Locus 6550

Sequence ID	3R_DroMel_CAF1
Location	17,254,957 – 17,255,152
Length	195
Max. P	0.947219

overview

Window 4

Location	17,254,957 – 17,255,073
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	91.76
Mean single sequence MFE	-34.33
Consensus MFE	-30.67
Energy contribution	-30.33
Covariance contribution	-0.33
Combinations/Pair	1.14
Mean z-score	-1.22
Structure conservation index	0.89
SVM decision value	0.06
SVM RNA-class probability	0.563874
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17254957 116 - 27905053
UACACAGAUACACGACGGCUGCAGAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU----
................((..(((((((((((((...(((((((.(....)))))))).)))))))......(((((.(.....).)))))...............))))))))...---- ( -36.60)
>DroSec_CAF1 51505 116 - 1
UACACAGAUACUCGCCGGCUGAAAAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUACACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU----
....((((...((((((.((....)).)).))))..(((((...(.((((((((.....)))).)))).).(((((.(.....).))))).)))))..........))))......---- ( -33.10)
>DroSim_CAF1 52104 116 - 1
UACACAGAUACUCGCCGGCUGAAAAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU----
................(((.(((((((((((((...(((((((.(....)))))))).)))))))))))..(((((.(.....).)))))................)).)))....---- ( -34.60)
>DroEre_CAF1 53479 116 - 1
UACACAGAUACUCGACGGCUGAAGAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU----
................(((.(((((((((((((...(((((((.(....)))))))).)))))))).....(((((.(.....).)))))...........)))))...)))....---- ( -36.20)
>DroYak_CAF1 74419 116 - 1
UACACAGAUACUCACCAGCUGAGAAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU----
.................((.(((((((((((((...(((((((.(....)))))))).)))))))......(((((.(.....).)))))............)))))).)).....---- ( -35.90)
>DroAna_CAF1 42244 111 - 1
UACUCGGAUACAC---------AGAGGUGUGCGAAAGCAACGCACUGAAGGUGUUACCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUUUCUGCCCAAAGGAG
...(((.((((..---------....)))).)))..(((((...(.((((((((.....)))).)))).).(((((.(.....).))))).))))).....((((((......)))))). ( -29.60)
>consensus
UACACAGAUACUCGCCGGCUGAAAAGGUGUGCGAAAGCGACGCACUGAAGGUGUUGCCUGCACGCUUUUGAUGAGCACUAAUUGAGCUCAAGUUGCAUUUUUCUUCUCUGCCCAUU____
....((((..............(((((((((((...(((((((.(....)))))))).)))))))))))..(((((.(.....).)))))................)))).......... (-30.67 = -30.33 +  -0.33)

alignment

secondary structure

dotplot

Window 5

Location	17,255,033 – 17,255,152
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.30
Mean single sequence MFE	-39.12
Consensus MFE	-20.32
Energy contribution	-22.68
Covariance contribution	2.36
Combinations/Pair	1.19
Mean z-score	-2.19
Structure conservation index	0.52
SVM decision value	1.37
SVM RNA-class probability	0.947219
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17255033 119 + 27905053
UCGCUUUCGCACACCUCUGCAGCCGUCGUGUAUCUGUGUACCUGGGUA-UCUGGGCAUCUGGGUAUCUGGGUAUCUAAGUAUCUGAGCGUCUCAGAUACUGAUGCGAGUAUAUGCUGGCC
........(((......))).((((.((((((..((((((((..((((-((..(....)..))))))..)))))...((((((((((...))))))))))...)))..)))))).)))). ( -48.00)
>DroSec_CAF1 51581 119 + 1
UCGCUUUCGCACACCUUUUCAGCCGGCGAGUAUCUGUGUACCUGGGUA-UCUGCGCAUCUGGGUAUCUGGGUAUCUAAGUAUCUGAGCGUCUCAGAUACUGAUGCGAGAAUCUGCUGGCC
..((....))...........(((((((.(((((...(((((..((((-(((........)))))))..)))))...((((((((((...)))))))))))))))(.....)))))))). ( -45.60)
>DroSim_CAF1 52180 119 + 1
UCGCUUUCGCACACCUUUUCAGCCGGCGAGUAUCUGUGUACCUGGGUA-UCUGCGCAUCUGGGUAUCUGGGUAUCUAAGUAUCUGAGCGUCUCAGAUACUGAUGCGAGUAUCUGCUGGCC
..((....))...........(((((((..((..((((((((..((((-(((........)))))))..)))))...((((((((((...))))))))))...)))..))..))))))). ( -46.90)
>DroEre_CAF1 53555 98 + 1
UCGCUUUCGCACACCUCUUCAGCCGUCGAGUAUCUGUGUACCUGGGUA-UCUUAGUAUCUAAGUAUCUGAGUAU----------------CUCGGU-----GUGCGAGUAUCUGCUGGCC
..((....))...........((((.((..((..((..((((.(((((-.((((((((....))).))))))))----------------)).)))-----)..))..))..)).)))). ( -28.70)
>DroAna_CAF1 42324 106 + 1
UUGCUUUCGCACACCUCU---------GUGUAUCCGAGUAUCUGGCUGGUC--UGCAUCU--GUAUCUAAGUAUCUGUGUAUCUUAGCAUCUCGG-UGUGUAUCUGAGCAUCUCCAGGCC
.(((((..(((((((...---------(......)(((......(((((..--(((((..--((((....))))..)))))..)))))..)))))-)))))....))))).......... ( -26.40)
>consensus
UCGCUUUCGCACACCUCUUCAGCCGGCGAGUAUCUGUGUACCUGGGUA_UCUGCGCAUCUGGGUAUCUGGGUAUCUAAGUAUCUGAGCGUCUCAGAUACUGAUGCGAGUAUCUGCUGGCC
..(((((((((..................(((((((.((((((((((.........)))))))))).)))))))...((((((((((...))))))))))..))))))........))). (-20.32 = -22.68 +   2.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:17 2006