Locus 5468

Sequence ID	X_DroMel_CAF1
Location	14,211,180 – 14,211,320
Length	140
Max. P	0.986506

overview

Window 8

Location	14,211,180 – 14,211,287
Length	107
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	87.31
Mean single sequence MFE	-35.54
Consensus MFE	-25.92
Energy contribution	-27.36
Covariance contribution	1.44
Combinations/Pair	1.11
Mean z-score	-2.32
Structure conservation index	0.73
SVM decision value	0.98
SVM RNA-class probability	0.894735
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14211180 107 + 22224390
UGAGCCUGGAGUC--UUC--UCCUCUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUUUUGGCCCAUUC
((((((.((((..--..)--)))....))))))..(.(((......))).).........((((((((((..((((.((.((....)).)).))))))))))))))..... ( -40.50)
>DroSec_CAF1 122356 109 + 1
UGAGCCUGGUGGUGUCUC--UCCUCUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCGCAUCCUCCAUUUUGGCCCAUUC
((((((.((.((......--.)).)).))))))..(.(((......))).).........((((((((((..((((.((.((....)).)).))))))))))))))..... ( -39.30)
>DroSim_CAF1 98518 109 + 1
UGAGCCUGGUGGUGUCUC--UCCUCUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCGCAUCCUCCAUUUUGGCCCAUUC
((((((.((.((......--.)).)).))))))..(.(((......))).).........((((((((((..((((.((.((....)).)).))))))))))))))..... ( -39.30)
>DroEre_CAF1 110031 96 + 1
------------UGUCUC--UUCUCUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUUUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUU-UGGACCAUUC
------------......--......(((..((((((..(((((((((.(((.....))).))...))))))).(((((.....))))).......))))-))..)))... ( -24.80)
>DroYak_CAF1 112261 108 + 1
UGGGUUUCA---UGUCUCUCCUUUUUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUUUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUGCAUUUUGGCCCAUUC
(((((((((---.(((((.....((((((((.((((((((......))).....))))).))))))))....))))))))..(((((......)))))....))))))... ( -33.80)
>consensus
UGAGCCUGG_G_UGUCUC__UCCUCUUGGCUUAAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUUUUGGCCCAUUC
((((((.....................))))))..(.(((......))).).........((((((((((..((((.((.((....)).)).))))))))))))))..... (-25.92 = -27.36 +   1.44)

alignment

secondary structure

dotplot

Window 9

Location	14,211,180 – 14,211,287
Length	107
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	87.31
Mean single sequence MFE	-35.36
Consensus MFE	-28.78
Energy contribution	-29.78
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.44
Structure conservation index	0.81
SVM decision value	2.04
SVM RNA-class probability	0.986506
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14211180 107 - 22224390
GAAUGGGCCAAAAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAGAGGA--GAA--GACUCCAGGCUCA
(((((((((((((((((((.(((((....))))).))))..))))))))))...........((((....))))))))).((((....(((--(..--..)))).)))).. ( -42.20)
>DroSec_CAF1 122356 109 - 1
GAAUGGGCCAAAAUGGAGGAUGCGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAGAGGA--GAGACACCACCAGGCUCA
(((((((((((((((((((.((.((....)).)).))))..))))))))))...........((((....))))))))).((((..(.((.--......)).)..)))).. ( -35.50)
>DroSim_CAF1 98518 109 - 1
GAAUGGGCCAAAAUGGAGGAUGCGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAGAGGA--GAGACACCACCAGGCUCA
(((((((((((((((((((.((.((....)).)).))))..))))))))))...........((((....))))))))).((((..(.((.--......)).)..)))).. ( -35.50)
>DroEre_CAF1 110031 96 - 1
GAAUGGUCCA-AAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAAAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAGAGAA--GAGACA------------
...((((..(-((((((((.(((((....))))).))))((((((...((.(((.....))).))))))))...)))))..))))......--......------------ ( -28.70)
>DroYak_CAF1 112261 108 - 1
GAAUGGGCCAAAAUGCAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAAAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAAAAAGGAGAGACA---UGAAACCCA
..(((((((((((((((((.(((((....))))).)))..))))))))))).......((((((((....))).........((......)))))))))---)........ ( -34.90)
>consensus
GAAUGGGCCAAAAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUUAAGCCAAGAGGA__GAGACA_C_CCAGGCUCA
(((((((((((((((((((.(((((....))))).))))..))))))))))...........((((....)))))))))................................ (-28.78 = -29.78 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	14,211,208 – 14,211,320
Length	112
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.12
Mean single sequence MFE	-33.30
Consensus MFE	-19.44
Energy contribution	-22.32
Covariance contribution	2.88
Combinations/Pair	1.10
Mean z-score	-2.03
Structure conservation index	0.58
SVM decision value	0.91
SVM RNA-class probability	0.880595
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14211208 112 + 22224390
AAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUUUUGGCCCAUUCACCUU--UUUGCCGGUCAGU--UUGGCAGUUG---GUAAU
...(.(((......))).).........((((((((((..((((.((.((....)).)).)))))))))))))).....(((..--.(((((((.....--)))))))..)---))... ( -38.50)
>DroSec_CAF1 122386 89 + 1
AAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCGCAUCCUCCAUUUUGGCCCAUUCACC---------------------------UG---GUAAU
...(.(((......))).).........((((((((((..((((.((.((....)).)).))))))))))))))........---------------------------..---..... ( -27.70)
>DroSim_CAF1 98548 112 + 1
AAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCGCAUCCUCCAUUUUGGCCCAUUCACCUU--UUUGCCGGUCAGU--UUGGCAGUUG---GUAAU
...(.(((......))).).........((((((((((..((((.((.((....)).)).)))))))))))))).....(((..--.(((((((.....--)))))))..)---))... ( -38.90)
>DroEre_CAF1 110049 111 + 1
AAAUGUGCAGCAUUGCAGAAAAUAUUUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUU-UGGACCAUUCACCUU--UUUGCCGGUCAGU--UUGGCAGUUG---GUAAU
......((((((((......)))...((((((..........)))))))))))((.(((.........-))).))....(((..--.(((((((.....--)))))))..)---))... ( -32.80)
>DroYak_CAF1 112290 112 + 1
AAAUGUGCAGCAUUGCAGAAAAUAUUUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUGCAUUUUGGCCCAUUCACCUU--UUUGCCGGUCACU--UUGGCAGUUG---GUAAU
...(.(((......))).).........(((((((((((.(((((((.....)))))..))..))))))))))).....(((..--.(((((((.....--)))))))..)---))... ( -40.30)
>DroAna_CAF1 122419 101 + 1
AAAUGUGCAACAUUGCAGAAUAUAUUUCAAC----AUCAU---------C-CCCGCCCGGCCUCA----GACCUUAUUCACCUGACUCGGCUGGUCAGUUUUUGGCAGUUGAUGAUAAU
.....((((....))))(((.....)))...----(((((---------(-...(.(((((((((----(...........))))...)))))).).((.....))....))))))... ( -21.60)
>consensus
AAAUGUGCAGCAUUGCAGAAAAUAUAUCGGCCAAAAUGCUGAGGCUGAGCUGCGGCCCAUCCUCCAUUUUGGCCCAUUCACCUU__UUUGCCGGUCAGU__UUGGCAGUUG___GUAAU
...(.(((......))).).........((((((((((..((((.((.((....)).)).)))))))))))))).............(((((((.......)))))))........... (-19.44 = -22.32 +   2.88)

