Locus 6863

Sequence ID	X_DroMel_CAF1
Location	17,121,588 – 17,121,727
Length	139
Max. P	0.986737

overview

Window 2

Location	17,121,588 – 17,121,696
Length	108
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	72.61
Mean single sequence MFE	-20.25
Consensus MFE	-13.71
Energy contribution	-13.03
Covariance contribution	-0.69
Combinations/Pair	1.41
Mean z-score	-1.97
Structure conservation index	0.68
SVM decision value	2.05
SVM RNA-class probability	0.986737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17121588 108 + 22224390
AUUAUAUUCUUAUAU-UCUUCUUGUGAUAAAUGGUCUUGCGAGCUAAAAAUUCCCGGUUUUUAUGGCUUGCACUUCUUGUGCAAAGCCGAUUGAUAAACAUAUAUAUUU
..(((((..((((..-((..((((((((.....)))..))))).(((((((.....))))))).(((((((((.....)))).)))))))...))))..)))))..... ( -21.40)
>DroSec_CAF1 3976 107 + 1
AUUAUAUUCUUAUAUAUAUUCUUGUGAUAAAUGGUCUUAAGAGUUAAAAAUUC--UAUUUUUAUGGCGUGUACUUCCUGUGCAAAGCUGAUUGAUAAGCAUAUAUAUUU
..(((((.(((((....(((((((.(((.....))).))))))).........--.........(((.(((((.....)))))..))).....))))).)))))..... ( -18.90)
>DroEre_CAF1 3798 94 + 1
----------U---U-CAUUCUUUUGAUAAAUGCUCUUGCGAGUCAAAAAUUCUCAGUUUUGAUAGCUUGCACUUCCUGUGCAGAGCUGAUUGAUAAA-AAAUAUCGUU
----------.---(-((......))).....((((..((..(((((((........))))))).)).(((((.....))))))))).....((((..-...))))... ( -20.40)
>DroYak_CAF1 3985 85 + 1
CU--------U---U-CCUUCUUUUGAUAA-----------AGUUAAAAACUCUCAGUUUUUAUGGCUUGCACUUCCUGUGCAGAGCCAAUUGAUAAA-AAAUAUCUUU
..--------.---.-.........((((.-----------...(((((((.....)))))))((((((((((.....))))).))))).........-...))))... ( -20.30)
>consensus
AU________U___U_CAUUCUUGUGAUAAAUGGUCUUGCGAGUUAAAAAUUCUCAGUUUUUAUGGCUUGCACUUCCUGUGCAAAGCCGAUUGAUAAA_AAAUAUAUUU
............................................(((((((.....)))))))((((((((((.....)))).)))))).................... (-13.71 = -13.03 +  -0.69)

alignment

secondary structure

dotplot

Window 3

Location	17,121,588 – 17,121,696
Length	108
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	72.61
Mean single sequence MFE	-18.38
Consensus MFE	-9.36
Energy contribution	-10.30
Covariance contribution	0.94
Combinations/Pair	1.17
Mean z-score	-1.99
Structure conservation index	0.51
SVM decision value	0.56
SVM RNA-class probability	0.781220
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17121588 108 - 22224390
AAAUAUAUAUGUUUAUCAAUCGGCUUUGCACAAGAAGUGCAAGCCAUAAAAACCGGGAAUUUUUAGCUCGCAAGACCAUUUAUCACAAGAAGA-AUAUAAGAAUAUAAU
.......(((((((.((....(((((.((((.....)))))))))....................(.((....)).)...........)).))-))))).......... ( -22.00)
>DroSec_CAF1 3976 107 - 1
AAAUAUAUAUGCUUAUCAAUCAGCUUUGCACAGGAAGUACACGCCAUAAAAAUA--GAAUUUUUAACUCUUAAGACCAUUUAUCACAAGAAUAUAUAUAAGAAUAUAAU
..((((((((.(((........(((((......)))))........(((((((.--..))))))).....................))).))))))))........... (  -9.20)
>DroEre_CAF1 3798 94 - 1
AACGAUAUUU-UUUAUCAAUCAGCUCUGCACAGGAAGUGCAAGCUAUCAAAACUGAGAAUUUUUGACUCGCAAGAGCAUUUAUCAAAAGAAUG-A---A----------
...((((...-..))))....((((.(((((.....))))))))).((((((........))))))(((....)))(((((.......)))))-.---.---------- ( -21.60)
>DroYak_CAF1 3985 85 - 1
AAAGAUAUUU-UUUAUCAAUUGGCUCUGCACAGGAAGUGCAAGCCAUAAAAACUGAGAGUUUUUAACU-----------UUAUCAAAAGAAGG-A---A--------AG
...((((...-..))))...(((((.(((((.....))))))))))(((((((.....))))))).((-----------((.......)))).-.---.--------.. ( -20.70)
>consensus
AAAGAUAUAU_UUUAUCAAUCAGCUCUGCACAGGAAGUGCAAGCCAUAAAAACUGAGAAUUUUUAACUCGCAAGACCAUUUAUCAAAAGAAGA_A___A________AU
...............((....((((.(((((.....))))))))).(((((((.....))))))).......................))................... ( -9.36 = -10.30 +   0.94)

