Locus 6360

Sequence ID	2L_DroMel_CAF1
Location	17,769,019 – 17,769,149
Length	130
Max. P	0.993734

overview

Window 4

Location	17,769,019 – 17,769,120
Length	101
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	75.34
Mean single sequence MFE	-15.46
Consensus MFE	-8.47
Energy contribution	-9.08
Covariance contribution	0.61
Combinations/Pair	1.17
Mean z-score	-1.82
Structure conservation index	0.55
SVM decision value	0.72
SVM RNA-class probability	0.833400
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17769019 101 - 22407834
UUUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUUACCCAUUCAA-----AAUCAGAGACCCUGCACUUUG-CCA
.(((((.......)))))......((((((((..((((........))))))))))))...................-----...(((((........)))))-... ( -14.40)
>DroSec_CAF1 68931 94 - 1
CUUUUGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUUACCCAUUCAA-----AAUCAGAGA-------CUUUG-CCA
.....((.((..............((((((((..((((........))))))))))))..............(((..-----.....))).-------))..)-).. ( -12.20)
>DroSim_CAF1 72804 99 - 1
-UUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCACAAAUAAUUAUGUGUAAGCCAACACUUAAUUACCCAU-CAA-----AAUCAGAGACCCAGCACUUUG-CCA
-(((((.......)))))......((((((((..((((........))))))))))))...............-...-----...(((((........)))))-... ( -14.60)
>DroEre_CAF1 78382 100 - 1
CUUUACCUAGCAGCUAAACAAUUAUUGGCUUUGCCGCAAAUAAUUGUGUGUAAGCCAAUACUUAAUUACCCAUUCAA-----AAUCAGAGAC-UGGCACUCUG-CCA
.........((((.........(((((((((.(((((((....))))).))))))))))).........(((.((..-----.......)).-)))....)))-).. ( -22.50)
>DroYak_CAF1 71273 100 - 1
CAUUAGCUAGAAACUAAACAUUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUUACCCAUUCAA-----AAUCAGAUAC-UGGCACUAUG-CCA
.....(((((..............((((((((..((((........))))))))))))...............((..-----.....))..)-))))......-... ( -17.50)
>DroMoj_CAF1 105249 88 - 1
CUUCUGUUAAGAAUU------UCUUUAACUU--CCCAACAGAAUUAAGAGAAAGCUAAAACUGAUCUAU----UAAGAUAUUAAACAGAUA-------UUUUCUUCA
.(((((((..(((..------........))--)..)))))))..(((((((..((.......((((..----..)))).......))...-------))))))).. ( -11.54)
>consensus
CUUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUUACCCAUUCAA_____AAUCAGAGAC___GCACUUUG_CCA
........................((((((((..((((........))))))))))))................................................. ( -8.47 =  -9.08 +   0.61)

