Locus 1616

Sequence ID	X_DroMel_CAF1
Location	4,624,931 – 4,625,086
Length	155
Max. P	0.997960

overview

Window 3

Location	4,624,931 – 4,625,031
Length	100
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	75.75
Mean single sequence MFE	-24.85
Consensus MFE	-14.96
Energy contribution	-15.20
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-1.80
Structure conservation index	0.60
SVM decision value	0.69
SVM RNA-class probability	0.825150
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4624931 100 + 22224390
CCAAG----CCCAUCCAGGACCAACCAUUU-----GGCCAAUCCCGCACCGUCU-------G-UCAUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUG
....(----(.......((.((((....))-----))))......)).......-------.-.................((((..((((((((((....))))).)))))..)))) ( -23.32)
>DroSec_CAF1 11462 91 + 1
-------------CCCAGGACCUCCCAUUU-----GGCCAAUCCCGCACCGUCU-------G-UCAUUAACGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUG
-------------....((.((........-----))))...............-------.-.................((((..((((((((((....))))).)))))..)))) ( -22.00)
>DroEre_CAF1 9431 100 + 1
CCAGG----CUCUACCAGGUCCUCCCAUUU-----GGCCAAUCCCUCACCGUCU-------G-CCAUUACUGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUGGUUG
.((((----(.......((.....((....-----)).....))......))))-------)-.................(((((.((((((((((....))))).))))).))))) ( -27.32)
>DroYak_CAF1 9817 107 + 1
GCAGG----CUCUGGCAGGACCUCCCAUUC-----GGUCAAUCCCGUACCGUCUGUCGCCUG-UCAUUAAUGUAAUUCAAUAACCUUCAUCUCGCCAGUUGGCCGUGAUGAUUGUUG
(((((----(...(((((((((........-----)))).....((...)).))))))))))-)................((((..(((((.((((....)).)).)))))..)))) ( -30.50)
>DroAna_CAF1 72772 106 + 1
CCACUUUCUCCCUUCUCCCACCCGCCACUUUCUCCGGCCAACC----GUCGUCC-------GACCAUUAAUGUAAUUUAAUAACCUCCAUCUGGCCAGUCGGCCAUGAUGAUUGUUG
.......................(((.........)))((((.----((((((.-------....(((((......)))))..........(((((....))))).)))))).)))) ( -21.10)
>consensus
CCAGG____CCCUUCCAGGACCUCCCAUUU_____GGCCAAUCCCGCACCGUCU_______G_UCAUUAAUGUAAUUCAAUAACCUUCAUCUGGCCAGUUGGCCAUGAUGAUUGUUG
................................................................................((((..((((((((((....))))).)))))..)))) (-14.96 = -15.20 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	4,624,931 – 4,625,031
Length	100
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	75.75
Mean single sequence MFE	-32.96
Consensus MFE	-19.26
Energy contribution	-20.58
Covariance contribution	1.32
Combinations/Pair	1.09
Mean z-score	-2.29
Structure conservation index	0.58
SVM decision value	1.97
SVM RNA-class probability	0.984334
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4624931 100 - 22224390
CAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACGUUAAUGA-C-------AGACGGUGCGGGAUUGGCC-----AAAUGGUUGGUCCUGGAUGGG----CUUGG
......(((((.(((((....))))))))))..((((((((......)))))))-)-------...(.((.((((((..(((-----....)))..)))))).)).).----..... ( -41.30)
>DroSec_CAF1 11462 91 - 1
CAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACGUUAAUGA-C-------AGACGGUGCGGGAUUGGCC-----AAAUGGGAGGUCCUGGG-------------
......(((((.(((((....))))))))))..((((((((......)))))))-)-------........(((((((..((-----....))..)))))))..------------- ( -32.00)
>DroEre_CAF1 9431 100 - 1
CAACCAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACAGUAAUGG-C-------AGACGGUGAGGGAUUGGCC-----AAAUGGGAGGACCUGGUAGAG----CCUGG
..(((.(((((.(((((....))))))))))..(((((((.....)))))))..-.-------....)))..(((....(((-----(...((.....))))))....----))).. ( -31.80)
>DroYak_CAF1 9817 107 - 1
CAACAAUCAUCACGGCCAACUGGCGAGAUGAAGGUUAUUGAAUUACAUUAAUGA-CAGGCGACAGACGGUACGGGAUUGACC-----GAAUGGGAGGUCCUGCCAGAG----CCUGC
......(((((.((.((....)))).)))))..((((((((......)))))))-)(((((.....)(((..((((((..((-----....))..)))))))))...)----))).. ( -32.60)
>DroAna_CAF1 72772 106 - 1
CAACAAUCAUCAUGGCCGACUGGCCAGAUGGAGGUUAUUAAAUUACAUUAAUGGUC-------GGACGAC----GGUUGGCCGGAGAAAGUGGCGGGUGGGAGAAGGGAGAAAGUGG
...((.((..(....((.(((.((((......(..((((((......))))))..)-------...(..(----((....)))..)....)))).))).)).....)..))...)). ( -27.10)
>consensus
CAACAAUCAUCAUGGCCAACUGGCCAGAUGAAGGUUAUUGAAUUACAUUAAUGA_C_______AGACGGUGCGGGAUUGGCC_____AAAUGGGAGGUCCUGGAAGAG____CCUGG
.(((..(((((.(((((....))))))))))..)))...................................(((((((..((.........))..)))))))............... (-19.26 = -20.58 +   1.32)

