Locus 4545

Sequence ID	X_DroMel_CAF1
Location	11,961,502 – 11,961,610
Length	108
Max. P	0.965401

overview

Window 5

Location	11,961,502 – 11,961,610
Length	108
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	74.17
Mean single sequence MFE	-22.27
Consensus MFE	-9.99
Energy contribution	-10.24
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.45
SVM decision value	0.74
SVM RNA-class probability	0.837518
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11961502 108 + 22224390
U--AAUU-----UAA-UUCUUCCUUUAAUUUCUUGAAUUUCGA-AAACUUAA--GAGAGAAGCACUUGCACUUACCGCACAAUGCAAUCAUUUUUGUAAGUGCACUUUUGUGCGCCCUA
.--....-----...-((((..(((...((((.........))-))....))--)..))))((((.(((((((((.....((((....))))...))))))))).....))))...... ( -22.70)
>DroSec_CAF1 826 109 + 1
C--AAUU-----UUA-UCCUUUUUUAAAUUUCUUUAAUUUCGGAAAACUUAA--GAAAGAAGCACUUGCUUUUACCACACAAUGCAAUUAUUUUUGUAAGUGCACUUUUGUGCGCCCUA
.--....-----...-..(((((((((.(((((........)))))..))))--)))))((((....))))...........(((((......))))).((((((....)))))).... ( -21.80)
>DroSim_CAF1 818 115 + 1
UUAAAUUAGAAAUUAUUCCUAAUUU---UUUUUUUAAAUUUGA-GAAAUUAAGAGACAGAAGCACUUGCACUUACCACACAAUGAAAUUAUUUUUGUAAGUGCACUUUUGUGCGCCCUA
(((((..((((((((....))))))---))..))))).(((((-....)))))..(((((((....(((((((((.....((((....))))...))))))))))))))))........ ( -22.80)
>DroEre_CAF1 1361 108 + 1
U--CAUU-UAAUUUA-----UACCUAAAUUUCUAUUAUUUUUA-GAAGCUAA--GAGUGAUGCACUUACUGCCGCCACACAAUGCACUUAUUUCUGAAAGUGCACUUCUGUGCGCCCUA
.--....-.......-----.............((((((((((-(...))))--)))))))(((.....))).((((((.(((((((((........))))))).)).)))).)).... ( -21.80)
>consensus
U__AAUU_____UUA_UCCUUACUUAAAUUUCUUUAAUUUCGA_AAACUUAA__GAGAGAAGCACUUGCACUUACCACACAAUGCAAUUAUUUUUGUAAGUGCACUUUUGUGCGCCCUA
.............................................................((((((((..........................))))))((((....)))))).... ( -9.99 = -10.24 +   0.25)

alignment

secondary structure

dotplot

Window 6

Location	11,961,502 – 11,961,610
Length	108
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	74.17
Mean single sequence MFE	-24.80
Consensus MFE	-13.73
Energy contribution	-14.22
Covariance contribution	0.50
Combinations/Pair	1.21
Mean z-score	-2.26
Structure conservation index	0.55
SVM decision value	1.58
SVM RNA-class probability	0.965401
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11961502 108 - 22224390
UAGGGCGCACAAAAGUGCACUUACAAAAAUGAUUGCAUUGUGCGGUAAGUGCAAGUGCUUCUCUC--UUAAGUUU-UCGAAAUUCAAGAAAUUAAAGGAAGAA-UUA-----AAUU--A
......((((.....(((((((((...((((....)))).....))))))))).))))((((..(--((.(((((-(..........)))))).)))..))))-...-----....--. ( -26.70)
>DroSec_CAF1 826 109 - 1
UAGGGCGCACAAAAGUGCACUUACAAAAAUAAUUGCAUUGUGUGGUAAAAGCAAGUGCUUCUUUC--UUAAGUUUUCCGAAAUUAAAGAAAUUUAAAAAAGGA-UAA-----AAUU--G
(((((((((((...(((((.(((......))).)))))))))))....((((....))))...))--)))((((((((....(((((....)))))....)))-..)-----))))--. ( -21.50)
>DroSim_CAF1 818 115 - 1
UAGGGCGCACAAAAGUGCACUUACAAAAAUAAUUUCAUUGUGUGGUAAGUGCAAGUGCUUCUGUCUCUUAAUUUC-UCAAAUUUAAAAAAA---AAAUUAGGAAUAAUUUCUAAUUUAA
(((((.((((.....(((((((((....(((((...)))))...))))))))).)))))))))............-...............---(((((((((.....))))))))).. ( -26.10)
>DroEre_CAF1 1361 108 - 1
UAGGGCGCACAGAAGUGCACUUUCAGAAAUAAGUGCAUUGUGUGGCGGCAGUAAGUGCAUCACUC--UUAGCUUC-UAAAAAUAAUAGAAAUUUAGGUA-----UAAAUUA-AAUG--A
...(.((((((...((((((((........)))))))))))))).)(((.(..((((...)))).--.).)))((-((.......))))((((((....-----)))))).-....--. ( -24.90)
>consensus
UAGGGCGCACAAAAGUGCACUUACAAAAAUAAUUGCAUUGUGUGGUAAGAGCAAGUGCUUCUCUC__UUAAGUUC_UCAAAAUUAAAGAAAUUUAAAUAAGGA_UAA_____AAUU__A
...((.((((.....(((((((((....((((.....))))...))))))))).)))).)).......................................................... (-13.73 = -14.22 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:48 2006