Locus 1965

Sequence ID	X_DroMel_CAF1
Location	5,380,891 – 5,381,102
Length	211
Max. P	0.971483

overview

Window 8

Location	5,380,891 – 5,380,983
Length	92
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	91.30
Mean single sequence MFE	-21.09
Consensus MFE	-17.57
Energy contribution	-18.24
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.83
SVM decision value	-0.00
SVM RNA-class probability	0.533273
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380891 92 - 22224390
UAGAGACAAAGGCGCUGAAAAGCGUGGAAAACUGGGAAAAAACUCAAAGGAUUUCGCGUAUACUCUGCCAAUAAAUAGCGCAAAUAUGAACC
..........((((((....)))((((((..((..((......))..))..)))))).........)))....................... ( -19.60)
>DroSec_CAF1 62210 92 - 1
UAGAGACAAAGGCGCUGAAAAGCGGUAAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUAUAUAGCGCAAAUAUUGAAU
...........((((((....((((.......((((......)))).......))))((........))......))))))........... ( -21.84)
>DroSim_CAF1 49168 92 - 1
UAGAGACAAAGGCGCUGAAAAGCGGUGAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUAUAUAGCGCAAAUAUUGAAU
...........((((((....((((.......((((......)))).......))))((........))......))))))........... ( -21.84)
>consensus
UAGAGACAAAGGCGCUGAAAAGCGGUGAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUAUAUAGCGCAAAUAUUGAAU
...........((((((....((((.......((((......)))).......))))((........))......))))))........... (-17.57 = -18.24 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	5,380,910 – 5,381,023
Length	113
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	90.90
Mean single sequence MFE	-28.81
Consensus MFE	-23.20
Energy contribution	-23.14
Covariance contribution	-0.06
Combinations/Pair	1.08
Mean z-score	-2.41
Structure conservation index	0.81
SVM decision value	1.23
SVM RNA-class probability	0.934110
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380910 113 - 22224390
GUUGGAAAUUGAAGUUUCAGCGAAAAAAAUGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGUGGAAAACUGGGAAAAAACUCAAAGGAUUUCGCGUAUACUCUGCCAAUA
(((((.........((((((((.......(((.......))).......-...)))))))).((((((((..((..((......))..))..))))))))........))))). ( -27.23)
>DroSec_CAF1 62229 113 - 1
GUUGGAAAUUGAAGUUCCAGCGAAAAAAGUGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGGUAAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUA
(((((((.......)))))))................((.(((((....-...((((....)))).......(((.(((....(.....)...))).)))...))))).))... ( -27.10)
>DroSim_CAF1 49187 113 - 1
GUUGGAAAUUGAAGUUCCAGCGAAAAAAGCGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGGUGAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUA
(((((((.......))))))).......(((((....(((..(((....-...((((....))))((....))((((......)))).....))).))).....)))))..... ( -28.90)
>DroEre_CAF1 55381 110 - 1
GU-GGAAAUUGAAGUUCCGGCGGAAAAAAUGGGAAGAUGCUAGAGACAAAAGGCGCUGAAAAGCGGGGAAAACUGGGGAAA-ACUCAAAGCACUCCUCGGAUACUCUGCCAA--
..-((((.......))))((((((.....((((.((.((((............((((....))))........((((....-.)))).)))))).)))).....))))))..-- ( -32.00)
>consensus
GUUGGAAAUUGAAGUUCCAGCGAAAAAAAUGGAAAGAUGCUAGAGACAA_AGGCGCUGAAAAGCGGGGAAAACUGGGGAAAAACUCAAAGGACUCCGCGGAUACUCUGCCAAUA
(((((((.......)))))))................((.(((((........((((....)))).......(((.(((..............))).)))...))))).))... (-23.20 = -23.14 +  -0.06)