alignment

secondary structure

dotplot

Window 5

Location	4,624,992 – 4,625,086
Length	94
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	73.07
Mean single sequence MFE	-28.20
Consensus MFE	-13.54
Energy contribution	-14.85
Covariance contribution	1.31
Combinations/Pair	1.14
Mean z-score	-2.97
Structure conservation index	0.48
SVM decision value	2.97
SVM RNA-class probability	0.997960
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4624992 94 + 22224390
AAUAACCU-UCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUUGUUUUUCAUGCU------AUGCCAGAGCGCCUCGAA-----AUUUGCAAUUAAUAAUUG------GUAC
....(((.-((((((((((....))))).)))))(((((((((((.((((.((((------.......))))....)))-----)...)))))))))))..)------)).. ( -30.10)
>DroPse_CAF1 41463 106 + 1
AAUAACCCAGCAUCUGGACAGUUGGAUA---UGAUUGCUGAUUGUUUUUCAUUCGCCAGAGCCGCCAGAGCGCUUC---GAGUGGGGUGCAAUUAAUGAUAUUCGAGUGCAC
......((((...)))).((.(((((((---(.((...(((((((.(..((((((...((((.((....)))))))---)))))..).))))))))).)))))))).))... ( -33.00)
>DroSec_CAF1 11514 94 + 1
AAUAACCU-UCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUUGUUUUUCAUGCG------AUGCCAGAGCGCCUCGAA-----AUUUGCAAUUAAUAAUUG------GCAC
........-((((((((((....))))).))))).(((..((((((.....((((------(.....(((...)))...-----..)))))...))))))..------))). ( -29.50)
>DroEre_CAF1 9492 87 + 1
AAUAACCU-UCAUCUGGCCAGUUGGCCAUGAUGAUGGUUGAUUGUUUUUCACGCG------AUGCCAGAGCGCCUCGAA------------AUUAAUAAUUG------CCAA
...((((.-((((((((((....))))).))))).))))(((((((.......((------(.((......)).)))..------------...))))))).------.... ( -27.30)
>DroYak_CAF1 9885 94 + 1
AAUAACCU-UCAUCUCGCCAGUUGGCCGUGAUGAUUGUUGAUUGUUUUUUAUGCG------AUGCCAUAGCGUCUCGCA-----AUUUGCAAUUAAUAAUUG------GCAC
.....((.-(((((.((((....)).)).)))))(((((((((((...((.((.(------((((....))))).)).)-----)...)))))))))))..)------)... ( -27.00)
>DroAna_CAF1 72839 75 + 1
AAUAACCU-CCAUCUGGCCAGUCGGCCAUGAUGAUUGUUGAUUGUUUUACG-------------------------AAA-----AUAUGCAAUUAAUAAUUG------GCAC
.....((.-.(((((((((....))))).))))((((((((((((......-------------------------...-----....)))))))))))).)------)... ( -22.32)
>consensus
AAUAACCU_UCAUCUGGCCAGUUGGCCAUGAUGAUUGUUGAUUGUUUUUCAUGCG______AUGCCAGAGCGCCUCGAA_____AUUUGCAAUUAAUAAUUG______GCAC
..........(((((((((....))))).))))((((((((((((...........................................))))))))))))............ (-13.54 = -14.85 +   1.31)

