Locus 2983

Sequence ID	X_DroMel_CAF1
Location	7,941,520 – 7,941,640
Length	120
Max. P	0.753850

overview

Window 3

Location	7,941,520 – 7,941,640
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	86.11
Mean single sequence MFE	-31.87
Consensus MFE	-23.57
Energy contribution	-27.40
Covariance contribution	3.83
Combinations/Pair	1.00
Mean z-score	-2.30
Structure conservation index	0.74
SVM decision value	0.48
SVM RNA-class probability	0.753850
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7941520 120 + 22224390
GGUUGCAUCUACUCCACAUGCAACUAGUACAUUUGUCCUGCUUACAGACUAUGUUCAUAAGAUAUAUGUAGAGUCGCGUGUGUGCUCCCUUUCGAUCCGGCAUGGAUCGAAAUGCAUUCU
(..(((((......(((((((.(((..(((((.((((......(((.....)))......)))).))))).))).)))))))........((((((((.....)))))))))))))..). ( -37.50)
>DroSim_CAF1 16977 120 + 1
GGUUGCAUCUACUCCACAUGCAACUAGUACAUUUGUCCUGCUUACAGACUAUGUUCAUAAGAUAUAUGUAGAGUCGCGUGUGUGCUCCCUUUCGAUCCGGCAUGGAUCGAAAUGCAUUCU
(..(((((......(((((((.(((..(((((.((((......(((.....)))......)))).))))).))).)))))))........((((((((.....)))))))))))))..). ( -37.50)
>DroYak_CAF1 19238 96 + 1
GGUUGCAUCUACUCCACAUGCAACUAGUACAUUUGUCCUGCUUACAGACUAUGUUCAUAAGAUAUAUGUAGAGUCGCGUAUGUGC--------------------AUCGAAA----UUCU
((((((((.........)))))))).((((((.(((...(((((((...((((((.....))))))))).)))).))).))))))--------------------.......----.... ( -20.60)
>consensus
GGUUGCAUCUACUCCACAUGCAACUAGUACAUUUGUCCUGCUUACAGACUAUGUUCAUAAGAUAUAUGUAGAGUCGCGUGUGUGCUCCCUUUCGAUCCGGCAUGGAUCGAAAUGCAUUCU
((.(((((......(((((((.(((..(((((.((((......(((.....)))......)))).))))).))).)))))))........((((((((.....))))))))))))).)). (-23.57 = -27.40 +   3.83)

alignment

secondary structure

dotplot

Window 4

Location	7,941,520 – 7,941,640
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.11
Mean single sequence MFE	-30.63
Consensus MFE	-23.55
Energy contribution	-26.50
Covariance contribution	2.95
Combinations/Pair	1.03
Mean z-score	-1.84
Structure conservation index	0.77
SVM decision value	0.05
SVM RNA-class probability	0.557088
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7941520 120 - 22224390
AGAAUGCAUUUCGAUCCAUGCCGGAUCGAAAGGGAGCACACACGCGACUCUACAUAUAUCUUAUGAACAUAGUCUGUAAGCAGGACAAAUGUACUAGUUGCAUGUGGAGUAGAUGCAACC
....(((((((((((((.....)))))))......((.((((.((((((.(((((...((....)).....((((.......))))..)))))..)))))).))))..)).))))))... ( -36.00)
>DroSim_CAF1 16977 120 - 1
AGAAUGCAUUUCGAUCCAUGCCGGAUCGAAAGGGAGCACACACGCGACUCUACAUAUAUCUUAUGAACAUAGUCUGUAAGCAGGACAAAUGUACUAGUUGCAUGUGGAGUAGAUGCAACC
....(((((((((((((.....)))))))......((.((((.((((((.(((((...((....)).....((((.......))))..)))))..)))))).))))..)).))))))... ( -36.00)
>DroYak_CAF1 19238 96 - 1
AGAA----UUUCGAU--------------------GCACAUACGCGACUCUACAUAUAUCUUAUGAACAUAGUCUGUAAGCAGGACAAAUGUACUAGUUGCAUGUGGAGUAGAUGCAACC
....----......(--------------------(((....(...(((((((((.((.((...(.((((..((((....))))....)))).).)).)).))))))))).).))))... ( -19.90)
>consensus
AGAAUGCAUUUCGAUCCAUGCCGGAUCGAAAGGGAGCACACACGCGACUCUACAUAUAUCUUAUGAACAUAGUCUGUAAGCAGGACAAAUGUACUAGUUGCAUGUGGAGUAGAUGCAACC
....(((((((((((((.....)))))))......((.((((.((((((.(((((...((....)).....((((.......))))..)))))..)))))).))))..)).))))))... (-23.55 = -26.50 +   2.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:19 2006