Locus 3233

Sequence ID	2R_DroMel_CAF1
Location	11,051,246 – 11,051,341
Length	95
Max. P	0.989809

overview

Window 2

Location	11,051,246 – 11,051,341
Length	95
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	72.62
Mean single sequence MFE	-17.55
Consensus MFE	-10.85
Energy contribution	-10.77
Covariance contribution	-0.08
Combinations/Pair	1.15
Mean z-score	-2.22
Structure conservation index	0.62
SVM decision value	2.18
SVM RNA-class probability	0.989809
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11051246 95 + 20766785
CGUCUCCACAGCUCCACUUCUCGUGGACGUCUUCUUUACCAUCAGGUAAAUAUAAUCAUUCGAUUA-UCUAAUGUA-UUUUGCUGAUCCAUUUGAAA
........((((.((((.....))))((((....((((((....)))))).((((((....)))))-)...)))).-....))))............ ( -18.50)
>DroSec_CAF1 1185 95 + 1
CGUCUCCACAGCUCCACUUCUAGUGGACGUCUUCUUUACCAUCAGGUAAAUAUAACCAUUCGAUUA-UCUAAAGUA-UUUUGCUGAUCCAUUUGAUA
........(((((((((.....))))).((..(.((((((....)))))).)..))..........-.........-....))))............ ( -16.90)
>DroSim_CAF1 1185 90 + 1
CGUCUCCACAGCUCCACUUCUCGUGGACGUCUUCUUUACCAUCAGGUAAAUAUAACCAUUCGAUUA-UCU-----A-UUUAUAUGAUCUGUUCAAUA
..........(((((((.....))))).))....((((((....))))))...........(((((-(..-----.-.....))))))......... ( -14.00)
>DroEre_CAF1 1197 95 + 1
CGUCUCUACAGCUCCACUUCUCGUGGAUGUCUUCUUUACCAUCAGGUAAACAUAAUCAUUCGAUUUGUUU-AAUGAUUUUAUCUAACCCAUUG-AUG
((((......(((((((.....))))).))..........((((..((((((.((((....)))))))))-).))))...............)-))) ( -16.70)
>DroWil_CAF1 1222 90 + 1
UGUGUCGUCCGCUCCACUUCUCGUGGAUGUGUUUUUUACUAUAAGGUAAGUGUAGCAA--GAAUUU-UAGAGUCUC-UCUUGCUAAUCUUUACU---
.(((..(..((((((((.....))))).)))..)..))).....((((((..((((((--((....-.........-))))))))...))))))--- ( -23.22)
>DroYak_CAF1 1193 81 + 1
CGUCUCCACAGCUCCACUUCUUGUGGAUGUUUUCUUUACCAUCAGGUAAUUAGAAUCAUUCCACUU--UU-AAGUA-UUUAUUUA------------
...............((((...(((((.(((((..(((((....)))))..)))))...)))))..--..-)))).-........------------ ( -16.00)
>consensus
CGUCUCCACAGCUCCACUUCUCGUGGACGUCUUCUUUACCAUCAGGUAAAUAUAACCAUUCGAUUA_UCU_AAGUA_UUUAGCUAAUCCAUUC_AUA
..........(((((((.....))))).))....((((((....))))))............................................... (-10.85 = -10.77 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	11,051,246 – 11,051,341
Length	95
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	72.62
Mean single sequence MFE	-20.67
Consensus MFE	-10.50
Energy contribution	-10.67
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.51
SVM decision value	1.69
SVM RNA-class probability	0.972184
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11051246 95 - 20766785
UUUCAAAUGGAUCAGCAAAA-UACAUUAGA-UAAUCGAAUGAUUAUAUUUACCUGAUGGUAAAGAAGACGUCCACGAGAAGUGGAGCUGUGGAGACG
............((((....-........(-(((((....)))))).((((((....)))))).......(((((.....))))))))).(....). ( -22.30)
>DroSec_CAF1 1185 95 - 1
UAUCAAAUGGAUCAGCAAAA-UACUUUAGA-UAAUCGAAUGGUUAUAUUUACCUGAUGGUAAAGAAGACGUCCACUAGAAGUGGAGCUGUGGAGACG
............((((....-..((((..(-(((((....)))))).((((((....))))))))))...(((((.....))))))))).(....). ( -23.40)
>DroSim_CAF1 1185 90 - 1
UAUUGAACAGAUCAUAUAAA-U-----AGA-UAAUCGAAUGGUUAUAUUUACCUGAUGGUAAAGAAGACGUCCACGAGAAGUGGAGCUGUGGAGACG
......((((.((.......-.-----..(-(((((....)))))).((((((....)))))))).....(((((.....))))).))))(....). ( -20.40)
>DroEre_CAF1 1197 95 - 1
CAU-CAAUGGGUUAGAUAAAAUCAUU-AAACAAAUCGAAUGAUUAUGUUUACCUGAUGGUAAAGAAGACAUCCACGAGAAGUGGAGCUGUAGAGACG
(((-((...(((.(((((.(((((((-..........))))))).)))))))))))))((.....((...(((((.....))))).))......)). ( -22.60)
>DroWil_CAF1 1222 90 - 1
---AGUAAAGAUUAGCAAGA-GAGACUCUA-AAAUUC--UUGCUACACUUACCUUAUAGUAAAAAACACAUCCACGAGAAGUGGAGCGGACGACACA
---.((.(((..((((((((-(........-...)))--))))))..))).((.....((.....))...(((((.....)))))..))))...... ( -17.30)
>DroYak_CAF1 1193 81 - 1
------------UAAAUAAA-UACUU-AA--AAGUGGAAUGAUUCUAAUUACCUGAUGGUAAAGAAAACAUCCACAAGAAGUGGAGCUGUGGAGACG
------------........-(((((-..--..(((((....((((..(((((....)))))))))....)))))...))))).......(....). ( -18.00)
>consensus
UAU_AAAUGGAUCAGAAAAA_UACUU_AGA_AAAUCGAAUGAUUAUAUUUACCUGAUGGUAAAGAAGACAUCCACGAGAAGUGGAGCUGUGGAGACG
................................................(((((....)))))........(((((.....)))))............ (-10.50 = -10.67 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:41 2006