alignment

secondary structure

dotplot

Window 6

Location	4,624,992 – 4,625,086
Length	94
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	73.07
Mean single sequence MFE	-22.08
Consensus MFE	-10.95
Energy contribution	-12.12
Covariance contribution	1.17
Combinations/Pair	1.13
Mean z-score	-1.58
Structure conservation index	0.50
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4624992 94 - 22224390
GUAC------CAAUUAUUAAUUGCAAAU-----UUCGAGGCGCUCUGGCAU------AGCAUGAAAAACAAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGA-AGGUUAUU
..((------(................(-----((((..((((....))..------.)).)))))............(((((.(((((....))))))))))-.))).... ( -21.40)
>DroPse_CAF1 41463 106 - 1
GUGCACUCGAAUAUCAUUAAUUGCACCCCACUC---GAAGCGCUCUGGCGGCUCUGGCGAAUGAAAAACAAUCAGCAAUCA---UAUCCAACUGUCCAGAUGCUGGGUUAUU
(((((.(..(......)..).)))))((((...---...(((.((((((((...(((...((((..............)))---)..))).))).))))))))))))..... ( -22.44)
>DroSec_CAF1 11514 94 - 1
GUGC------CAAUUAUUAAUUGCAAAU-----UUCGAGGCGCUCUGGCAU------CGCAUGAAAAACAAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGA-AGGUUAUU
((((------((((.....)))).....-----...((.((......)).)------)))))...........(((..(((((.(((((....))))))))))-..)))... ( -23.20)
>DroEre_CAF1 9492 87 - 1
UUGG------CAAUUAUUAAU------------UUCGAGGCGCUCUGGCAU------CGCGUGAAAAACAAUCAACCAUCAUCAUGGCCAACUGGCCAGAUGA-AGGUUAUU
....------..........(------------((((.(..((....))..------)...))))).......((((.(((((.(((((....))))))))))-.))))... ( -25.60)
>DroYak_CAF1 9885 94 - 1
GUGC------CAAUUAUUAAUUGCAAAU-----UGCGAGACGCUAUGGCAU------CGCAUAAAAAACAAUCAACAAUCAUCACGGCCAACUGGCGAGAUGA-AGGUUAUU
((((------((........((((....-----.)))).......))))))------................(((..(((((.((.((....)))).)))))-..)))... ( -22.16)
>DroAna_CAF1 72839 75 - 1
GUGC------CAAUUAUUAAUUGCAUAU-----UUU-------------------------CGUAAAACAAUCAACAAUCAUCAUGGCCGACUGGCCAGAUGG-AGGUUAUU
((((------.(((.....)))))))..-----...-------------------------............(((..(((((.(((((....))))))))))-..)))... ( -17.70)
>consensus
GUGC______CAAUUAUUAAUUGCAAAU_____UUCGAGGCGCUCUGGCAU______CGCAUGAAAAACAAUCAACAAUCAUCAUGGCCAACUGGCCAGAUGA_AGGUUAUU
.........................................((....))........................(((..(((((.(((((....))))))))))...)))... (-10.95 = -12.12 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:46 2006