Locus 5610

Sequence ID	2R_DroMel_CAF1
Location	17,875,527 – 17,875,662
Length	135
Max. P	0.998535

overview

Window 6

Location	17,875,527 – 17,875,624
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	96.49
Mean single sequence MFE	-31.08
Consensus MFE	-27.34
Energy contribution	-27.54
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-2.56
Structure conservation index	0.88
SVM decision value	3.13
SVM RNA-class probability	0.998535
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875527 97 + 20766785
UCGCCCAUUUGCUGACCGCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCC
..((...(((((((((((......)))(((.((((.......)))).)))((((((((........))))))))...........)).)))))))). ( -30.70)
>DroSec_CAF1 40395 97 + 1
UCGCCCAUUUGCUGACCGCAUUUACGGAGCUGGCCUCCAUUUGGCCAGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCC
..((...(((((((((((......)))((((((((.......))))))))((((((((........))))))))...........)).)))))))). ( -35.30)
>DroSim_CAF1 40853 97 + 1
UCGCCCAUUUGCUGACCGCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCC
..((...(((((((((((......)))(((.((((.......)))).)))((((((((........))))))))...........)).)))))))). ( -30.70)
>DroEre_CAF1 42785 97 + 1
UCGCCCAUUUGCUGACCGCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAGGCCAAGCC
..(((.....(((..(((......)))))).))).....(((((((((...(((((((........)))))))(((......))).))))))))).. ( -31.50)
>DroYak_CAF1 39548 97 + 1
UCGCCCAUUUGCUGACCGCAUUCACGAAGCUGGCCUCCAUUUGGCCUGCUUUGUCCGCAAUUAAAGCCAGGCAGUUCAAAGAAACUCAGGCAAAGCC
..(((.....((((.((......(((((((.((((.......)))).)))))))..((.......))..)))))).....(.....).)))...... ( -27.20)
>consensus
UCGCCCAUUUGCUGACCGCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCC
..((...((((((....((....(((((((.((((.......)))).)))))))((((........))))))((((......))))..)))))))). (-27.34 = -27.54 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	17,875,527 – 17,875,624
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	96.49
Mean single sequence MFE	-32.74
Consensus MFE	-28.94
Energy contribution	-29.02
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.88
SVM decision value	1.02
SVM RNA-class probability	0.901861
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875527 97 - 20766785
GGCUUUGCUUGAGUUUCUUUGAACUGCCUGCUUUUAAUUGCAGACAAAGCAGGCCAAAUGGAGGCCAGCUCCGUGAAUGCGGUCAGCAAAUGGGCGA
((((((..((((((((....)))))(((((((((...........))))))))))))...)))))).((.((((...(((.....))).)))))).. ( -32.50)
>DroSec_CAF1 40395 97 - 1
GGCUUUGCUUGAGUUUCUUUGAACUGCCUGCUUUUAAUUGCAGACAAAGCUGGCCAAAUGGAGGCCAGCUCCGUAAAUGCGGUCAGCAAAUGGGCGA
.((((((((.((............((.((((........)))).)).((((((((.......))))))))((((....)))))))))))...))).. ( -32.80)
>DroSim_CAF1 40853 97 - 1
GGCUUUGCUUGAGUUUCUUUGAACUGCCUGCUUUUAAUUGCAGACAAAGCAGGCCAAAUGGAGGCCAGCUCCGUGAAUGCGGUCAGCAAAUGGGCGA
((((((..((((((((....)))))(((((((((...........))))))))))))...)))))).((.((((...(((.....))).)))))).. ( -32.50)
>DroEre_CAF1 42785 97 - 1
GGCUUGGCCUGAGUUUCUUUGAACUGCCUGCUUUUAAUUGCAGACAAAGCAGGCCAAAUGGAGGCCAGCUCCGUGAAUGCGGUCAGCAAAUGGGCGA
((((((((((((((((....)))))..((((........))))......)))))))......)))).((.((((...(((.....))).)))))).. ( -35.00)
>DroYak_CAF1 39548 97 - 1
GGCUUUGCCUGAGUUUCUUUGAACUGCCUGGCUUUAAUUGCGGACAAAGCAGGCCAAAUGGAGGCCAGCUUCGUGAAUGCGGUCAGCAAAUGGGCGA
....((((((.(((((....)))))((.(((((.((.(..(((....(((.((((.......)))).))))))..).)).)))))))....)))))) ( -30.90)
>consensus
GGCUUUGCUUGAGUUUCUUUGAACUGCCUGCUUUUAAUUGCAGACAAAGCAGGCCAAAUGGAGGCCAGCUCCGUGAAUGCGGUCAGCAAAUGGGCGA
.((((((....(((((....)))))..((((........)))).)))))).((((.......)))).((.((((...(((.....))).)))))).. (-28.94 = -29.02 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	17,875,544 – 17,875,662
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.79
Mean single sequence MFE	-33.74
Consensus MFE	-24.40
Energy contribution	-24.84
Covariance contribution	0.44
Combinations/Pair	1.05
Mean z-score	-2.68
Structure conservation index	0.72
SVM decision value	1.31
SVM RNA-class probability	0.940516
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17875544 118 + 20766785
GCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCCAAGUACACUGGGGAAA--AAACCCUCCCAAUGCUGCUAAG
(((((...((((.....))))(((((((.((((((((((((........)))))))(((......)))..)))))..)))))))......((((..--......)))))))))....... ( -36.40)
>DroSec_CAF1 40412 107 + 1
GCAUUUACGGAGCUGGCCUCCAUUUGGCCAGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCCAAGUACACUGGGGAAA--AAACCAUCCCA-----------
((......((((((((((.......))))))))))((((((........)))))).................))................((((..--......)))).----------- ( -35.10)
>DroSim_CAF1 40870 109 + 1
GCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCCAAGUACACUGGGGAAAAAAAACCCUCCCA-----------
........((((.....))))(((((((.((((((((((((........)))))))(((......)))..)))))..)))))))......((((..........)))).----------- ( -31.90)
>DroEre_CAF1 42802 107 + 1
GCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAGGCCAAGCCGAGUACACUGGGGAAA--AUACUGGCUCA-----------
.........((((..(......(((((((((...(((((((........)))))))(((......))).)))))))))((.((....)).))....--...)..)))).----------- ( -37.70)
>DroYak_CAF1 39565 102 + 1
GCAUUCACGAAGCUGGCCUCCAUUUGGCCUGCUUUGUCCGCAAUUAAAGCCAGGCAGUUCAAAGAAACUCAGGCAAAGCCAAGUACACUGUGGAAA--AU-----CUCA-----------
.......((((((.((((.......)))).))))))(((((.......(((..(.((((......))))).))).......((....)))))))..--..-----....----------- ( -27.60)
>consensus
GCAUUCACGGAGCUGGCCUCCAUUUGGCCUGCUUUGUCUGCAAUUAAAAGCAGGCAGUUCAAAGAAACUCAAGCAAAGCCAAGUACACUGGGGAAA__AAACCCUCCCA___________
((......(((((.((((.......)))).)))))((((((........)))))).................))....((.((....)).))............................ (-24.40 = -24.84 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:53 2006