Locus 10069

Sequence ID	3R_DroMel_CAF1
Location	26,964,531 – 26,964,630
Length	99
Max. P	0.922233

overview

Window 5

Location	26,964,531 – 26,964,630
Length	99
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.41
Mean single sequence MFE	-30.67
Consensus MFE	-17.75
Energy contribution	-19.33
Covariance contribution	1.59
Combinations/Pair	1.20
Mean z-score	-1.53
Structure conservation index	0.58
SVM decision value	0.07
SVM RNA-class probability	0.566670
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26964531 99 + 27905053
AGCAGGACACGCGUCGCAUUAAUGCGUACACGGAUUUCGCAGGCUCAGAGAUCCACGGGCUCGAGCCUGCGAGUGCAGCCAGAAUCUACACUC----AAAUAC
....(((..((.((((((....)))).)).))...)))((((((((.(((.((....)))))))))))))(((((.((.......)).)))))----...... ( -36.80)
>DroSec_CAF1 12082 102 + 1
AGCAGGACACGCGUCGCAUUAAUGCGUACAUGGAUUUCACAGGCUCAGAGAUCC-CAGGCUCCAGCGUGCGAGUGCAGCCAAAAUCUACACUCCCCGAACUGC
.(((((.(((((((((((....)))).))..(((((((.........)))))))-.........))))))(((((.((.......)).)))))......)))) ( -31.60)
>DroSim_CAF1 12375 103 + 1
AGCAGGACACGCGUCGCAUUAAUGCGUACACGGAUUUCCCAGGCUCAGAGAUCCACGGGCUCCAGCCUGCGAGUGCAGCCAAUCUCUACACUCCUCGAACUGC
.((((..(..((((((((....)))).))..(((((((.........)))))))..((((....))))))(((((.((.......)).)))))...)..)))) ( -31.80)
>DroEre_CAF1 14134 76 + 1
AGCAGGACACGCGUCGCAUUAAUGCGAACAGGGAUUUCCCAGGC----------------UCGAGCCUGCGAGUGCAGCCAAAAUCUACACU-----------
.(((((.(.((.((((((....))).....(((....))).)))----------------.)).)))))).((((.((.......)).))))----------- ( -24.80)
>DroYak_CAF1 12136 103 + 1
AGCAGGACACGCGUCGCAUUAAUGCGUACACGGAUUUCCCAGGCUCGCAGAUCCACGGGCUCGAGCCUCCGAGUGCAGCCAAAAUCUACACUCCUCGAACUGC
.((((..(.((.((((((....)))).)).))((......(((((((.((.((....)))))))))))..(((((.((.......)).))))).)))..)))) ( -32.70)
>DroAna_CAF1 12881 101 + 1
AGUAGAACACGCGUCGCAUUAAUGCGUACACGGAUUUUCCUGGCUAGGAAAUUCAGUAGGCUGGCCCAACAAGUGCAGCCUAAAGAUACACUUG--GAAAAAU
((.((((..((.((((((....)))).)).))..)))).))..(((((....((..(((((((((.......)).)))))))..))....))))--)...... ( -26.30)
>consensus
AGCAGGACACGCGUCGCAUUAAUGCGUACACGGAUUUCCCAGGCUCAGAGAUCCACGGGCUCGAGCCUGCGAGUGCAGCCAAAAUCUACACUCC__GAACUGC
.(((((......((((((....)))).))..(((((((.........)))))))...........)))))(((((.((.......)).))))).......... (-17.75 = -19.33 +   1.59)

alignment

secondary structure

dotplot

Window 6

Location	26,964,531 – 26,964,630
Length	99
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.41
Mean single sequence MFE	-36.70
Consensus MFE	-23.62
Energy contribution	-24.45
Covariance contribution	0.84
Combinations/Pair	1.14
Mean z-score	-1.89
Structure conservation index	0.64
SVM decision value	1.15
SVM RNA-class probability	0.922233
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26964531 99 - 27905053
GUAUUU----GAGUGUAGAUUCUGGCUGCACUCGCAGGCUCGAGCCCGUGGAUCUCUGAGCCUGCGAAAUCCGUGUACGCAUUAAUGCGACGCGUGUCCUGCU
......----((((((((.......))))))))(((((((((((.(....)..))).))))))))......(((((.((((....)))))))))......... ( -41.10)
>DroSec_CAF1 12082 102 - 1
GCAGUUCGGGGAGUGUAGAUUUUGGCUGCACUCGCACGCUGGAGCCUG-GGAUCUCUGAGCCUGUGAAAUCCAUGUACGCAUUAAUGCGACGCGUGUCCUGCU
((((......((((((((.......))))))))((((((((((.(.((-((.((...)).)))).)...)))).((.((((....)))))))))))).)))). ( -37.50)
>DroSim_CAF1 12375 103 - 1
GCAGUUCGAGGAGUGUAGAGAUUGGCUGCACUCGCAGGCUGGAGCCCGUGGAUCUCUGAGCCUGGGAAAUCCGUGUACGCAUUAAUGCGACGCGUGUCCUGCU
((((..((.(((((((((.......))))))((.((((((((((.(....)..)))).)))))).))..)))((((.((((....)))))))).))..)))). ( -42.80)
>DroEre_CAF1 14134 76 - 1
-----------AGUGUAGAUUUUGGCUGCACUCGCAGGCUCGA----------------GCCUGGGAAAUCCCUGUUCGCAUUAAUGCGACGCGUGUCCUGCU
-----------(((((((.......))))))).((((((.(((----------------((..(((....))).))))(((....))).....).).))))). ( -28.20)
>DroYak_CAF1 12136 103 - 1
GCAGUUCGAGGAGUGUAGAUUUUGGCUGCACUCGGAGGCUCGAGCCCGUGGAUCUGCGAGCCUGGGAAAUCCGUGUACGCAUUAAUGCGACGCGUGUCCUGCU
((((..((..((((((((.......))))))))(((..((((.((.(((......))).)).))))...)))((((.((((....)))))))).))..)))). ( -41.30)
>DroAna_CAF1 12881 101 - 1
AUUUUUC--CAAGUGUAUCUUUAGGCUGCACUUGUUGGGCCAGCCUACUGAAUUUCCUAGCCAGGAAAAUCCGUGUACGCAUUAAUGCGACGCGUGUUCUACU
.......--..((((..((..(((((((..((....))..)))))))..)).((((((....))))))...(((((.((((....))))))))).....)))) ( -29.30)
>consensus
GCAGUUC__GGAGUGUAGAUUUUGGCUGCACUCGCAGGCUCGAGCCCGUGGAUCUCUGAGCCUGGGAAAUCCGUGUACGCAUUAAUGCGACGCGUGUCCUGCU
..........((((((((.......))))))))(((((((..................)))))((((....(((((.((((....)))))))))..)))))). (-23.62 = -24.45 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:48:12 2006