Locus 862

Sequence ID	X_DroMel_CAF1
Location	2,442,891 – 2,443,028
Length	137
Max. P	0.980656

overview

Window 9

Location	2,442,891 – 2,443,011
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.06
Mean single sequence MFE	-42.83
Consensus MFE	-41.03
Energy contribution	-41.37
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.99
Structure conservation index	0.96
SVM decision value	1.87
SVM RNA-class probability	0.980656
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2442891 120 + 22224390
UUAAACUUCCACUUCUAACCCUCAGCCGCUGAUAAACUAAUCAAAAUCUGGGGAGCAUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGG
...........(((((...((((((....((((......))))....))))))......(((........)))))))).......(((((((((.((((.....))))..))))))))). ( -39.90)
>DroSec_CAF1 3802 120 + 1
UUAAACUUCCACUUCUACUCCUCAGCCGCUGAUAAACUAAUCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGG
...........(((((..(((((((....((((......))))....)))))))(((......))).......))))).......(((((((((.((((.....))))..))))))))). ( -44.60)
>DroSim_CAF1 5955 120 + 1
UUAAACUUCCACUUCUAUCCCUCAGCCGCUGAUAAACUAAUCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGG
...........(((((.((((.(((....((((......))))....)))))))(((......))).......))))).......(((((((((.((((.....))))..))))))))). ( -44.00)
>consensus
UUAAACUUCCACUUCUAACCCUCAGCCGCUGAUAAACUAAUCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGG
...........(((((...((((((....((((......))))....)))))).(((......))).......))))).......(((((((((.((((.....))))..))))))))). (-41.03 = -41.37 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	2,442,931 – 2,443,028
Length	97
Sequences	3
Columns	97
Reading direction	forward
Mean pairwise identity	99.31
Mean single sequence MFE	-36.57
Consensus MFE	-35.50
Energy contribution	-35.83
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.97
SVM decision value	0.77
SVM RNA-class probability	0.845234
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2442931 97 + 22224390
UCAAAAUCUGGGGAGCAUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGGAGCUCAGACUCGCGACU
......((((((((((...(((........)))..........(((((((((((.((((.....))))..)))))))))))))))...)))).)).. ( -34.50)
>DroSec_CAF1 3842 97 + 1
UCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGGAGCUCAGACUCGCGACU
......((((((..(((......)))................((((((((((((.((((.....))))..))))))))))))))))))......... ( -37.60)
>DroSim_CAF1 5995 97 + 1
UCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGGAGCUCAGACUCGCGACU
......((((((..(((......)))................((((((((((((.((((.....))))..))))))))))))))))))......... ( -37.60)
>consensus
UCAAAAUCUGGGGAGCCUACGAUGGCAAGUUCGAGAAGACCAUUUCGGGCCACAAGCUGGGCAUCAGCGAUGUGGCCUGGAGCUCAGACUCGCGACU
......((((((..(((......)))................((((((((((((.((((.....))))..))))))))))))))))))......... (-35.50 = -35.83 +   0.33)

alignment

secondary structure

dotplot

Window 1

Location	2,442,931 – 2,443,028
Length	97
Sequences	3
Columns	97
Reading direction	reverse
Mean pairwise identity	99.31
Mean single sequence MFE	-32.77
Consensus MFE	-31.70
Energy contribution	-31.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.97
SVM decision value	-0.02
SVM RNA-class probability	0.521083
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2442931 97 - 22224390
AGUCGCGAGUCUGAGCUCCAGGCCACAUCGCUGAUGCCCAGCUUGUGGCCCGAAAUGGUCUUCUCGAACUUGCCAUCGUAUGCUCCCCAGAUUUUGA
....((((((.((((..((((((((((..((((.....)))).))))))).....)))....)))).))))))........................ ( -31.70)
>DroSec_CAF1 3842 97 - 1
AGUCGCGAGUCUGAGCUCCAGGCCACAUCGCUGAUGCCCAGCUUGUGGCCCGAAAUGGUCUUCUCGAACUUGCCAUCGUAGGCUCCCCAGAUUUUGA
((((((((((.((((..((((((((((..((((.....)))).))))))).....)))....)))).)))))).......((....)).)))).... ( -33.30)
>DroSim_CAF1 5995 97 - 1
AGUCGCGAGUCUGAGCUCCAGGCCACAUCGCUGAUGCCCAGCUUGUGGCCCGAAAUGGUCUUCUCGAACUUGCCAUCGUAGGCUCCCCAGAUUUUGA
((((((((((.((((..((((((((((..((((.....)))).))))))).....)))....)))).)))))).......((....)).)))).... ( -33.30)
>consensus
AGUCGCGAGUCUGAGCUCCAGGCCACAUCGCUGAUGCCCAGCUUGUGGCCCGAAAUGGUCUUCUCGAACUUGCCAUCGUAGGCUCCCCAGAUUUUGA
....((((((.((((..((((((((((..((((.....)))).))))))).....)))....)))).))))))........................ (-31.70 = -31.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:34 2006