Locus 2508

Sequence ID	2R_DroMel_CAF1
Location	8,943,598 – 8,943,747
Length	149
Max. P	0.832838

overview

Window 9

Location	8,943,598 – 8,943,712
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.90
Mean single sequence MFE	-26.70
Consensus MFE	-16.74
Energy contribution	-16.52
Covariance contribution	-0.22
Combinations/Pair	1.10
Mean z-score	-2.89
Structure conservation index	0.63
SVM decision value	0.58
SVM RNA-class probability	0.788219
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8943598 114 + 20766785
UUCCGCCAGCCGCGACGGCGUCUAAAAAUACCGACAU-AG----ACAUAGGAAUAAGUAGGUUUUUUUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAAAAUUCA
.(((((..((((...))))(((((............)-))----))....((((((((((((((..((((((.....)))))).)))))))))))))))))))..-.............. ( -36.40)
>DroPse_CAF1 10093 108 + 1
UUCCCCCAGCUACGACGCGCUCUAAAAAUACCAGCAUCAA----ACACAGGAAUAAGUA----U--UUUGGAUUCAUUCCAAUCGUAUUUACUUAUUUGUGGAUU-UCAUAUAC-AUACA
........((......))(((...........))).....----...((.(((((((((----.--.(((((.....))))).......))))))))).))....-........-..... ( -17.00)
>DroEre_CAF1 17341 111 + 1
UUCUGCCAGCCGCGACGGCGUCUAAAAAUACCACCAU-AG----ACAUAGGAAUAAGUAGGUAU--UUUGGAUUCAUUCCAAGCAAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCA
.(((((..((((...))))(((((............)-))----))....((((((((((((..--((((((.....))))))...)))))))))))))))))..-........-..... ( -32.00)
>DroYak_CAF1 12374 115 + 1
UUCCGCCAGCCGCGACGGCGUCUAAAAAUACAACCGU-AAAAAUACAUGGGAAUAAGUAGGUAU--UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCA
.(((((..((((...))))..............((((-........))))((((((((((((..--((((((.....))))))...)))))))))))))))))..-........-..... ( -33.20)
>DroAna_CAF1 14978 102 + 1
UUCCGCCGGACACGACGGCAUCUAAAAAUACCAGC-----------AUAGGAAUAAGUA----U--UUUGGAUUCAUUCCAAGCACAUUUACUUAUUUGUGGAUUUUCAUAUAA-AUCCA
....((((.......))))................-----------..(.(((((((((----.--((((((.....))))))......))))))))).)((((((......))-)))). ( -24.60)
>DroPer_CAF1 10168 108 + 1
UUCCCCCAGCUACGACGCGCUCUAAAAAUACCAGCAUCAA----ACACAGGAAUAAGUA----U--UUUGGAUUCAUUCCAAUCGUAUUUACUUAUUUGUGGAUU-UCAUAUAC-AUACA
........((......))(((...........))).....----...((.(((((((((----.--.(((((.....))))).......))))))))).))....-........-..... ( -17.00)
>consensus
UUCCGCCAGCCACGACGGCGUCUAAAAAUACCAGCAU_AA____ACAUAGGAAUAAGUA____U__UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU_UCAUAUAA_AUUCA
.........((((((.....))............................(((((((((.......((((((.....))))))......))))))))))))).................. (-16.74 = -16.52 +  -0.22)

alignment

secondary structure

dotplot

Window 0

Location	8,943,637 – 8,943,747
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.75
Mean single sequence MFE	-28.34
Consensus MFE	-21.18
Energy contribution	-21.43
Covariance contribution	0.25
Combinations/Pair	1.11
Mean z-score	-2.71
Structure conservation index	0.75
SVM decision value	0.72
SVM RNA-class probability	0.832838
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8943637 110 + 20766785
----ACAUAGGAAUAAGUAGGUUUUUUUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAAAAUUCAACA-----GCCGCAGGAAUGCCAAAUGGUGUGCAUUUUGA
----......((((((((((((((..((((((.....)))))).))))))))))))))((((...-.................-----.)))).(((((((((.....)).))))))).. ( -30.80)
>DroSec_CAF1 17904 108 + 1
----ACAUAGGAAUAAGUAGGUUUU-UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCAACA-----GCCGCAGGAAUGCCAAAUGGAGUGCAUCUUGU
----......((((((((((((((.-((((((.....)))))).))))))))))))))..(((((-(.....))-))))....-----...((((((.((((.......).))))))))) ( -31.40)
>DroSim_CAF1 12181 108 + 1
----ACAUAGGAAUAAGUAGGUUUU-UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCAACA-----GCCGCAGGAAUGCCAAAUGGAGUGCAUGUUGU
----......((((((((((((((.-((((((.....)))))).))))))))))))))..(((((-(.....))-)))).(((-----((.(((......((....))..)))..))))) ( -30.10)
>DroEre_CAF1 17380 104 + 1
----ACAUAGGAAUAAGUAGGUAU--UUUGGAUUCAUUCCAAGCAAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCA--------GCCGCAGAAAUGCCAAAUGGAGUGCAUGAUAU
----.(((..((((((((((((..--((((((.....))))))...))))))))))))(((((((-(.....))-)))).--------...(((....)))..........))))).... ( -26.80)
>DroYak_CAF1 12413 108 + 1
AAAUACAUGGGAAUAAGUAGGUAU--UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU-UCAUAUAA-AUUCA--------ACCGCAGGAAUGCCCAAUGGAGUGCAUGCUAU
.....(((((((((((((((((..--((((((.....))))))...)))))))))))(((((...-........-.....--------.)))))......))).))).(((....))).. ( -28.43)
>DroAna_CAF1 15013 107 + 1
------AUAGGAAUAAGUA----U--UUUGGAUUCAUUCCAAGCACAUUUACUUAUUUGUGGAUUUUCAUAUAA-AUCCAAAACAAAUUCCGUUGAAAUGCCUAAUAAAGUGAGUUCACA
------.((((((((((((----.--((((((.....))))))......))))))))..(((((((......))-)))))....................)))).....(((....))). ( -22.50)
>consensus
____ACAUAGGAAUAAGUAGGUUU__UUUGGAUUCAUUCCAAGCGAACUUACUUAUUUGCGGAUU_UCAUAUAA_AUUCAACA_____GCCGCAGGAAUGCCAAAUGGAGUGCAUGUUGU
..........((((((((((((....((((((.....))))))...))))))))))))((((...........................))))....(((((.......).))))..... (-21.18 = -21.43 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:50 2006