Locus 8474

Sequence ID	X_DroMel_CAF1
Location	21,039,479 – 21,039,663
Length	184
Max. P	0.999904

overview

Window 1

Location	21,039,479 – 21,039,594
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.19
Mean single sequence MFE	-30.49
Consensus MFE	-25.04
Energy contribution	-24.96
Covariance contribution	-0.08
Combinations/Pair	1.11
Mean z-score	-2.27
Structure conservation index	0.82
SVM decision value	2.06
SVM RNA-class probability	0.987024
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21039479 115 - 22224390
AAUUAAGCAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCCUCAAAAGUUCCCUCGGAUUUAUUAACGUAACAGAGAAGUGCUCAAUUAUGACC-----AAGUCCGAGCAAACGGAAUUU
((((.(((.....(((((((((((((.((....((((((((..............)))))))).)).)))))))))))))))).))))......-----...((((......)))).... ( -25.94)
>DroSec_CAF1 10001 113 - 1
AAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUCCUCA--AGUUCCCUCGGACUUAUUAACGUAACAGAGAAGUGCUCAAUUGUGACC-----AAGUCCGUGCAAACGGAAUUU
......((.....(((((((((((((....(((((((((((...--.........))))))))))).)))))))))))))((......))..))-----...(((((....))))).... ( -33.40)
>DroSim_CAF1 10495 113 - 1
AAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUCCUCA--AGUUGCCUUGGAUUUAUUAACGUAACAGAGAAGUGCUCAAUUAUGACC-----AAGUCCGUGCAAACGGAAUUU
......((.....(((((((((((((....(((((((((((...--.........))))))))))).)))))))))))))..(((....)))))-----...(((((....))))).... ( -31.40)
>DroEre_CAF1 10730 113 - 1
AAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGAGCCCUCA--AAUUCCCUCGGAUUUAUUAAUGUAACAGAGAAGUGCUCAAUUAUGGCC-----GAGUCCGUGCAAACGGAAUUU
.....(((.....((((((((((((((((....((((..((...--.........))..)))).)))))))))))))))).)))..........-----...(((((....))))).... ( -28.30)
>DroYak_CAF1 11687 118 - 1
AAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCUUCA--AAUCCCCUCGGAUUUAUUAAUGUAACAGAGAAGUGCUCAAUUAUGGCCAAGCCAAGUCCGUGCAAACGGAAUUU
.....(((.....((((((((((((((((....((((((((...--.........)))))))).)))))))))))))))).))).....((((...))))..(((((....))))).... ( -33.40)
>consensus
AAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCCUCA__AGUUCCCUCGGAUUUAUUAACGUAACAGAGAAGUGCUCAAUUAUGACC_____AAGUCCGUGCAAACGGAAUUU
.............(((((((((((((.((....((((((((..............)))))))).)).)))))))))))))......................(((((....))))).... (-25.04 = -24.96 +  -0.08)

