Locus 6295

Sequence ID	3L_DroMel_CAF1
Location	16,775,656 – 16,775,796
Length	140
Max. P	0.771829

overview

Window 6

Location	16,775,656 – 16,775,776
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.97
Mean single sequence MFE	-37.78
Consensus MFE	-26.86
Energy contribution	-26.03
Covariance contribution	-0.83
Combinations/Pair	1.28
Mean z-score	-1.44
Structure conservation index	0.71
SVM decision value	0.09
SVM RNA-class probability	0.578516
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16775656 120 - 23771897
CUCCUCUUUUUCCAUUCGAAUUAUACAGAGCGCUGCUUCCGGCUCACUGCUGUUGACGGCAGCGAAUCUGGAACGCUUUGCGGAGAUCCACAAGAAGCAGGAGCGACACAACAAGAUGCU
(((((((((((..............(((((((....((((((.((.((((((....)))))).))..))))))))))))).((....))..)))))).)))))................. ( -37.80)
>DroVir_CAF1 23839 109 - 1
CUCU-----------CUCUGCUGUAUAGAGCGCCGCUUCCGGCUCACUGCUGCUGACGGCAGCGAAUCUGGAGCGGUUCGCGGAGAUACACAAGAAACAGGAGCGUCAGCACAAGAUGCU
...(-----------((((((.((.....))((((((((.(..((.((((((....)))))).))..).))))))))..)))))))...............((((((.......)))))) ( -42.40)
>DroPse_CAF1 24812 107 - 1
CUCUUCU----A---------CAUAUAGAGCGCUGCUUCCGGCUCACUGCUGCUAACGGCAGCGAAUCUGGAGCGCUUCGCGGAGAUCCACAAGAAGCAGGAGCGGCACAACAAGAUGUU
((((...----.---------.....)))).((((((((..((((..((((((.....))))))......))))(((((..((....))....))))).))))))))............. ( -38.00)
>DroGri_CAF1 24567 109 - 1
UUCU-----------UGGACAAUUACAGAGCGCCGCUUCUGGUUCACUGCUGCUGACGGCAGCGAAUCUGGAACGCUUUGCGGAGAUCCACAAGAAACAGGAGCGUCAGCACAAAAUGAU
((((-----------((........(((((((...((...(((((.((((((....)))))).))))).))..))))))).((....)).))))))......((....)).......... ( -34.50)
>DroAna_CAF1 24496 106 - 1
CUCUU-----UA---------CAUAUAGAGUGCUGCUUCCGGCUCACUGCUGUUGACGGCGGCGAAUCUGGAACGCUUCGCGGAGAUCCACAAGAAGCAGGAGCGCCGCAACAAGAUGCU
.....-----..---------......(.(((((.(((((((.((.((((((....)))))).))..)))))..(((((..((....))....))))))).))))))(((......))). ( -36.00)
>DroPer_CAF1 25118 107 - 1
CUCUUCU----A---------CAUAUAGAGCGCUGCUUCCGGCUCACUGCUGCUGACGGCAGCGAAUCUGGAGCGCUUCGCGGAGAUCCACAAGAAGCAGGAGCGGCACAACAAGAUGUU
((((...----.---------.....)))).((((((((..((((..((((((.....))))))......))))(((((..((....))....))))).))))))))............. ( -38.00)
>consensus
CUCUU______A_________CAUAUAGAGCGCUGCUUCCGGCUCACUGCUGCUGACGGCAGCGAAUCUGGAACGCUUCGCGGAGAUCCACAAGAAGCAGGAGCGGCACAACAAGAUGCU
((((.........................(((..((((((((.((.((((((....)))))).))..)))))).))..)))((....))..........))))................. (-26.86 = -26.03 +  -0.83)

alignment

secondary structure

dotplot

Window 7

Location	16,775,696 – 16,775,796
Length	100
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	80.65
Mean single sequence MFE	-26.95
Consensus MFE	-22.68
Energy contribution	-22.18
Covariance contribution	-0.50
Combinations/Pair	1.14
Mean z-score	-1.48
Structure conservation index	0.84
SVM decision value	0.53
SVM RNA-class probability	0.771829
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16775696 100 - 23771897
GCCGUGACUCAA---CAAACAUUCUCCUCUUUUUCCAUUCGAAUUAUACAGAGCGCUGCUUCCGGCUCACUGCUGUUGACGGCAGCGAAUCUGGAACGCUUUG
...((......)---)................................(((((((....((((((.((.((((((....)))))).))..))))))))))))) ( -25.80)
>DroPse_CAF1 24852 87 - 1
---GUGACUCACGUCGAAACAUUCUCUUCU----A---------CAUAUAGAGCGCUGCUUCCGGCUCACUGCUGCUAACGGCAGCGAAUCUGGAGCGCUUCG
---.((((....))))..............----.---------......((((((....(((((.((.((((((....)))))).))..))))))))))).. ( -26.30)
>DroEre_CAF1 24937 98 - 1
ACCGUGACUCAA---CAAACAUUCUCCU--UUUUCCAUUUGAAUCACACAGAGCGCUGCUUCCGGCUCACUGCUGUUGACGGCAGCGAAUCUGGAACGCUUUG
...((((.((((---.............--........)))).)))).(((((((....((((((.((.((((((....)))))).))..))))))))))))) ( -30.90)
>DroYak_CAF1 24701 99 - 1
ACCGUGACUCAA---CAAACAUUCUCCUC-UUUUCCAUUCGAAUUAUACAGAGCGCUGCUUCCGGCUCACUGCUGUUGACGGCAGCGAAUCUGGAACGCUUUG
...((......)---).............-..................(((((((....((((((.((.((((((....)))))).))..))))))))))))) ( -25.80)
>DroAna_CAF1 24536 86 - 1
ACCGUGACUCAA---CGAACAUUCUCUU-----UA---------CAUAUAGAGUGCUGCUUCCGGCUCACUGCUGUUGACGGCGGCGAAUCUGGAACGCUUCG
..(((......)---))..((((((.(.-----..---------...).))))))..((((((((.((.((((((....)))))).))..)))))).)).... ( -24.70)
>DroPer_CAF1 25158 87 - 1
---GUGACUCACGUCGAAACAUUCUCUUCU----A---------CAUAUAGAGCGCUGCUUCCGGCUCACUGCUGCUGACGGCAGCGAAUCUGGAGCGCUUCG
---(((.(((..((.(((........))).----)---------)...((((.(((((((..((((........))))..)))))))..)))))))))).... ( -28.20)
>consensus
ACCGUGACUCAA___CAAACAUUCUCCUC____UA_________CAUACAGAGCGCUGCUUCCGGCUCACUGCUGUUGACGGCAGCGAAUCUGGAACGCUUCG
...(((.(((........................................)))))).((((((((.((.((((((....)))))).))..)))))).)).... (-22.68 = -22.18 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:56 2006