Locus 1251

Sequence ID	3L_DroMel_CAF1
Location	3,584,693 – 3,584,788
Length	95
Max. P	0.997889

overview

Window 0

Location	3,584,693 – 3,584,788
Length	95
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	75.59
Mean single sequence MFE	-28.45
Consensus MFE	-16.00
Energy contribution	-18.12
Covariance contribution	2.11
Combinations/Pair	1.13
Mean z-score	-3.49
Structure conservation index	0.56
SVM decision value	2.95
SVM RNA-class probability	0.997889
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3584693 95 + 23771897
AUACUAAAUUCCGUUUUUCCCGAGGA----CCUGCAUUCAUUAGCA-GA-CCUCCU-AUCGGAUG---------------CCACUCGGUAAAUGGAAACAUUUCCGAAAAAAGGAAA
........((((.((((((..((((.----.((((........)))-).-))))..-...(((((---------------((....))))((((....))))))))))))).)))). ( -29.30)
>DroPse_CAF1 154942 108 + 1
ACAUUCACUUCCGACAG---CCAGGAUACUCGGGUAUUCAUUAGGAAGAGCCGCCC-AUUCGCUUUCUCUGGGCGAAAGAACAUUUUGUAAAUGGAAACAGUUUCGAGAAA-----G
...(((.((((((....---.).((((((....))))))....)))))...(((((-(...........))))))...)))..(((((....((....))....)))))..-----. ( -27.40)
>DroSec_CAF1 114540 95 + 1
AUACUAAAUUCCGUUUUUCCCGAGGA----CCUGCAUUCAUUAGCA-GA-CCGCCU-AUCGGAUG---------------CCACUCGGUAAAUGGAAACAUUUCCGAAAAAAGGAAA
........((((.(((((((((((..----...((((((((..((.-..-..))..-)).)))))---------------)..))))).(((((....)))))..)))))).)))). ( -28.70)
>DroSim_CAF1 120392 95 + 1
AUACUAAAUUCCGUUUUUCCCGAGGA----CCUGCAUUUAUUAGCA-GA-CCUCCU-AUCGGAUG---------------CCACUCGGUAAAUGGAAACAUUUCCAAAAAAAGGAAA
........((((((((...(((((..----.((((........)))-).-..(((.-...)))..---------------...))))).))))))))...(((((.......))))) ( -26.00)
>DroEre_CAF1 135903 86 + 1
-------CUUCCGUCUUUCCCGAGGA----CCUGCAUUCAUUAGCA-GA-CCUCCU-AUCGGAUG---------------CCACUCGGUAAAUGGAAACAUUUCCGAA--AAGGAUA
-------..(((((((.....((((.----.((((........)))-).-))))..-...)))).---------------....((((.(((((....))))))))).--..))).. ( -27.50)
>DroYak_CAF1 118905 89 + 1
-------CUUCCGUUUAUCCCGAGGA----CCUGCAUUCAUUAGCA-GA-CCUCCUCAUCGGAUG---------------CCACUCGGUAAAUGGAAACAUUUCCGAAAAAAGGAAA
-------.((((...(((((.(((((----.((((........)))-).-..)))))...)))))---------------....((((.(((((....))))))))).....)))). ( -31.80)
>consensus
AUACUAAAUUCCGUUUUUCCCGAGGA____CCUGCAUUCAUUAGCA_GA_CCUCCU_AUCGGAUG_______________CCACUCGGUAAAUGGAAACAUUUCCGAAAAAAGGAAA
........((((.......(((((((......(((........)))......)))...))))......................((((.(((((....))))))))).....)))). (-16.00 = -18.12 +   2.11)

alignment

secondary structure

dotplot

Window 1

Location	3,584,693 – 3,584,788
Length	95
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	75.59
Mean single sequence MFE	-29.52
Consensus MFE	-12.32
Energy contribution	-15.38
Covariance contribution	3.06
Combinations/Pair	1.12
Mean z-score	-2.37
Structure conservation index	0.42
SVM decision value	1.02
SVM RNA-class probability	0.902168
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3584693 95 - 23771897
UUUCCUUUUUUCGGAAAUGUUUCCAUUUACCGAGUGG---------------CAUCCGAU-AGGAGG-UC-UGCUAAUGAAUGCAGG----UCCUCGGGAAAAACGGAAUUUAGUAU
.((((.((((((((((....)))).....(((((.((---------------(.(((...-.)))..-.(-(((........)))))----))))))))))))).))))........ ( -33.10)
>DroPse_CAF1 154942 108 - 1
C-----UUUCUCGAAACUGUUUCCAUUUACAAAAUGUUCUUUCGCCCAGAGAAAGCGAAU-GGGCGGCUCUUCCUAAUGAAUACCCGAGUAUCCUGG---CUGUCGGAAGUGAAUGU
.-----.................(((((((....(((((....(((((..(....)...)-))))((.....))....))))).((((((......)---)..))))..))))))). ( -22.00)
>DroSec_CAF1 114540 95 - 1
UUUCCUUUUUUCGGAAAUGUUUCCAUUUACCGAGUGG---------------CAUCCGAU-AGGCGG-UC-UGCUAAUGAAUGCAGG----UCCUCGGGAAAAACGGAAUUUAGUAU
.((((.((((((((((....)))).....(((((.((---------------(..(((..-...)))-.(-(((........)))))----))))))))))))).))))........ ( -32.30)
>DroSim_CAF1 120392 95 - 1
UUUCCUUUUUUUGGAAAUGUUUCCAUUUACCGAGUGG---------------CAUCCGAU-AGGAGG-UC-UGCUAAUAAAUGCAGG----UCCUCGGGAAAAACGGAAUUUAGUAU
.((((.((((((((((....)))).....(((((.((---------------(.(((...-.)))..-.(-(((........)))))----))))))))))))).))))........ ( -30.60)
>DroEre_CAF1 135903 86 - 1
UAUCCUU--UUCGGAAAUGUUUCCAUUUACCGAGUGG---------------CAUCCGAU-AGGAGG-UC-UGCUAAUGAAUGCAGG----UCCUCGGGAAAGACGGAAG-------
..(((((--(((((((....)))).....(((((.((---------------(.(((...-.)))..-.(-(((........)))))----))))))))))))..)))..------- ( -29.10)
>DroYak_CAF1 118905 89 - 1
UUUCCUUUUUUCGGAAAUGUUUCCAUUUACCGAGUGG---------------CAUCCGAUGAGGAGG-UC-UGCUAAUGAAUGCAGG----UCCUCGGGAUAAACGGAAG-------
.((((.(((.((((((....)))).....(((((.((---------------(.(((.....)))..-.(-(((........)))))----))))))))).))).)))).------- ( -30.00)
>consensus
UUUCCUUUUUUCGGAAAUGUUUCCAUUUACCGAGUGG_______________CAUCCGAU_AGGAGG_UC_UGCUAAUGAAUGCAGG____UCCUCGGGAAAAACGGAAGUUAGUAU
..(((.((((((((((....)))).....(((((....................(((.....)))......(((........)))........))))))))))).)))......... (-12.32 = -15.38 +   3.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:07 2006