Locus 5020

Sequence ID	X_DroMel_CAF1
Location	13,130,921 – 13,131,153
Length	232
Max. P	0.930479

overview

Window 5

Location	13,130,921 – 13,131,040
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	80.74
Mean single sequence MFE	-26.83
Consensus MFE	-17.86
Energy contribution	-20.87
Covariance contribution	3.00
Combinations/Pair	1.09
Mean z-score	-1.65
Structure conservation index	0.67
SVM decision value	0.05
SVM RNA-class probability	0.560006
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13130921 119 + 22224390
UACAAAUUAUUGAAAAUCACGACUUGUGGUGAACAGUCACGACCAAAGCAGUGACCUUAAGAAUUGCCCGCUCCAGCGUUAUCGAUAACACACCGAUAACGACUGCUAACGCAUACACA
....((((.((((...((((..(((((.((((....)))).))..)))..))))..)))).))))((......(((((((((((.........)))))))).))).....))....... ( -26.20)
>DroSim_CAF1 2161 112 + 1
-------UAUAAAAAAUCGUGACUUGUGGUGAACAGUUACGACCGCAGCAGUGACCUCAAGAAUUACCCGCUCCAGCGUUAUCGAUAAACCGCCGAUAACGAGUGCUAACGCAUACACA
-------.........((((((((.((.....))))))))))........(((..(((...........((....))(((((((.........))))))))))(((....)))..))). ( -28.70)
>DroEre_CAF1 21519 115 + 1
AA---A-AAUGUAAAAACGUGACUCCCGGUGAACGGUCACGACCGCAGAAGUGACCUUAAAAAUAGCCCGCACUAGCAUUAUCGAUAACGCACCGAUAACGACUGCUAACGCAUACACA
..---.-...........(((.....(((((...((((((..........)))))).............((....)).............)))))........(((....)))..))). ( -25.60)
>consensus
_A___A_UAUAAAAAAUCGUGACUUGUGGUGAACAGUCACGACCGCAGCAGUGACCUUAAGAAUUGCCCGCUCCAGCGUUAUCGAUAACACACCGAUAACGACUGCUAACGCAUACACA
.................((((((.(((.....))))))))).........(((.......................((((((((.........))))))))..(((....)))..))). (-17.86 = -20.87 +   3.00)

alignment

secondary structure

dotplot

Window 6

Location	13,131,001 – 13,131,113
Length	112
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	94.22
Mean single sequence MFE	-35.28
Consensus MFE	-32.35
Energy contribution	-31.72
Covariance contribution	-0.62
Combinations/Pair	1.09
Mean z-score	-1.98
Structure conservation index	0.92
SVM decision value	1.21
SVM RNA-class probability	0.930479
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13131001 112 - 22224390
GUGUGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGAUGUGUAUGCGUUAGCAGUCGUUAUCGG-UGUGUUAUCGAU
...((((((......)))....((((((.(((((.((((((.......))))))....((((......)))).))))).)))))).)))......(((((-((...))))))) ( -32.20)
>DroSim_CAF1 2234 112 - 1
GUGUGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUCGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGAUGUGUAUGCGUUAGCACUCGUUAUCGG-CGGUUUAUCGAU
(.(((((((......)))....((((((.(((((.((((((.......))))))....((((......)))).))))).)))))).)))).)...(((((-.......))))) ( -36.00)
>DroEre_CAF1 21595 112 - 1
GUGCGCGCGGGAAAUCGCGAAAAAUGCACGCACAACUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGAUGUGUAUGCGUUAGCAGUCGUUAUCGG-UGCGUUAUCGAU
..((((((.((.(((.((....((((((..((((.((((((.......))))))....((((......)))).))))..))))))....)).))).)).)-)))))....... ( -37.70)
>DroYak_CAF1 8980 113 - 1
GUGCGCGCGGGAAAACGCGGAAAAUGCACGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGAUGUGUAUGCGUUAGCAGUCGUUAUCGGAAGUGUUAUCGAU
.(((.((((......))))...((((((..((((.((((((.......))))))....((((......)))).))))..)))))).)))((((.((.(....)...)).)))) ( -35.20)
>consensus
GUGCGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGAUGUGUAUGCGUUAGCAGUCGUUAUCGG_UGUGUUAUCGAU
.(((.((((......))))...((((((.(((((.((((((.......))))))....((((......)))).))))).)))))).)))......(((((........))))) (-32.35 = -31.72 +  -0.62)

alignment

secondary structure

dotplot

Window 7

Location	13,131,040 – 13,131,153
Length	113
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	93.81
Mean single sequence MFE	-34.18
Consensus MFE	-30.54
Energy contribution	-30.48
Covariance contribution	-0.06
Combinations/Pair	1.10
Mean z-score	-1.77
Structure conservation index	0.89
SVM decision value	0.72
SVM RNA-class probability	0.832308
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13131040 113 - 22224390
UUACUAUUGGGCGCAUUAAUUUUACGGCUACCGAAGGAUUGUGUGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGA
......(((((((((((((((((.(((...))).)))))).....((((......))))...)))))........((((((.......)))))).....))))))........ ( -30.10)
>DroSim_CAF1 2273 113 - 1
UUACUAUUGGGCGCAUUAAUUUCACGGCUGCCGAAGGAUUGUGUGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUCGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGA
......(((((((((((.....(((((((......)).)))))..((((......))))...)))))........((((((.......)))))).....))))))........ ( -31.60)
>DroEre_CAF1 21634 113 - 1
UCACUAUUGGGCGCAUUAAUUUCACGGCUGCCGGAGGAUUGUGCGCGCGGGAAAUCGCGAAAAAUGCACGCACAACUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGA
((.(((((((((((...(((((..(((...)))..)))))((((((((((....))))).....)))))))....((((((.......)))))).....))))))..))).)) ( -36.60)
>DroYak_CAF1 9020 113 - 1
UCACGAUUGGGCGCAUCAAUUUUACGGCUGCCGUAGGAUUGUGCGCGCGGGAAAACGCGGAAAAUGCACGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGA
...(((((((((((...((((((((((...))))))))))(((((((((......)))).....)))))))....((((((.......)))))).....)))).))))).... ( -38.40)
>consensus
UCACUAUUGGGCGCAUUAAUUUCACGGCUGCCGAAGGAUUGUGCGCGCGGGAAAACGCGAAAAAUGCAAGCACAAUUUGCAAUUUACAUGCGAGAAAAUGCCCAAAUUGGCGA
......(((((((((((((((((.(((...))).)))))))....((((......))))....))))........((((((.......)))))).....))))))........ (-30.54 = -30.48 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:21 2006