Locus 6804

Sequence ID	X_DroMel_CAF1
Location	16,942,829 – 16,942,938
Length	109
Max. P	0.718159

overview

Window 5

Location	16,942,829 – 16,942,938
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.45
Mean single sequence MFE	-40.53
Consensus MFE	-30.90
Energy contribution	-30.65
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-1.73
Structure conservation index	0.76
SVM decision value	0.39
SVM RNA-class probability	0.718159
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16942829 109 + 22224390
GUUAGCCGGUUUCCAUAAAAAGCAGCU--CAGACAGGCGAAAAGAGAGGGAUUCUCCAUUCCCCAUUCUCG---------AUUCUCGAGUGAGUGGGUCACUUGUGGUGUCUGCGGCUGG
..(((((((...)).......(((((.--(..(((((.((...(((.(((....))).)))((((((((((---------.....)))..))))))))).))))).).).))))))))). ( -35.40)
>DroSec_CAF1 25656 111 + 1
UUUAGCCGGUUUCCAUAAAAAGCAGCUCUCAGACAGGCGAAAAGAGAGGGAUUCUCCAUUCCCCAUUUUCG---------AUUCUCGAGUGAGUGGGUCACUUGUGGUGGCUGCGGCUGG
..(((((((...)).......((((((..((......((((((..(.((((........))))).))))))---------.....(((((((.....)))))))))..))))))))))). ( -38.00)
>DroEre_CAF1 12601 118 + 1
UUUAGCCGGUUUCCAUAAAAAGCAGCU--CAGACAGGCGCAAAGAGAGGGAUUCCCGAUUCCCGACUCACGAUUCACUCGAUUCUCGAGUGAGUGGGUCAUUUGUGGUGGCUGCGGCUGA
.(((((((((..(((((((..((.(((--......))))).......((((........))))(((((((...(((((((.....)))))))))))))).)))))))..))..))))))) ( -49.50)
>DroYak_CAF1 12329 116 + 1
UUUAGCCGGUUUCCAUAAAAAGCAGCU--CAGACAGGCGGAAAGAGAGGGAUUCUCUAUUCUCCAUUCUCGAUUC--UCCAUUCUCGAGUGAGUGGGUCACUUGUGGUGGCUGCGGCUGG
..(((((((...)).......((((((--...(((((.((((.((((((((..........))).)))))..)))--(((((((......))))))).).)))))...))))))))))). ( -39.20)
>consensus
UUUAGCCGGUUUCCAUAAAAAGCAGCU__CAGACAGGCGAAAAGAGAGGGAUUCUCCAUUCCCCAUUCUCG_________AUUCUCGAGUGAGUGGGUCACUUGUGGUGGCUGCGGCUGG
.((((((((...)).......((((((................((((((((........))))...))))............((.(((((((.....))))))).)).)))))))))))) (-30.90 = -30.65 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	16,942,829 – 16,942,938
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.45
Mean single sequence MFE	-35.38
Consensus MFE	-24.31
Energy contribution	-25.50
Covariance contribution	1.19
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.69
SVM decision value	0.16
SVM RNA-class probability	0.612981
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16942829 109 - 22224390
CCAGCCGCAGACACCACAAGUGACCCACUCACUCGAGAAU---------CGAGAAUGGGGAAUGGAGAAUCCCUCUCUUUUCGCCUGUCUG--AGCUGCUUUUUAUGGAAACCGGCUAAC
..((((((((.(((.....))).....((((((((.....---------))))...((.(((.(((((.....))))).))).))....))--)))))).......(....).))))... ( -34.10)
>DroSec_CAF1 25656 111 - 1
CCAGCCGCAGCCACCACAAGUGACCCACUCACUCGAGAAU---------CGAAAAUGGGGAAUGGAGAAUCCCUCUCUUUUCGCCUGUCUGAGAGCUGCUUUUUAUGGAAACCGGCUAAA
..((((((((((((.....))).....((((.(((.....---------)))....((.(((.(((((.....))))).))).))....)))).))))).......(....).))))... ( -34.40)
>DroEre_CAF1 12601 118 - 1
UCAGCCGCAGCCACCACAAAUGACCCACUCACUCGAGAAUCGAGUGAAUCGUGAGUCGGGAAUCGGGAAUCCCUCUCUUUGCGCCUGUCUG--AGCUGCUUUUUAUGGAAACCGGCUAAA
..(((((((((((..(((...(((.((((((((((.....)))))))...))).)))((((........))))............))).))--.))))).......(....).))))... ( -39.40)
>DroYak_CAF1 12329 116 - 1
CCAGCCGCAGCCACCACAAGUGACCCACUCACUCGAGAAUGGA--GAAUCGAGAAUGGAGAAUAGAGAAUCCCUCUCUUUCCGCCUGUCUG--AGCUGCUUUUUAUGGAAACCGGCUAAA
..(((((((((((..(((.(((..(((....(((((.......--...)))))..))).(((.(((((.....))))))))))).))).))--.))))).......(....).))))... ( -33.60)
>consensus
CCAGCCGCAGCCACCACAAGUGACCCACUCACUCGAGAAU_________CGAGAAUGGGGAAUGGAGAAUCCCUCUCUUUUCGCCUGUCUG__AGCUGCUUUUUAUGGAAACCGGCUAAA
..(((((((((.....(.(((((.....))))).).....................((.(((.(((((.....))))).))).)).........))))).......(....).))))... (-24.31 = -25.50 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:24 2006