Locus 3152

Sequence ID	X_DroMel_CAF1
Location	8,369,476 – 8,369,654
Length	178
Max. P	0.862344

overview

Window 5

Location	8,369,476 – 8,369,589
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.85
Mean single sequence MFE	-23.40
Consensus MFE	-18.74
Energy contribution	-18.74
Covariance contribution	0.00
Combinations/Pair	1.09
Mean z-score	-1.77
Structure conservation index	0.80
SVM decision value	0.83
SVM RNA-class probability	0.862344
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8369476 113 - 22224390
UAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAAUGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--UGCUACCAGCAUUUCGACAUAACUCAAUCGAGAAAACUGUU
.((-----((((....(((((((.....((((....(((....(((((.....(((((........))))).)))))--))).....))))...((......))...))))))))))))) ( -24.80)
>DroSec_CAF1 34609 113 - 1
UAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--UGCUACCAGCAUUUCCACAUAACUCAAUCGGGAAAACUGUU
.((-----((((....((((((((((..((((....)))).............(((((........)))))))))..--(((.....)))..................)))))))))))) ( -24.00)
>DroSim_CAF1 37828 113 - 1
UAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--UGCUACCAGCAUUUCCACAUAACUCAAUCGGGAAAACUGUU
.((-----((((....((((((((((..((((....)))).............(((((........)))))))))..--(((.....)))..................)))))))))))) ( -24.00)
>DroEre_CAF1 31269 117 - 1
UAGUAGUGUAAUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCA---UGCUACCAGCAUUUUCACAUUACUUAAUCGAGGAAACUGUU
.((((((((.............((((..((((....)))).............(((((........)))))))))(---(((.....))))....))))))))......((....))... ( -25.00)
>DroYak_CAF1 33694 112 - 1
--------UAAUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCGGUGAAUUAAGAAUGGGCAUUGUGCUACCAGCAUUUUCACAUUACUCAAUCGUGGAAACUGUU
--------............................((((..((((((.....((((..........)))).))))))))))....((((((((((((((....))).))))))).)))) ( -19.20)
>consensus
UAG_____CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU__UGCUACCAGCAUUUCCACAUAACUCAAUCGAGAAAACUGUU
................((((((((((..((((....)))).............(((((........)))))))))....(((.....)))..................))))))...... (-18.74 = -18.74 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	8,369,516 – 8,369,615
Length	99
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.64
Mean single sequence MFE	-26.29
Consensus MFE	-13.12
Energy contribution	-13.32
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.50
SVM decision value	-0.04
SVM RNA-class probability	0.515536
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8369516 99 + 22224390
A--AUGCCCAUUCUUAAUUUAUAGAAUUUAUUGGCAUUUAAUGCAUUGGCAUGAGGGCGAGAAAUUACACUG-----CUAUG--------------CAGCAUAAAUGCGCCAAUAAAAAA
.--.......((((........))))(((((((((......(((((.((((.(...(..(....)..).)))-----)))))--------------))(((....))))))))))))... ( -24.20)
>DroSec_CAF1 34649 111 + 1
A--AUGCCCAUUCUUAAUUUAUAGAAUUUAUUGGCAUUUAAUGCGUUGGCAUGAGGGCGAGAAAUUACACUG-----CUAUGCUCCGUCGCAUUUGCAGCAUAAAUGCGCCAAUAAAA--
.--.......((((........))))(((((((((....((((((..((((((.(((..(....)..).)).-----.))))))....)))))).(((.......)))))))))))).-- ( -29.60)
>DroSim_CAF1 37868 111 + 1
A--AUGCCCAUUCUUAAUUUAUAGAAUUUAUUGGCAUUUAAUGCGUUGGCAUGAGGGCGAGAAAUUACACUG-----CUAUGCUCCGUCGCAUUUACAGCAUAAAUGCGCCAAUAAAA--
.--.......((((........))))(((((((((....((((((..((((((.(((..(....)..).)).-----.))))))....))))))....(((....)))))))))))).-- ( -29.30)
>DroEre_CAF1 31309 108 + 1
A---UGCCCAUUCUUAAUUUAUAGAAUUUAUUGGCAUUUAAUGCGUUGGCAUGAGGGCGAGAAAUUACAUUACACUACUAUGCU-----GCCAUUGCAGUAUAAAUG--CCGAUAAAA--
.---......((((........))))((((((((((((((.((((.(((((.....(((((................)).))))-----)))).))))...))))))--)))))))).-- ( -28.59)
>DroYak_CAF1 33734 101 + 1
ACAAUGCCCAUUCUUAAUUCACCGAAUUUAUUGGCAUUUAAUGCGUUGGCAUGAGGGCGAGAAAUUACAUUA----------CU-----ACCAUUGCGGCAUAAAUG--GCAAUAAAA--
..........................(((((((.((((((.((((.(((.......(..(....)..)....----------..-----.))).))))...))))))--.))))))).-- ( -19.74)
>consensus
A__AUGCCCAUUCUUAAUUUAUAGAAUUUAUUGGCAUUUAAUGCGUUGGCAUGAGGGCGAGAAAUUACACUG_____CUAUGCU_____GCAAUUGCAGCAUAAAUGCGCCAAUAAAA__
....((((((((((........))))).............((((....))))..)))))............................................................. (-13.12 = -13.32 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	8,369,516 – 8,369,615
