Locus 6354

Sequence ID	3R_DroMel_CAF1
Location	16,648,311 – 16,648,476
Length	165
Max. P	0.972765

overview

Window 1

Location	16,648,311 – 16,648,416
Length	105
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.31
Mean single sequence MFE	-28.18
Consensus MFE	-20.44
Energy contribution	-21.00
Covariance contribution	0.56
Combinations/Pair	1.18
Mean z-score	-1.15
Structure conservation index	0.73
SVM decision value	0.18
SVM RNA-class probability	0.619457
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16648311 105 + 27905053
CAACUC------AGGGAUUUAGAGGUUGCAUUUACCUGGAGGCUUUGCGUUCCC-CCAGACGCUUAGCCUAGUCAUUAAUAAAUGCUAGAUA-AAGUGCCAGAAUCGGACAUU
....((------.((.(((((.((((.......))))..(((((..(((((...-...)))))..))))).........))))).)).))..-.((((((......)).)))) ( -26.10)
>DroPse_CAF1 795 112 + 1
CAUAGCACAAUAUGUGCUUUCGCAUCCGCAUUUACCUGGAGGCUUUGUGUUCCG-CCAGACGCUUAGCCUAGUCUUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUU
...(((((.....)))))......((((((((((...(((((((..(((((...-...)))))..))))...)))....)))))))(((......)))........))).... ( -27.10)
>DroEre_CAF1 873 105 + 1
CAUCUC------GAGGAUUCCGAAGUUGCAUUUACCUGGAGGCUUUGCGUGACC-CCAGACGCUUAGCCUAGUCAUAAAUAAAUGCCAGAUA-AAGCGCCUGAGUCGGACAUU
......------......(((((((.(((.((((.(((((((((..((((....-....))))..)))))...(((......))))))).))-))))).))...))))).... ( -29.90)
>DroYak_CAF1 859 105 + 1
CACCUC------AGGGAUUCUAAUGUUGCAUUUACCUGGAGGCUUUGCGUGACC-CCAGACGCUUAGCCUAGUCAUUUAUAAAUGCCAGAUA-AAGUGCCUGAAUCGGACAUU
..((((------(((.(((...((.(.(((((((..((((((((..((((....-....))))..)))))..)))....))))))).).)).-.))).)))))...))..... ( -29.60)
>DroAna_CAF1 7523 105 + 1
CUUUCC------A-GCUUCCUGAAUUUGCAUUUACCUGGAGGCUUCGCGUGCCUGCAAGACGCCUAGCCUAGUCAUUAAUAAAUGCUAGAGA-AAAUGCCUGAAUCGGACAUU
......------.-.....((((.((.((((((.((((((((((..((((.........))))..)))))...((((....)))))))).).-))))))..)).))))..... ( -25.40)
>DroPer_CAF1 812 112 + 1
CACAGCACAAUAUGUGCUUUCGAGUCCGCAUUUACCUGGAGGCUUUGUGUUCCG-CCAGACGCUUAGCCUAGUCUUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUU
...(((((.....))))).....(((((((((((...(((((((..(((((...-...)))))..))))...)))....)))))))(((......)))........))))... ( -31.00)
>consensus
CAUCUC______AGGGAUUCCGAAGUUGCAUUUACCUGGAGGCUUUGCGUGCCC_CCAGACGCUUAGCCUAGUCAUUAAUAAAUGCCAGAGA_AAAUGCCUGAAUCGGACAUU
..................(((((....((((((..(((((((((..((((.........))))..)))))...((((....))))))))....)))))).....))))).... (-20.44 = -21.00 +   0.56)

