Locus 1295

Sequence ID	2R_DroMel_CAF1
Location	5,039,206 – 5,039,341
Length	135
Max. P	0.960018

overview

Window 6

Location	5,039,206 – 5,039,301
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.92
Mean single sequence MFE	-29.66
Consensus MFE	-21.95
Energy contribution	-21.48
Covariance contribution	-0.47
Combinations/Pair	1.15
Mean z-score	-1.47
Structure conservation index	0.74
SVM decision value	1.04
SVM RNA-class probability	0.904633
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5039206 95 + 20766785
G--CG-------CCCAA-GUUU-----UCCG----UUUGCA----CAGUAA--AGUAAUUUCCGUCAGGACUACCAGCGGCACAUAGCGGUGCUCAAGGAAUCGCUAUGUGCCAAAGAGG
(--(.-------....(-((((-----(.((----.((((.----......--.))))....))..))))))....))(((((((((((((.(.....).)))))))))))))....... ( -29.40)
>DroVir_CAF1 17106 110 + 1
GCGCG----AA-UCCAAAAACAGUUCAAUUGUU-CCAUGCA----CAGUAAAAAAUAACUUUCGUUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGG
((..(----(.-(((............(((((.-......)----))))......((((....)))))))...)).))(((((((((((..((((...)))))))))))))))....... ( -31.00)
>DroPse_CAF1 13409 102 + 1
G--GGCCUCAAUCCAAA-AAUA-----GUCG----UUUGCA----CAGUAA--CGUAAUUCCCGCUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGG
.--..((((........-.(((-----(((.----(..((.----......--..........)).).))))))....(((((((((((..((((...)))))))))))))))...)))) ( -34.53)
>DroGri_CAF1 17451 107 + 1
G--CG----AA-UCCAA--AUUGUUCAAUUGUCCCCAUGCA----CAGUAAAAUAUAACUUUCGUUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGG
(--((----((-(....--...))))....((((..(((..----.(((........)))..)))..)))).....))(((((((((((..((((...)))))))))))))))....... ( -32.80)
>DroWil_CAF1 14312 106 + 1
G--CG-------GCCAA-AAUUGUUAACCCA----UUUGCAGAAACAGUAAAAAAUAACUCUCAUUAGGACUAUCAGCGGCAUAUAGCGGUGCUCAAGGAAUCGCUAUGCGCCAAAGAAG
(--((-------(((..-....((((.....----(((((.......)))))...))))........)).))....))(((.(((((((((.(.....).))))))))).)))....... ( -20.34)
>DroAna_CAF1 14154 95 + 1
G--CG-------UCGAA-GUUA-----GUCG----UUUGCA----CAGUAA--AGUAAUUCCCAUUAGGACUACCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGG
(--((-------.(((.-....-----.)))----..))).----..((..--.(((..(((.....))).)))..))(((((((((((..((((...)))))))))))))))....... ( -29.90)
>consensus
G__CG_______UCCAA_AAUA_____AUCG____UUUGCA____CAGUAA__AAUAACUCCCGUUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGG
......................................((......(((........))).((....)).......))((((((((((((..(.....)..))))))))))))....... (-21.95 = -21.48 +  -0.47)

