Locus 1374

Sequence ID	X_DroMel_CAF1
Location	4,114,678 – 4,114,829
Length	151
Max. P	0.982750

overview

Window 1

Location	4,114,678 – 4,114,789
Length	111
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	92.19
Mean single sequence MFE	-45.07
Consensus MFE	-41.29
Energy contribution	-41.40
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-3.19
Structure conservation index	0.92
SVM decision value	1.92
SVM RNA-class probability	0.982750
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114678 111 + 22224390
AGCACCAACACGUGCAGCGAUCAGGGGCAAGGACAUGGAUCUGGGAUUGGACUUGGUGACCCAAAGCGGGACCAAAGCCAAGUCCACUACGCCCAUGACCCUGCCCAGGAU
.((((......))))....(((..(((((.((.(((((...(((...((((((((((..(((.....)))......)))))))))))))...))))).)).)))))..))) ( -47.50)
>DroSec_CAF1 6017 111 + 1
AGCACCAACACGUGCAGCGAUCAGGGGCAAGGACAUGGAUCUGGGAUUGGACUUGGUGACCCAAAGCGGGACCAAAGCCAAGUCCACUACGCCCAUGACCCUGCCCAGGAU
.((((......))))....(((..(((((.((.(((((...(((...((((((((((..(((.....)))......)))))))))))))...))))).)).)))))..))) ( -47.50)
>DroYak_CAF1 1357 102 + 1
---------ACGUGCAGCGAUCAGGGGCAAGGACAUGGAUCUGGCAUUGGGCUUGGUGACCCAAAGCGGACCCAAAGCCAAGUCCACUACGCCCAUGACCCUGCCCAGGAU
---------..(.((((.(.(((.((((..((...((((..((((.(((((.((.((........)).))))))).))))..))))))..)))).))).))))).)..... ( -40.20)
>consensus
AGCACCAACACGUGCAGCGAUCAGGGGCAAGGACAUGGAUCUGGGAUUGGACUUGGUGACCCAAAGCGGGACCAAAGCCAAGUCCACUACGCCCAUGACCCUGCCCAGGAU
..........((.....))(((..(((((.((.(((((...(((...((((((((((..(((.....)))......)))))))))))))...))))).)).)))))..))) (-41.29 = -41.40 +   0.11)

alignment

secondary structure

dotplot

Window 2

Location	4,114,678 – 4,114,789
Length	111
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	92.19
Mean single sequence MFE	-51.07
Consensus MFE	-43.49
Energy contribution	-44.93
Covariance contribution	1.45
Combinations/Pair	1.03
Mean z-score	-3.84
Structure conservation index	0.85
SVM decision value	1.45
SVM RNA-class probability	0.955381
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114678 111 - 22224390
AUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUCCUUGCCCCUGAUCGCUGCACGUGUUGGUGCU
(((..((((((((.(((((((....(((((((((...((..((......))..)))))))))))......).)))))).))))))))..)))....((((......)))). ( -52.00)
>DroSec_CAF1 6017 111 - 1
AUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUCCUUGCCCCUGAUCGCUGCACGUGUUGGUGCU
(((..((((((((.(((((((....(((((((((...((..((......))..)))))))))))......).)))))).))))))))..)))....((((......)))). ( -52.00)
>DroYak_CAF1 1357 102 - 1
AUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGGUCCGCUUUGGGUCACCAAGCCCAAUGCCAGAUCCAUGUCCUUGCCCCUGAUCGCUGCACGU---------
.......(((((((((.(((((..(((((.(((((.((((((.....((((....)))))))))).))))).))))).....))))).))))).))))....--------- ( -49.20)
>consensus
AUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUCCUUGCCCCUGAUCGCUGCACGUGUUGGUGCU
(((..((((((((.(((((((....(((((((((...((..((......))..)))))))))))......).)))))).))))))))..)))....((((......)))). (-43.49 = -44.93 +   1.45)

alignment

secondary structure

dotplot

Window 3

Location	4,114,709 – 4,114,829
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-41.62
Consensus MFE	-36.69
Energy contribution	-37.00
Covariance contribution	0.31
Combinations/Pair	1.03
Mean z-score	-1.84
Structure conservation index	0.88
SVM decision value	0.41
SVM RNA-class probability	0.724188
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114709 120 - 22224390
ACAUUCCAGUACAACUCUUGACAUUCGGUGAAUCGCCAUUAUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUC
.....((((..((.....))......((((...))))......))))((((((((.((((.....(((((((((...((..((......))..)))))))))))..))))))))).))). ( -41.90)
>DroSec_CAF1 6048 120 - 1
ACAUUCCAGUACAACUCCUGACAUUCGGUGAAUCGCCAUUAUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUC
.....((((..((.....))......((((...))))......))))((((((((.((((.....(((((((((...((..((......))..)))))))))))..))))))))).))). ( -42.10)
>DroSim_CAF1 1496 120 - 1
ACAUUCCAGUACAACUCCUGACAUUCGGUGAAUCGCCAUUAUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUC
.....((((..((.....))......((((...))))......))))((((((((.((((.....(((((((((...((..((......))..)))))))))))..))))))))).))). ( -42.10)
>DroYak_CAF1 1379 120 - 1
UCAAUUCAUUACAACUCUUGACAUUCGGUGAAUCGCCAUUAUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGGUCCGCUUUGGGUCACCAAGCCCAAUGCCAGAUCCAUGUC
.........(((..(((.((((....((((...)))).....(((....))))))).))).)))(((((.(((((.((((((.....((((....)))))))))).))))).)))))... ( -40.40)
>consensus
ACAUUCCAGUACAACUCCUGACAUUCGGUGAAUCGCCAUUAUCCUGGGCAGGGUCAUGGGCGUAGUGGACUUGGCUUUGGUCCCGCUUUGGGUCACCAAGUCCAAUCCCAGAUCCAUGUC
...................(((((..........(((.........))).(((((.((((.....(((((((((...((..((......))..)))))))))))..)))))))))))))) (-36.69 = -37.00 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:45 2006