Locus 3942

Sequence ID	2R_DroMel_CAF1
Location	13,015,592 – 13,015,708
Length	116
Max. P	0.968885

overview

Window 4

Location	13,015,592 – 13,015,708
Length	116
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	73.96
Mean single sequence MFE	-16.77
Consensus MFE	-6.51
Energy contribution	-8.14
Covariance contribution	1.63
Combinations/Pair	1.06
Mean z-score	-3.07
Structure conservation index	0.39
SVM decision value	1.15
SVM RNA-class probability	0.922512
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13015592 116 + 20766785
AAGUGUAUUCUGUAUCAAAA---CUAAUCAUCUAGUUAUCAUACCAGAUCACUGACCCACAUAUCUAUGAUCCAUCUACACAAAAAUAUUAUAGAGAAAAACCAUAGAUACAGAAAUCA
.......(((((((((....---.........((((.(((......))).)))).........((((((((................))))))))...........))))))))).... ( -19.89)
>DroSec_CAF1 29325 117 + 1
AAAUGAAUCCUGUAUCAAAUCAUCUAAUCAUUCAGUUAUCAUACUUAACCAUUGACCCACAUAUCUGUGUUCCAUCUACACA--UAUAUUUUACAGAAAACCCAUAGAUACAGAAAUCA
...(((...(((((((...........(((....((((.......))))...))).....((((.(((((.......)))))--.)))).................)))))))...))) ( -17.00)
>DroSim_CAF1 25708 114 + 1
AAAUGCAUCCUGUAUCAAAA---GUAAUCAUCCAGUUAUCAUACUUAACCAAUGACCCACAUAUCUGUGUUCCAUAUACAUA--AAUAUUUUACAGAAAAACCAUAGAUACAGAAAUCU
.........(((((((....---((..((((...((((.......))))..))))...))...((((((....((((.....--.))))..)))))).........)))))))...... ( -17.80)
>DroEre_CAF1 25215 100 + 1
-AAAGCAUCCCGUUUCCAAA---UU-ACCAUCCAGUUAU---ACUCAGCCACUGACCCACAUAUCUGUGUUCUAUCUACAAA--A---------AUCGAGAUCAUACACAAUGGAAUAA
-............(((((..---..-......((((...---........))))...........(((((...((((.(...--.---------...)))))...))))).)))))... ( -12.40)
>consensus
AAAUGCAUCCUGUAUCAAAA___CUAAUCAUCCAGUUAUCAUACUUAACCACUGACCCACAUAUCUGUGUUCCAUCUACACA__AAUAUUUUACAGAAAAACCAUAGAUACAGAAAUCA
.......(((((((((..................((((..............)))).((((....)))).....................................))))))))).... ( -6.51 =  -8.14 +   1.63)

alignment

secondary structure

dotplot

Window 5

Location	13,015,592 – 13,015,708
Length	116
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	73.96
Mean single sequence MFE	-27.17
Consensus MFE	-15.15
Energy contribution	-15.15
Covariance contribution	0.00
Combinations/Pair	1.35
Mean z-score	-2.24
Structure conservation index	0.56
SVM decision value	1.63
SVM RNA-class probability	0.968885
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13015592 116 - 20766785
UGAUUUCUGUAUCUAUGGUUUUUCUCUAUAAUAUUUUUGUGUAGAUGGAUCAUAGAUAUGUGGGUCAGUGAUCUGGUAUGAUAACUAGAUGAUUAG---UUUUGAUACAGAAUACACUU
(((((..(((((((((((((..(((.(((((.....))))).)))..)))))))))))))..)))))(((.((((.(((.(.((((((....))))---)).).))))))).))).... ( -35.60)
>DroSec_CAF1 29325 117 - 1
UGAUUUCUGUAUCUAUGGGUUUUCUGUAAAAUAUA--UGUGUAGAUGGAACACAGAUAUGUGGGUCAAUGGUUAAGUAUGAUAACUGAAUGAUUAGAUGAUUUGAUACAGGAUUCAUUU
(((.(((((((((...(((((.(((.....((((.--(((((.......))))).))))...(((((..(((((.......)))))...)))))))).)))))))))))))).)))... ( -25.70)
>DroSim_CAF1 25708 114 - 1
AGAUUUCUGUAUCUAUGGUUUUUCUGUAAAAUAUU--UAUGUAUAUGGAACACAGAUAUGUGGGUCAUUGGUUAAGUAUGAUAACUGGAUGAUUAC---UUUUGAUACAGGAUGCAUUU
.(..(((((((((...(((...(((((...(((((--((.....((((..((((....))))..))))....)))))))....)).))).....))---)...)))))))))..).... ( -26.80)
>DroEre_CAF1 25215 100 - 1
UUAUUCCAUUGUGUAUGAUCUCGAU---------U--UUUGUAGAUAGAACACAGAUAUGUGGGUCAGUGGCUGAGU---AUAACUGGAUGGU-AA---UUUGGAAACGGGAUGCUUU-
....((((((((((...(((((((.---------.--.))).))))...))))))....((.(.((((...)))).)---...)))))).(((-(.---((((....)))).))))..- ( -20.60)
>consensus
UGAUUUCUGUAUCUAUGGUUUUUCUGUAAAAUAUU__UGUGUAGAUGGAACACAGAUAUGUGGGUCAGUGGUUAAGUAUGAUAACUGGAUGAUUAG___UUUUGAUACAGGAUGCAUUU
....(((((((((................................(((..((((....))))..))).(.(((.(((......))).))).)...........)))))))))....... (-15.15 = -15.15 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:54 2006