alignment

secondary structure

dotplot

Window 4

Location	17,121,616 – 17,121,727
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.71
Mean single sequence MFE	-23.73
Consensus MFE	-15.92
Energy contribution	-15.28
Covariance contribution	-0.64
Combinations/Pair	1.32
Mean z-score	-1.63
Structure conservation index	0.67
SVM decision value	0.29
SVM RNA-class probability	0.671389
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17121616 111 + 22224390
AAUGGUCUUGCGAGCUAAAAAUUCCCGGUUUUUAUGGCUUGCACUUCUUGUGCAAAGCCGAUUGAUAAACAUAUAUAUUUAUAAUU---------GCUUUAAUUAUGCUAUAUAAGUGGC
...((((........(((((((.....))))))).(((((((((.....)))).)))))))))......(((.(((((.(((((((---------(...))))))))..))))).))).. ( -23.60)
>DroSec_CAF1 4005 107 + 1
AAUGGUCUUAAGAGUUAAAAAUUC--UAUUUUUAUGGCGUGUACUUCCUGUGCAAAGCUGAUUGAUAAGCAUAUAUAUUUAUAAUU---------GCUUUAAUUAUGCUA--UAAAUGGC
....(((...(((((.....))))--)...((((((((((((((.....)))))....(((((((..((((((((....))))..)---------)))))))))))))))--)))).))) ( -21.20)
>DroSim_CAF1 3981 109 + 1
UAUCGUCUAAAGAGUUAAAAAUUCUCUGUUUUUAUGGCUUGCACUUCCUGUGCAAAGCUGAUUGAUAAGCAUAUAUAUUUAUAAUU---------GCUUUAAUUAUGCUA--UAAAUGGC
....(((...((((.........))))...((((((((((((((.....))))))...(((((((..((((((((....))))..)---------)))))))))).))))--)))).))) ( -24.20)
>DroEre_CAF1 3813 117 + 1
AAUGCUCUUGCGAGUCAAAAAUUCUCAGUUUUGAUAGCUUGCACUUCCUGUGCAGAGCUGAUUGAUAAA-AAAUAUCGUUAUAAUUCUAAGAAGUGCUUUGCUUAUGCUA--UAAAUGGC
...((....(((((.((....((((.((..(((.((((((((((.....))))).)))))...((((..-...))))....)))..)).)))).)).)))))....))..--........ ( -26.30)
>DroYak_CAF1 4002 106 + 1
A-----------AGUUAAAAACUCUCAGUUUUUAUGGCUUGCACUUCCUGUGCAGAGCCAAUUGAUAAA-AAAUAUCUUUACAAUUGCAAGAACUGCUUUACUUAUGCUA--UAAAUGGC
.-----------(((..........((((((((.((((((((((.....))))).)))))...((((..-...))))...........))))))))..........))).--........ ( -23.35)
>consensus
AAUGGUCUUAAGAGUUAAAAAUUCUCAGUUUUUAUGGCUUGCACUUCCUGUGCAAAGCUGAUUGAUAAACAUAUAUAUUUAUAAUU_________GCUUUAAUUAUGCUA__UAAAUGGC
...........(((((((((((.....)))))))((((((((((.....)))).))))))...................................)))).......((((......)))) (-15.92 = -15.28 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:43 2006