alignment

secondary structure

dotplot

Window 0

Location	5,380,944 – 5,381,063
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.21
Mean single sequence MFE	-26.74
Consensus MFE	-20.22
Energy contribution	-20.82
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-2.76
Structure conservation index	0.76
SVM decision value	1.68
SVM RNA-class probability	0.971483
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380944 119 - 22224390
AAUAGCGAAAAAAGUUCGCGAGCGUUAAACUCAUAUGAAAGUUGGAAAUUGAAGUUUCAGCGAAAAAAAUGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGUGGAAAACUGGGAAA
....(((((.....))))).((((((....((((......(((((((.......))))))).......))))...))))))........-..(((((....))))).............. ( -25.22)
>DroSec_CAF1 62263 114 - 1
----GCGA-AAAAGUUCGCGAGCGUUAAACUCAUAUGAAAGUUGGAAAUUGAAGUUCCAGCGAAAAAAGUGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGGUAAAAACUGGGGAA
----((((-(....))))).((((((....((((......(((((((.......))))))).......))))...))))))........-...((((....))))............... ( -26.62)
>DroSim_CAF1 49221 114 - 1
----GCGA-AAAAGUUCGCGAGCGUUAAACUCAUAUGAAAGUUGGAAAUUGAAGUUCCAGCGAAAAAAGCGGAAAGAUGCUAGAGACAA-AGGCGCUGAAAAGCGGUGAAAACUGGGGAA
----((((-(....))))).((((((...(((........(((((((.......)))))))......((((......)))).)))....-.))))))......((((....))))..... ( -30.30)
>DroEre_CAF1 55412 116 - 1
AAA-GCGA--AAAGUGCGCGACCGUUAAACUCAUAUGAAAGU-GGAAAUUGAAGUUCCGGCGGAAAAAAUGGGAAGAUGCUAGAGACAAAAGGCGCUGAAAAGCGGGGAAAACUGGGGAA
...-(((.--......)))..(((((...(((..........-((((.......))))((((...............)))).)))........((((....)))).....))).)).... ( -19.96)
>DroYak_CAF1 54957 119 - 1
AAUGGCGA-AAAAGUUCGCGAGCGUUAAACUCAUAUGAAAGUUGGAAAUUGAAGUUCCAGCGGAAAAAAUGGGAAGAUGCCGGAGACAAAAGGCGCUGAAAAGCGAGGAAAACUGGCGAA
....((((-(....))))).((((((...(((((......(((((((.......))))))).......)))))........(....)....)))))).....((.((.....)).))... ( -31.62)
>consensus
AA__GCGA_AAAAGUUCGCGAGCGUUAAACUCAUAUGAAAGUUGGAAAUUGAAGUUCCAGCGAAAAAAAUGGAAAGAUGCUAGAGACAA_AGGCGCUGAAAAGCGGGGAAAACUGGGGAA
....((((.......)))).((((((....((((......(((((((.......))))))).......))))...))))))............((((....))))............... (-20.22 = -20.82 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	5,380,983 – 5,381,102
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.67
Mean single sequence MFE	-22.75
Consensus MFE	-7.74
Energy contribution	-8.74
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.78
Structure conservation index	0.34
SVM decision value	0.10
SVM RNA-class probability	0.582986
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5380983 119 + 22224390
GCAUCUUUCCAUUUUUUUCGCUGAAACUUCAAUUUCCAACUUUCAUAUGAGUUUAACGCUCGCGAACUUUUUUCGCUAUUUCACUCGCUG-AAAAAGAAGGCUAAAAAGCUCACUGAAAA
.....((((..(((((((((((((((......................((((.....))))(((((.....)))))..)))))...)).)-))))))).((((....))))....)))). ( -20.40)
>DroSec_CAF1 62302 104 + 1
GCAUCUUUCCACUUUUUUCGCUGGAACUUCAAUUUCCAACUUUCAUAUGAGUUUAACGCUCGCGAACUUUU-UCGC------------UC--AAAAGAAGGCCGA-AAGCUCGCUGAAAC
((..(((((............(((((.......))))).(((((....((((.....))))(((((....)-))))------------..--....)))))..))-)))...))...... ( -21.10)
>DroSim_CAF1 49260 104 + 1
GCAUCUUUCCGCUUUUUUCGCUGGAACUUCAAUUUCCAACUUUCAUAUGAGUUUAACGCUCGCGAACUUUU-UCGC------------UC--AAAAGAAGGCCGA-AAGCUCGCCGAAAC
((..(((((.((((((((...(((((.......)))))..........((((.....))))(((((....)-))))------------..--..)))))))).))-)))...))...... ( -24.30)
>DroEre_CAF1 55452 105 + 1
GCAUCUUCCCAUUUUUUCCGCCGGAACUUCAAUUUCC-ACUUUCAUAUGAGUUUAACGGUCGCGCACUUU--UCGC-UUUUCGUGCGCUGGAAAAAGAAGGAUGA-AAGC----------
...((.(((..(((((((((((((((.......))))-((((......)))).....))).((((((...--....-.....)))))).))))))))..))).))-....---------- ( -29.30)
>DroYak_CAF1 54997 94 + 1
GCAUCUUCCCAUUUUUUCCGCUGGAACUUCAAUUUCCAACUUUCAUAUGAGUUUAACGCUCGCGAACUUUU-UCGCCAUUUCACUCGAUG--------------A-AAGA----------
.....................(((((.......))))).(((((((.(((((.........(((((....)-))))......))))))))--------------)-))).---------- ( -18.66)
>consensus
GCAUCUUUCCAUUUUUUUCGCUGGAACUUCAAUUUCCAACUUUCAUAUGAGUUUAACGCUCGCGAACUUUU_UCGC__UUUC___CG_UG__AAAAGAAGGCCGA_AAGCUC_C_GAAA_
................((((((((((.......)))))..........((((.....)))))))))...................................................... ( -7.74 =  -8.74 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:03 2006