alignment

secondary structure

dotplot

Window 2

Location	16,648,341 – 16,648,448
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	75.81
Mean single sequence MFE	-29.25
Consensus MFE	-25.44
Energy contribution	-23.20
Covariance contribution	-2.24
Combinations/Pair	1.61
Mean z-score	-1.43
Structure conservation index	0.87
SVM decision value	1.34
SVM RNA-class probability	0.943595
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16648341 107 + 27905053
UGGAGGCUUUGCGUUCC-C-CCAGACGCUUAGCCUAGUCAUUAAUAAAUGCUAGAUA-AAGUGCCAGAAUCGGACAUUAUUCCCGCACUGAUCG-ACUGCAGAGCUGGAAU
...(((((..(((((..-.-...)))))..)))))((.((((....)))))).....-.((((((......)).))))(((((.((.(((....-....))).)).))))) ( -29.90)
>DroVir_CAF1 1170 107 + 1
UGGAGGUUUUGUGUGCCUG-CUUGCCACUUAGCCUAGUCAAUAUUAAAUGCUAGAUC-AAAUGCUUGAGUUGGACAUUAUUUUCACAUUGAG--AUAAACAGUGUGAAGAU
...(((((..(((.((...-...)))))..)))))...........((((((((.((-((....)))).)))).))))((((((((((((..--.....)))))))))))) ( -29.60)
>DroPse_CAF1 831 108 + 1
UGGAGGCUUUGUGUUCC-G-CCAGACGCUUAGCCUAGUCUUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUUAUUCCCACAUUGACUG-CCAACAGUGCGGGAAU
...(((((..(((((..-.-...)))))..))))).((((.........((.((......)))).......))))...((((((.(((((....-....))))).)))))) ( -28.69)
>DroMoj_CAF1 1178 107 + 1
UGGAGGCUUCCUGCGCCUG-CUUGCCGCUUAGCCUAGUCAUUAAUAAAUGCCAGAUC-AAAUGCAUAAAUUGGACAUUAUUUUCACACUGAA--ACAAUUAGUGUAAAGAU
...(((((....(((.(..-...).)))..))))).(((..((((..((((......-....))))..)))))))...(((((.(((((((.--....))))))).))))) ( -22.80)
>DroAna_CAF1 7552 107 + 1
UGGAGGCUUCGCGUGCC-UGCAAGACGCCUAGCCUAGUCAUUAAUAAAUGCUAGAGA-AAAUGCCUGAAUCGGACAUUACUUUGGCCCUGAUU--CUCCCAGGGUCAGAGU
...((((.((...((..-..)).)).))))...((((.((((....))))))))...-.((((((......)).))))((((((((((((...--....)))))))))))) ( -35.80)
>DroPer_CAF1 848 108 + 1
UGGAGGCUUUGUGUUCC-G-CCAGACGCUUAGCCUAGUCUUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUUAUUCCCACAUUGACUG-CCAACAGUGCGGGAAU
...(((((..(((((..-.-...)))))..))))).((((.........((.((......)))).......))))...((((((.(((((....-....))))).)))))) ( -28.69)
>consensus
UGGAGGCUUUGUGUGCC_G_CCAGACGCUUAGCCUAGUCAUUAAUAAAUGCCAGAGA_AAAUGCUUGAAUCGGACAUUAUUCCCACACUGACU__CCAACAGUGCGAGAAU
...(((((..(((.((.......)))))..)))))........................((((((......)).))))((((((((((((.........)))))))))))) (-25.44 = -23.20 +  -2.24)

alignment

secondary structure

dotplot

Window 3

Location	16,648,378 – 16,648,476
Length	98
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	80.85
Mean single sequence MFE	-30.73
Consensus MFE	-26.69
Energy contribution	-26.08
Covariance contribution	-0.61
Combinations/Pair	1.13
Mean z-score	-4.39
Structure conservation index	0.87
SVM decision value	1.65
SVM RNA-class probability	0.969637
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16648378 98 + 27905053
AUUAAUAAAUGCUAGAUA-AAGUGCCAGAAUCGGACAUUAUUCCCGCACUGAUCGACUGCAGAGCUGGAAUAUCACAUGGUUCAGGCUACAAUACC-CAU
..................-..(((((.((((((.....((((((.((.(((........))).)).)))))).....)))))).))).))......-... ( -25.00)
>DroPse_CAF1 868 100 + 1
UUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUUAUUCCCACAUUGACUGCCAACAGUGCGGGAAUAUUAUAUGGUUCAAGCGAUAAUUGACUAA
......................(((((((((((.....(((((((.(((((........))))).))))))).....)))))))))))............ ( -30.40)
>DroSec_CAF1 922 96 + 1
AUUAAUAAAUGCUAGAUA-AAGUGCCUGAAUCGGACAUUAUUCCCGCACUGAUUGACUCCAGAGCAGGAAUAUCACAUGGUUCAGGCUACAAUAAA-A--
..................-..((((((((((((.....((((((.((.(((........))).)).)))))).....)))))))))).))......-.-- ( -30.50)
>DroSim_CAF1 923 98 + 1
AUUAAUAAAUGCUAGAUA-AAGUGCCUGAAUCGGACAUUAUUCCCGCACUGAUUGACUCCAGAGCAGGAAUAUCACAUGGUUCAGGCUACAGUACC-CGU
..................-..((((((((((((.....((((((.((.(((........))).)).)))))).....)))))))))).))......-... ( -30.50)
>DroYak_CAF1 926 96 + 1
AUUUAUAAAUGCCAGAUA-AAGUGCCUGAAUCGGACAUUAUUCCUGCGCUGAUU-ACUUCAGAGCAGGAAUAUCAAAUGGUUCAGGCUACAAAUCC--CU
..................-..((((((((((((.....(((((((((.((((..-...)))).))))))))).....)))))))))).))......--.. ( -37.60)
>DroPer_CAF1 885 100 + 1
UUUAAUAAAUGCCAUAGAAAAAUGCUUGAAUCGGACAUUAUUCCCACAUUGACUGCCAACAGUGCGGGAAUAUUAUAUGGUUCAAGCGAUAAUUGACUAA
......................(((((((((((.....(((((((.(((((........))))).))))))).....)))))))))))............ ( -30.40)
>consensus
AUUAAUAAAUGCCAGAUA_AAGUGCCUGAAUCGGACAUUAUUCCCGCACUGAUUGACUACAGAGCAGGAAUAUCACAUGGUUCAGGCUACAAUACA_CAU
.....................((((((((((((.....((((((.((.(((........))).)).)))))).....)))))))))).)).......... (-26.69 = -26.08 +  -0.61)

