Locus 1535

Sequence ID	X_DroMel_CAF1
Location	4,444,808 – 4,444,998
Length	190
Max. P	0.966558

overview

Window 9

Location	4,444,808 – 4,444,928
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.28
Mean single sequence MFE	-38.77
Consensus MFE	-30.13
Energy contribution	-29.93
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.28
Structure conservation index	0.78
SVM decision value	1.40
SVM RNA-class probability	0.950366
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444808 120 + 22224390
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGGCAGAGUGGAAGGGGAACGGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAGCCC
((((....((((.(..(((.....)))...)...)))))))).....((((((((((.((((.....................))))...))))))).)))(((((....)))))..... ( -35.40)
>DroSec_CAF1 46453 113 + 1
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGG-AGGGUGGAAGGG------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCC
................(((.....))).(((...(((((((..(..((.(((((..(((((......-.)))))..))))------)))..)..)))))))(((((....)))))..))) ( -42.10)
>DroSim_CAF1 47648 113 + 1
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGG-AGGGUGGAAGGG------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCC
................(((.....))).(((...(((((((..(..((.(((((..(((((......-.)))))..))))------)))..)..)))))))(((((....)))))..))) ( -42.10)
>DroEre_CAF1 48275 109 + 1
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGG-AUG------GUGGAGGGGGAAGGAGAGGGUGCAGGUGGGGGACUAUCA----
.............(..(((.....)))..)....(((((((........((((((((..(((.....-.))------)..))))))))......)))))))(((((....))))).---- ( -35.44)
>DroYak_CAF1 47083 117 + 1
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGG-AGAACGAAAGGGGGUGGGGAACGAGAGGGUGCAGGUGGGGGACUACCAU--C
((((....((((.(..(((.....)))...)...)))))))).....((((((((((.(((...((.-....))...)))....(....)))))))).)))(((((....)))))..--. ( -38.80)
>consensus
CAGAAAGUUACAGCAGCGAUAAAUUCGAGGGAAAUGUAUCUGACGAUUGUCCCUCUCACCCGGAUGG_AGGGUGGAAGGGG___GGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCC
((((....((((.(..(((.....)))...)...)))))))).....((((((((((.(((................)))..........))))))).)))(((((....)))))..... (-30.13 = -29.93 +  -0.20)

alignment

secondary structure

dotplot

Window 0

Location	4,444,848 – 4,444,967
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.63
Mean single sequence MFE	-47.74
Consensus MFE	-33.33
Energy contribution	-33.13
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.63
Structure conservation index	0.70
SVM decision value	1.27
SVM RNA-class probability	0.938312
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444848 119 + 22224390
UGACGAUUGUCCCUCUCACCCGGAUGGCAGAGUGGAAGGGGAACGGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAGCCCAA-UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGA
((((.....(((((..(((.(........).)))..)))))...((((..(((..((.((.(((((....))))).))))..-)))..)))).....))))...(((((.....))))). ( -47.50)
>DroSec_CAF1 46493 112 + 1
UGACGAUUGUCCCUCUCACCCGGAUGG-AGGGUGGAAGGG------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA-UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGA
((((.....(((((..(((((......-.)))))..))))------)....((((((....((..(((.........)))..-.))...))))))..))))...(((((.....))))). ( -50.30)
>DroSim_CAF1 47688 112 + 1
UGACGAUUGUCCCUCUCACCCGGAUGG-AGGGUGGAAGGG------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA-UCCAAUCCCACCGAGUCACCCCAUCCGACAAGGAUGA
((((.....(((((..(((((......-.)))))..))))------)..(((..((((...(((((....))))).))))..-)))...........))))...(((((.....))))). ( -49.00)
>DroEre_CAF1 48315 107 + 1
UGACGAUUGUCCCUCUCACCCGGAUGG-AUG------GUGGAGGGGGAAGGAGAGGGUGCAGGUGGGGGACUAUCA------ACCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGA
((((......(((((.((((.......-..)------))))))))(((.(((..((((...(((((....))))).------))))..))).)))..))))...(((((.....))))). ( -48.40)
>DroYak_CAF1 47123 117 + 1
UGACGAUUGUCCCUCUCACCCGGAUGG-AGAACGAAAGGGGGUGGGGAACGAGAGGGUGCAGGUGGGGGACUACCAU--CAAUCCCAAUCCCACCAAGUCACCCCAUCCGACAAGGAUGA
((((...((((((((((.(((...((.-....))...)))....(....)))))))).)))(((((((((.......--...)))....))))))..))))...(((((.....))))). ( -43.50)
>consensus
UGACGAUUGUCCCUCUCACCCGGAUGG_AGGGUGGAAGGGG___GGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA_UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGA
((((...((((((((((.(((................)))..........))))))).)))(((((....)))))......................))))...(((((.....))))). (-33.33 = -33.13 +  -0.20)

