Locus 914

Sequence ID	3R_DroMel_CAF1
Location	3,078,412 – 3,078,545
Length	133
Max. P	0.552825

overview

Window 7

Location	3,078,412 – 3,078,505
Length	93
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	79.77
Mean single sequence MFE	-18.38
Consensus MFE	-12.25
Energy contribution	-12.17
Covariance contribution	-0.08
Combinations/Pair	1.20
Mean z-score	-1.27
Structure conservation index	0.67
SVM decision value	0.04
SVM RNA-class probability	0.552825
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3078412 93 - 27905053
AAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAG--------AAUCCAAGCGAAAAUUACAGCGAGUA-----AAAUUUUAAGC-GAA-A
...(..((((((.(((((((((((....)))))).((((....)))).....--------.))))).)))....((((.....)))-----)....)))..)-...-. ( -22.30)
>DroVir_CAF1 4391 87 - 1
AAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAUGAA--------AAUUCCAUCAAGAAUUACUGCA-----------AAAUUAAGC-GAA-A
...((((.((((((....)).))))))))(((.....(((((((((..(((.--------.......))).)))))))).).-----------......)))-...-. ( -16.20)
>DroPse_CAF1 4073 93 - 1
AAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAA--------AUUCCAA-CGAAAAUUACUACAAAUU-----CAAAUUUAAGC-GAAAA
.........(((....((((((((....))))))))..((((((((..((..--------.......-.)))))))))).......-----.........))-).... ( -19.10)
>DroGri_CAF1 4423 104 - 1
AAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAA---ACAAAAACAAUUCCAUCAAAAAUUACUGCAAGAAAGCUACAAAAUUAAGAACAA-A
..(.(((....((((((((((.((....)).)))))..((((((((...---...................)))))))).........)))))......))).)..-. ( -16.75)
>DroAna_CAF1 4488 91 - 1
AAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAA--------AAUC--AGCGAAAAUGAUUGCAAAUA-----AAAUUUUAAAC-GAA-A
..((((.....(((.(((((((((....)))))).((((....)))).....--------.)))--.))).....)))).......-----...........-...-. ( -16.80)
>DroPer_CAF1 4085 93 - 1
AAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAA--------AUUCCAA-CGAAAAUUACUACAAAUU-----CAAAUUUAAGC-GAAAA
.........(((....((((((((....))))))))..((((((((..((..--------.......-.)))))))))).......-----.........))-).... ( -19.10)
>consensus
AAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAA________AAUCCAA_CGAAAAUUACUGCAAAUA_____CAAAUUUAAGC_GAA_A
............((((.(((((((....)))))))((((....))))..............................))))........................... (-12.25 = -12.17 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	3,078,442 – 3,078,545
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.70
Mean single sequence MFE	-31.15
Consensus MFE	-21.95
Energy contribution	-22.12
Covariance contribution	0.17
Combinations/Pair	1.17
Mean z-score	-1.07
Structure conservation index	0.70
SVM decision value	0.03
SVM RNA-class probability	0.549053
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3078442 103 - 27905053
UGAGAAGGGCGCCUACCUGCUGAAGAGGGCCUGGGGCGCCAAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAG-----------------AAUCCAAGCGA
..(((..(((((((....(((......)))...)))))))....)))..(((.(((((((((((....)))))).((((....)))).....-----------------.))))).))). ( -40.20)
>DroVir_CAF1 4415 103 - 1
GGAGAAGGGCGCCUAUCUAUUGAAACGGGCCUGGGGCGCCAAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAUGAA-----------------AAUUCCAUCAA
((((...((((((............(((((((((....)).)))))))((((((....)).)))))).)))).((((((....))).)))..-----------------..))))..... ( -28.10)
>DroGri_CAF1 4459 108 - 1
CGAGAAGGGAGCCUAUCUGCUGAAACGAGCCUGGGGCGCCAAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAA------------ACAAAAACAAUUCCAUCAA
..(((..((.((((....(((......)))...)))).))....))).....(((((((((.((....)).))))((((....))))..------------...........)))))... ( -25.40)
>DroWil_CAF1 11851 103 - 1
AGAGAAGGGCUCCUAUCUGCUCAAGAGAGCCUGGGGUGCUAAGGUCUGACGAUUGGAUGCAACGUGGACACUGCAUAGAGUAAUUUAAAUGA-----------------AAAAAAAACAA
...(((..((((((....((((....))))...))((((....((((.(((.(((....))))))))))...)))).))))..)))......-----------------........... ( -23.10)
>DroMoj_CAF1 4611 120 - 1
CGAAAAGGGCGCCUAUCUGCUGAAACGGGCCUGGGGAGCCAAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAAAGAAUAAACAAAACAAAACCAAUUCCAUGAA
.......((((......))))....(((((((((....)).)))))))....(((((((((.((....)).))))((((....)))).........................)))))... ( -27.40)
>DroAna_CAF1 4518 101 - 1
CGAGCGGGGCGCCUACCUGCUGAAGCGGGCAUGGGGCGCCAAGGUCUGACGCGUGGAUGCGACGUGGACGUUGCAUAGAGUAAUUUAAUCAA-----------------AAUC--AGCGA
.((.(..(((((((.(((((....)))))....)))))))..).))...(((...(((((((((....)))))).((((....)))).....-----------------.)))--.))). ( -42.70)
>consensus
CGAGAAGGGCGCCUAUCUGCUGAAACGGGCCUGGGGCGCCAAGGUCUGACGUGUGGAUGCAACGUGGACGCUGCAUAGAGUAAUUUAAACAA_________________AAUUCCAUCAA
.......(((((((....(((......)))...)))))))...((((.((((((....))).)))))))......((((....))))................................. (-21.95 = -22.12 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:16 2006