Locus 8608

Sequence ID	X_DroMel_CAF1
Location	21,386,781 – 21,387,003
Length	222
Max. P	0.989802

overview

Window 1

Location	21,386,781 – 21,386,887
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	74.46
Mean single sequence MFE	-40.20
Consensus MFE	-22.52
Energy contribution	-22.64
Covariance contribution	0.12
Combinations/Pair	1.17
Mean z-score	-1.70
Structure conservation index	0.56
SVM decision value	-0.08
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21386781 106 + 22224390
CGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAACUGAACUGAGUUCAGUUCAGUUGGCCAGGACCAAAAGGCAUUGGCCCGU---UGGUGG---------CGGGUGGGUG--GUGCC
....(..(((((((((....))))....((((((((((((((((....))))))))))))))))))))......((((.((((((---.....)---------))))).))))--)..). ( -52.70)
>DroSec_CAF1 35067 97 + 1
CGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAAC----------UCAGUUCAGUUGGCCAGGACCAAAA-GCAUUGGGCCGU---CGGUGG---------UGGCCCGUCGUUUGGCC
........(((..(((.(((((((.....((((((((----------(......))))))))))))))....-.....(((((..---(...).---------.))))))).)))..))) ( -41.10)
>DroEre_CAF1 22999 88 + 1
CGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAAC----------UCAGUUCAGUGGCCCAGGACCAAAAAGCGUUGGCUCGU------------------CGGAUGGGUG----GGC
(((((((((((...)))))(((((......(((((.(----------(......)))))))..))))).....))))))((((..------------------(.....)..)----))) ( -27.20)
>DroYak_CAF1 23735 106 + 1
CGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAAC----------UCAGUUCACUUGGCCAGGACCGAAAAGCGUUGGCCCUUGGCCCGUGUUGGCUUGGGUGGCUGGGUG----UUC
.((.((..(((..((..(((...))).))..))).))----------))....((((..((((...((((..((((..((((...))))..))))...)))).))))..))))----... ( -39.80)
>consensus
CGAUGUGCGGUUGAAUUGCGGUUCGCUUUUGGCCAAC__________UCAGUUCAGUUGGCCAGGACCAAAAAGCAUUGGCCCGU___CGGUGG_________CGGCUGGGUG____GCC
(((((((((((...)))))(((((.....((((((((..................))))))))))))).....))))))(((((.......................)))))........ (-22.52 = -22.64 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	21,386,781 – 21,386,887
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	74.46
Mean single sequence MFE	-33.74
Consensus MFE	-16.68
Energy contribution	-18.19
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.81
Structure conservation index	0.49
SVM decision value	2.18
SVM RNA-class probability	0.989802
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21386781 106 - 22224390
GGCAC--CACCCACCCG---------CCACCA---ACGGGCCAAUGCCUUUUGGUCCUGGCCAACUGAACUGAACUCAGUUCAGUUGGCCAAAAGCGAACCGCAAUUCAACCGCACAUCG
(((..--.........)---------))....---..(((((((......)))))))(((((((((((((((....)))))))))))))))...(((..............)))...... ( -44.54)
>DroSec_CAF1 35067 97 - 1
GGCCAAACGACGGGCCA---------CCACCG---ACGGCCCAAUGC-UUUUGGUCCUGGCCAACUGAACUGA----------GUUGGCCAAAAGCGAACCGCAAUUCAACCGCACAUCG
(((((((.(..(((((.---------......---..)))))....)-.))))))).(((((((((......)----------))))))))...(((..............)))...... ( -34.84)
>DroEre_CAF1 22999 88 - 1
GCC----CACCCAUCCG------------------ACGAGCCAACGCUUUUUGGUCCUGGGCCACUGAACUGA----------GUUGGCCAAAAGCGAACCGCAAUUCAACCGCACAUCG
(((----((.....(((------------------(.((((....)))).))))...)))))...((((.((.----------(((.((.....)).)))..)).))))........... ( -23.50)
>DroYak_CAF1 23735 106 - 1
GAA----CACCCAGCCACCCAAGCCAACACGGGCCAAGGGCCAACGCUUUUCGGUCCUGGCCAAGUGAACUGA----------GUUGGCCAAAAGCGAACCGCAAUUCAACCGCACAUCG
...----......((.......((((((...(((((.(((((..........)))))))))).((....))..----------)))))).....(((...))).........))...... ( -32.10)
>consensus
GGC____CACCCAGCCA_________CCACCG___ACGGGCCAACGCUUUUUGGUCCUGGCCAACUGAACUGA__________GUUGGCCAAAAGCGAACCGCAAUUCAACCGCACAUCG
.....................................(((((((......)))))))((((((((..................))))))))...(((..............)))...... (-16.68 = -18.19 +   1.50)

