Locus 796

Sequence ID	2R_DroMel_CAF1
Location	3,791,397 – 3,791,554
Length	157
Max. P	0.954705

overview

Window 4

Location	3,791,397 – 3,791,487
Length	90
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	78.05
Mean single sequence MFE	-24.04
Consensus MFE	-13.22
Energy contribution	-14.14
Covariance contribution	0.92
Combinations/Pair	1.10
Mean z-score	-2.10
Structure conservation index	0.55
SVM decision value	0.92
SVM RNA-class probability	0.881587
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3791397 90 - 20766785
UACCUUAUAUGCAUCCCUAUA--------UACG-------------CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAUCUAUGCACGCAUA--------UCCUUUGCAUGUAACCUCC
....(((((((((........--------((((-------------((....))))))...(((.((.....(((....))).)).)))...--------.....)))))))))..... ( -20.70)
>DroSec_CAF1 48001 97 - 1
CACCUUAUAUGCAUCCCUAUA--------UACA-------------CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAUCUAUGCACGCACAAAAGCCUUUCCUUUGCAUGUAAGCUC-
...((((((((((........--------((((-------------((....))))))...(((.((.....(((....))).)).)))................))))))))))...- ( -23.80)
>DroSim_CAF1 61497 105 - 1
CACCUUAUAUGCAUCCCUAUAUACCUUUAUACA-------------CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAUCUAUGCACGCACAGAAGCCUUUCCUUUGCAUGUAAGCUC-
...((((((((((......((((((((((....-------------..))))))))))...(((.((.....(((....))).)).)))................))))))))))...- ( -26.00)
>DroEre_CAF1 49321 117 - 1
CACCUCAUAUGCAUCCCUAUAU-CCUAUAUACAUAGGAAUACACGCCCUAGAGGUGUGCGCGUGAGCCA-AUUAGAAAUCUAUGCACGCACAGAAGCGUGUCCUUUGCAUGCAAACGCU
.......((((((........(-(((((....))))))..((((((.......((((((((....))..-..(((....))).))))))......))))))....))))))........ ( -34.12)
>DroYak_CAF1 43626 102 - 1
CACCUUAUAUGCAUCCCUAUA--------UACAU--------ACUCUCUAGAGAUGUGCCCGUGAGCCA-AUUAAAAAUCUACUCAAGCACAGAAGCGUUACCUUUGAAAGUAAGUUCU
...(((((((((.((......--------.....--------.(((....))).(((((...((((...-............)))).))))))).))))...........))))).... ( -15.56)
>consensus
CACCUUAUAUGCAUCCCUAUA________UACA_____________CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAUCUAUGCACGCACAGAAGCCUUUCCUUUGCAUGUAAGCUC_
...((((((((((.................................((....))(((((.(....)......(((....))).....))))).............)))))))))).... (-13.22 = -14.14 +   0.92)

alignment

secondary structure

dotplot

Window 5

Location	3,791,429 – 3,791,522
Length	93
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	86.21
Mean single sequence MFE	-17.48
Consensus MFE	-12.36
Energy contribution	-12.43
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.51
Structure conservation index	0.71
SVM decision value	0.07
SVM RNA-class probability	0.567540
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3791429 93 - 20766785
CAAGCGCCCCUCGC-ACACACAC--ACACACACAUGUGUACCUUAUAUGCAUCCCUAUA--------UACG-----CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAU
...((((.((((((-......((--(((......)))))....((((((......))))--------)).)-----)...)))).)))).(....)............. ( -18.10)
>DroSec_CAF1 48040 94 - 1
CAAGCGCCCCUCGGAACACACAC--ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA--------UACA-----CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAU
...((((.((((((..((((...--.........))))..)).((((((......))))--------))..-----....)))).)))).(....)............. ( -17.40)
>DroSim_CAF1 61536 104 - 1
CAAGCGCCCCUCGCAACACACACACACACACACAUGUGCACCUUAUAUGCAUCCCUAUAUACCUUUAUACA-----CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAU
.........(((((.....................(((((.......))))).....((((((((((....-----..))))))))))...)))))............. ( -18.90)
>DroYak_CAF1 43666 94 - 1
CAAGCGCCCCUCGCACCA----C--ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA--------UACAUACUCUCUAGAGAUGUGCCCGUGAGCCA-AUUAAAAAU
...(((.....)))....----.--.......((((.((((..((((((......))))--------))....(((....)))..)))).)))).....-......... ( -15.50)
>consensus
CAAGCGCCCCUCGCAACACACAC__ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA________UACA_____CCUAGAGGUGUGCCCGUGAGCCAAAUUAGAAAU
...((((.((((...............(((....)))(((.......)))..............................)))).)))).(....)............. (-12.36 = -12.43 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	3,791,462 – 3,791,554
Length	92
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	85.40
Mean single sequence MFE	-18.26
Consensus MFE	-14.62
Energy contribution	-14.82
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.23
Structure conservation index	0.80
SVM decision value	1.45
SVM RNA-class probability	0.954705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3791462 92 - 20766785
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCGCACAAGCGCCCCUCGC-ACACACAC--ACACACACAUGUGUACCUUAUAUGCAUCCCUAUA--------UACG------
...............((.(((.(((..((((....)))).......-......((--(((......)))))........))).)))))...--------....------ ( -18.20)
>DroSec_CAF1 48073 93 - 1
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCGCACAAGCGCCCCUCGGAACACACAC--ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA--------UACA------
...........(((((((....))...((((....))))...)))))........--..........(((((.......))))).......--------....------ ( -18.70)
>DroSim_CAF1 61569 103 - 1
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCGCACAAGCGCCCCUCGCAACACACACACACACACACAUGUGCACCUUAUAUGCAUCCCUAUAUACCUUUAUACA------
...............((.(((.(((..((((....)))).................((((......)))).........))).)))))...............------ ( -16.40)
>DroEre_CAF1 49400 99 - 1
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCACACAAGCGCCCCUCGCA-------C--ACACACACACGUGCACCUCAUAUGCAUCCCUAUAU-CCUAUAUACAUAGGAA
...............((.(((.(((..((......)).......(((-------(--..........))))........))).)))))...(-(((((....)))))). ( -19.90)
>DroYak_CAF1 43702 90 - 1
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCGCACAAGCGCCCCUCGCACCA----C--ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA--------UACAU-----
...............((.(((.(((..((((....)))).....((((..----.--..........))))........))).)))))...--------.....----- ( -18.12)
>consensus
ACGAAAUUAAAUCUGAGCGGAAGCAAAGCGCACAAGCGCCCCUCGCAACACACAC__ACACACACAUGUGCACCUUAUAUGCAUCCCUAUA________UACA______
...............((.(((.(((..((((....))))...................(((......))).........))).)))))..................... (-14.62 = -14.82 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:37 2006