alignment

secondary structure

dotplot

Window 2

Location	21,039,514 – 21,039,629
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.56
Mean single sequence MFE	-26.04
Consensus MFE	-18.41
Energy contribution	-17.69
Covariance contribution	-0.72
Combinations/Pair	1.18
Mean z-score	-2.26
Structure conservation index	0.71
SVM decision value	0.67
SVM RNA-class probability	0.817680
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21039514 115 + 22224390
ACUUCUCUGUUACGUUAAUAAAUCCGAGGGAACUUUUGAGGACCCAUAAAAAAUGUAACAAAAAAGCCAUUUGCUUAAUUUGCAAAUAGUUUCUUCAAGCACGAAGCUGAAAGGG-----
.......(((((((((...........(((..((....))..)))......)))))))))...((((.((((((.......)))))).))))(((..(((.....)))..)))..----- ( -22.43)
>DroSec_CAF1 10036 113 + 1
ACUUCUCUGUUACGUUAAUAAGUCCGAGGGAACU--UGAGGACCCAUCAAAAAUGUAACAAAAAAGCCAUUUCCUUAAUUUGGAAAUAGUUUCUUCAAGCAAGAAGCUGAAAAGG-----
.(((.(((((((((((.....(((((((....))--)..))))........)))))))))........((((((.......))))))((((((((.....)))))))))).))).----- ( -27.42)
>DroSim_CAF1 10530 113 + 1
ACUUCUCUGUUACGUUAAUAAAUCCAAGGCAACU--UGAGGACCCAUCAAAAAUGUAACAAAAAAGCCAUUUCCUUAAUUUGGAAAUAGUUCCUUCAAGCAAGAAGCUGAAAAGG-----
.......(((((((((........((((....))--)).(....)......)))))))))....(((.((((((.......)))))).)))((((..(((.....)))...))))----- ( -25.50)
>DroEre_CAF1 10765 113 + 1
ACUUCUCUGUUACAUUAAUAAAUCCGAGGGAAUU--UGAGGGCUCAUAAAAAAUGUAACAAAAAAGCCAUUUCCCUAAUUUGGAAAUAGUUUCCCCAAGCGUGAAGCCGAGAAGG-----
.((((((.(((.(((.......((((((((((..--....((((....................))))..))))))....))))....((((....))))))).))).)))))).----- ( -26.15)
>DroYak_CAF1 11727 118 + 1
ACUUCUCUGUUACAUUAAUAAAUCCGAGGGGAUU--UGAAGACCCAUAAAAAAUGUAACAAAAAAGCCAUUUCCCUAAUUUGGAAAUAGUUUCUCCAAGCAUGAAGCUUGGAAUAUUUAG
.......(((((((((...((((((....)))))--)(......)......)))))))))...((((.((((((.......)))))).)))).(((((((.....)))))))........ ( -28.70)
>consensus
ACUUCUCUGUUACGUUAAUAAAUCCGAGGGAACU__UGAGGACCCAUAAAAAAUGUAACAAAAAAGCCAUUUCCUUAAUUUGGAAAUAGUUUCUUCAAGCAAGAAGCUGAAAAGG_____
.((((..(((((((((...........(((..((....))..)))......)))))))))...((((.((((((.......)))))).))))..........)))).............. (-18.41 = -17.69 +  -0.72)

alignment

secondary structure

dotplot

Window 3

Location	21,039,514 – 21,039,629
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.56
Mean single sequence MFE	-35.23
Consensus MFE	-31.52
Energy contribution	-29.80
Covariance contribution	-1.72
Combinations/Pair	1.24
Mean z-score	-4.39
Structure conservation index	0.89
SVM decision value	4.47
SVM RNA-class probability	0.999904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21039514 115 - 22224390
-----CCCUUUCAGCUUCGUGCUUGAAGAAACUAUUUGCAAAUUAAGCAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCCUCAAAAGUUCCCUCGGAUUUAUUAACGUAACAGAGAAGU
-----..((((.(((.....))).))))...((((((((.......))))))))((((((((((((.((....((((((((..............)))))))).)).)))))))))))). ( -31.44)
>DroSec_CAF1 10036 113 - 1
-----CCUUUUCAGCUUCUUGCUUGAAGAAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUCCUCA--AGUUCCCUCGGACUUAUUAACGUAACAGAGAAGU
-----..((((((((.....)).))))))..((((((((.......))))))))((((((((((((....(((((((((((...--.........))))))))))).)))))))))))). ( -36.80)
>DroSim_CAF1 10530 113 - 1
-----CCUUUUCAGCUUCUUGCUUGAAGGAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUCCUCA--AGUUGCCUUGGAUUUAUUAACGUAACAGAGAAGU
-----(((((..(((.....))).)))))..((((((((.......))))))))((((((((((((....(((((((((((...--.........))))))))))).)))))))))))). ( -36.60)
>DroEre_CAF1 10765 113 - 1
-----CCUUCUCGGCUUCACGCUUGGGGAAACUAUUUCCAAAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGAGCCCUCA--AAUUCCCUCGGAUUUAUUAAUGUAACAGAGAAGU
-----..((((((((.....)).))))))..((((((((.......))))))))(((((((((((((((....((((..((...--.........))..)))).))))))))))))))). ( -31.90)
>DroYak_CAF1 11727 118 - 1
CUAAAUAUUCCAAGCUUCAUGCUUGGAGAAACUAUUUCCAAAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCUUCA--AAUCCCCUCGGAUUUAUUAAUGUAACAGAGAAGU
.......((((((((.....))))))))...((((((((.......))))))))(((((((((((((((....((((((((...--.........)))))))).))))))))))))))). ( -39.40)
>consensus
_____CCUUUUCAGCUUCAUGCUUGAAGAAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUCCUCA__AGUUCCCUCGGAUUUAUUAACGUAACAGAGAAGU
.......((((.(((.....))).))))...((((((((.......))))))))((((((((((((.((....((((((((..............)))))))).)).)))))))))))). (-31.52 = -29.80 +  -1.72)

