Locus 6011

Sequence ID	3L_DroMel_CAF1
Location	16,044,054 – 16,044,206
Length	152
Max. P	0.933344

overview

Window 2

Location	16,044,054 – 16,044,172
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	95.57
Mean single sequence MFE	-36.88
Consensus MFE	-35.51
Energy contribution	-35.53
Covariance contribution	0.03
Combinations/Pair	1.04
Mean z-score	-1.13
Structure conservation index	0.96
SVM decision value	1.23
SVM RNA-class probability	0.933344
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044054 118 + 23771897
UU--AUUUUUUUUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGA
..--..................((((((........))))))((((.((......))))))..((((((((.....(((((......)))))(((........)))...))))))))... ( -36.40)
>DroSec_CAF1 14471 116 + 1
UU--AUUUU--UUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUUUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGA
..--.....--.........((((((((........))))))))...(..(((....)))..)((((((((.....(((((......)))))(((........)))...))))))))... ( -35.60)
>DroAna_CAF1 10775 118 + 1
UUUUAUUUU--CUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGACCGUCUGCGAGCCGAGAAUCGGGCCCUCACCCGGGUCGUCUCGAAGCUGACCACCUCGGCUCAGA
.......((--((((.((..((((((((........))))))))))))))))...........((((((((...((((......))))(((((.(.....).)))))..))))))))... ( -38.50)
>DroSim_CAF1 11978 116 + 1
UU--AUUUU--UUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGA
..--.....--...........((((((........))))))((((.((......))))))..((((((((.....(((((......)))))(((........)))...))))))))... ( -36.40)
>DroEre_CAF1 14444 115 + 1
UU--AUUA---UUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUUACGCGGGUCGUCUCCAAGCUGACAACCUCGGCUCAGA
..--....---...........((((((........))))))((((.((......))))))..((((((((.....(((((......)))))(((........)))...))))))))... ( -37.30)
>DroYak_CAF1 36918 115 + 1
UU--AUUC---UUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUCACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGA
(.--.(((---((.((....((((((((........)))))))))).)))))..)........((((((((.....(((((......)))))(((........)))...))))))))... ( -37.10)
>consensus
UU__AUUUU__UUUGUGUGAUUUUAGCUAUUGCAGAAGCUAAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGA
......................((((((........))))))((((.((......))))))..((((((((.....(((((......)))))(((........)))...))))))))... (-35.51 = -35.53 +   0.03)

