Locus 4133

Sequence ID	2L_DroMel_CAF1
Location	11,892,965 – 11,893,088
Length	123
Max. P	0.898677

overview

Window 2

Location	11,892,965 – 11,893,059
Length	94
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	74.15
Mean single sequence MFE	-27.55
Consensus MFE	-12.16
Energy contribution	-12.97
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-1.79
Structure conservation index	0.44
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11892965 94 + 22407834
UAGGGGGUUUGGU-AUGU-UAUAGUCUGCUGCUGGCAGUUGGUGGCAGAGCAGAAAAUCAAUGUUGCCAGCAACAACA-----------GCAUUGGCAG-GAAGAACA-----
.............-.(((-(....((((((((((...((((.(((((..(((.........)))))))).))))..))-----------))...)))))-)...))))----- ( -29.60)
>DroVir_CAF1 100736 87 + 1
-AAUGUGU------GCGAUUGUGCGCUGUGGGUGGCAUUUAGUAGCAGAGCUGAAAAUCAAUGUAGCCGCCAACAAGA--------------AGGGCAAAUGAGAACA-----
-..(((..------.((.((((.(..(((.((((((.((((((......)))))).((....)).)))))).)))...--------------.).)))).))...)))----- ( -21.40)
>DroSec_CAF1 115762 91 + 1
UGGGGGGUUUGGU-AUGU-UAUAGUCUG---CUGGCAGUUGGUGGCAGAGUAGAAAAUCAAUGUUGCCAGCAACAACA-----------GCAUUGGCAG-GAAGAACA-----
......((((...-.(((-((.....((---(((...((((.((((((.((.(.....).)).)))))).))))..))-----------))).))))).-...)))).----- ( -27.30)
>DroSim_CAF1 81267 94 + 1
UGGGGGGUUUGGU-AUGU-UAUAGUCUGCUGCUGGCAGUUGGUGGCAGAGUAGAAAAUCAAUGUUGCCAGCAACAACA-----------GCAUUGGCAG-GAAGAACA-----
.............-.(((-(....((((((((((...((((.((((((.((.(.....).)).)))))).))))..))-----------))...)))))-)...))))----- ( -29.80)
>DroYak_CAF1 83629 100 + 1
UGUGGGGUUGGGUUUUGG-UAUAGUCUGCAGGUGGCAGUUGGUGGCAGGGCAGAAAAUCAAUGUUGCCAGCAACAACA-----------GCAUGGGCAG-GAAGAACAGGGAG
((((..(((((...((((-(....(((((..((.((.....)).))...)))))..))))).....)))))..).)))-----------((....))..-............. ( -24.50)
>DroAna_CAF1 96959 104 + 1
UU-AAGGUUCAGG-AGGC-UAUAGUCUGCUGCUGGCAUUCGGUGGCAAAGCAGAAAAUCAAUGUUGCCAGCAACAACAUUGCCAGCGCGGCAUUGGCAG-AAACAACC-----
..-..((((....-..((-((..(.((((.(((((((...(.((((((....(.....)....)))))).)........))))))))))))..))))..-....))))----- ( -32.70)
>consensus
UGGGGGGUUUGGU_AUGU_UAUAGUCUGCUGCUGGCAGUUGGUGGCAGAGCAGAAAAUCAAUGUUGCCAGCAACAACA___________GCAUUGGCAG_GAAGAACA_____
..............................(((((((((((((..(......)...))))))..))))))).......................................... (-12.16 = -12.97 +   0.81)