alignment

secondary structure

dotplot

Window 7

Location	5,039,206 – 5,039,301
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.92
Mean single sequence MFE	-31.24
Consensus MFE	-22.48
Energy contribution	-22.15
Covariance contribution	-0.33
Combinations/Pair	1.25
Mean z-score	-1.89
Structure conservation index	0.72
SVM decision value	1.51
SVM RNA-class probability	0.960018
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5039206 95 - 20766785
CCUCUUUGGCACAUAGCGAUUCCUUGAGCACCGCUAUGUGCCGCUGGUAGUCCUGACGGAAAUUACU--UUACUG----UGCAAA----CGGA-----AAAC-UUGGG-------CG--C
.......(((((((((((.............)))))))))))(((((((.(((....)))...))))--...(((----(....)----))).-----....-...))-------).--. ( -30.32)
>DroVir_CAF1 17106 110 - 1
CCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAACGAAAGUUAUUUUUUACUG----UGCAUGG-AACAAUUGAACUGUUUUUGGA-UU----CGCGC
.......(((((((((((.(((...)))...)))))))))))((.((..((((((((....))))..........----.....((-((((.......)))))).)))-))----))).. ( -33.10)
>DroPse_CAF1 13409 102 - 1
CCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAGCGGGAAUUACG--UUACUG----UGCAAA----CGAC-----UAUU-UUUGGAUUGAGGCC--C
((((...(((((((((((.(((...)))...)))))))))))...(((((((.(((((.......))--)))..(----(....)----))))-----))))-........))))..--. ( -35.80)
>DroGri_CAF1 17451 107 - 1
CCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAACGAAAGUUAUAUUUUACUG----UGCAUGGGGACAAUUGAACAAU--UUGGA-UU----CG--C
..((..((((((((((((.(((...)))...))))))))))))..)).(((((((((....))))........((----(.((((....))..)).)))..--..)))-))----..--. ( -34.70)
>DroWil_CAF1 14312 106 - 1
CUUCUUUGGCGCAUAGCGAUUCCUUGAGCACCGCUAUAUGCCGCUGAUAGUCCUAAUGAGAGUUAUUUUUUACUGUUUCUGCAAA----UGGGUUAACAAUU-UUGGC-------CG--C
.......((((.((((((.............)))))).))))((.((((((..((((....))))......))))))...))...----..((((((.....-)))))-------).--. ( -24.62)
>DroAna_CAF1 14154 95 - 1
CCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGGUAGUCCUAAUGGGAAUUACU--UUACUG----UGCAAA----CGAC-----UAAC-UUCGA-------CG--C
.......(((((((((((.(((...)))...)))))))))))((.((((((((.....)).))))))--......----.))...----(((.-----....-.))).-------..--. ( -28.90)
>consensus
CCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAACGAAAAUUACU__UUACUG____UGCAAA____CGAC_____AAUU_UUGGA_______CG__C
.......(((((((((((.(((...)))...)))))))))))((...((((..((((....))))......)))).....))...................................... (-22.48 = -22.15 +  -0.33)

alignment

secondary structure

dotplot

Window 8

Location	5,039,227 – 5,039,341
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.59
Mean single sequence MFE	-35.38
Consensus MFE	-27.75
Energy contribution	-27.70
Covariance contribution	-0.05
Combinations/Pair	1.10
Mean z-score	-2.02
Structure conservation index	0.78
SVM decision value	0.83
SVM RNA-class probability	0.862101
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5039227 114 + 20766785
A----CAGUAA--AGUAAUUUCCGUCAGGACUACCAGCGGCACAUAGCGGUGCUCAAGGAAUCGCUAUGUGCCAAAGAGGAGCACUACAACAUGCUGCAGACGGACGUCGAGGAGAUGCG
.----......--.......((((((.((....)).(((((((((((((((.(.....).))))))))))))).......((((........)))))).))))))((((.....)))).. ( -42.10)
>DroPse_CAF1 13437 114 + 1
A----CAGUAA--CGUAAUUCCCGCUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGGAGCACUACAACAUGCUGCAUUCGGACGUGGAGGAGAUGCG
.----......--((((.((((..(((.(.((......(((((((((((..((((...))))))))))))))).....(.((((........)))).)....)).).))).)))).)))) ( -39.10)
>DroGri_CAF1 17482 116 + 1
A----CAGUAAAAUAUAACUUUCGUUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGGAGCACUACAAUAUGCUGCAGACGGAUGUCGAGGAGAUGCG
.----..(((.....((((....)))).(((.(((..((((((((((((..((((...))))))))))))))).....(.((((........)))).).)...)))))).......))). ( -35.90)
>DroEre_CAF1 2 93 + 1
---------------------------GGACUACCAGCGGCACAUAGCGGUGCUCAAGGAGUCGCUAUGUGCCAAAGAGGAGCACUACAACAUGCUGCAGACCGAUGUCGAGGAGAUGCG
---------------------------...((.((.(((((((((((((..((((...))))))))))))))).......((((........)))))).(((....)))..))))..... ( -33.10)
>DroWil_CAF1 14338 120 + 1
AGAAACAGUAAAAAAUAACUCUCAUUAGGACUAUCAGCGGCAUAUAGCGGUGCUCAAGGAAUCGCUAUGCGCCAAAGAAGAGCACUACAACAUGCUGCAAACGGAUGUGGAGGAGAUGCG
..................((((((((.((.....).(((((((...(..((((((.......(((...)))........))))))..)...)))))))...).)))).))))........ ( -28.06)
>DroMoj_CAF1 2 93 + 1
---------------------------GGACUAUCAGCGGCACAUAGCGGUACUUAAGGAAUCGCUAUGUGCCAAAGAGGAGCACUACAACAUGCUGCAGACGGACGUGGAGGAGAUGCG
---------------------------...........(((((((((((((.(.....).)))))))))))))........(((((.(..(((((((....))).))))..).)).))). ( -34.00)
>consensus
A____CAGUAA____UAA_U__CGUUAGGACUAUCAGCGGCACAUAGCGGUGCUCAAGGAAUCGCUAUGUGCCAAAGAGGAGCACUACAACAUGCUGCAGACGGACGUCGAGGAGAUGCG
....................................(((((((((((((((.(.....).))))))))))))).....(.((((........)))).)...................)). (-27.75 = -27.70 +  -0.05)

