Locus 872

Sequence ID	X_DroMel_CAF1
Location	2,452,971 – 2,453,251
Length	280
Max. P	0.964553

overview

Window 5

Location	2,452,971 – 2,453,091
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-42.77
Consensus MFE	-42.23
Energy contribution	-42.23
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.99
SVM decision value	0.51
SVM RNA-class probability	0.762724
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2452971 120 - 22224390
CAUCGGAGACCCGAAAGCUGUCCGCCAAUGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCGAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUAC
..((((....))))..((((...((((((((((((((....))))))))(....)))))))...((((..(((((((((......)))).))))).))))))))................ ( -43.70)
>DroSec_CAF1 13428 120 - 1
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ ( -42.30)
>DroSim_CAF1 15885 120 - 1
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ ( -42.30)
>consensus
CAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCAAUUGACCACGUUCUCGUUGGCAUAGGUGAUCAGGCCCUGGCCAAACGGGUGCUUGCCAUCCAGCACAAAGUUAAUGAUUC
..((((....))))..((((...(((((.((((((((....))))))))(....).)))))...((((..(((((((((......)))).))))).))))))))................ (-42.23 = -42.23 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	2,453,051 – 2,453,171
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.78
Mean single sequence MFE	-50.13
Consensus MFE	-47.16
Energy contribution	-46.50
Covariance contribution	-0.66
Combinations/Pair	1.07
Mean z-score	-2.34
Structure conservation index	0.94
SVM decision value	1.10
SVM RNA-class probability	0.915593
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453051 120 + 22224390
UGGCUGACCACAUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGUCUGCAGUUCAAGCUCUUUCACAAGCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAG
(((.(((((((((.(((.........((((....))))(((...((((.((((((....))))))...))))..)))...)))(((((((.....)))))))....))))))))).))). ( -50.20)
>DroSec_CAF1 13508 120 + 1
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). ( -50.10)
>DroSim_CAF1 15965 120 + 1
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). ( -50.10)
>consensus
UGGCUGACCACCUUGGCGGACAGCUUUCGGGUCUCCGAUGAUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAG
(((.(((((((..((((((((.((..((((....))))......((((.......)))))).))))..(((((((((......(((....)))))))))))).)))).))))))).))). (-47.16 = -46.50 +  -0.66)

alignment

secondary structure

dotplot

Window 7

Location	2,453,051 – 2,453,171
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.78
Mean single sequence MFE	-50.50
Consensus MFE	-47.20
Energy contribution	-47.87
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.86
Structure conservation index	0.93
SVM decision value	1.57
SVM RNA-class probability	0.964553
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453051 120 - 22224390
CUGGGUGACCACAUAACUGCCCUUCCAGCUGAAGAGCGGCUUGUGAAAGAGCUUGAACUGCAGACGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAUGUGGUCAGCCA
..((.(((((((((..((((..(((..(((....)))(((((......))))).)))..))))..(((((((..........((((....)))))))))))......))))))))).)). ( -44.10)
>DroSec_CAF1 13508 120 - 1
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))..(.(((((.....))))).)...)..)))).....((((....))))..((((.((((....)))).)))).. ( -53.70)
>DroSim_CAF1 15965 120 - 1
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))..(.(((((.....))))).)...)..)))).....((((....))))..((((.((((....)))).)))).. ( -53.70)
>consensus
CUGGGUGACCACAUAGCUGCCCUUCCAGCUGAAGAGCGGCUUGUGGAAGAGCUUGAACUGCAGGCGCAGCUUGCCCAUAUCAUCGGAGACCCGAAAGCUGUCCGCCAAGGUGGUCAGCCA
.((((..((((((.((((((.((((.....)))).)))))))))))...........((((....)))).)..)))).....((((....))))..((((.((((....)))).)))).. (-47.20 = -47.87 +   0.67)

alignment

secondary structure

dotplot

Window 8

Location	2,453,091 – 2,453,211
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.61
Mean single sequence MFE	-37.37
Consensus MFE	-36.41
Energy contribution	-35.97
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-1.29
Structure conservation index	0.97
SVM decision value	0.02
SVM RNA-class probability	0.542796
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453091 120 + 22224390
AUAUGGGCAAGCUGCGUCUGCAGUUCAAGCUCUUUCACAAGCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAGGUGAGUAAUUUCCAAUUUCCUCCAUUUCGUUCGCUCGAUU
...(((((.((((((....))))))..(((....((((((((.(((((((.....))))))).))).)))))((((....))))........................))).)))))... ( -33.10)
>DroSec_CAF1 13548 112 + 1
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUU
...((((((((((((....)))))..((((....((((((((.(((((((.....))))))).))).)))))((((....))))......-------......))))..))-)))))... ( -39.50)
>DroSim_CAF1 16005 112 + 1
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUU
...((((((((((((....)))))..((((....((((((((.(((((((.....))))))).))).)))))((((....))))......-------......))))..))-)))))... ( -39.50)
>consensus
AUAUGGGCAAGCUGCGCCUGCAGUUCAAGCUCUUCCACAAGCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU_______CCCUCCGUUUCGUU_GCUCGAUU
....((((.((((((....))))))...))))..((((((((.(((((((.....))))))).))).)))))((((....))))......................(((......))).. (-36.41 = -35.97 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	2,453,131 – 2,453,251
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	90.34
Mean single sequence MFE	-42.37
Consensus MFE	-36.56
Energy contribution	-35.90
Covariance contribution	-0.66
Combinations/Pair	1.09
Mean z-score	-1.66
Structure conservation index	0.86
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2453131 120 + 22224390
GCCGCUCUUCAGCUGGAAGGGCAGUUAUGUGGUCACCCAGGUGAGUAAUUUCCAAUUUCCUCCAUUUCGUUCGCUCGAUUUGUCGUCGAAUGAGUGGGCCUUUGGGGAAUUCCGCAAACA
...(((((((.....))))))).(((.(((((((((....))))....(..((((.....((((((.((((((..(((....))).))))))))))))...))))..)...)))))))). ( -43.10)
>DroSec_CAF1 13588 112 + 1
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))....(((....)))(((((((((((-------((((((..((((((-(((((.....))))).))))))..)).....))))))))..))))))) ( -42.00)
>DroSim_CAF1 16045 112 + 1
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU-------CCCUCCGUUUCGUU-GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))....(((....)))(((((((((((-------((((((..((((((-(((((.....))))).))))))..)).....))))))))..))))))) ( -42.00)
>consensus
GCCGCUCUUCAGCUGGAAGGGCAGCUAUGUGGUCACCCAGGUGAGUAAUU_______CCCUCCGUUUCGUU_GCUCGAUUUGUGGGCGAAUGAGUGGGCCUUUGGGGAAUUCCACUCACU
((.(((((((.....))))))).))...((((((((....))))...............(((((....(((.((((.(((((....))))))))).)))...)))))....))))..... (-36.56 = -35.90 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:58 2006