alignment

secondary structure

dotplot

Window 4

Location	21,039,554 – 21,039,663
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.55
Mean single sequence MFE	-23.18
Consensus MFE	-15.96
Energy contribution	-15.96
Covariance contribution	-0.00
Combinations/Pair	1.30
Mean z-score	-1.76
Structure conservation index	0.69
SVM decision value	1.33
SVM RNA-class probability	0.943085
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21039554 109 - 22224390
UAUUGGAUUGUUGUGCUUAAUGUAGCUUC---CUUUC--------CCCUUUCAGCUUCGUGCUUGAAGAAACUAUUUGCAAAUUAAGCAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUC
..........(..((...((((((((...---.....--------..((((.(((.....))).))))...((((((((.......)))))))).......))))))))...))..)... ( -22.50)
>DroSec_CAF1 10074 109 - 1
UAUUGGAUUGUUCUGCUUAAUGUAGCUUG---CUUUC--------CCUUUUCAGCUUCUUGCUUGAAGAAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUC
....(((..((.((((.....))))...)---)..))--------)((..(((((.....))..((((((.((((((((.......)))))))).))))))..........)))..)).. ( -23.70)
>DroSim_CAF1 10568 109 - 1
UAUUGGAUUGUUCUGCUUAAUGUAGCUUG---CUUUC--------CCUUUUCAGCUUCUUGCUUGAAGGAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUGAUGGGUC
.....((((..((.....((((((((...---.....--------(((((..(((.....))).)))))..((((((((.......)))))))).......))))))))...))..)))) ( -25.30)
>DroEre_CAF1 10803 91 - 1
------------------AAUUUCUAUUG---CUUUG--------CCUUCUCGGCUUCACGCUUGGGGAAACUAUUUCCAAAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGAGCC
------------------..(((((...(---(...(--------((.....))).....))...))))).((((((((.......)))))))).......(((.(((.....)))))). ( -17.80)
>DroYak_CAF1 11765 102 - 1
------------------GAUUUCUAUCGGAACUGUGCUGCUAAAUAUUCCAAGCUUCAUGCUUGGAGAAACUAUUUCCAAAUUAGGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUC
------------------....(((((..(((.((((..........((((((((.....))))))))...((((((((.......)))))))).........)))).)))..))))).. ( -26.60)
>consensus
UAUUGGAUUGUU_UGCUUAAUGUAGCUUG___CUUUC________CCUUUUCAGCUUCAUGCUUGAAGAAACUAUUUCCAAAUUAAGGAAAUGGCUUUUUUGUUACAUUUUUUAUGGGUC
..................((((((((.....................((((.(((.....))).))))...((((((((.......)))))))).......))))))))........... (-15.96 = -15.96 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:56 2006