Locus 4417

Sequence ID	X_DroMel_CAF1
Location	11,652,870 – 11,653,003
Length	133
Max. P	0.989340

overview

Window 7

Location	11,652,870 – 11,652,976
Length	106
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	96.44
Mean single sequence MFE	-23.81
Consensus MFE	-20.83
Energy contribution	-21.43
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.87
SVM decision value	1.35
SVM RNA-class probability	0.945536
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11652870 106 + 22224390
UUGCCUCUUUGUUUUCCAGCUGAAUUCGAGGGCAAAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
.(((((..(((..(((.....)))..))))))))(((((((((.((((.....))))))((((.(((...((--(((.......))))).))).))))...))))))) ( -27.40)
>DroSec_CAF1 26191 106 + 1
UUGCCUCUUUGUUUUCCAGCUGAAUUCGAGGGCAAAAGCAAGAACAGCAAAAUGAUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
((((((..(((..(((.....)))..)))))))))..((.......))((((..((...((((.(((...((--(((.......))))).))).))))..))..)))) ( -21.00)
>DroSim_CAF1 22276 106 + 1
UUGCCUCUUUGUUUUCCAGCUGAAUUCGAGGGCAAAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
.(((((..(((..(((.....)))..))))))))(((((((((.((((.....))))))((((.(((...((--(((.......))))).))).))))...))))))) ( -27.40)
>DroEre_CAF1 28371 108 + 1
UUGCCUCUUUGUUUUCAAGCUGUAUUCGAGGGCAAAAGCAACAACAGCAAAAUGCUGUCGUGUAAUCAAAAAAAAAAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
.(((((((.((((((...(((.(.....).)))....(((...(((((.....)))))..))).................))))))...))).))))........... ( -20.80)
>DroYak_CAF1 25655 106 + 1
UUGCCUCUUUGUUUUCCAGCUGUAUUCGAGGGCAAAAGCAACAACAGCAAAAUGCUGUCGUGUAAUCAAAAA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
.((((.(((..................)))))))(((((((..(((((.....))))).((((.(((...((--(((.......))))).))).))))...))))))) ( -22.47)
>consensus
UUGCCUCUUUGUUUUCCAGCUGAAUUCGAGGGCAAAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA__AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUU
.(((((..(((..(((.....)))..))))))))(((((((..(((((.....))))).((((..(((((................)))))...))))...))))))) (-20.83 = -21.43 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	11,652,870 – 11,652,976
Length	106
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	96.44
Mean single sequence MFE	-21.68
Consensus MFE	-18.98
Energy contribution	-18.94
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.37
Structure conservation index	0.88
SVM decision value	0.35
SVM RNA-class probability	0.699045
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11652870 106 - 22224390
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUAU--UCUUUGAUUACACGACAGCAUUUUGCUGUUCUUGCUUUUGCCCUCGAAUUCAGCUGGAAAACAAAGAGGCAA
...........((((...((((....))))....--((((((........(((((.....)))))(((.(((((((....))))...))).)))...)))))))))). ( -22.50)
>DroSec_CAF1 26191 106 - 1
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUAU--UCUUUGAUUACACGACAUCAUUUUGCUGUUCUUGCUUUUGCCCUCGAAUUCAGCUGGAAAACAAAGAGGCAA
...........((((...((((....))))....--((((((.......(....).((..(((((((..((....))....)))..))))..))...)))))))))). ( -17.40)
>DroSim_CAF1 22276 106 - 1
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUAU--UCUUUGAUUACACGACAGCAUUUUGCUGUUCUUGCUUUUGCCCUCGAAUUCAGCUGGAAAACAAAGAGGCAA
...........((((...((((....))))....--((((((........(((((.....)))))(((.(((((((....))))...))).)))...)))))))))). ( -22.50)
>DroEre_CAF1 28371 108 - 1
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUUUUUUUUUUGAUUACACGACAGCAUUUUGCUGUUGUUGCUUUUGCCCUCGAAUACAGCUUGAAAACAAAGAGGCAA
...........((((.........(((((((((((...(((((....((((((((.....)))))))).((....))..)))))........))))))))))))))). ( -23.90)
>DroYak_CAF1 25655 106 - 1
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUAU--UUUUUGAUUACACGACAGCAUUUUGCUGUUGUUGCUUUUGCCCUCGAAUACAGCUGGAAAACAAAGAGGCAA
...........((((...((((....))))....--((((((.......((((((.....))))))((((..((((....))))..)))).......)))))))))). ( -22.10)
>consensus
AAAACAAUUUGUGCCAUCCAAAUAUUUUUGUUAU__UCUUUGAUUACACGACAGCAUUUUGCUGUUCUUGCUUUUGCCCUCGAAUUCAGCUGGAAAACAAAGAGGCAA
...........((((...((((....))))......((((((.......((((((.....))))))...(((((((....))))...))).......)))))))))). (-18.98 = -18.94 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	11,652,904 – 11,653,003
Length	99
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	96.19
Mean single sequence MFE	-18.32
Consensus MFE	-15.70
Energy contribution	-15.90
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.20
Structure conservation index	0.86
SVM decision value	2.16
SVM RNA-class probability	0.989340
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11652904 99 + 22224390
AAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCGUUUACAAAAUUUAAAACGCA
(((((((((.((((.....))))))((((.(((...((--(((.......))))).))).))))...))))))).....(((((..........))))).. ( -19.90)
>DroSec_CAF1 26225 99 + 1
AAAGCAAGAACAGCAAAAUGAUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCAUUUACAAAAUUUAAAACGCA
.((((.(((((((((......))).((((.(((...((--(((.......))))).))).))))....)))))).))))...................... ( -16.00)
>DroSim_CAF1 22310 98 + 1
AAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCAUUUACAA-AUUUAAAACGCA
...((..((.((((.....))))))((((.(((...((--(((.......))))).))).)))).....(((((((.((........)-).))))))))). ( -19.10)
>DroEre_CAF1 28405 101 + 1
AAAGCAACAACAGCAAAAUGCUGUCGUGUAAUCAAAAAAAAAAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCGUUUACAAAAUUUAAAACGCA
...((.((.(((((.....))))).))((((.(...........((((....))))((.(((.((((....)))))))))).))))............)). ( -18.50)
>DroYak_CAF1 25689 99 + 1
AAAGCAACAACAGCAAAAUGCUGUCGUGUAAUCAAAAA--AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCAUUUACAAAAUUUAAAACGCA
...((....(((((.....))))).((((.(((...((--(((.......))))).))).)))).....((((((..........)))))).......)). ( -18.10)
>consensus
AAAGCAAGAACAGCAAAAUGCUGUCGUGUAAUCAAAGA__AUAACAAAAAUAUUUGGAUGGCACAAAUUGUUUUGGCUUCAUUUACAAAAUUUAAAACGCA
...((....(((((.....)))))..(((((.............((((....))))((.(((.((((....)))))))))..)))))...........)). (-15.70 = -15.90 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:32 2006