Locus 2352

Sequence ID	2R_DroMel_CAF1
Location	8,560,061 – 8,560,229
Length	168
Max. P	0.995106

overview

Window 4

Location	8,560,061 – 8,560,179
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	98.31
Mean single sequence MFE	-30.42
Consensus MFE	-29.70
Energy contribution	-29.94
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.98
SVM decision value	1.07
SVM RNA-class probability	0.910994
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8560061 118 - 20766785
CGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGAGCUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCCAAAA
...(((((.(((((....((((.....))))..((..((((....))))..)).)))))..........(((((((..(((((......)))))..))).))))......)))))... ( -32.40)
>DroSec_CAF1 35803 118 - 1
CGAUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGAGCUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCCAAAA
...(((((.(((((....((((.....))))..((..((((....))))..)).)))))..........(((((((..(((((......)))))..))).))))......)))))... ( -32.50)
>DroSim_CAF1 39096 118 - 1
CGGUGGCCAGAAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGAGCUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCCAAAA
...(((((.....................(((((...((((....)))).....)))))..........(((((((..(((((......)))))..))).))))......)))))... ( -29.00)
>DroEre_CAF1 24539 118 - 1
CGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGAGUUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCGAAAA
.....(((.(((((....((((.....))))..((..((((....))))..)).)))))..........(((((((..(((((......)))))..))).))))......)))..... ( -25.80)
>DroYak_CAF1 39083 118 - 1
CGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGGGCUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCCAAAA
...(((((.(((((....((((.....))))..((..((((....))))..)).)))))..........(((((((..(((((......)))))..))).))))......)))))... ( -32.40)
>consensus
CGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUGGCAAACCAAUCUGAGCUGUGAUUAUUUUAGCUGGCAGGUGGAAAAAGCAUUUCAAAUGUGCAGCGGACAAGGCCAAAA
...(((((.(((((....((((.....))))..((..((((....))))..)).)))))..........(((((((..(((((......)))))..))).))))......)))))... (-29.70 = -29.94 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	8,560,139 – 8,560,229
Length	90
Sequences	5
Columns	91
Reading direction	forward
Mean pairwise identity	80.09
Mean single sequence MFE	-21.76
Consensus MFE	-10.88
Energy contribution	-14.00
Covariance contribution	3.12
Combinations/Pair	1.11
Mean z-score	-2.60
Structure conservation index	0.50
SVM decision value	1.45
SVM RNA-class probability	0.955393
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8560139 90 + 20766785
CAAAUUGCUAUUUAUUAAAAAUCAAUGCUGCUGGCCACCGCCGGCCAACGUAAUCGCAA-UGGACGGCGACAACGCCAGCAACAGCAAAUC
....(((((((((.....))))....(.(((((((...(((((.(((.((....))...-))).))))).....))))))).))))))... ( -27.70)
>DroSec_CAF1 35881 90 + 1
CAAAUUGCUAUUUAUUAAAAAUCAAUGCUGCUGGCCAUCGCCGACCAACGUAAUCGCAA-UGGACGGCGACAACGCCAGCAACAGCAAAUC
....(((((((((.....))))....(.(((((((..((((((.(((.((....))...-))).))))))....))))))).))))))... ( -29.30)
>DroSim_CAF1 39174 90 + 1
CAAAUUGCUAUUUAUUAAAAAUCAAUGCUUCUGGCCACCGCCGACCAACGUAAUCGCAA-UGGACGGCGACAACGCCAGCAACAGCAAAUC
.........................((((.(((((...(((((.(((.((....))...-))).))))).....)))))....)))).... ( -22.80)
>DroEre_CAF1 24617 88 + 1
CAAAUUGCUAUUUAUUAAAAAUCAAUGCUGCUGGCCACCGA---GCGACGUGAUCGCAAAAGGACGACGACAACGCCAGCAACAGCAAAUC
....(((((((((.....))))....(.(((((((......---((((.....))))....(.....)......))))))).))))))... ( -19.40)
>DroWil_CAF1 3973 79 + 1
CAAAUGGCAAUUUAUUAAAAAUCAAUGCCUGUCGUU----CCAACACACAAAACAGG-A-UG--UGAAGAGAA---UA-GAACAGAAAAUC
..........((((((.....(((...(((((.((.----.......))...)))))-.-..--)))....))---))-)).......... (  -9.60)
>consensus
CAAAUUGCUAUUUAUUAAAAAUCAAUGCUGCUGGCCACCGCCGACCAACGUAAUCGCAA_UGGACGGCGACAACGCCAGCAACAGCAAAUC
.........................((.(((((((...(((((.(((.((....))....))).))))).....))))))).))....... (-10.88 = -14.00 +   3.12)

alignment

secondary structure

dotplot

Window 6

Location	8,560,139 – 8,560,229
Length	90
Sequences	5
Columns	91
Reading direction	reverse
Mean pairwise identity	80.09
Mean single sequence MFE	-29.68
Consensus MFE	-17.92
Energy contribution	-21.48
Covariance contribution	3.56
Combinations/Pair	1.13
Mean z-score	-3.01
Structure conservation index	0.60
SVM decision value	2.54
SVM RNA-class probability	0.995106
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8560139 90 - 20766785
GAUUUGCUGUUGCUGGCGUUGUCGCCGUCCA-UUGCGAUUACGUUGGCCGGCGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUG
...((((((((((((((..(..(((((.(((-..(((....)))))).)))))..))))))))))....((((.....))))))))).... ( -36.50)
>DroSec_CAF1 35881 90 - 1
GAUUUGCUGUUGCUGGCGUUGUCGCCGUCCA-UUGCGAUUACGUUGGUCGGCGAUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUG
...((((((((((((((...(((((((.(((-..(((....)))))).))))))).)))))))))....((((.....))))))))).... ( -39.10)
>DroSim_CAF1 39174 90 - 1
GAUUUGCUGUUGCUGGCGUUGUCGCCGUCCA-UUGCGAUUACGUUGGUCGGCGGUGGCCAGAAGCAUUGAUUUUUAAUAAAUAGCAAUUUG
...(((((((((((.(.((..((((((.(((-..(((....)))))).))))))..)))...)))(((((...))))).)))))))).... ( -32.80)
>DroEre_CAF1 24617 88 - 1
GAUUUGCUGUUGCUGGCGUUGUCGUCGUCCUUUUGCGAUCACGUCGC---UCGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUG
...((((((((((((((...((.(((((......))))).))..(((---...))))))))))))....((((.....))))))))).... ( -26.70)
>DroWil_CAF1 3973 79 - 1
GAUUUUCUGUUC-UA---UUCUCUUCA--CA-U-CCUGUUUUGUGUGUUGG----AACGACAGGCAUUGAUUUUUAAUAAAUUGCCAUUUG
.......(((((-((---....(..((--((-.-.......)))).).)))----))))...((((................))))..... ( -13.29)
>consensus
GAUUUGCUGUUGCUGGCGUUGUCGCCGUCCA_UUGCGAUUACGUUGGUCGGCGGUGGCCAGCAGCAUUGAUUUUUAAUAAAUAGCAAUUUG
...((((((((((((((....((((((.(((...(((....)))))).))))))..))))))))))...((((.....)))).)))).... (-17.92 = -21.48 +   3.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:48 2006