Locus 5903

Sequence ID	3L_DroMel_CAF1
Location	15,855,782 – 15,856,017
Length	235
Max. P	0.993322

overview

Window 1

Location	15,855,782 – 15,855,897
Length	115
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	82.97
Mean single sequence MFE	-28.95
Consensus MFE	-24.74
Energy contribution	-25.17
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.90
Structure conservation index	0.85
SVM decision value	1.00
SVM RNA-class probability	0.897209
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15855782 115 - 23771897
CGGAGCAAUGCUGGCCACGUCAUGAAUGACUGCCCAUCGAAUGCUCAAAUGCUCGAUUGCCAAGCGGAAAAAGUGCUGAGAAAAGCGGUAGCUCAAAAAACUGAAAAGGAAAA-AA
..((((..(((((((...((((....)))).....(((((..((......))))))).))).)))).....(.((((......)))).).))))......((....)).....-.. ( -28.40)
>DroSim_CAF1 64610 116 - 1
CGGAGCAAUGCUGGCCACGUCAUGAAUGACUGCCCAUCGAAUGCUCAAAUGCUCGAAUGCCAAGCGGAAAAAGUGCUGAGAAAAGCGGUAGCUCAAAAAACUGAAAAGAAAAAAAA
..((((..(((((((...((((....))))......((((..((......))))))..))).)))).....(.((((......)))).).))))......((....))........ ( -27.80)
>DroEre_CAF1 62728 88 - 1
CGGAGCAAUGCUGGCCACGUCAUGAAUGACUGCCCAUCGAGUG--------CUCGAGUGCCAAGCGGAAAAAUUGCUGAGAAAAGCGGUAGCUCAA--------------------
..((((..(((((((.((((((....))))......((((...--------.))))))))).)))).....((((((......)))))).))))..-------------------- ( -28.80)
>DroYak_CAF1 104357 103 - 1
CGGAGCAAUGCUGGCCACGUCAUGAAUGACUGCCCAUCGAAGG--------CUCGAAUGCCAAGCGGAAAAACUGCUGAGAAAAGCGGUAGCUCAAACAACUGAAAAGGAA-----
..((((..((((((.((.((((....)))))).))......((--------(......))).)))).....((((((......)))))).))))......((....))...----- ( -30.80)
>consensus
CGGAGCAAUGCUGGCCACGUCAUGAAUGACUGCCCAUCGAAUG________CUCGAAUGCCAAGCGGAAAAAGUGCUGAGAAAAGCGGUAGCUCAAAAAACUGAAAAGGAA_____
..((((..(((((((...((((....))))......((((............))))..))).)))).....((((((......)))))).))))...................... (-24.74 = -25.17 +   0.44)

