Locus 4675

Sequence ID	2R_DroMel_CAF1
Location	15,300,418 – 15,300,538
Length	120
Max. P	0.981065

overview

Window 8

Location	15,300,418 – 15,300,514
Length	96
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	75.22
Mean single sequence MFE	-24.00
Consensus MFE	-17.19
Energy contribution	-16.92
Covariance contribution	-0.28
Combinations/Pair	1.16
Mean z-score	-2.00
Structure conservation index	0.72
SVM decision value	1.88
SVM RNA-class probability	0.981065
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15300418 96 - 20766785
AA-GGCCACGCGUCAAUUAUACUGAAGUAGAUG---UAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACCAUGCGCACUGGAUUUCAUCG---G--GGCA
..-(((((.((((.......))(((((((.((.---....)).)))))))...)).)))))..................((.((.(((...))).---)--))). ( -20.90)
>DroVir_CAF1 123881 98 - 1
GA-GGCCACGCGUCAAUUAAACUGAAGUGCAUG---UAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCGCCAA-GUAUAUUUGAUUCGUGC--GGAA
..-.((.(((.(((((.((...((((((((((.---....))))))))))...(((((((...((......))...)))))-)).)).))))).)))))--.... ( -27.00)
>DroPse_CAF1 131714 99 - 1
AAGGGCCACGCGUCAAUUAGACUGAAGUGCAUG---UAAAAUGUGUUUUAAAAGCCGGGCCAAUAUUAUCUUACUUUGCACUCUGGAUGGUAUCA---GCCAACA
...(((.....(((.....)))(((((..(((.---....)))..)))))...))).(((..(((((((((.............)))))))))..---))).... ( -25.32)
>DroWil_CAF1 205988 88 - 1
AA-GGCCACGCGUCAAUUAAAUUGAAGUGCAUG---UAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUGUAUUACUGUGAGCACA--------UCA---G--AGAA
..-(((((.((..........(((((((((((.---....)))))))))))..)).)))))............((.(((.....--------)))---.--)).. ( -23.70)
>DroMoj_CAF1 122627 98 - 1
GA-GGCCACGCGUCAAUUAAAUUGAAGUGCAUG---UAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCUCCAA--UACAUUUGAUUCGUGU-AAGAA
..-(((((.((..........(((((((((((.---....)))))))))))..)).))))).......((((((.(..(((--.....)))....).))-)))). ( -22.30)
>DroAna_CAF1 78970 96 - 1
AG-GGCCACGCGUCAAUUAGAUUGAAGUACAUGGUAAAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUGCUUCACU------ACUAGAUUUCAUCGACGG--GGCA
..-(((((.((.((.....))(((((((((((........)))))))))))..)).))))).....((((((...------................))--)))) ( -24.81)
>consensus
AA_GGCCACGCGUCAAUUAAACUGAAGUGCAUG___UAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCUGCACACUAGAUUUCAUCA___G__AGAA
...(((((.((((.......))((((((((((........))))))))))...)).)))))............................................ (-17.19 = -16.92 +  -0.28)

alignment

secondary structure

dotplot

Window 9

Location	15,300,438 – 15,300,538
Length	100
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	75.87
Mean single sequence MFE	-22.14
Consensus MFE	-16.36
Energy contribution	-16.28
Covariance contribution	-0.08
Combinations/Pair	1.16
Mean z-score	-1.09
Structure conservation index	0.74
SVM decision value	0.58
SVM RNA-class probability	0.787234
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15300438 100 - 20766785
UUUCCUUGUC-UCGACUAUAUCACA------------AA-GGCCACGCGUCAAUUAUACUGAAGUAGAUGUAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACCAUGCG
..........-..............------------..-(((((.((((.......))(((((((.((.....)).)))))))...)).)))))................... ( -15.60)
>DroVir_CAF1 123903 109 - 1
UUUCGCCUGC-CUUUCAAUAUAACAGU---GGAACACGA-GGCCACGCGUCAAUUAAACUGAAGUGCAUGUAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCGCCA
..(((....(-(...............---))....)))-(((((.((((.......))((((((((((.....))))))))))...)).)))))................... ( -22.16)
>DroPse_CAF1 131736 100 - 1
UUUCGCUGCCUUCGAG--UAUUACA------------AAGGGCCACGCGUCAAUUAGACUGAAGUGCAUGUAAAAUGUGUUUUAAAAGCCGGGCCAAUAUUAUCUUACUUUGCA
.......((....(((--((.....------------...((((..(((((.....)))(((((..(((.....)))..)))))...))..))))..........))))).)). ( -22.87)
>DroWil_CAF1 206000 112 - 1
UUUCACUUGC-CUUCCAAUAUUACAAAAAACAGAAAAAA-GGCCACGCGUCAAUUAAAUUGAAGUGCAUGUAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUGUAUUACUGUGAG
..((((....-....(((((((.(........)......-(((((.((..........(((((((((((.....)))))))))))..)).)))))))))))).......)))). ( -24.86)
>DroMoj_CAF1 122649 99 - 1
UUUCGCUCGA----GCAAUA----------GGAAGACGA-GGCCACGCGUCAAUUAAAUUGAAGUGCAUGUAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCUCCA
....((.(((----((....----------....((((.-(....).)))).......(((((((((((.....)))))))))))..))))))).................... ( -24.50)
>DroPer_CAF1 90362 100 - 1
UUUCGCUGCCUUCGAG--UAUUACA------------AAGGGCCACGCGUCAAUUAGACUGAAGUGCAUGUAAAAUGUGUUUUAAAAGCCGGGCCAAUAUUAUCUUACUUUGCA
.......((....(((--((.....------------...((((..(((((.....)))(((((..(((.....)))..)))))...))..))))..........))))).)). ( -22.87)
>consensus
UUUCGCUGGC_UCGACAAUAUUACA____________AA_GGCCACGCGUCAAUUAAACUGAAGUGCAUGUAAAAUGUAUUUUAAAAGCUUGGCCAAUAUUAUUUUACUCUGCA
........................................(((((.((((.......))((((((((((.....))))))))))...)).)))))................... (-16.36 = -16.28 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:24 2006