alignment

secondary structure

dotplot

Window 5

Location	17,769,053 – 17,769,149
Length	96
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	75.50
Mean single sequence MFE	-25.65
Consensus MFE	-12.43
Energy contribution	-11.79
Covariance contribution	-0.63
Combinations/Pair	1.48
Mean z-score	-2.56
Structure conservation index	0.48
SVM decision value	1.89
SVM RNA-class probability	0.981505
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17769053 96 + 22407834
AAUUAAGUGUUGGCUUACACAUAAUUAUUUGCGGUUAAGCCAAUAAUUGUUUAGUUUCUAGCUAAAAUGCAGAUAUGCUUG----UG-AGCUGG---GAUUAGG--
.....(((.(..(((((((......(((((((((.....))........((((((.....))))))..)))))))....))----))-)))..)---.)))...-- ( -26.30)
>DroSec_CAF1 68958 96 + 1
AAUUAAGUGUUGGCUUACACAUAAUUAUUUGCGGUUAAGCCAAUAAUUGUUUAGUUUCUAGCAAAAGUGCAGAUAUGCUUG----UG-AGCUGG---CUUUAGG--
..(((((.((..(((((((.(((((((((.((......)).)))))))))..(((.(((.(((....))))))...)))))----))-)))..)---)))))).-- ( -28.30)
>DroSim_CAF1 72837 98 + 1
AAUUAAGUGUUGGCUUACACAUAAUUAUUUGUGGUUAAGCCAAUAAUUGUUUAGUUUCUAGCUAAA-UGCAGAUAUGCUUG----UGGAGCUGG---GAUUAGGUG
.......((((((((((..(((((....)))))..))))))))))...(..(((((.((((((...-.(((....)))...----...))))))---)))))..). ( -30.10)
>DroEre_CAF1 78415 96 + 1
AAUUAAGUAUUGGCUUACACACAAUUAUUUGCGGCAAAGCCAAUAAUUGUUUAGCUGCUAGGUAAAGUUCAGCUGUGAUUG----UG-AACUGG---GAUGGGG--
...(((((....)))))..(((((((((..(((((.((((........)))).)))))..(((........))))))))))----))-......---.......-- ( -20.50)
>DroYak_CAF1 71306 96 + 1
AAUUAAGUGUUGGCUUACACAUAAUUAUUUGCGGUUAAGCCAAUAAAUGUUUAGUUUCUAGCUAAUGUUUAGUUGUGAUUG----UG-AGCUGG---GAUUAGG--
.....(((.(..(((((((((((((((...((((.....)).........(((((.....))))).)).))))))))..))----))-)))..)---.)))...-- ( -24.80)
>DroMoj_CAF1 105278 95 + 1
AGAUCAGUUUUAGCUUUCUCUUAAUUCUGUUGGG--AAGUUAAAGA------AAUUCUUAACAGAAGUUGAGAUUUGGAUGAUCGAU-AAUUGGGCUAUUUAGC--
.(((((..(((((...((((....((((((((((--((........------..))))))))))))...)))).))))))))))...-......(((....)))-- ( -23.90)
>consensus
AAUUAAGUGUUGGCUUACACAUAAUUAUUUGCGGUUAAGCCAAUAAUUGUUUAGUUUCUAGCUAAAGUGCAGAUAUGCUUG____UG_AGCUGG___GAUUAGG__
.......((((((((((..(.(((....))).)..))))))))))............((((((.....(((....)))..........))))))............ (-12.43 = -11.79 +  -0.63)

alignment

secondary structure

dotplot

Window 6

Location	17,769,053 – 17,769,149
Length	96
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	75.50
Mean single sequence MFE	-16.53
Consensus MFE	-8.47
Energy contribution	-9.08
Covariance contribution	0.61
Combinations/Pair	1.17
Mean z-score	-2.82
Structure conservation index	0.51
SVM decision value	2.42
SVM RNA-class probability	0.993734
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17769053 96 - 22407834
--CCUAAUC---CCAGCU-CA----CAAGCAUAUCUGCAUUUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUU
--.......---..((((-..----...(((....))).....))))................((((((((..((((........))))))))))))......... ( -16.80)
>DroSec_CAF1 68958 96 - 1
--CCUAAAG---CCAGCU-CA----CAAGCAUAUCUGCACUUUUGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUU
--....(((---((((((-..----..)))...((((((....))).)))..............))))))..........(((((.((((......)))).))))) ( -18.10)
>DroSim_CAF1 72837 98 - 1
CACCUAAUC---CCAGCUCCA----CAAGCAUAUCUGCA-UUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCACAAAUAAUUAUGUGUAAGCCAACACUUAAUU
.........---...(((...----..)))...(((((.-....)).))).............((((((((..((((........))))))))))))......... ( -16.80)
>DroEre_CAF1 78415 96 - 1
--CCCCAUC---CCAGUU-CA----CAAUCACAGCUGAACUUUACCUAGCAGCUAAACAAUUAUUGGCUUUGCCGCAAAUAAUUGUGUGUAAGCCAAUACUUAAUU
--.......---......-..----.......(((((..((......))))))).......(((((((((.(((((((....))))).)))))))))))....... ( -21.00)
>DroYak_CAF1 71306 96 - 1
--CCUAAUC---CCAGCU-CA----CAAUCACAACUAAACAUUAGCUAGAAACUAAACAUUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUU
--.......---..((((-..----..................))))................((((((((..((((........))))))))))))......... ( -12.55)
>DroMoj_CAF1 105278 95 - 1
--GCUAAAUAGCCCAAUU-AUCGAUCAUCCAAAUCUCAACUUCUGUUAAGAAUU------UCUUUAACUU--CCCAACAGAAUUAAGAGAAAGCUAAAACUGAUCU
--(((....)))......-...((((.......((((...(((((((..(((..------........))--)..)))))))....)))).((......)))))). ( -13.90)
>consensus
__CCUAAUC___CCAGCU_CA____CAAGCAUAUCUGAACUUUAGCUAGAAACUAAACAAUUAUUGGCUUAACCGCAAAUAAUUAUGUGUAAGCCAACACUUAAUU
...............................................................((((((((..((((........))))))))))))......... ( -8.47 =  -9.08 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:15 2006