Locus 2227

Sequence ID	3R_DroMel_CAF1
Location	6,343,917 – 6,344,017
Length	100
Max. P	0.919638

overview

Window 7

Location	6,343,917 – 6,344,017
Length	100
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	71.16
Mean single sequence MFE	-20.89
Consensus MFE	-11.15
Energy contribution	-11.65
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.53
SVM decision value	1.13
SVM RNA-class probability	0.919638
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6343917 100 + 27905053
--AAU-----GCCCCUGCC--CCACCCUUCCCGCCAGUCUUCUUCGACCGCCCUCUAUGGCUUCCUUUUGGCCAUUUUGCCACGGCUUAACAUUUCGCGCUCUCCGCA--C
--...-----.........--...........(((.(((......))).((.....((((((.......))))))...))...)))..........(((.....))).--. ( -18.20)
>DroPse_CAF1 106266 100 + 1
--ACCUA--GCCCCCUACC--UCCCCCCUUCAAC----CACCUCAUAUCUCGCACUAUGGCUUCCU-UUGGCCAUUUUGCCAUGGCUUAACGUUUCGCGCUUUGCGCAGUC
--.....--..........--.............----.............(((..((((((....-..))))))..)))................((((...)))).... ( -17.90)
>DroSim_CAF1 122255 100 + 1
--AAU-----GCCCCUGCC--CCGCCCUUCCCGCCAGGCCCCUUCGACCGCCCUCUAUGGCUUCCUUUUGGCCAUUUUGCCACGGCUUAACAUUUCGCGCUCUGCGCA--C
--...-----(((...(((--..((.......))..)))..........((.....((((((.......))))))...))...)))..........((((...)))).--. ( -22.50)
>DroEre_CAF1 119873 86 + 1
CUCAA----------UGUC--UC-CCCUUUC-------CGCAAGC---CUCCCUCUAUGGCUUCCUUUUGGCCAUUUUUCCACGGCUCAACAUUUCGCGCUCUGCGCA--C
.....----------....--..-.......-------....(((---(.......((((((.......))))))........)))).........((((...)))).--. ( -17.66)
>DroYak_CAF1 109427 92 + 1
--AAA-----GCCCCUGCC--CC-CACCAAC-------CCCCUGCCAACGCCCUCUAUGGCUUCCUUUUGGCCAUUUUGCCACGGCUUAACAUUUCGCGCUCUGCGCA--C
--.((-----(((......--..-.......-------.....((((..........)))).......((((......)))).)))))........((((...)))).--. ( -20.40)
>DroAna_CAF1 110808 102 + 1
--ACAUGCGUCCCCCUGCCGUCCGGCAUUGUGGCAGUGCC---CCCAUCCACCUCCAUGGCUUCCU-UUGGCCAUUUUGCCGUGGCUUAACAUUUCGCGCU-UGCACA--C
--.((.((((......((((..(((((..(((((......---.((((........))))......-...)))))..)))))))))..........)))).-))....--. ( -28.68)
>consensus
__AAA_____GCCCCUGCC__CC_CCCUUCC_GC____CCCCUCCCACCGCCCUCUAUGGCUUCCUUUUGGCCAUUUUGCCACGGCUUAACAUUUCGCGCUCUGCGCA__C
........................................................((((((.......))))))...((....))..........((((...)))).... (-11.15 = -11.65 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	6,343,917 – 6,344,017
Length	100
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	71.16
Mean single sequence MFE	-29.03
Consensus MFE	-11.69
Energy contribution	-12.25
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-1.76
Structure conservation index	0.40
SVM decision value	-0.00
SVM RNA-class probability	0.532307
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6343917 100 - 27905053
G--UGCGGAGAGCGCGAAAUGUUAAGCCGUGGCAAAAUGGCCAAAAGGAAGCCAUAGAGGGCGGUCGAAGAAGACUGGCGGGAAGGGUGG--GGCAGGGGC-----AUU--
(--(((.....))))..((((((..(((.((.(....(.(((........(((......)))((((......))))))).)....).)).--)))...)))-----)))-- ( -31.60)
>DroPse_CAF1 106266 100 - 1
GACUGCGCAAAGCGCGAAACGUUAAGCCAUGGCAAAAUGGCCAA-AGGAAGCCAUAGUGCGAGAUAUGAGGUG----GUUGAAGGGGGGA--GGUAGGGGGC--UAGGU--
...(((((...)))))........((((.((((......)))).-....((((((.(((.....)))...)))----)))..........--.......)))--)....-- ( -22.50)
>DroSim_CAF1 122255 100 - 1
G--UGCGCAGAGCGCGAAAUGUUAAGCCGUGGCAAAAUGGCCAAAAGGAAGCCAUAGAGGGCGGUCGAAGGGGCCUGGCGGGAAGGGCGG--GGCAGGGGC-----AUU--
(--(((.....))))..((((((..(((.((.(....(.((((.......(((......)))((((.....)))))))).)....).)).--)))...)))-----)))-- ( -36.00)
>DroEre_CAF1 119873 86 - 1
G--UGCGCAGAGCGCGAAAUGUUGAGCCGUGGAAAAAUGGCCAAAAGGAAGCCAUAGAGGGAG---GCUUGCG-------GAAAGGG-GA--GACA----------UUGAG
(--(((.....))))..(((((((.(((((......))))))....(.(((((.........)---)))).).-------.......-..--))))----------))... ( -24.00)
>DroYak_CAF1 109427 92 - 1
G--UGCGCAGAGCGCGAAAUGUUAAGCCGUGGCAAAAUGGCCAAAAGGAAGCCAUAGAGGGCGUUGGCAGGGG-------GUUGGUG-GG--GGCAGGGGC-----UUU--
(--(((.....))))........(((((.(.((....(.(((((......((((..........)))).....-------.))))).-).--.)).).)))-----)).-- ( -27.20)
>DroAna_CAF1 110808 102 - 1
G--UGUGCA-AGCGCGAAAUGUUAAGCCACGGCAAAAUGGCCAA-AGGAAGCCAUGGAGGUGGAUGGG---GGCACUGCCACAAUGCCGGACGGCAGGGGGACGCAUGU--
(--(((...-.))))...((((...(((.(((((..(((((...-.....)))))....((((.(((.---....)))))))..)))))...)))..(....)))))..-- ( -32.90)
>consensus
G__UGCGCAGAGCGCGAAAUGUUAAGCCGUGGCAAAAUGGCCAAAAGGAAGCCAUAGAGGGCGAUCGAAGGGG____GC_GAAAGGG_GG__GGCAGGGGC_____UUU__
...(((((...))))).........(((.((((......))))........((.....))................................)))................ (-11.69 = -12.25 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:22 2006