alignment

secondary structure

dotplot

Window 1

Location	4,444,848 – 4,444,967
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.63
Mean single sequence MFE	-45.74
Consensus MFE	-34.30
Energy contribution	-35.22
Covariance contribution	0.92
Combinations/Pair	1.10
Mean z-score	-2.55
Structure conservation index	0.75
SVM decision value	1.60
SVM RNA-class probability	0.966558
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444848 119 - 22224390
UCAUCCUUGUCGGAUGGGGUGACUCGGAGGGAUUGGA-UUGGGCUGAUAGUCCCCCACCUGCACCCUCCCCUUCCCGUUCCCCUUCCACUCUGCCAUCCGGGUGAGAGGGACAAUCGUCA
......(((((((((((((......((((((...((.-..((((.....))))....))....))))))...)))))))).(((..(((((........)))))..))))))))...... ( -43.90)
>DroSec_CAF1 46493 112 - 1
UCAUCCUUGUCGGAUGGGGUGACUCGGAGGGAUUGGA-UUGGGUUGAUAGUCCCCCACCUGCACCCUCCCCUUU------CCCUUCCACCCU-CCAUCCGGGUGAGAGGGACAAUCGUCA
((((((.....))))))..((((..((((((...((.-..(((........)))...))....))))))....(------((((..(((((.-......)))))..))))).....)))) ( -45.80)
>DroSim_CAF1 47688 112 - 1
UCAUCCUUGUCGGAUGGGGUGACUCGGUGGGAUUGGA-UUGGGUUGAUAGUCCCCCACCUGCACCCUCCCCUUU------CCCUUCCACCCU-CCAUCCGGGUGAGAGGGACAAUCGUCA
.(((((.....)))))(((((....((((((...(((-(((......))))))))))))..))))).......(------((((..(((((.-......)))))..)))))......... ( -50.20)
>DroEre_CAF1 48315 107 - 1
UCAUCCUUGUCGGAUGGGGUGACUCGGAGGGAUUGGGU------UGAUAGUCCCCCACCUGCACCCUCUCCUUCCCCCUCCAC------CAU-CCAUCCGGGUGAGAGGGACAAUCGUCA
......((((((((.((((((....((.(((((((...------...))))))))).....)))))).))).....(((((((------(..-.......)))).)))))))))...... ( -43.40)
>DroYak_CAF1 47123 117 - 1
UCAUCCUUGUCGGAUGGGGUGACUUGGUGGGAUUGGGAUUG--AUGGUAGUCCCCCACCUGCACCCUCUCGUUCCCCACCCCCUUUCGUUCU-CCAUCCGGGUGAGAGGGACAAUCGUCA
.(((((.....)))))(((((....((((((....((((((--....))))))))))))..)))))..............((((((((..(.-......)..)))))))).......... ( -45.40)
>consensus
UCAUCCUUGUCGGAUGGGGUGACUCGGAGGGAUUGGA_UUGGGUUGAUAGUCCCCCACCUGCACCCUCCCCUUCCC___CCCCUUCCACCCU_CCAUCCGGGUGAGAGGGACAAUCGUCA
.(((((.....)))))(((((....((.(((((((............))))))))).....)))))..............(((((.(((((........))))).))))).......... (-34.30 = -35.22 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	4,444,888 – 4,444,998
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.29
Mean single sequence MFE	-46.42
Consensus MFE	-37.01
Energy contribution	-38.25
Covariance contribution	1.24
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.507365
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4444888 110 + 22224390
GAACGGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAGCCCAA-UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGCGCG---------
....(((..((((.((((((.((.((((((............-)))...))).))..).)))))(((((.....)))))...))))..))).((.((......)).))...--------- ( -42.90)
>DroSec_CAF1 46532 113 + 1
------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA-UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGCGCGGCACAAAAA
------...((((.((((((.((.((((((............-)))...))).))..).)))))(((((.....))))).))))((((((....)))))).((((......))))..... ( -44.80)
>DroSim_CAF1 47727 113 + 1
------AAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA-UCCAAUCCCACCGAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGCGCGGCACAAAAA
------...((((.((((((.(((((((((............-)))...))))))..).)))))(((((.....))))).))))((((((....)))))).((((......))))..... ( -48.80)
>DroEre_CAF1 48348 114 + 1
GAGGGGGAAGGAGAGGGUGCAGGUGGGGGACUAUCA------ACCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGCGUGGCACAAAAA
..((((((.(((..((((...(((((....))))).------))))..))).))).........(((((.....))))).))).((((((....)))))).((((......))))..... ( -48.60)
>DroYak_CAF1 47162 118 + 1
GGUGGGGAACGAGAGGGUGCAGGUGGGGGACUACCAU--CAAUCCCAAUCCCACCAAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGAGCGGCACAAAAA
...((((.......((((((.(((((((((.......--...)))....))))))..).)))))(((((.....))))).))))((((((....)))))).((((......))))..... ( -47.00)
>consensus
G___GGGAAGGGGAGGGUGCAGGUGGGGGACUAUCAACCCAA_UCCAAUCCCUCCGAGUCACCCCAUCCGACAAGGAUGACCCCCCGACCCUGCGGUUGGCGUGCGGCGCGGCACAAAAA
.........((((.(((((.(..(((((((..................)))).)))..))))))(((((.....))))).))))((((((....)))))).((((......))))..... (-37.01 = -38.25 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:43 2006