Locus 4245

Sequence ID	X_DroMel_CAF1
Location	11,131,525 – 11,131,633
Length	108
Max. P	0.999788

overview

Window 4

Location	11,131,525 – 11,131,633
Length	108
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	70.65
Mean single sequence MFE	-22.88
Consensus MFE	-14.79
Energy contribution	-15.71
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-3.23
Structure conservation index	0.65
SVM decision value	4.08
SVM RNA-class probability	0.999788
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11131525 108 + 22224390
CCUAC-AAAAAAA----AAGAAUAAAAAUUAUAGCUUGGACAACAGUACGUAUGAGUAACAUCUUAGCUCACAGAUUGCUCAUACGCACCGUUGUU-UCCACUUGCGAG--UCAUU
.....-.......----................((.((((((((.((.((((((((((..((((........)))))))))))))).)).))))..-))))...))...--..... ( -26.40)
>DroSec_CAF1 46691 109 + 1
CCUAU-AACUACA----AAUAAUAAUAAUUAUAACCUGUACAACAGUACGUAUGGGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUGAGAG--UCAUU
.....-.......----......................(((((.((.(((((((((((................))))))))))).)).)))))(((((....)))))--..... ( -19.49)
>DroSim_CAF1 15175 109 + 1
CCUAU-AACUACA----AAUAAUAAUAAUUAUAACCUGCACAACAGUGCGUAUGAGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUUUUUCACUUCAGAG--UCAUU
.....-.......----......................(((((.((((((((((((((................)))))))))))))).)))))..............--..... ( -25.69)
>DroYak_CAF1 49471 112 + 1
CUUUCAAACUAAAUUACAAUAAUAAUAAUUAGAAACUGUACAACAGUACGUAUGAGUAAUAC-UUAGCAUUCAGAUUGCUCAUACGCACCGUUGUU-UUCACUGAAGAC--UCAUU
.(((((.............((((....))))((((....(((((.((.((((((((((((.(-(........)))))))))))))).)).))))))-)))..)))))..--..... ( -24.90)
>DroAna_CAF1 48171 90 + 1
----G-AACUCUA----AACAGUUAUU-CCAUAACGC---CCACACUGCGUAUACGUAUUAU------------AUUACUCAUACGCACUGUUGCC-UCCAACCAGGACCUUGUUU
----.-......(----(((((((((.-..)))))((---..(((.(((((((..(((....------------..)))..))))))).))).)).-(((.....)))...))))) ( -17.90)
>consensus
CCUAC_AACUAAA____AAUAAUAAUAAUUAUAACCUGUACAACAGUACGUAUGAGUAACAUCUUAGCUCACAAAUUGCUCAUACGCACCGUUGUU_UUCACUUAAGAG__UCAUU
.......................................(((((.((.(((((((((((................))))))))))).)).)))))..................... (-14.79 = -15.71 +   0.92)

alignment

secondary structure

dotplot

Window 5

Location	11,131,525 – 11,131,633
Length	108
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	70.65
Mean single sequence MFE	-31.36
Consensus MFE	-22.20
Energy contribution	-22.70
Covariance contribution	0.50
Combinations/Pair	1.24
Mean z-score	-3.49
Structure conservation index	0.71
SVM decision value	3.96
SVM RNA-class probability	0.999731
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11131525 108 - 22224390
AAUGA--CUCGCAAGUGGA-AACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAGAUGUUACUCAUACGUACUGUUGUCCAAGCUAUAAUUUUUAUUCUU----UUUUUUU-GUAGG
.....--..(....)((((-..((((((((((((((((..((((........))))....))))))))))))))))))))..((((((...........----.....))-)))). ( -34.39)
>DroSec_CAF1 46691 109 - 1
AAUGA--CUCUCAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACCCAUACGUACUGUUGUACAGGUUAUAAUUAUUAUUAUU----UGUAGUU-AUAGG
.((((--((..(((((((...(((((((((((((((((((.((((.....)))).))))...)))))))))))))))...(((.......))).)))))----)).))))-))... ( -29.90)
>DroSim_CAF1 15175 109 - 1
AAUGA--CUCUGAAGUGAAAAACAACGGUGCGUAUGAGCAAUUUGUGAGCUAAGAUGUUACUCAUACGCACUGUUGUGCAGGUUAUAAUUAUUAUUAUU----UGUAGUU-AUAGG
.....--.((((.........(((((((((((((((((..((((........))))....))))))))))))))))).))))((((((((((.......----.))))))-)))). ( -35.90)
>DroYak_CAF1 49471 112 - 1
AAUGA--GUCUUCAGUGAA-AACAACGGUGCGUAUGAGCAAUCUGAAUGCUAA-GUAUUACUCAUACGUACUGUUGUACAGUUUCUAAUUAUUAUUAUUGUAAUUUAGUUUGAAAG
.....--...(((((....-.(((((((((((((((((.(((((........)-).))).))))))))))))))))).......((((..(((((....))))))))).))))).. ( -31.30)
>DroAna_CAF1 48171 90 - 1
AAACAAGGUCCUGGUUGGA-GGCAACAGUGCGUAUGAGUAAU------------AUAAUACGUAUACGCAGUGUGG---GCGUUAUGG-AAUAACUGUU----UAGAGUU-C----
(((((.(.(((......((-.((.(((.((((((((.(((..------------....))).)))))))).)))..---)).))..))-)....)))))----)......-.---- ( -25.30)
>consensus
AAUGA__CUCUCAAGUGAA_AACAACGGUGCGUAUGAGCAAUCUGUGAGCUAAGAUGUUACUCAUACGUACUGUUGUACAGGUUAUAAUUAUUAUUAUU____UGUAGUU_AUAGG
.....................(((((((((((((((((..((((........))))....)))))))))))))))))....................................... (-22.20 = -22.70 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:06 2006