Locus 837

Sequence ID	3R_DroMel_CAF1
Location	2,871,888 – 2,872,088
Length	200
Max. P	0.905110

overview

Window 9

Location	2,871,888 – 2,872,008
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-34.65
Consensus MFE	-34.65
Energy contribution	-34.65
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	1.00
SVM decision value	1.04
SVM RNA-class probability	0.905110
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2871888 120 - 27905053
CAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGUUCUCGGGCCAGAUAAAUCAAUAGGUGCACCAAAACAUGCC
.....(((((((((...((((...(((((((.....))))))).((.(((((.(((...(((((.((.....)).))))).))).)))))))..))))....))))).))))........ ( -35.10)
>DroSec_CAF1 3082 120 - 1
CAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGUUCUCGGGCCAGAUAAAUCAAUAGGUGCACCAAAACAUGUC
.....(((((((((...((((...(((((((.....))))))).((.(((((.(((...(((((.((.....)).))))).))).)))))))..))))....))))).))))........ ( -35.10)
>DroSim_CAF1 3457 120 - 1
CAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGUUCUCGGGCCAGAUAAAUCAAUAGGUGCACCAAAACAUGUC
.....(((((((((...((((...(((((((.....))))))).((.(((((.(((...(((((.((.....)).))))).))).)))))))..))))....))))).))))........ ( -35.10)
>DroEre_CAF1 4027 120 - 1
CAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGUUCUCAGGCCAGAUAAAUCAAUAGGUGCACCAAAACAUGUC
.....(((((((((...((((...(((((((.....))))))).((.(((((.(((...(((((.((.....)).))))).))).)))))))..))))....))))).))))........ ( -33.30)
>consensus
CAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGUUCUCGGGCCAGAUAAAUCAAUAGGUGCACCAAAACAUGUC
.....(((((((((...((((...(((((((.....))))))).((.(((((.(((...(((((.((.....)).))))).))).)))))))..))))....))))).))))........ (-34.65 = -34.65 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	2,871,928 – 2,872,048
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	100.00
Mean single sequence MFE	-40.00
Consensus MFE	-40.00
Energy contribution	-40.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	1.00
SVM decision value	0.32
SVM RNA-class probability	0.685145
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2871928 120 - 27905053
GCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGU
..((((((((.(((.....))))))))))).((((((((.......((((.(((.((((((......))))))...))))))).....))))))))...(((((.((.....)).))))) ( -40.00)
>DroSec_CAF1 3122 120 - 1
GCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGU
..((((((((.(((.....))))))))))).((((((((.......((((.(((.((((((......))))))...))))))).....))))))))...(((((.((.....)).))))) ( -40.00)
>DroSim_CAF1 3497 120 - 1
GCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGU
..((((((((.(((.....))))))))))).((((((((.......((((.(((.((((((......))))))...))))))).....))))))))...(((((.((.....)).))))) ( -40.00)
>DroEre_CAF1 4067 120 - 1
GCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGU
..((((((((.(((.....))))))))))).((((((((.......((((.(((.((((((......))))))...))))))).....))))))))...(((((.((.....)).))))) ( -40.00)
>consensus
GCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUUUCAUUCAUGGCCGGGGCAUACGUAAAUGGAAAAUAUAUGU
..((((((((.(((.....))))))))))).((((((((.......((((.(((.((((((......))))))...))))))).....))))))))...(((((.((.....)).))))) (-40.00 = -40.00 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	2,871,968 – 2,872,088
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.31
Mean single sequence MFE	-43.49
Consensus MFE	-35.28
Energy contribution	-35.77
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.07
Structure conservation index	0.81
SVM decision value	0.61
SVM RNA-class probability	0.798490
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2871968 120 - 27905053
UUGGAGCGCCAACCCCGGGCCCCACCCACAAGUUGGCCAUGCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUU
....((((((......(((.....))).(((...((((..(.((((((((.(((.....))))))))))).)...))))......))))))))).((((((......))))))....... ( -44.80)
>DroSec_CAF1 3162 119 - 1
UUGGAGCACCA-CUCCGCGACCCACCCACAAGGUGGCCAUGCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUU
..((((.....-))))(((.((((((.....)))((((..(.((((((((.(((.....))))))))))).)...))))........))))))..((((((......))))))....... ( -44.60)
>DroSim_CAF1 3537 119 - 1
UUGGAGCACCA-CUCCGCGACCCACCCACAAGUUGGCCAUGCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUU
..((((.....-))))(((.((((..........((((..(.((((((((.(((.....))))))))))).)...)))).......)))))))..((((((......))))))....... ( -42.43)
>DroEre_CAF1 4107 114 - 1
UCGGAGCGCCC------AGCCCCACCCACCAUUUGGCCAUGCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUU
(((((.((((.------(((((((..........((((..(.((((((((.(((.....))))))))))).)...)))).......)))).)))))))....)))))............. ( -42.13)
>consensus
UUGGAGCACCA_CUCCGCGACCCACCCACAAGUUGGCCAUGCGUGCGUGUGUUGGCCAACAAACGCGCACUCUCCGGCCUCAUUAUUGGGCGCUGGCGAUUAUUUGAAAUUGCAAAAGUU
....((((((........................((((..(.((((((((.(((.....))))))))))).)...)))).((....)))))))).((((((......))))))....... (-35.28 = -35.77 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:21 2006