alignment

secondary structure

dotplot

Window 2

Location	15,855,897 – 15,856,017
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-36.23
Consensus MFE	-28.54
Energy contribution	-28.65
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.88
Structure conservation index	0.79
SVM decision value	0.50
SVM RNA-class probability	0.759174
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15855897 120 + 23771897
GCCUAAUCCUCCACUGCCGUUUUGCCUGCCAAAUCGGCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGCGCUAUUUGGCAGGCUUUUGCCUGCUUUUCAUGGUUUAC
...........(((.((((.((((.....)))).)))).)))((((.(((.................(((((((.....)))))))...(((((((....)))))))))).))))..... ( -36.70)
>DroPse_CAF1 61801 120 + 1
GCGUAAUCCUCGACUGCCGCUUUGCCUGCCAAAUCGUCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGUGCUAUUUGGCAGGCUUUUGUCUGCGCUUCAAGGCUUAC
..((((.(((.((..((.((...(((((((((((.......((((......................))))((((.....)))).)))))))))))........)))).)).))).)))) ( -37.35)
>DroSim_CAF1 64726 120 + 1
GCCUAAUCCUCUACUGCCGUUUUGCCUGCCAAAUCGGCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGCGCUAUUUGGCAGGCUUUUGUCUGCUUUUCAUGGUUUAC
...(((.((......((.(....((((((((((..(((...))).......................(((((((.....)))))))))))))))))......).)).......)).))). ( -33.22)
>DroEre_CAF1 62816 120 + 1
GCCUAAUCCUCUACUGCCGUUUUGCCUGCCAAAUCGGCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGCGCUAUUUGGCAGGCUUUUGUCUGCUUUUCAGCGUUUAC
...............((((.((((.....)))).))))(((((((......................)))))))......(((((....(((((((....)))))))....))))).... ( -34.25)
>DroYak_CAF1 104460 120 + 1
GCCUAAUCCUCCACUGCCGUUUUGCCUGCCAAAUCGGCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGCGCUAUUUGGCAGGCUUUUGUCUGCUGUUCAGGGUUUAC
....((((((..((.((.(....((((((((((..(((...))).......................(((((((.....)))))))))))))))))......).)).))..))))))... ( -38.50)
>DroPer_CAF1 63692 120 + 1
GCGUAAUCCUCGACUGCCGCUUUGCCUGCCAAAUCGUCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGUGCUAUUUGGCAGGCUUUUGUCUGCGCUUCAAGGCUUAC
..((((.(((.((..((.((...(((((((((((.......((((......................))))((((.....)))).)))))))))))........)))).)).))).)))) ( -37.35)
>consensus
GCCUAAUCCUCCACUGCCGUUUUGCCUGCCAAAUCGGCUGUGCCAUCAAAUUAAACGACAACUAAAUUGGCGCACAUUUUGCGCUAUUUGGCAGGCUUUUGUCUGCUUUUCAAGGUUUAC
...............((.(....((((((((((..(((...))).......................(((((((.....)))))))))))))))))......).)).............. (-28.54 = -28.65 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	15,855,897 – 15,856,017
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-40.17
Consensus MFE	-34.03
Energy contribution	-33.81
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-3.13
Structure conservation index	0.85
SVM decision value	2.39
SVM RNA-class probability	0.993322
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15855897 120 - 23771897
GUAAACCAUGAAAAGCAGGCAAAAGCCUGCCAAAUAGCGCAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGCCGAUUUGGCAGGCAAAACGGCAGUGGAGGAUUAGGC
.....((((.....((((((....))))(((.....((((.....))))(((((.(..(((((((((......)))))))..))..).))))).)))......)).)))).......... ( -37.30)
>DroPse_CAF1 61801 120 - 1
GUAAGCCUUGAAGCGCAGACAAAAGCCUGCCAAAUAGCACAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGACGAUUUGGCAGGCAAAGCGGCAGUCGAGGAUUACGC
((((.((((((...((........(((((((((((.((((.....))))((((.((.(((((.....))))).)))))).......)))))))))))......))..)))))).)))).. ( -45.74)
>DroSim_CAF1 64726 120 - 1
GUAAACCAUGAAAAGCAGACAAAAGCCUGCCAAAUAGCGCAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGCCGAUUUGGCAGGCAAAACGGCAGUAGAGGAUUAGGC
.....((.................(((((((((((.(((((.....))))).......((..(((.......)))..)).......)))))))))))...((....))...))....... ( -34.90)
>DroEre_CAF1 62816 120 - 1
GUAAACGCUGAAAAGCAGACAAAAGCCUGCCAAAUAGCGCAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGCCGAUUUGGCAGGCAAAACGGCAGUAGAGGAUUAGGC
((....(((....)))........(((((((((((.(((((.....))))).......((..(((.......)))..)).......)))))))))))......))............... ( -38.40)
>DroYak_CAF1 104460 120 - 1
GUAAACCCUGAACAGCAGACAAAAGCCUGCCAAAUAGCGCAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGCCGAUUUGGCAGGCAAAACGGCAGUGGAGGAUUAGGC
......(((..((.((........(((((((((((.(((((.....))))).......((..(((.......)))..)).......)))))))))))......)).))..)))....... ( -38.94)
>DroPer_CAF1 63692 120 - 1
GUAAGCCUUGAAGCGCAGACAAAAGCCUGCCAAAUAGCACAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGACGAUUUGGCAGGCAAAGCGGCAGUCGAGGAUUACGC
((((.((((((...((........(((((((((((.((((.....))))((((.((.(((((.....))))).)))))).......)))))))))))......))..)))))).)))).. ( -45.74)
>consensus
GUAAACCAUGAAAAGCAGACAAAAGCCUGCCAAAUAGCGCAAAAUGUGCGCCAAUUUAGUUGUCGUUUAAUUUGAUGGCACAGCCGAUUUGGCAGGCAAAACGGCAGUAGAGGAUUAGGC
..............((........(((((((((((.((((.....))))((((.((.(((((.....))))).)))))).......)))))))))))......))............... (-34.03 = -33.81 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:26 2006