Locus 8691

Sequence ID	3R_DroMel_CAF1
Location	23,206,173 – 23,206,273
Length	100
Max. P	0.993692

overview

Window 7

Location	23,206,173 – 23,206,273
Length	100
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	70.98
Mean single sequence MFE	-27.34
Consensus MFE	-8.46
Energy contribution	-8.32
Covariance contribution	-0.14
Combinations/Pair	1.20
Mean z-score	-2.98
Structure conservation index	0.31
SVM decision value	2.42
SVM RNA-class probability	0.993692
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23206173 100 + 27905053
AGCAAUCGCAUCAAAGAAAAUCAU-AAGAAAUGCCACAAAUGAAAGGAUAUUUC-UUGAUAUUUUUUGCGUCAUUUGCAUGGCAACAAAGCCAAGC------------UAAAAU
.((((.((((...(((((.((((.-.(((((((((..........)).))))))-))))).)))))))))....)))).((((......))))...------------...... ( -24.10)
>DroPse_CAF1 3767 108 + 1
----GGCGCUCCAUCAGUAAUCAUUGCUAAAUUCAGCAAAUGAAUGAAAAUUCUCUGGAAUU--UUUCUUUCAUUUGCAUUGCAGAUAAACCAUGGGAAGGAAUCUGGCAGAAU
----...................((((((.((((.(((((((((.((((((((....)))))--)))..))))))))).((.((.........)).))..)))).))))))... ( -26.80)
>DroSec_CAF1 3839 100 + 1
AGCAAUCGCAUCAAAGAAAAUCAU-GGGGAAUGCCGCAAAUGAAAGGAAAUUUC-UGGAUAUUUUUUGCGGCAUUUGCCUGGCAACAAAGCCAAGC------------UAAAAU
(((.....................-((.((((((((((((.....(((....))-)........)))))))))))).))((((......)))).))------------)..... ( -30.92)
>DroSim_CAF1 3851 100 + 1
AGCAAUCGCAUCAAAGAAAAUCAU-GGGGAAUGCCGCAAAUGAAAGGAAAUUUC-UGGAUAUUUUUUGCGGCAUUUGCCUGGCAACAAAGCCAAGC------------UAAAAU
(((.....................-((.((((((((((((.....(((....))-)........)))))))))))).))((((......)))).))------------)..... ( -30.92)
>DroEre_CAF1 3715 101 + 1
AGCAAUCGCAUCAAAGGAAAUCAU-ACGGAAUGCCGCAAAUGAAAGGAAAUUUUUUGGAUAUUUUUUGCGGCAUUUGCCUGGCAACAAAGCCAAGC------------UAAAAU
.((....))...............-...((((((((((((........((....))........))))))))))))((.((((......)))).))------------...... ( -25.79)
>DroPer_CAF1 3779 108 + 1
----GGCGCUCCAUCAGUAAUCAUUGCUAAAUUUAGCAAAUGAAUGAAAAUUCUCUGGAAUU--UUUCUUUCAUUUGCAUUGCAGAUAAACCAUGGGAAGGAAUCUGGCAGAAU
----...................((((........(((((((((.((((((((....)))))--)))..)))))))))....(((((...((.......)).)))))))))... ( -25.50)
>consensus
AGCAAUCGCAUCAAAGAAAAUCAU_GCGAAAUGCCGCAAAUGAAAGGAAAUUUC_UGGAUAUUUUUUGCGGCAUUUGCAUGGCAACAAAGCCAAGC____________UAAAAU
...............................(((((((((((...(.(((..............))).)..)))))))..)))).............................. ( -8.46 =  -8.32 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	23,206,173 – 23,206,273
Length	100
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	70.98
Mean single sequence MFE	-25.23
Consensus MFE	-9.77
Energy contribution	-10.53
Covariance contribution	0.75
Combinations/Pair	1.24
Mean z-score	-2.37
Structure conservation index	0.39
SVM decision value	1.70
SVM RNA-class probability	0.972929
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23206173 100 - 27905053
AUUUUA------------GCUUGGCUUUGUUGCCAUGCAAAUGACGCAAAAAAUAUCAA-GAAAUAUCCUUUCAUUUGUGGCAUUUCUU-AUGAUUUUCUUUGAUGCGAUUGCU
......------------((.((((......)))).))......((((..(((.(((((-(((((..((........).)..)))))).-.))))....)))..))))...... ( -20.90)
>DroPse_CAF1 3767 108 - 1
AUUCUGCCAGAUUCCUUCCCAUGGUUUAUCUGCAAUGCAAAUGAAAGAAA--AAUUCCAGAGAAUUUUCAUUCAUUUGCUGAAUUUAGCAAUGAUUACUGAUGGAGCGCC----
....((((((((.((.......))...)))))....(((((((((.((((--(.(((....)))))))).)))))))))........)))....................---- ( -23.10)
>DroSec_CAF1 3839 100 - 1
AUUUUA------------GCUUGGCUUUGUUGCCAGGCAAAUGCCGCAAAAAAUAUCCA-GAAAUUUCCUUUCAUUUGCGGCAUUCCCC-AUGAUUUUCUUUGAUGCGAUUGCU
......------------(((((((......))))))).(((((((((((.........-..............)))))))))))....-...............((....)). ( -26.80)
>DroSim_CAF1 3851 100 - 1
AUUUUA------------GCUUGGCUUUGUUGCCAGGCAAAUGCCGCAAAAAAUAUCCA-GAAAUUUCCUUUCAUUUGCGGCAUUCCCC-AUGAUUUUCUUUGAUGCGAUUGCU
......------------(((((((......))))))).(((((((((((.........-..............)))))))))))....-...............((....)). ( -26.80)
>DroEre_CAF1 3715 101 - 1
AUUUUA------------GCUUGGCUUUGUUGCCAGGCAAAUGCCGCAAAAAAUAUCCAAAAAAUUUCCUUUCAUUUGCGGCAUUCCGU-AUGAUUUCCUUUGAUGCGAUUGCU
......------------(((((((......))))))).(((((((((((........................))))))))))).(((-((.(.......).)))))...... ( -30.66)
>DroPer_CAF1 3779 108 - 1
AUUCUGCCAGAUUCCUUCCCAUGGUUUAUCUGCAAUGCAAAUGAAAGAAA--AAUUCCAGAGAAUUUUCAUUCAUUUGCUAAAUUUAGCAAUGAUUACUGAUGGAGCGCC----
....((((((((.((.......))...)))))....(((((((((.((((--(.(((....)))))))).)))))))))........)))....................---- ( -23.10)
>consensus
AUUUUA____________GCUUGGCUUUGUUGCCAGGCAAAUGACGCAAAAAAUAUCCA_AAAAUUUCCUUUCAUUUGCGGCAUUCCGC_AUGAUUUCCUUUGAUGCGAUUGCU
..................(((((((......))))))).((((.((((((........................)))))).))))............................. ( -9.77 = -10.53 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:22 2006