Locus 3311

Sequence ID	2L_DroMel_CAF1
Location	9,559,928 – 9,560,024
Length	96
Max. P	0.999861

overview

Window 8

Location	9,559,928 – 9,560,024
Length	96
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	70.56
Mean single sequence MFE	-23.70
Consensus MFE	-10.58
Energy contribution	-10.97
Covariance contribution	0.39
Combinations/Pair	1.10
Mean z-score	-2.48
Structure conservation index	0.45
SVM decision value	2.69
SVM RNA-class probability	0.996400
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9559928 96 + 22407834
UUUUUUGGGGGAAAAAAAAUAUGUGAAAUGGGAAAAACGUGUGU-----AUGUGUGUGUGUGUGUUUUAGCCGCACA----CGCACACACACGUUAAAAAUAGCA
((((((......)))))).................(((((((((-----..(((((((((((.((....))))))))----)))))))))))))).......... ( -32.00)
>DroPse_CAF1 13035 101 + 1
UUUGUUAAG---AAAAAAAUAUGUGAGAUUUGAAAAUGUUGUAUUGUCGAAGUAUGUGUGUGUGCCAC-ACCGCACAGCAGCACACACACACGGUAAAAAUAGCU
...((((..---.........((..(.(((....))).)..))((..((.....(((((((((((..(-........)..)))))))))))))..))...)))). ( -21.80)
>DroSec_CAF1 10363 94 + 1
UUUUUUGGG--UAAAAAAAUAUGUGAAAUGGGAAAGACGUGUGU-----AUGUGUGUGUGUGUGUUUUAGCCGCACA----CGCACACACACGUUAAAAAUAGCA
..(((((.(--((......))).))))).......(((((((((-----..(((((((((((.((....))))))))----)))))))))))))).......... ( -32.70)
>DroMoj_CAF1 22131 80 + 1
UC-GUUAGA---AAAAAAAUUUAAGAAA--GAAAGAAAUUGUGA----AAAAUUUUUGUG-----UUUGGCCGC----------ACACACACGUUAAAAAUAGCA
..-((((..---................--...(((((((....----..)))))))(((-----(.((.....----------.)).))))........)))). ( -10.20)
>DroPer_CAF1 12940 101 + 1
UUUGUUAAG---AAAAAAAUAUGUGAGAUUUGAAAAUGUUGUAUUGUCGAAGUAUGUGUGUGUGCCAC-ACCGCACAGCAGCACACACACACGGUAAAAAUAGCU
...((((..---.........((..(.(((....))).)..))((..((.....(((((((((((..(-........)..)))))))))))))..))...)))). ( -21.80)
>consensus
UUUGUUAGG___AAAAAAAUAUGUGAAAUGGGAAAAACUUGUGU_____AAGUAUGUGUGUGUGCUUU_GCCGCACA____CACACACACACGUUAAAAAUAGCA
......................................................((((((((((.................)))))))))).............. (-10.58 = -10.97 +   0.39)

alignment

secondary structure

dotplot

Window 9

Location	9,559,928 – 9,560,024
Length	96
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	70.56
Mean single sequence MFE	-21.52
Consensus MFE	-10.01
Energy contribution	-10.64
Covariance contribution	0.63
Combinations/Pair	1.15
Mean z-score	-3.26
Structure conservation index	0.47
SVM decision value	4.29
SVM RNA-class probability	0.999861
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9559928 96 - 22407834
UGCUAUUUUUAACGUGUGUGUGCG----UGUGCGGCUAAAACACACACACACACAU-----ACACACGUUUUUCCCAUUUCACAUAUUUUUUUUCCCCCAAAAAA
..........((((((((((((.(----((((.(...........).))))).)))-----)))))))))................................... ( -25.80)
>DroPse_CAF1 13035 101 - 1
AGCUAUUUUUACCGUGUGUGUGUGCUGCUGUGCGGU-GUGGCACACACACAUACUUCGACAAUACAACAUUUUCAAAUCUCACAUAUUUUUUU---CUUAACAAA
.............((((((((((((..(........-)..)))))))))))).........................................---......... ( -25.40)
>DroSec_CAF1 10363 94 - 1
UGCUAUUUUUAACGUGUGUGUGCG----UGUGCGGCUAAAACACACACACACACAU-----ACACACGUCUUUCCCAUUUCACAUAUUUUUUUA--CCCAAAAAA
...........(((((((((((.(----((((.(...........).))))).)))-----)))))))).........................--......... ( -25.00)
>DroMoj_CAF1 22131 80 - 1
UGCUAUUUUUAACGUGUGUGU----------GCGGCCAAA-----CACAAAAAUUUU----UCACAAUUUCUUUC--UUUCUUAAAUUUUUUU---UCUAAC-GA
............(((..((((----------........)-----)))((((((((.----..............--......))))))))..---....))-). (  -6.00)
>DroPer_CAF1 12940 101 - 1
AGCUAUUUUUACCGUGUGUGUGUGCUGCUGUGCGGU-GUGGCACACACACAUACUUCGACAAUACAACAUUUUCAAAUCUCACAUAUUUUUUU---CUUAACAAA
.............((((((((((((..(........-)..)))))))))))).........................................---......... ( -25.40)
>consensus
UGCUAUUUUUAACGUGUGUGUGCG____UGUGCGGC_AAAACACACACACACACUU_____ACACAACUUUUUCCAAUUUCACAUAUUUUUUU___CCUAACAAA
.............(((((((((......((((.........)))))))))))))................................................... (-10.01 = -10.64 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:31 2006