Locus 7266

Sequence ID	3R_DroMel_CAF1
Location	19,193,803 – 19,193,918
Length	115
Max. P	0.985881

overview

Window 0

Location	19,193,803 – 19,193,918
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.58
Mean single sequence MFE	-41.75
Consensus MFE	-35.00
Energy contribution	-36.50
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-3.10
Structure conservation index	0.84
SVM decision value	2.02
SVM RNA-class probability	0.985881
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19193803 115 + 27905053
AAAUCGUUGGCGAAAAAUGUGCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU-UAC----CAGGCUGCCAGUUAGCCUGGCCAGGCGGCGCUUU
...(((....))).......((((((....((((((((((((..........))))))))))))..))..(((((((.-..(----(((((((.....)))))))))))))))))))... ( -46.20)
>DroSec_CAF1 5776 119 + 1
AAAUCGUUGGCGAAAAAUGUUCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU-UACCAACCAGACUGCCAGUUAGCCUGGCCAGGCGGCGCUUU
.........(((((.....)))))......((((((((((((..........))))))))))))..(((.((((((((-(........))).(((((.....))))))))))).)))... ( -37.80)
>DroSim_CAF1 6174 119 + 1
AAAUCGUUGGCGAAAAAUGUGCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU-UACCAACCAGGCUGCCAGUUAGCCUGGCCAGGCGGCGCUUU
...(((....))).......((((((....((((((((((((..........))))))))))))..))..(((((((.-......((((((((.....)))))))))))))))))))... ( -44.81)
>DroEre_CAF1 7122 115 + 1
AAAUCGUUGGCGAAAAAUGUGCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU-UAC----CAGGCUGCCAGUUAGCCCGGCCAGGCGGCGCUUU
...(((....))).......((((((....((((((((((((..........))))))))))))..))..(((((((.-..(----(.(((((.....))))).)))))))))))))... ( -41.60)
>DroYak_CAF1 9737 116 + 1
AAAUCGUUGGCGAAAAAUGUGCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGUUUAC----CAGGCUGCCAGUUAGCCUGGCCAGGCGGCGCUUU
...(((....))).......((((((....((((((((((((..........))))))))))))..))..(((((((....(----(((((((.....)))))))))))))))))))... ( -45.80)
>DroAna_CAF1 11907 101 + 1
---------GCGAAAAAUGUGCGCGCGAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU-UAC----CAGGCUGCCAGUUAU-----CCAGGCGGCGCUUU
---------...........(((((((...((((((((((((..........)))))))))))).)))..(((((((.-.((----..((...)).))...-----)))))))))))... ( -34.30)
>consensus
AAAUCGUUGGCGAAAAAUGUGCGCGCUAUAAAUUUAUGUUGGCAACAUCAAAUCGACGUAAAUUACGCGACGCCUGGU_UAC____CAGGCUGCCAGUUAGCCUGGCCAGGCGGCGCUUU
........((((.........((((.....((((((((((((..........)))))))))))).)))).((((((((........(((((((.....))))))))))))))).)))).. (-35.00 = -36.50 +   1.50)

alignment

secondary structure

dotplot

Window 1

Location	19,193,803 – 19,193,918
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.58
Mean single sequence MFE	-37.91
Consensus MFE	-30.42
Energy contribution	-30.83
Covariance contribution	0.42
Combinations/Pair	1.08
Mean z-score	-2.19
Structure conservation index	0.80
SVM decision value	0.03
SVM RNA-class probability	0.550127
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19193803 115 - 27905053
AAAGCGCCGCCUGGCCAGGCUAACUGGCAGCCUG----GUA-ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGCACAUUUUUCGCCAACGAUUU
...(((.((((((((((((((.......))))))----)..-.))))))).)))........((((((...(((((((((..............).))).)))))..)))...))).... ( -39.54)
>DroSec_CAF1 5776 119 - 1
AAAGCGCCGCCUGGCCAGGCUAACUGGCAGUCUGGUUGGUA-ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGAACAUUUUUCGCCAACGAUUU
...(((.(((((((....((((((..(....)..)))))).-.))))))).)))((.....(((((.....))))).....))...........(.(((((.....))))))........ ( -38.10)
>DroSim_CAF1 6174 119 - 1
AAAGCGCCGCCUGGCCAGGCUAACUGGCAGCCUGGUUGGUA-ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGCACAUUUUUCGCCAACGAUUU
...(((((((((....))))....((((((((((((.....-)))))))((((((((...)))).)))).......))))).............).)))).......(((....)))... ( -40.00)
>DroEre_CAF1 7122 115 - 1
AAAGCGCCGCCUGGCCGGGCUAACUGGCAGCCUG----GUA-ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGCACAUUUUUCGCCAACGAUUU
...(((.((((((((((((((.......))))))----)..-.))))))).)))........((((((...(((((((((..............).))).)))))..)))...))).... ( -38.84)
>DroYak_CAF1 9737 116 - 1
AAAGCGCCGCCUGGCCAGGCUAACUGGCAGCCUG----GUAAACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGCACAUUUUUCGCCAACGAUUU
...(((((((((....))))....((((((((((----(....))))))((((((((...)))).)))).......))))).............).)))).......(((....)))... ( -39.40)
>DroAna_CAF1 11907 101 - 1
AAAGCGCCGCCUGG-----AUAACUGGCAGCCUG----GUA-ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUCGCGCGCACAUUUUUCGC---------
...((((.((.(((-----((...((((((((((----(..-.))))))((((((((...)))).)))).......)))))......)))))..))))))...........--------- ( -31.60)
>consensus
AAAGCGCCGCCUGGCCAGGCUAACUGGCAGCCUG____GUA_ACCAGGCGUCGCGUAAUUUACGUCGAUUUGAUGUUGCCAACAUAAAUUUAUAGCGCGCACAUUUUUCGCCAACGAUUU
...((((.((((....))))....((((((((((..........)))))((((((((...)))).)))).......))))).............))))...................... (-30.42 = -30.83 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:42 2006