alignment

secondary structure

dotplot

Window 3

Location	21,386,861 – 21,386,963
Length	102
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	72.74
Mean single sequence MFE	-28.89
Consensus MFE	-17.76
Energy contribution	-17.92
Covariance contribution	0.16
Combinations/Pair	1.13
Mean z-score	-1.57
Structure conservation index	0.61
SVM decision value	0.48
SVM RNA-class probability	0.752643
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21386861 102 - 22224390
UCCCUUCCUCCGAAAAGGGAGAAACUUUUUCGAUUAUUGUGCUUGUGAAAGUU-UUCGGUGUUUGUGC-GCAAACACAGGCAC--CACCCACCCG---------CCACCA---ACGGG
((((((........))))))(((((((((.(((.........))).)))))))-)).((((((((((.-.....)))))))))--).....((((---------......---.)))) ( -32.80)
>DroSec_CAF1 35136 103 - 1
UCCCUUCCCCCGAAAAGGGAGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUU-UUCGGUGUUUGUGC-GCAAACACUGGCCAAACGACGGGCCA---------CCACCG---ACGGC
((((((........))))))(((((((((.(((....-....))).)))))))-))(((((((((...-.)))))))))(((...((..((....---------))..))---..))) ( -31.30)
>DroEre_CAF1 23069 94 - 1
UCCCUGCCCCCGAAAAGGGAGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUUUUUCGGUGUUUGUGC-GCAAACACAGCC----CACCCAUCCG------------------ACGAG
................(((((((((((((.(((....-....))).))))))))))).(((((((...-.)))))))...)----).........------------------..... ( -22.40)
>DroYak_CAF1 23805 112 - 1
UCCCCUUCCCCGAAAAGGGAGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUUUUUCGGUGUUUGUGC-GCAAACACAGAA----CACCCAGCCACCCAAGCCAACACGGGCCAAGGG
..(((((.((((....(((((((((((((.(((....-....))).)))))))))))((((((((((.-.....))))).)----))))............))....))))..))))) ( -36.10)
>DroAna_CAF1 31466 82 - 1
A-CCCCCCCCCGAAAAUACACAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUUUUUGGGUGUUUGUGCAGUAAACAUGGA----------------------------------GGGA
.-(((.(((((((((((.(((((.(............-..).)))))...)))))))))((((((.....)))))).)).----------------------------------))). ( -21.84)
>consensus
UCCCUUCCCCCGAAAAGGGAGAAACUUUUUCGAUUAU_AUGCUUGUGAAAGUUUUUCGGUGUUUGUGC_GCAAACACAGAC____CACCCAGCCA__________CAC_____ACGGG
.........((.......(((((((((((.(((.........))).))))))))))).(((((((.....)))))))......................................)). (-17.76 = -17.92 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	21,386,887 – 21,387,003
Length	116
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	77.56
Mean single sequence MFE	-30.72
Consensus MFE	-14.99
Energy contribution	-15.82
Covariance contribution	0.83
Combinations/Pair	1.04
Mean z-score	-1.95
Structure conservation index	0.49
SVM decision value	0.38
SVM RNA-class probability	0.714575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21386887 116 - 22224390
UUUGGCUUGUUUUGGGACAGUUUACCAGAACUCCCAGAACUCCCUUCCUCCGAAAAGGG-AGAAACUUUUUCGAUUAUUGUGCUUGUGAAAGUU-UUCGGUGUUUGUGCGCAAACACA
(((((...(((((((.........)))))))..))))).(((((((........)))))-))((((((((.(((.........))).)))))))-)...(((((((....))))))). ( -36.10)
>DroSec_CAF1 35164 115 - 1
UUUGGCUUGUUUUGGGACAGUUUACCAGAACUCGCAGAACUCCCUUCCCCCGAAAAGGG-AGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUU-UUCGGUGUUUGUGCGCAAACACU
....((..(((((((.........)))))))..)).((.(((((((........)))))-))((((((((.(((....-....))).)))))))-)))((((((((....)))))))) ( -35.90)
>DroEre_CAF1 23087 107 - 1
UUUGGCUUGUUUGAGGACAGUUUACCAGAA---------CUCCCUGCCCCCGAAAAGGG-AGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUUUUUCGGUGUUUGUGCGCAAACACA
.......((((((.(.((((..((((.(((---------((((((..........))))-))((((((((.(((....-....))).))))))))))))))).)))).).)))))).. ( -30.90)
>DroYak_CAF1 23841 107 - 1
CUUGGCUUGUUUUGGGACAGUUUACCAGAA---------CUCCCCUUCCCCGAAAAGGG-AGAAACUUUUUCGAUUAU-AUGCUUGUGAAAGUUUUUCGGUGUUUGUGCGCAAACACA
...((...(((((((.........))))))---------)...))....((.....))(-((((((((((.(((....-....))).))))))))))).(((((((....))))))). ( -31.30)
>DroMoj_CAF1 20548 96 - 1
-----------AUAGGAAAGGAAAUCAAAAAUAGAGGA-CGUUCCGU-ACCGAAAAGGGUAGAAACUUUUUCGAUUAU-AUGCUCGUAAAAGUU-UUCGAUGUUUGUCC--AG-----
-----------...(((......(((.........((.-....)).(-(((......))))(((((((((.(((....-....))).)))))))-)).))).....)))--..----- ( -19.40)
>consensus
UUUGGCUUGUUUUGGGACAGUUUACCAGAA_U____GA_CUCCCUUCCCCCGAAAAGGG_AGAAACUUUUUCGAUUAU_AUGCUUGUGAAAGUU_UUCGGUGUUUGUGCGCAAACACA
.......(((((..(.((((..((((........................((((((((.......))))))))........((((....)))).....)))).)))).)..))))).. (-14.99 = -15.82 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:27 2006