Locus 7904

Sequence ID	X_DroMel_CAF1
Location	19,685,285 – 19,685,388
Length	103
Max. P	0.998908

overview

Window 8

Location	19,685,285 – 19,685,388
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	96.46
Mean single sequence MFE	-36.80
Consensus MFE	-33.90
Energy contribution	-34.14
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.23
Structure conservation index	0.92
SVM decision value	3.28
SVM RNA-class probability	0.998908
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19685285 103 + 22224390
AAACCACUUCCUUGCUCUCUCGCUCUGGCUCCCUUGCUCUUCUAUACCGCUCUCUCUCUCGCUCGCCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAG
..........(((((((((((.(((((((......))..........(((((.(.(...((((.....))))..).).)))))....)))))))))))))))) ( -38.30)
>DroSec_CAF1 58921 101 + 1
AAACCACUUCCUUGCUCUCUCGCUCUGGCUCCCUUGGUCUUCUAUACCGCUCUC--UCUCGCUCGCCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAA
...........((((((((((((.(((((......(((.......)))((....--....))..))))))).((((((......))))))..)))))))))). ( -37.30)
>DroSim_CAF1 46130 101 + 1
AAACCACUUCCUUGCUCUCUCGCUCUGGCUCCCUUGCUCUUCUAUACCGCUCUC--UCUCGCUCACCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAA
...........((((((((((.(((((((......)).................--..(((((((((((...))).))))))))...))))))))))))))). ( -36.10)
>DroEre_CAF1 70096 101 + 1
AAACCACUUCCUUGCUCUCUCGCUCUGGCUCCCUUGCUCUUUUAUACCGCUCUC--UCUCGCUCGCCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAA
...........((((((((((.(((((((......))..........((.((.(--((.(((.(((...)))..))).))).)).))))))))))))))))). ( -36.80)
>DroYak_CAF1 72221 101 + 1
AAACCACUUCCUUGCUCUCUCGCUCCGGCUCCACUGCUCUUCUAUACCGCUCUC--UCUCGCUCGCCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAA
...........((((((((((.....(((......)))...............(--(((((.(((((..(((...))).))))).)).)))))))))))))). ( -35.50)
>consensus
AAACCACUUCCUUGCUCUCUCGCUCUGGCUCCCUUGCUCUUCUAUACCGCUCUC__UCUCGCUCGCCAGGCGUUGCGUGGGCGAACGUAGGGGAGAGAGCAAA
...........((((((((((.(((((((......)).....................(((((((((((...))).))))))))...))))))))))))))). (-33.90 = -34.14 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	19,685,285 – 19,685,388
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	96.46
Mean single sequence MFE	-38.60
Consensus MFE	-36.90
Energy contribution	-36.82
Covariance contribution	-0.08
Combinations/Pair	1.10
Mean z-score	-1.76
Structure conservation index	0.96
SVM decision value	2.46
SVM RNA-class probability	0.994218
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19685285 103 - 22224390
CUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGCGAGCGAGAGAGAGAGCGGUAUAGAAGAGCAAGGGAGCCAGAGCGAGAGAGCAAGGAAGUGGUUU
(((((((((((((((.((((((((...((...))..)))))))).........((...........)).)))).((....))))))))))))).......... ( -41.40)
>DroSec_CAF1 58921 101 - 1
UUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGCGAGCGAGA--GAGAGCGGUAUAGAAGACCAAGGGAGCCAGAGCGAGAGAGCAAGGAAGUGGUUU
(((((((((((((((.((((((((...((...))..))))))))...--......(((.......))).)))).((....))))))))))))).......... ( -40.20)
>DroSim_CAF1 46130 101 - 1
UUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGUGAGCGAGA--GAGAGCGGUAUAGAAGAGCAAGGGAGCCAGAGCGAGAGAGCAAGGAAGUGGUUU
(((((((((((((((.((((((((...((...))..))))))))...--....((...........)).)))).((....))))))))))))).......... ( -37.00)
>DroEre_CAF1 70096 101 - 1
UUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGCGAGCGAGA--GAGAGCGGUAUAAAAGAGCAAGGGAGCCAGAGCGAGAGAGCAAGGAAGUGGUUU
(((((((((((((((.((((((((...((...))..))))))))...--....((...........)).)))).((....))))))))))))).......... ( -38.90)
>DroYak_CAF1 72221 101 - 1
UUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGCGAGCGAGA--GAGAGCGGUAUAGAAGAGCAGUGGAGCCGGAGCGAGAGAGCAAGGAAGUGGUUU
((((((((((((((..((((((((...((...))..))))))))...--..(.((..(((.(.....).)))..))))).).))))))))))).......... ( -35.50)
>consensus
UUUGCUCUCUCCCCUACGUUCGCCCACGCAACGCCUGGCGAGCGAGA__GAGAGCGGUAUAGAAGAGCAAGGGAGCCAGAGCGAGAGAGCAAGGAAGUGGUUU
(((((((((((((((.((((((((...((...))..)))))))).........((...........)).)))).((....))))))))))))).......... (-36.90 = -36.82 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:27 2006