alignment

secondary structure

dotplot

Window 9

Location	5,039,227 – 5,039,341
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.59
Mean single sequence MFE	-33.16
Consensus MFE	-25.62
Energy contribution	-25.70
Covariance contribution	0.08
Combinations/Pair	1.14
Mean z-score	-2.03
Structure conservation index	0.77
SVM decision value	0.81
SVM RNA-class probability	0.856912
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5039227 114 - 20766785
CGCAUCUCCUCGACGUCCGUCUGCAGCAUGUUGUAGUGCUCCUCUUUGGCACAUAGCGAUUCCUUGAGCACCGCUAUGUGCCGCUGGUAGUCCUGACGGAAAUUACU--UUACUG----U
.(((...........((((((.(((((((......))))).......(((((((((((.............))))))))))))).((....)).)))))).......--....))----) ( -36.57)
>DroPse_CAF1 13437 114 - 1
CGCAUCUCCUCCACGUCCGAAUGCAGCAUGUUGUAGUGCUCCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAGCGGGAAUUACG--UUACUG----U
.((((.((..........)))))).(((.((((((((..(((.....(((((((((((.(((...)))...)))))))))))((((.......))))))).))))))--..))))----) ( -34.40)
>DroGri_CAF1 17482 116 - 1
CGCAUCUCCUCGACAUCCGUCUGCAGCAUAUUGUAGUGCUCCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAACGAAAGUUAUAUUUUACUG----U
...........(((....(((.(((((((......))))).......(((((((((((.(((...)))...))))))))))))).))).))).((((....))))..........----. ( -35.30)
>DroEre_CAF1 2 93 - 1
CGCAUCUCCUCGACAUCGGUCUGCAGCAUGUUGUAGUGCUCCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGGUAGUCC---------------------------
...........(((((((((((((((....))))))...........(((((((((((.(((...)))...))))))))))))))))).))).--------------------------- ( -34.30)
>DroWil_CAF1 14338 120 - 1
CGCAUCUCCUCCACAUCCGUUUGCAGCAUGUUGUAGUGCUCUUCUUUGGCGCAUAGCGAUUCCUUGAGCACCGCUAUAUGCCGCUGAUAGUCCUAAUGAGAGUUAUUUUUUACUGUUUCU
.((.((((........(..((.((.((((((.(..((((((.....(.((.....)).)......))))))..).)))))).)).))..).......))))))................. ( -29.16)
>DroMoj_CAF1 2 93 - 1
CGCAUCUCCUCCACGUCCGUCUGCAGCAUGUUGUAGUGCUCCUCUUUGGCACAUAGCGAUUCCUUAAGUACCGCUAUGUGCCGCUGAUAGUCC---------------------------
..............(.(..((.(((((((......))))).......(((((((((((.............))))))))))))).))..).).--------------------------- ( -29.22)
>consensus
CGCAUCUCCUCCACAUCCGUCUGCAGCAUGUUGUAGUGCUCCUCUUUGGCACAUAGCGACUCCUUGAGCACCGCUAUGUGCCGCUGAUAGUCCUAACG__A_UUA____UUACUG____U
..................(((.(((((((......))))).......(((((((((((.............))))))))))))).)))................................ (-25.62 = -25.70 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:26 2006