alignment

secondary structure

dotplot

Window 4

Location	16,648,378 – 16,648,476
Length	98
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	80.85
Mean single sequence MFE	-28.80
Consensus MFE	-25.05
Energy contribution	-24.77
Covariance contribution	-0.28
Combinations/Pair	1.21
Mean z-score	-3.09
Structure conservation index	0.87
SVM decision value	1.70
SVM RNA-class probability	0.972765
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16648378 98 - 27905053
AUG-GGUAUUGUAGCCUGAACCAUGUGAUAUUCCAGCUCUGCAGUCGAUCAGUGCGGGAAUAAUGUCCGAUUCUGGCACUU-UAUCUAGCAUUUAUUAAU
.((-((((..((.(((.(((........((((((.((.(((........))).)).))))))........))).)))))..-))))))............ ( -24.89)
>DroPse_CAF1 868 100 - 1
UUAGUCAAUUAUCGCUUGAACCAUAUAAUAUUCCCGCACUGUUGGCAGUCAAUGUGGGAAUAAUGUCCGAUUCAAGCAUUUUUCUAUGGCAUUUAUUAAA
...((((......(((((((.(..(((.(((((((((((((....))))....))))))))).)))..).))))))).........)))).......... ( -27.26)
>DroSec_CAF1 922 96 - 1
--U-UUUAUUGUAGCCUGAACCAUGUGAUAUUCCUGCUCUGGAGUCAAUCAGUGCGGGAAUAAUGUCCGAUUCAGGCACUU-UAUCUAGCAUUUAUUAAU
--.-..((..((.(((((((........(((((((((.((((......)))).)))))))))........)))))))))..-))................ ( -28.09)
>DroSim_CAF1 923 98 - 1
ACG-GGUACUGUAGCCUGAACCAUGUGAUAUUCCUGCUCUGGAGUCAAUCAGUGCGGGAAUAAUGUCCGAUUCAGGCACUU-UAUCUAGCAUUUAUUAAU
..(-((((..((.(((((((........(((((((((.((((......)))).)))))))))........)))))))))..-)))))............. ( -32.49)
>DroYak_CAF1 926 96 - 1
AG--GGAUUUGUAGCCUGAACCAUUUGAUAUUCCUGCUCUGAAGU-AAUCAGCGCAGGAAUAAUGUCCGAUUCAGGCACUU-UAUCUGGCAUUUAUAAAU
..--((((..((.(((((((........(((((((((.((((...-..)))).)))))))))........)))))))))..-.))))............. ( -32.79)
>DroPer_CAF1 885 100 - 1
UUAGUCAAUUAUCGCUUGAACCAUAUAAUAUUCCCGCACUGUUGGCAGUCAAUGUGGGAAUAAUGUCCGAUUCAAGCAUUUUUCUAUGGCAUUUAUUAAA
...((((......(((((((.(..(((.(((((((((((((....))))....))))))))).)))..).))))))).........)))).......... ( -27.26)
>consensus
AUA_GGAAUUGUAGCCUGAACCAUGUGAUAUUCCUGCUCUGGAGUCAAUCAGUGCGGGAAUAAUGUCCGAUUCAGGCACUU_UAUCUAGCAUUUAUUAAU
.............(((((((........(((((((((.(((........))).)))))))))........)))))))....................... (-25.05 = -24.77 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:28 2006