probability	0.996328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6275661 95 + 27905053
UUUGGUGCGUGGAAUAGUUAAGUAACUAUUUUCUUGCACUGUG-GAAAAAAAAC-GGGUCUUAGUAG-AACCACU----UUUUGUUUAAUAUAAAGUUGUUA
...((((((.(((((((((....)))))))))..))))))...-.......(((-((.(((....))-).))(((----((.(((...))).))))).))). ( -19.30)
>DroSec_CAF1 40909 94 + 1
UUUGGUGCGUGGAAUAGUUAAGUAACUAUUUUCUUGCACUGUG-AAAAA--UACAGGGUAUUAGUAG-AACCACU----UUCUGUUUAAUAUAUAGUGGUUA
...((((((.(((((((((....)))))))))..))))))...-...((--(((...))))).....-(((((((----...(((.....))).))))))). ( -21.90)
>DroEre_CAF1 46288 84 + 1
UUUGGUGCGUGGAAUAGCAA----ACUAUUUUCUUGCACAGCG-GAAAA--AGC-UGCUAGUAGUUG-AA-CACU----AUUUGUUUACU----ACUUUUUA
....(((((.(((((((...----.)))))))..)))))((((-(....--..)-))))((((((.(-((-((..----...))))))))----)))..... ( -24.10)
>DroYak_CAF1 42711 92 + 1
UUUGGUGCGUGGAAUAGCAAAGUAACUAUUUUCUUGCACAGUGGGAAAA--AGU-UGCUAGUAGUUG-GACCACU----AUUUGCUUAAU--AAACUUGUUA
........((((..((((..(((((((.((((((..(...)..))))))--)))-))))....))))-..)))).----...........--.......... ( -21.90)
>DroAna_CAF1 46771 92 + 1
UUUGGUGCGUGGAAUAGUGAAGUAACUAU-UUCAUGCACUGCU-GAAAA--AAA-UGGUAGUGAUAUGGGCUAAAAAACAAAUUAA-----AAAAGGGAUGA
((((((((((((((((((......)))))-)))))))((((((-.....--...-.)))))).......))))))...........-----........... ( -24.80)
>consensus
UUUGGUGCGUGGAAUAGUAAAGUAACUAUUUUCUUGCACUGUG_GAAAA__AAC_UGGUAGUAGUAG_AACCACU____AUUUGUUUAAU__AAAGUUGUUA
....(((((.(((((((........)))).))).)))))............................................................... ( -9.78 =  -9.78 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	6,275,661 – 6,275,756
Length	95
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	70.89
Mean single sequence MFE	-14.69
Consensus MFE	-7.46
Energy contribution	-7.42
Covariance contribution	-0.04
Combinations/Pair	1.10
Mean z-score	-2.26
Structure conservation index	0.51
SVM decision value	2.20
SVM RNA-class probability	0.990181
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6275661 95 - 27905053
UAACAACUUUAUAUUAAACAAAA----AGUGGUU-CUACUAAGACCC-GUUUUUUUUC-CACAGUGCAAGAAAAUAGUUACUUAACUAUUCCACGCACCAAA
...................((((----(((((.(-((....))).))-)))))))...-....((((.....(((((((....)))))))....)))).... ( -14.30)
>DroSec_CAF1 40909 94 - 1
UAACCACUAUAUAUUAAACAGAA----AGUGGUU-CUACUAAUACCCUGUA--UUUUU-CACAGUGCAAGAAAAUAGUUACUUAACUAUUCCACGCACCAAA
.(((((((...............----)))))))-................--.....-....((((.....(((((((....)))))))....)))).... ( -14.66)
>DroEre_CAF1 46288 84 - 1
UAAAAAGU----AGUAAACAAAU----AGUG-UU-CAACUACUAGCA-GCU--UUUUC-CGCUGUGCAAGAAAAUAGU----UUGCUAUUCCACGCACCAAA
.....(((----(((((((...(----((((-..-....)))))(((-((.--.....-.)))))...........))----))))))))............ ( -18.30)
>DroYak_CAF1 42711 92 - 1
UAACAAGUUU--AUUAAGCAAAU----AGUGGUC-CAACUACUAGCA-ACU--UUUUCCCACUGUGCAAGAAAAUAGUUACUUUGCUAUUCCACGCACCAAA
.....(((..--...(((....(----(((((..-...))))))...-.))--)......)))((((.....((((((......))))))....)))).... ( -15.30)
>DroAna_CAF1 46771 92 - 1
UCAUCCCUUUU-----UUAAUUUGUUUUUUAGCCCAUAUCACUACCA-UUU--UUUUC-AGCAGUGCAUGAA-AUAGUUACUUCACUAUUCCACGCACCAAA
...........-----...............................-...--.....-....((((.((.(-(((((......)))))).)).)))).... ( -10.90)
>consensus
UAACAACUUU__AUUAAACAAAU____AGUGGUU_CUACUACUACCA_GUU__UUUUC_CACAGUGCAAGAAAAUAGUUACUUAACUAUUCCACGCACCAAA
...............................................................((((.....((((((......))))))....)))).... ( -7.46 =  -7.42 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:41 2006