Locus 5773

Sequence ID	3R_DroMel_CAF1
Location	15,045,238 – 15,045,331
Length	93
Max. P	0.998991

overview

Window 8

Location	15,045,238 – 15,045,331
Length	93
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	72.24
Mean single sequence MFE	-26.72
Consensus MFE	-8.68
Energy contribution	-9.55
Covariance contribution	0.87
Combinations/Pair	1.27
Mean z-score	-2.55
Structure conservation index	0.32
SVM decision value	1.53
SVM RNA-class probability	0.961357
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15045238 93 + 27905053
CUGUGGAGCAGAAAAAAAAAGGA-GUUGGGAAAAUUGUUAUCCU-CGUGACAAGGGGCUU-----UUUGCCCAGUUAACUCUCUUACCUCUUCCACAGUC
((((((((.((.......(((((-(((((.....(((((((...-.))))))).((((..-----...))))..))))))).)))..)).)))))))).. ( -29.80)
>DroPse_CAF1 50729 92 + 1
CUGAC----AAAAAA-AAGAAGAAGAGAAGAAAAGUUUCAUUAACUCU---GAGCGGCUUGCGGGUCUCCUCCUUCUCCUCUCUUACCUCUUCCACAGUC
.....----......-((((.((.((((((...((((.....))))..---(((.((((....))))..))))))))).))))))............... ( -17.00)
>DroSim_CAF1 47444 92 + 1
CUGUGGAGCAGAAAA-AAGAGGA-GUUGGGCAAAUAGUUCUCCU-CGUGACAACGGGCUU-----UUUGCCCAGUUAACUCUCUUACCUCUUCCACAGUC
((((((((.((..((-.((((..-.(((((((((.((.....((-(((....))))))).-----)))))))))....)))).))..)).)))))))).. ( -34.70)
>DroEre_CAF1 49553 92 + 1
CUGUGGAGCAGAAAA-AAGGAGA-GUUGGGAAAAUAGUUCUCCA-CAUGACAGGGGGCUU-----UUUCCCCAGUUAACUCUCUUACCUCUUCCACAGUC
((((((((.((....-.((((((-((((((((((.(((((.((.-.......))))))))-----)))))).....)))))))))..)).)))))))).. ( -35.80)
>DroYak_CAF1 71362 92 + 1
CUGUGGAACAGAAAA-AAGGAGA-GAUGGAAAAAUAGUUAUCCA-UAUGACAGCGGGCUU-----UUUCUCCAGUUAACUCUCUUACCUCUUCCACAGUC
((((((((.((....-.((((((-((((((.((....)).))))-).((((.(.(((...-----...)))).)))).)))))))..)).)))))))).. ( -26.00)
>DroPer_CAF1 50773 91 + 1
CUGAC----AAAA-A-AAGAAGAAGAGAAGAAAAGUUUCAUUAACUCU---GAGCGGCUUGCGGGUCUCCUCCUUCUCCUCUCUUACCUCUUCCACAGUC
.....----....-.-((((.((.((((((...((((.....))))..---(((.((((....))))..))))))))).))))))............... ( -17.00)
>consensus
CUGUGGAGCAGAAAA_AAGAAGA_GAUGGGAAAAUAGUUAUCCA_CAUGACAAGGGGCUU_____UUUCCCCAGUUAACUCUCUUACCUCUUCCACAGUC
((((((((.((.....(((.(((.((((((.......................................))))))....))))))..)).)))))))).. ( -8.68 =  -9.55 +   0.87)

alignment

secondary structure

dotplot

Window 9

Location	15,045,238 – 15,045,331
Length	93
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	72.24
Mean single sequence MFE	-31.60
Consensus MFE	-16.31
Energy contribution	-15.90
Covariance contribution	-0.41
Combinations/Pair	1.36
Mean z-score	-3.27
Structure conservation index	0.52
SVM decision value	3.32
SVM RNA-class probability	0.998991
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15045238 93 - 27905053
GACUGUGGAAGAGGUAAGAGAGUUAACUGGGCAAA-----AAGCCCCUUGUCACG-AGGAUAACAAUUUUCCCAAC-UCCUUUUUUUUUCUGCUCCACAG
..((((((((((((.(((.(((((....((((...-----..))))........(-(((((....))))))..)))-)))))....)))))..))))))) ( -27.80)
>DroPse_CAF1 50729 92 - 1
GACUGUGGAAGAGGUAAGAGAGGAGAAGGAGGAGACCCGCAAGCCGCUC---AGAGUUAAUGAAACUUUUCUUCUCUUCUUCUU-UUUUUU----GUCAG
(((...((((((((.(((((((((((((...(((...(....)...)))---.............)))))))))))))))))))-))....----))).. ( -32.09)
>DroSim_CAF1 47444 92 - 1
GACUGUGGAAGAGGUAAGAGAGUUAACUGGGCAAA-----AAGCCCGUUGUCACG-AGGAGAACUAUUUGCCCAAC-UCCUCUU-UUUUCUGCUCCACAG
..((((((((((((.((((((((....((((((((-----.(((((((....)))-.))....)).))))))))))-).)))))-.)))))..))))))) ( -35.30)
>DroEre_CAF1 49553 92 - 1
GACUGUGGAAGAGGUAAGAGAGUUAACUGGGGAAA-----AAGCCCCCUGUCAUG-UGGAGAACUAUUUUCCCAAC-UCUCCUU-UUUUCUGCUCCACAG
..((((((((((((.(((((((((.((.((((...-----....)))).))...(-.(((((.....)))))))))-))).)))-.)))))..))))))) ( -32.70)
>DroYak_CAF1 71362 92 - 1
GACUGUGGAAGAGGUAAGAGAGUUAACUGGAGAAA-----AAGCCCGCUGUCAUA-UGGAUAACUAUUUUUCCAUC-UCUCCUU-UUUUCUGUUCCACAG
..((((((((.(((.(((((((.....((((((((-----.((.(((........-)))....)).)))))))).)-))).)))-...))).)))))))) ( -28.90)
>DroPer_CAF1 50773 91 - 1
GACUGUGGAAGAGGUAAGAGAGGAGAAGGAGGAGACCCGCAAGCCGCUC---AGAGUUAAUGAAACUUUUCUUCUCUUCUUCUU-U-UUUU----GUCAG
(((...((((((((.(((((((((((((...(((...(....)...)))---.............)))))))))))))))))))-)-)...----))).. ( -32.79)
>consensus
GACUGUGGAAGAGGUAAGAGAGUUAACUGGGGAAA_____AAGCCCCUUGUCACA_UGGAUAACAAUUUUCCCAAC_UCUUCUU_UUUUCUGCUCCACAG
..((((((((((((...(((((.....((((((((...............................)))))))).....)))))..)))))..))))))) (-16.31 = -15.90 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:24 2006