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	82.64
Mean single sequence MFE	-26.74
Consensus MFE	-12.58
Energy contribution	-12.98
Covariance contribution	0.40
Combinations/Pair	1.10
Mean z-score	-2.41
Structure conservation index	0.47
SVM decision value	0.17
SVM RNA-class probability	0.618287
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8369516 99 - 22224390
UUUUUUAUUGGCGCAUUUAUGCUG--------------CAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAAUGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--U
.........((((...((((((((--------------(...)-----)))))))).....))))...((((....))))..((((((.....(((((........))))).)))))--) ( -25.50)
>DroSec_CAF1 34649 111 - 1
--UUUUAUUGGCGCAUUUAUGCUGCAAAUGCGACGGAGCAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--U
--.......((((...(((((((((..((((......)))).)-----)))))))).....))))...((((....))))..((((((.....(((((........))))).)))))--) ( -31.50)
>DroSim_CAF1 37868 111 - 1
--UUUUAUUGGCGCAUUUAUGCUGUAAAUGCGACGGAGCAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU--U
--.......((((...(((((((((..((((......)))).)-----)))))))).....))))...((((....))))..((((((.....(((((........))))).)))))--) ( -29.90)
>DroEre_CAF1 31309 108 - 1
--UUUUAUCGG--CAUUUAUACUGCAAUGGC-----AGCAUAGUAGUGUAAUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCA---U
--........(--((((.(((((((.(((..-----..))).))))))))))))........((((..((((....)))).............(((((........))))))))).---. ( -25.10)
>DroYak_CAF1 33734 101 - 1
--UUUUAUUGC--CAUUUAUGCCGCAAUGGU-----AG----------UAAUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCGGUGAAUUAAGAAUGGGCAUUGU
--..(((((((--((((........))))))-----))----------)))...........((((...........(((..(((........)))..)))..........))))..... ( -21.70)
>consensus
__UUUUAUUGGCGCAUUUAUGCUGCAAAGGC_____AGCAUAG_____CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAUUAAAUGCCAAUAAAUUCUAUAAAUUAAGAAUGGGCAU__U
................((((((((........................))))))))......((((..((((....)))).............(((((........)))))))))..... (-12.58 = -12.98 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	8,369,554 – 8,369,654
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.09
Mean single sequence MFE	-24.06
Consensus MFE	-6.04
Energy contribution	-7.24
Covariance contribution	1.20
Combinations/Pair	1.11
Mean z-score	-1.77
Structure conservation index	0.25
SVM decision value	0.16
SVM RNA-class probability	0.610074
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8369554 100 - 22224390
CUAAUUUCC-CCGCAGUGUGGAAAAUUCAUUUUUCUUUUUUUUUUUAUUGGCGCAUUUAUGCUG--------------CAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAAUGCAU
.........-..(((((((((((((.....)))))..............((((...((((((((--------------(...)-----)))))))).....))))..)))))...))).. ( -22.40)
>DroSec_CAF1 34687 104 - 1
CUAAUUCCC-CCGCGCCGUGGAAAACUCAUUU----------UUUUAUUGGCGCAUUUAUGCUGCAAAUGCGACGGAGCAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAU
.........-..(((((((((((((.....))----------))))).))))))..(((((((((..((((......)))).)-----))))))))............((((....)))) ( -29.20)
>DroSim_CAF1 37906 104 - 1
CUAAUUUCC-CCGCGCCGUGGAAAACUCAUUU----------UUUUAUUGGCGCAUUUAUGCUGUAAAUGCGACGGAGCAUAG-----CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAU
.........-..(((((((((((((.....))----------))))).))))))..(((((((((..((((......)))).)-----))))))))............((((....)))) ( -27.60)
>DroEre_CAF1 31346 101 - 1
CUAAUUUGC-CCGAGCUGUGGAAAAUUCA-UU----------UUUUAUCGG--CAUUUAUACUGCAAUGGC-----AGCAUAGUAGUGUAAUGUAAUUUCUCGCCCUCAUGCCAACGCAU
.........-.((((((((((((((....-))----------))))).)))--)..(((((((((.(((..-----..))).))))))))).........))).....((((....)))) ( -21.00)
>DroYak_CAF1 33774 93 - 1
CUAAUUUCCACCGAGCUGUGGAAAAUUCAAUU----------UUUUAUUGC--CAUUUAUGCCGCAAUGGU-----AG----------UAAUGUAAUUUCUCGCCCUCAUGCCAACGCAU
............(((..(((..(((((((...----------..(((((((--((((........))))))-----))----------))))).)))))..))).)))((((....)))) ( -20.10)
>consensus
CUAAUUUCC_CCGCGCUGUGGAAAAUUCAUUU__________UUUUAUUGGCGCAUUUAUGCUGCAAAGGC_____AGCAUAG_____CAGUGUAAUUUCUCGCCCUCAUGCCAACGCAU
..........(((.....)))............................((((...((((((((........................)))))))).....))))...((((....)))) ( -6.04 =  -7.24 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:23 2006