alignment

secondary structure

dotplot

Window 3

Location	16,044,054 – 16,044,172
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	95.57
Mean single sequence MFE	-34.67
Consensus MFE	-31.60
Energy contribution	-31.80
Covariance contribution	0.20
Combinations/Pair	1.03
Mean z-score	-1.02
Structure conservation index	0.91
SVM decision value	0.03
SVM RNA-class probability	0.550562
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044054 118 - 23771897
UCUGAGCCGAGGUGGUCAGCUUGGAGACGACCCGCGUUAGGGCCCGAUUCUCGGCUCGCAGACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAAAAAAAAU--AA
...(((((((((.((((.(((((....)))...)).....))))....)))))))))...(((((......)).)))(((((((........))))))).................--.. ( -33.90)
>DroSec_CAF1 14471 116 - 1
UCUGAGCCGAGGUGGUCAGCUUGGAGACGACCCGCGUUAGGGCCCGAUUCUCGGCUCGCAAACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAA--AAAAU--AA
...(((((((((.((((.(((((....)))...)).....))))....))))))))).................(..(((((((........)))))))..).......--.....--.. ( -32.50)
>DroAna_CAF1 10775 118 - 1
UCUGAGCCGAGGUGGUCAGCUUCGAGACGACCCGGGUGAGGGCCCGAUUCUCGGCUCGCAGACGGUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAG--AAAAUAAAA
.(((((.((((((.....)))))).(((((((.(..((.(((((........))))).))..)))))))))))))..(((((((........)))))))..........--......... ( -38.90)
>DroSim_CAF1 11978 116 - 1
UCUGAGCCGAGGUGGUCAGCUUGGAGACGACCCGCGUUAGGGCCCGAUUCUCGGCUCGCAGACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAA--AAAAU--AA
...(((((((((.((((.(((((....)))...)).....))))....)))))))))...(((((......)).)))(((((((........)))))))..........--.....--.. ( -33.90)
>DroEre_CAF1 14444 115 - 1
UCUGAGCCGAGGUUGUCAGCUUGGAGACGACCCGCGUAAGGGCCCGAUUCUCGGCUCGCAGACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAA---UAAU--AA
.(((((....(((((((((((.((((.((.(((......)))..)).)))).))))....)))))))...)))))..(((((((........)))))))..........---....--.. ( -34.20)
>DroYak_CAF1 36918 115 - 1
UCUGAGCCGAGGUGGUCAGCUUGGAGACGACCCGCGUGAGGGCCCGAUUCUCGGCUCGCAGACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAA---GAAU--AA
((((((((((((.((((...(((....)))....(....)))))....)))))))))...(((((......)).)))(((((((........))))))).........)---))..--.. ( -34.60)
>consensus
UCUGAGCCGAGGUGGUCAGCUUGGAGACGACCCGCGUUAGGGCCCGAUUCUCGGCUCGCAGACGAUCGUUCUCAGUCUUUAGCUUCUGCAAUAGCUAAAAUCACACAAA__AAAAU__AA
...(((((((((..(((...(((....)))(((......)))...))))))))))))...(((((......)).)))(((((((........)))))))..................... (-31.60 = -31.80 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	16,044,092 – 16,044,206
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.13
Mean single sequence MFE	-40.21
Consensus MFE	-36.26
Energy contribution	-36.32
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-1.28
Structure conservation index	0.90
SVM decision value	0.47
SVM RNA-class probability	0.748090
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16044092 114 + 23771897
AAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGAGCAAAUAG------GCGCAGAUCAG
.....((((((....)).(((((((((((((.....(((((......)))))(((........)))...)))))))).......(((.((.....)).....)------))))))))))) ( -40.80)
>DroSec_CAF1 14507 114 + 1
AAAGACUGAGAACGAUCGUUUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAG------GCGCAGAUCAG
...(((((..(((....)))..)((((((((.....(((((......)))))(((........)))...))))))))..))))..((((((...........)------)).)))..... ( -40.00)
>DroAna_CAF1 10813 120 + 1
AAAGACUGAGAACGACCGUCUGCGAGCCGAGAAUCGGGCCCUCACCCGGGUCGUCUCGAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAGAUCAGAGCUGAGACCCC
.....((((........((((..((((((((...((((......))))(((((.(.....).)))))..)))))))).(.(((....)))).))))........))))............ ( -38.79)
>DroSim_CAF1 12014 114 + 1
AAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAG------GCGCAGAUCAG
.....((((((....)).(((((((((((((.....(((((......)))))(((........)))...))))))))...((((..(((......)))..).)------))))))))))) ( -41.00)
>DroEre_CAF1 14479 113 + 1
AAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUUACGCGGGUCGUCUCCAAGCUGACAACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAG------GCGCAGAUCA-
.................((((((((((((((.....(((((......)))))(((........)))...))))))))...((((..(((......)))..).)------))))))))..- ( -40.80)
>DroYak_CAF1 36953 113 + 1
AAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUCACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAG------GCGCAGAUCA-
.................((((((((((((((.....(((((......)))))(((........)))...))))))))...((((..(((......)))..).)------))))))))..- ( -39.90)
>consensus
AAAGACUGAGAACGAUCGUCUGCGAGCCGAGAAUCGGGCCCUAACGCGGGUCGUCUCCAAGCUGACCACCUCGGCUCAGAGUCAGCUGGCCAAGACCAAAUAG______GCGCAGAUCAG
.................((((((((((((((.....(((((......)))))(((........)))...)))))))).(.(((....))))....................))))))... (-36.26 = -36.32 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:42 2006