Locus 5067

Sequence ID	3R_DroMel_CAF1
Location	13,354,298 – 13,354,398
Length	100
Max. P	0.858965

overview

Window 2

Location	13,354,298 – 13,354,398
Length	100
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	70.72
Mean single sequence MFE	-27.28
Consensus MFE	-13.41
Energy contribution	-14.72
Covariance contribution	1.31
Combinations/Pair	1.29
Mean z-score	-1.80
Structure conservation index	0.49
SVM decision value	0.82
SVM RNA-class probability	0.858965
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13354298 100 + 27905053
GAGUUGGAACA-------------GCACAAGGAGCUGGAACUGCCCAGCAGUAACUGGGAACUAGGACUGGAAGUGGAAGUGGAAGUGGAUAUGGAGCAUCUGCUGGCCGGAA
.((((....((-------------((.......))))......(((((......)))))))))....((((.((..((.((....((....))...)).))..))..)))).. ( -26.20)
>DroSec_CAF1 99077 94 + 1
GAGCUGGAACA-------------GCAGAAGGAGCUGGAACUGCCCAGCAGUAACUAGUAACUAG------ACAUGGAAGUGGAAGUGGAUGUGAAGCAUCUGCUGGCCGGAA
...((((..((-------------(((((....(((((......))))).((.((.....(((..------.(((....)))..)))....))...)).))))))).)))).. ( -28.40)
>DroSim_CAF1 104791 94 + 1
GAGCUGGAACA-------------GCAGAAGGAGCUGGAACUGCCCAGCAGUAACUGGUAACUAG------ACAUGGAAGUGGAAGUGGAUGUGGAGCAUCUGCUGGCCGGAA
..((((...))-------------)).......(((((......))))).....(((((......------.(((....)))..((..((((.....))))..)).))))).. ( -29.30)
>DroEre_CAF1 106731 100 + 1
GAGCUGGAAGAAGGAAGGCAGAAGGCAGAAGGAGCAGGAACUGCCCUGCAGUAACUAGGA-CUGAAAGUA------------GAUGUGGAUGUGGAGCAUCUGCUGGCCGGAA
...((((....((....((((..(((((............))))))))).....))....-.....((((------------(((((.........)))))))))..)))).. ( -27.50)
>DroYak_CAF1 116656 99 + 1
GAACUGGAACA-------------GCAGAAGAAGCUGGAACUGCCCUAUAGUAACUAGGA-CUGGAAGUGGUUGUGGAUAUGGAUGUGGAUGUGGAGCAUCUGCUGGCCGGAA
...((((..((-------------(((((.(...(((.(.(..(.(((((....(((.((-((......)))).))).)))))..)..).).)))..).))))))).)))).. ( -30.00)
>DroPer_CAF1 107787 85 + 1
GAACAGGAACA-------------AAAGCCAGGGCUGGAACUG--------------AAA-CUGAAUGUGGAGGUGGCAGUGGCAGUGGAAGUGGAGCAUCUGUUCGCCGAAA
(((((((..((-------------....(((..(((...((((--------------..(-((.........)))..)))))))..)))...)).....)))))))....... ( -22.30)
>consensus
GAGCUGGAACA_____________GCAGAAGGAGCUGGAACUGCCCAGCAGUAACUAGGA_CUAGAAGUG_ACGUGGAAGUGGAAGUGGAUGUGGAGCAUCUGCUGGCCGGAA
...((((..........................(((((......)))))....................................(..((((.....))))..)...)))).. (-13.41 = -14.72 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	13,354,298 – 13,354,398
Length	100
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	70.72
Mean single sequence MFE	-20.29
Consensus MFE	-6.45
Energy contribution	-7.57
Covariance contribution	1.11
Combinations/Pair	1.25
Mean z-score	-1.99
Structure conservation index	0.32
SVM decision value	0.18
SVM RNA-class probability	0.621697
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13354298 100 - 27905053
UUCCGGCCAGCAGAUGCUCCAUAUCCACUUCCACUUCCACUUCCAGUCCUAGUUCCCAGUUACUGCUGGGCAGUUCCAGCUCCUUGUGC-------------UGUUCCAACUC
....((.(((((.(.(((..............(((...((.....))...))).((((((....)))))).......)))....).)))-------------))..))..... ( -20.20)
>DroSec_CAF1 99077 94 - 1
UUCCGGCCAGCAGAUGCUUCACAUCCACUUCCACUUCCAUGU------CUAGUUACUAGUUACUGCUGGGCAGUUCCAGCUCCUUCUGC-------------UGUUCCAGCUC
....((.(((((((.(((..((((..............))))------..)))...........((((((....))))))....)))))-------------))..))..... ( -22.34)
>DroSim_CAF1 104791 94 - 1
UUCCGGCCAGCAGAUGCUCCACAUCCACUUCCACUUCCAUGU------CUAGUUACCAGUUACUGCUGGGCAGUUCCAGCUCCUUCUGC-------------UGUUCCAGCUC
....((.(((((((.(((..((....(((...((......))------..)))..(((((....)))))...))...)))....)))))-------------))..))..... ( -23.00)
>DroEre_CAF1 106731 100 - 1
UUCCGGCCAGCAGAUGCUCCACAUCCACAUC------------UACUUUCAG-UCCUAGUUACUGCAGGGCAGUUCCUGCUCCUUCUGCCUUCUGCCUUCCUUCUUCCAGCUC
....((...(((((.((..............------------......(((-(.......)))).(((((((...)))).)))...))..)))))...))............ ( -18.40)
>DroYak_CAF1 116656 99 - 1
UUCCGGCCAGCAGAUGCUCCACAUCCACAUCCAUAUCCACAACCACUUCCAG-UCCUAGUUACUAUAGGGCAGUUCCAGCUUCUUCUGC-------------UGUUCCAGUUC
....((.(((((((.....................................(-(((((.......))))))(((....)))...)))))-------------))..))..... ( -20.30)
>DroPer_CAF1 107787 85 - 1
UUUCGGCGAACAGAUGCUCCACUUCCACUGCCACUGCCACCUCCACAUUCAG-UUU--------------CAGUUCCAGCCCUGGCUUU-------------UGUUCCUGUUC
...(((.(((((((.(((...((...((((..((((.............)))-)..--------------))))...))....))).))-------------))))))))... ( -17.52)
>consensus
UUCCGGCCAGCAGAUGCUCCACAUCCACUUCCACUUCCACGU_CACUUCCAG_UCCUAGUUACUGCUGGGCAGUUCCAGCUCCUUCUGC_____________UGUUCCAGCUC
....((..((((((((.....)))).......................................((((((....))))))......................))))))..... ( -6.45 =  -7.57 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:23 2006