alignment

secondary structure

dotplot

Window 1

Location	14,211,208 – 14,211,320
Length	112
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	78.12
Mean single sequence MFE	-34.75
Consensus MFE	-19.00
Energy contribution	-21.58
Covariance contribution	2.59
Combinations/Pair	1.10
Mean z-score	-2.52
Structure conservation index	0.55
SVM decision value	1.46
SVM RNA-class probability	0.955951
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14211208 112 - 22224390
AUUAC---CAACUGCCAA--ACUGACCGGCAAA--AAGGUGAAUGGGCCAAAAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUU
.((((---(...((((..--.......))))..--..)))))((.((((((((((((((.(((((....))))).))))..)))))))))).))........((((....))))..... ( -40.50)
>DroSec_CAF1 122386 89 - 1
AUUAC---CA---------------------------GGUGAAUGGGCCAAAAUGGAGGAUGCGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUU
.....---..---------------------------...(((((((((((((((((((.((.((....)).)).))))..))))))))))...........((((....))))))))) ( -29.40)
>DroSim_CAF1 98548 112 - 1
AUUAC---CAACUGCCAA--ACUGACCGGCAAA--AAGGUGAAUGGGCCAAAAUGGAGGAUGCGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAUAUAUUUUCUGCAAUGCUGCACAUUU
.((((---(...((((..--.......))))..--..)))))((.((((((((((((((.((.((....)).)).))))..)))))))))).))........((((....))))..... ( -36.90)
>DroEre_CAF1 110049 111 - 1
AUUAC---CAACUGCCAA--ACUGACCGGCAAA--AAGGUGAAUGGUCCA-AAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAAAUAUUUUCUGCAAUGCUGCACAUUU
.((((---(...((((..--.......))))..--..))))).(((((.(-((((((((.(((((....))))).))))..))))).)))))..........((((....))))..... ( -33.10)
>DroYak_CAF1 112290 112 - 1
AUUAC---CAACUGCCAA--AGUGACCGGCAAA--AAGGUGAAUGGGCCAAAAUGCAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAAAUAUUUUCUGCAAUGCUGCACAUUU
.((((---(...((((..--.......))))..--..)))))(((((((((((((((((.(((((....))))).)))..)))))))))))...........((((....))))))).. ( -40.40)
>DroAna_CAF1 122419 101 - 1
AUUAUCAUCAACUGCCAAAAACUGACCAGCCGAGUCAGGUGAAUAAGGUC----UGAGGCCGGGCGGG-G---------AUGAU----GUUGAAAUAUAUUCUGCAAUGUUGCACAUUU
..(((((((..(((((.....((((((....).)))))........(((.----....))).))))).-)---------)))))----).............((((....))))..... ( -28.20)
>consensus
AUUAC___CAACUGCCAA__ACUGACCGGCAAA__AAGGUGAAUGGGCCAAAAUGGAGGAUGGGCCGCAGCUCAGCCUCAGCAUUUUGGCCGAAAUAUUUUCUGCAAUGCUGCACAUUU
............((((...........)))).........(((((((((((((((((((.((.((....)).)).))))..))))))))))...........((((....))))))))) (-19.00 = -21.58 +   2.59)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:40 2006