Locus 3540

Sequence ID	3L_DroMel_CAF1
Location	10,371,020 – 10,371,123
Length	103
Max. P	0.995015

overview

Window 7

Location	10,371,020 – 10,371,123
Length	103
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	74.02
Mean single sequence MFE	-26.98
Consensus MFE	-17.76
Energy contribution	-17.68
Covariance contribution	-0.08
Combinations/Pair	1.19
Mean z-score	-2.02
Structure conservation index	0.66
SVM decision value	1.89
SVM RNA-class probability	0.981574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10371020 103 + 23771897
--GCCAC------------AACUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGCUAAAAUACUGGCCAUCCAGCGUCCCGAGGCAUUGAUUAAAAUGGCUUCUUUU
--((((.------------....((((((((((((((((....)).)))))))).)))..((((((...(..((((....))))..).....))))))))).....))))....... ( -33.30)
>DroVir_CAF1 285265 102 + 1
--ACCUCUAGCUGUUGCCUGUCUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGUAAAA--------CAUUCAA-----CGAGGCAUUGAUUAAAAUUGUUUUCCUA
--.((((((((((((((.((((...(.((((....)))).).)))).).))))).)))).((((.....--------))))...-----.))))....................... ( -25.50)
>DroGri_CAF1 263937 102 + 1
--GUUGCAAGCUGUUGCCGUCCUGUCAACUGCUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGUAAAA--------CAUUCAA-----CGAGGCAUUGAUUAAAAUUGUUUCCUUU
--((((.((....((((((..((((((.....)))))).))(((((((....)))))))....))))..--------..)))))-----)((((((...........)))))).... ( -25.00)
>DroWil_CAF1 385188 92 + 1
UUGCUUU------------AGCUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGUUAAA--------CAUCUUG-----CAAGGCAUUGAUUAAAAUUGUUUUUAUU
.((((((------------.((....(((((((((((((....)).)))))))).)))...(((.....--------)))...)-----)))))))..................... ( -24.40)
>DroMoj_CAF1 322283 102 + 1
--GCCACUAGCUGUUGCCUGUCUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUUAAAUGUAAAA--------CAUUCAG-----CGAAGCAUUGAUUAAAAUUGCUUUCCUU
--.......((((.............(((((((((((((....)).)))))))).)))..((((.....--------)))))))-----)((((((...........)))))).... ( -26.80)
>DroAna_CAF1 250974 100 + 1
--GCUGA------------AACUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGCUAAAAUGCCGGCCAUCCAC---CAAGAGGCAUUGAUUAAAAUUUUUCCUUUU
--(((((------------.....)))))((((((((((....)).)))))))).((......))...((((((..........---.....))))))................... ( -26.86)
>consensus
__GCCAC____________AACUGUCAGCUGUUGACAGCCGUGGCAUGUCAACAUGCUAAAAUGUAAAA________CAUCCAG_____CGAGGCAUUGAUUAAAAUUGUUUCCUUU
..........................(((((((((((((....)).)))))))).)))................................((((((((......))).))))).... (-17.76 = -17.68 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	10,371,020 – 10,371,123
Length	103
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.02
Mean single sequence MFE	-29.44
Consensus MFE	-18.63
Energy contribution	-18.52
Covariance contribution	-0.11
Combinations/Pair	1.13
Mean z-score	-2.63
Structure conservation index	0.63
SVM decision value	2.53
SVM RNA-class probability	0.995015
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10371020 103 - 23771897
AAAAGAAGCCAUUUUAAUCAAUGCCUCGGGACGCUGGAUGGCCAGUAUUUUAGCAUUUUAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGUU------------GUGGC--
.......(((((.......(((((...((((..((((....))))..)))).)))))(((((.((((((((.((....))))))))))))))).....------------)))))-- ( -35.70)
>DroVir_CAF1 285265 102 - 1
UAGGAAAACAAUUUUAAUCAAUGCCUCG-----UUGAAUG--------UUUUACAUUUUAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGACAGGCAACAGCUAGAGGU--
......................((((((-----(((..((--------(((......(((((.((((((((.((....))))))))))))))).)))))..)))).....)))))-- ( -30.90)
>DroGri_CAF1 263937 102 - 1
AAAGGAAACAAUUUUAAUCAAUGCCUCG-----UUGAAUG--------UUUUACAUUUUAGCAUGUUGACAUGCCACGGCUGUCAGCAGUUGACAGGACGGCAACAGCUUGCAAC--
...(....)..................(-----(((((((--------.....)).)))))).((((((((.((....))))))))))((((.((((..(....)..))))))))-- ( -27.90)
>DroWil_CAF1 385188 92 - 1
AAUAAAAACAAUUUUAAUCAAUGCCUUG-----CAAGAUG--------UUUAACAUUUUAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGCU------------AAAGCAA
.....................(((.(((-----(..((((--------.....))))(((((.((((((((.((....)))))))))))))))..)).------------)).))). ( -24.90)
>DroMoj_CAF1 322283 102 - 1
AAGGAAAGCAAUUUUAAUCAAUGCUUCG-----CUGAAUG--------UUUUACAUUUAAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGACAGGCAACAGCUAGUGGC--
...(((.(((...........))))))(-----(((..((--------(((........(((.((((((((.((....))))))))))))).......))))).)))).......-- ( -27.16)
>DroAna_CAF1 250974 100 - 1
AAAAGGAAAAAUUUUAAUCAAUGCCUCUUG---GUGGAUGGCCGGCAUUUUAGCAUUUUAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGUU------------UCAGC--
......................(((....)---)).((((((((((((.(((((((......))))))).)))))..)))))))....(((((.....------------)))))-- ( -30.10)
>consensus
AAAAAAAACAAUUUUAAUCAAUGCCUCG_____CUGAAUG________UUUAACAUUUUAGCAUGUUGACAUGCCACGGCUGUCAACAGCUGACAGAU____________GAAGC__
.........................................................(((((.((((((((.((....)))))))))))))))........................ (-18.63 = -18.52 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:37 2006