Locus 1839

Sequence ID	X_DroMel_CAF1
Location	5,079,199 – 5,079,338
Length	139
Max. P	0.854844

overview

Window 2

Location	5,079,199 – 5,079,298
Length	99
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	67.25
Mean single sequence MFE	-19.93
Consensus MFE	-16.09
Energy contribution	-15.78
Covariance contribution	-0.30
Combinations/Pair	1.15
Mean z-score	-0.73
Structure conservation index	0.81
SVM decision value	0.80
SVM RNA-class probability	0.854844
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5079199 99 - 22224390
GAGAUGAGCAUCUGCAGCACGUCGUGCAGGUUCUCGUCCUGAAAGU--CAAACCAAAACGAGCGAUGAAAAACAGAAUGCCAAUUAAUUAAAAAGCAGUUA----
..((((((.(((((((........))))))).))))))(((....(--((...............)))....)))..(((..............)))....---- ( -18.60)
>DroVir_CAF1 54960 94 - 1
GAGAUGAGCAUCUGCAGCACAUCGUGCAGAUUCUCGUCCUGUGCAAAUGA---CA--AAAGGAGUUUCAAAU--AAAUAUAAUUUAAU----UAGCAGCCACUGU
((((((((.(((((((........))))))).))).((((.(((....).---))--..)))))))))....--..............----..((((...)))) ( -20.00)
>DroPse_CAF1 39693 81 - 1
GAGAUGAGCAUUUGCAGCACAUCGUGCAGGUUCUCGUCCUGAAAAU--A----CGAAAUGCGAAGUCCAAAUC-CGAUAU-------------AGAACUCC----
((..((..(.((((((.....(((((((((.......))))....)--)----)))..)))))))..))..))-......-------------........---- ( -16.20)
>DroEre_CAF1 42651 99 - 1
GAGAUAAGCAUCUGCAGCACGUCGUGCAGAUUCUCGUCCUGAAAGU--CAAACCAAAACGAGGGGGGGAAAUCAUGAUGUUAAUUAAUUAAAUAGUUGUUA----
..(((.((((((....((((...)))).(((((((.((((......--............)))).))).))))..)))))).)))................---- ( -20.37)
>DroYak_CAF1 44518 96 - 1
GAGAUGAGCAUCUGCAGCACGUCAUGCAGAUUCUCGUCCUGGAAGU--UAAACCAAAACGAGG---GCAAAACAUGAUGUCAAUCAAUUAAAUAGCGGCUA----
..((((((.(((((((........))))))).)))))).(((..((--((..((.......))---........((((....))))......))))..)))---- ( -24.60)
>DroPer_CAF1 39472 81 - 1
GAGAUGAGCAUUUGCAGCACAUCGUGCAGGUUCUCGUCCUGAAAAU--A----CGAAAUGCGAAGUGCAAAUC-CGAUAU-------------AGAACUCC----
(.(((..((((((...(((..(((((((((.......))))....)--)----)))..))).))))))..)))-).....-------------........---- ( -19.80)
>consensus
GAGAUGAGCAUCUGCAGCACAUCGUGCAGAUUCUCGUCCUGAAAAU__AA___CAAAACGAGAGGUGCAAAUC_CGAUAU_AAUUAAU____UAGCAGUCA____
..((((((.(((((((........))))))).))))))................................................................... (-16.09 = -15.78 +  -0.30)