alignment

secondary structure

dotplot

Window 3

Location	11,892,965 – 11,893,059
Length	94
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	74.15
Mean single sequence MFE	-20.53
Consensus MFE	-10.49
Energy contribution	-10.71
Covariance contribution	0.22
Combinations/Pair	1.29
Mean z-score	-1.98
Structure conservation index	0.51
SVM decision value	1.00
SVM RNA-class probability	0.898677
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11892965 94 - 22407834
-----UGUUCUUC-CUGCCAAUGC-----------UGUUGUUGCUGGCAACAUUGAUUUUCUGCUCUGCCACCAACUGCCAGCAGCAGACUAUA-ACAU-ACCAAACCCCCUA
-----((((....-((((...(((-----------((..((((.(((((.....(.....).....))))).))))...))))))))).....)-))).-............. ( -22.70)
>DroVir_CAF1 100736 87 - 1
-----UGUUCUCAUUUGCCCU--------------UCUUGUUGGCGGCUACAUUGAUUUUCAGCUCUGCUACUAAAUGCCACCCACAGCGCACAAUCGC------ACACAUU-
-----................--------------...(((.((.(((......(.....)(((...))).......))).)).)))(((......)))------.......- ( -12.00)
>DroSec_CAF1 115762 91 - 1
-----UGUUCUUC-CUGCCAAUGC-----------UGUUGUUGCUGGCAACAUUGAUUUUCUACUCUGCCACCAACUGCCAG---CAGACUAUA-ACAU-ACCAAACCCCCCA
-----........-.......(((-----------((..((((.(((((.....(.....).....))))).))))...)))---)).......-....-............. ( -17.70)
>DroSim_CAF1 81267 94 - 1
-----UGUUCUUC-CUGCCAAUGC-----------UGUUGUUGCUGGCAACAUUGAUUUUCUACUCUGCCACCAACUGCCAGCAGCAGACUAUA-ACAU-ACCAAACCCCCCA
-----((((....-((((...(((-----------((..((((.(((((.....(.....).....))))).))))...))))))))).....)-))).-............. ( -22.70)
>DroYak_CAF1 83629 100 - 1
CUCCCUGUUCUUC-CUGCCCAUGC-----------UGUUGUUGCUGGCAACAUUGAUUUUCUGCCCUGCCACCAACUGCCACCUGCAGACUAUA-CCAAAACCCAACCCCACA
.............-((((....((-----------.((((..((.((((............))))..))...)))).)).....))))......-.................. ( -16.70)
>DroAna_CAF1 96959 104 - 1
-----GGUUGUUU-CUGCCAAUGCCGCGCUGGCAAUGUUGUUGCUGGCAACAUUGAUUUUCUGCUUUGCCACCGAAUGCCAGCAGCAGACUAUA-GCCU-CCUGAACCUU-AA
-----((((((.(-(((((......).(((((((......(((.((((((....(.....)....)))))).))).))))))).)))))..)))-))).-..........-.. ( -31.40)
>consensus
_____UGUUCUUC_CUGCCAAUGC___________UGUUGUUGCUGGCAACAUUGAUUUUCUGCUCUGCCACCAACUGCCAGCAGCAGACUAUA_ACAU_ACCAAACCCCCCA
.....................................((((.(((((((...(((.................))).))))))).))))......................... (-10.49 = -10.71 +   0.22)

alignment

secondary structure

dotplot

Window 4

Location	11,892,998 – 11,893,088
Length	90
Sequences	3
Columns	90
Reading direction	forward
Mean pairwise identity	97.04
Mean single sequence MFE	-22.17
Consensus MFE	-19.40
Energy contribution	-19.73
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.02
Structure conservation index	0.88
SVM decision value	0.18
SVM RNA-class probability	0.621363
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11892998 90 + 22407834
CAGUUGGUGGCAGAGCAGAAAAUCAAUGUUGCCAGCAACAACAGCAUUGGCAGGAAGAACAGUAGGAGCUGGAGGAACUGGAGGAGCAGG
..((((.(((((..(((.........)))))))).))))....((.((..(((......((((....))))......)))..)).))... ( -23.80)
>DroSec_CAF1 115792 90 + 1
CAGUUGGUGGCAGAGUAGAAAAUCAAUGUUGCCAGCAACAACAGCAUUGGCAGGAAGAACAGGAGGAGCUGGAGGAACUGGAGGAACAGG
..((((.((((((.((.(.....).)).)))))).))))..((((.((..(..(.....)..)..))))))......(((......))). ( -22.80)
>DroSim_CAF1 81300 90 + 1
CAGUUGGUGGCAGAGUAGAAAAUCAAUGUUGCCAGCAACAACAGCAUUGGCAGGAAGAACAGGAGGAGCUGGAGGAAGUGGAGGAACAGG
..((((.((((((.((.(.....).)).)))))).))))..((((.((..(..(.....)..)..))))))......((......))... ( -19.90)
>consensus
CAGUUGGUGGCAGAGUAGAAAAUCAAUGUUGCCAGCAACAACAGCAUUGGCAGGAAGAACAGGAGGAGCUGGAGGAACUGGAGGAACAGG
..((((.((((((....(.....)....)))))).))))..((((.((..(.(......).)..)).))))......(((......))). (-19.40 = -19.73 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:24 2006