Locus 1706

Sequence ID	3R_DroMel_CAF1
Location	4,898,254 – 4,898,402
Length	148
Max. P	0.852728

overview

Window 0

Location	4,898,254 – 4,898,371
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	77.95
Mean single sequence MFE	-47.74
Consensus MFE	-24.88
Energy contribution	-24.02
Covariance contribution	-0.86
Combinations/Pair	1.38
Mean z-score	-1.95
Structure conservation index	0.52
SVM decision value	0.35
SVM RNA-class probability	0.698586
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4898254 117 - 27905053
CCGGCGACUGCAGCAGCUGCUCAGGCAGCGGUGGCCGCGGCUGCCAACAAUAUGUUCGGAUCCAACAGCUCGAUCUUCUCGAAUCCCCUGGCCAUUCCGGGUACCGCAGCUGUGGCA
.........((.((((((((...((((((.((....)).)))))).......((..((((.....(((.((((.....)))).....))).....))))..))..)))))))).)). ( -46.80)
>DroGri_CAF1 8707 117 - 1
CCGGCAACAGCAGCAGCCGCACAGGCGGCCGUUGCCGCGGCGGCCAACAAUAUGUUUGGCUCGAACAGUUCGCUCUUCUCGAGCCAUCUGGCCAUGCCGGGCACCACACCAGCAGCA
((((((...(((((.(((((....))))).)))))......(((((((.....)))((((((((..((......))..))))))))...)))).))))))((.........)).... ( -51.80)
>DroWil_CAF1 7479 110 - 1
CCCACCACAGCGGCAGCUGCUCAGGCUGCUGUGGCAGCCGCUGCAAAUAACAUGUUCGGCUCGAAUAGUUCCCUUUUCUCCAAUCAUCUGGCCAUACCGGGAACCGCUG---U----
......(((((((((((......((((((....)))))))))))........((((((...))))))((((((......(((......))).......)))))))))))---)---- ( -40.72)
>DroYak_CAF1 6330 117 - 1
CCGGCGACUGCAGCAGCUGCCCAGGCAGCGGUGGCCGCGGCUGCCAACAAUAUGUUCGGAUCCAACAGCUCGAUCUUCUCGAACCCCCUGGCCAUUCCGGGUACCGCAGCCGUGGCA
((.((.......)).(((((....)))))))..(((((((((((.........(((((((((.........))))....)))))..(((((.....)))))....))))))))))). ( -49.80)
>DroMoj_CAF1 7557 117 - 1
CCGGCCACAGCGGCAGCGGCCCAGGCGGCAGUUGCGGCCGCAGCGAACAAUAUGUUCGGGUCGAACAGUUCGCUCUUCUCGAAUCACUUGGCGCUGCCGGGCACAACGCCCGCCGCC
.((((......(((((((.((.(((((((.......)))))(((((((....((((((...)))))))))))))............)).)))))))))((((.....)))))))).. ( -57.20)
>DroAna_CAF1 1666 117 - 1
CCGGCAACAGCAGCAGCUGCCCAGGCAGCCGUGGCCGCCGCCGCCAAUAAUAUGUUCGGCUCGAAUAGCUCACUAUUUUCGAAUCACCUGGCCAUCCCGGGAACUGCAGCAGUGGCU
..(((..(.((.((.(((((....))))).)).)).)..)))((((......(((((((.((((((((....))))..))))....(((((.....)))))..))).)))).)))). ( -40.10)
>consensus
CCGGCAACAGCAGCAGCUGCCCAGGCAGCCGUGGCCGCCGCUGCCAACAAUAUGUUCGGCUCGAACAGCUCGCUCUUCUCGAAUCACCUGGCCAUGCCGGGAACCGCAGCAGUGGCA
.........(((((.(((((....))))).(((((....)))))........((((((...)))))))))................(((((.....))))).............)). (-24.88 = -24.02 +  -0.86)

alignment

secondary structure

dotplot

Window 1

Location	4,898,294 – 4,898,402
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	70.47
Mean single sequence MFE	-42.26
Consensus MFE	-19.35
Energy contribution	-19.03
Covariance contribution	-0.32
Combinations/Pair	1.61
Mean z-score	-1.87
Structure conservation index	0.46
SVM decision value	0.79
SVM RNA-class probability	0.852728
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4898294 108 - 27905053
GCAACAACAGCAGCUGGCCGCCGUUGGUCUGCCGGCGACUGCAGCAGCUGCUCAGGCAGCGGUGGCCGCGGCUGCCAACAAUAUGUUCGGAUCCAACAGCUCGAUCUU
((.....((((.((.(((((((....(.((((.(....).))))).(((((....)))))))))))))).))))(((((.....))).))........))........ ( -44.70)
>DroPse_CAF1 33800 88 - 1
-----AACGACAGAUGG---CCGUGGGCCUGCCGGCCACCGCUGCGGCUGCCCAGG------------CGGCCGUCAACAACAUGUUCGGCUCAAACAGCUCGCUGUU
-----.......(((((---((((((((..((((((....))..)))).))))..)------------))))))))...((((.((..((((.....)))).)))))) ( -36.90)
>DroGri_CAF1 8747 95 - 1
----------CAGCUGG---CUGUGGGCCUGCCGGCAACAGCAGCAGCCGCACAGGCGGCCGUUGCCGCGGCGGCCAACAAUAUGUUUGGCUCGAACAGUUCGCUCUU
----------.(((..(---((((.((((.((((....).(((((.(((((....))))).)))))...)))))))..(((.....)))......)))))..)))... ( -43.40)
>DroWil_CAF1 7512 98 - 1
----------CAAUUGGCUGCCGUUGGCUUGCCCACCACAGCGGCAGCUGCUCAGGCUGCUGUGGCAGCCGCUGCAAAUAACAUGUUCGGCUCGAAUAGUUCCCUUUU
----------.....(((((((((((............)))))))))))((...((((((....))))))...))....(((.((((((...)))))))))....... ( -39.10)
>DroMoj_CAF1 7597 95 - 1
----------CAGCUGG---CGGUCGGUCUGCCGGCCACAGCGGCAGCGGCCCAGGCGGCAGUUGCGGCCGCAGCGAACAAUAUGUUCGGGUCGAACAGUUCGCUCUU
----------..((((.---.((((((....)))))).))))....(((((((((.(....)))).))))))(((((((....((((((...)))))))))))))... ( -47.20)
>consensus
__________CAGCUGG___CCGUGGGCCUGCCGGCCACAGCAGCAGCUGCCCAGGCGGC_GUGGCCGCGGCUGCCAACAAUAUGUUCGGCUCGAACAGUUCGCUCUU
...........(((((.....(((.((....)).)))......((((((((................)))))))).....................)))))....... (-19.35 = -19.03 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:22 2006