alignment

secondary structure

dotplot

Window 3

Location	5,079,229 – 5,079,338
Length	109
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.70
Mean single sequence MFE	-30.78
Consensus MFE	-21.54
Energy contribution	-22.07
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-1.70
Structure conservation index	0.70
SVM decision value	0.73
SVM RNA-class probability	0.834937
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5079229 109 + 22224390
UUUUCAUCGCUCGUUUUGGUUUG--ACUUUCAGGACGAGAACCUGCACGACGUGCUGCAGAUGCUCAUCUCGCUGAUGUCGGAGCAUCCCAGCUCCAUGGUACCUGCCUUU
.........((((((((((....--....)))))))))).....((((...)))).((((.((((((((.....))))..(((((......)))))..)))).)))).... ( -35.20)
>DroVir_CAF1 54988 106 + 1
UUUGAAACUCCUUU--UG---UCAUUUGCACAGGACGAGAAUCUGCACGAUGUGCUGCAGAUGCUCAUCUCGUUGAUGUCGGAGCAUCCGAGCUCAAUGGUACCUGCCUUC
..............--..---.........(((((((((.(((((((........))))))).)))....((((((..((((.....))))..)))))))).))))..... ( -31.30)
>DroPse_CAF1 39709 105 + 1
UUUGGACUUCGCAUUUCG----U--AUUUUCAGGACGAGAACCUGCACGAUGUGCUGCAAAUGCUCAUCUCAUUGAUGUCGGAGCAUCCCAGCUCCAUGGUACCUGCCUUC
....(((.((((((((((----(--.........))))))...)))..((((.((.......)).)))).....)).)))(((((......)))))..(((....)))... ( -29.20)
>DroGri_CAF1 23956 101 + 1
UAUAUAUAUCUUGU--U--------CUGUUUAGGACGAGAAUCUGCACGAUGUUCUGCAGAUGCUCAUCUCACUGAUGUCGGAGCACCCGAGCUCAAUGGUACCUGCCUUC
........((((((--(--------((....)))))))))(((((((.(.....))))))))((.((((.....))))((((.....)))))).....(((....)))... ( -28.50)
>DroAna_CAF1 16534 103 + 1
CUUGC---UCC-----UGCUCUUACUCUUACAGGACGAGAACCUGCACGACGUCCUGCAGAUGCUCAUCUCCCUGAUGUCGGAGCACCCCAGCUCCAUGGUACCUGCCUUC
((((.---(((-----((............))))))))).(((.....((((((..(.((((....)))).)..))))))(((((......)))))..))).......... ( -31.00)
>DroPer_CAF1 39488 105 + 1
UUUGCACUUCGCAUUUCG----U--AUUUUCAGGACGAGAACCUGCACGAUGUGCUGCAAAUGCUCAUCUCAUUGAUGUCGGAGCAUCCCAGCUCCAUGGUACCUGCCUUC
((((((....((((.(((----(--.....((((.......)))).)))).))))))))))....((((.....))))..(((((......)))))..(((....)))... ( -29.50)
>consensus
UUUGCACCUCCCAU__UG____U__AUUUUCAGGACGAGAACCUGCACGAUGUGCUGCAGAUGCUCAUCUCACUGAUGUCGGAGCAUCCCAGCUCCAUGGUACCUGCCUUC
..............................(((((((((...(((((........)))))...)))..............(((((......)))))...)).))))..... (-21.54 = -22.07 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	5,079,229 – 5,079,338
Length	109
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.70
Mean single sequence MFE	-32.34
Consensus MFE	-26.03
Energy contribution	-26.08
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-1.53
Structure conservation index	0.80
SVM decision value	0.73
SVM RNA-class probability	0.835023
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5079229 109 - 22224390
AAAGGCAGGUACCAUGGAGCUGGGAUGCUCCGACAUCAGCGAGAUGAGCAUCUGCAGCACGUCGUGCAGGUUCUCGUCCUGAAAGU--CAAACCAAAACGAGCGAUGAAAA
.......(((.....(((((......)))))(((.((((...((((((.(((((((........))))))).))))))))))..))--)..)))................. ( -35.40)
>DroVir_CAF1 54988 106 - 1
GAAGGCAGGUACCAUUGAGCUCGGAUGCUCCGACAUCAACGAGAUGAGCAUCUGCAGCACAUCGUGCAGAUUCUCGUCCUGUGCAAAUGA---CA--AAAGGAGUUUCAAA
...((......)).((((((((.((((......)))).(((.((((((.(((((((........))))))).)))))).)))........---..--....))).))))). ( -30.20)
>DroPse_CAF1 39709 105 - 1
GAAGGCAGGUACCAUGGAGCUGGGAUGCUCCGACAUCAAUGAGAUGAGCAUUUGCAGCACAUCGUGCAGGUUCUCGUCCUGAAAAU--A----CGAAAUGCGAAGUCCAAA
....((((((....((((((......)))))).((((.....))))...)))))).(((..(((((((((.......))))....)--)----)))..))).......... ( -30.40)
>DroGri_CAF1 23956 101 - 1
GAAGGCAGGUACCAUUGAGCUCGGGUGCUCCGACAUCAGUGAGAUGAGCAUCUGCAGAACAUCGUGCAGAUUCUCGUCCUAAACAG--------A--ACAAGAUAUAUAUA
............((((((..((((.....))))..)))))).((((((.((((((((.....).))))))).))))))........--------.--.............. ( -29.10)
>DroAna_CAF1 16534 103 - 1
GAAGGCAGGUACCAUGGAGCUGGGGUGCUCCGACAUCAGGGAGAUGAGCAUCUGCAGGACGUCGUGCAGGUUCUCGUCCUGUAAGAGUAAGAGCA-----GGA---GCAAG
((..((..((((...(((((......)))))(((.((..(.((((....)))).)..)).)))))))..))..)).((((((..........)))-----)))---..... ( -36.90)
>DroPer_CAF1 39488 105 - 1
GAAGGCAGGUACCAUGGAGCUGGGAUGCUCCGACAUCAAUGAGAUGAGCAUUUGCAGCACAUCGUGCAGGUUCUCGUCCUGAAAAU--A----CGAAAUGCGAAGUGCAAA
....((((((....((((((......)))))).((((.....))))...)))))).((((.((((.((((.......)))).....--.----......)))).))))... ( -32.02)
>consensus
GAAGGCAGGUACCAUGGAGCUGGGAUGCUCCGACAUCAAUGAGAUGAGCAUCUGCAGCACAUCGUGCAGGUUCUCGUCCUGAAAAU__A____CA__ACGAGAAAUGCAAA
.....(((......((((((......))))))..........((((((.(((((((........))))))).))))))))).............................. (-26.03 = -26.08 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:59 2006