Locus 5722

Sequence ID	X_DroMel_CAF1
Location	14,811,779 – 14,812,032
Length	253
Max. P	0.894205

overview

Window 2

Location	14,811,779 – 14,811,896
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.25
Mean single sequence MFE	-30.90
Consensus MFE	-20.16
Energy contribution	-19.84
Covariance contribution	-0.32
Combinations/Pair	1.28
Mean z-score	-1.88
Structure conservation index	0.65
SVM decision value	0.96
SVM RNA-class probability	0.889717
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14811779 117 - 22224390
GGCCACCCAUGGGCCACCCAUACCCGUGAAUGGCCCCAUCCCUCCAACGACCAUU--GUGGUCAUUCUUAAAUGGCCUUUUACUUAAUGCUAAGUGUCGUUUGACUGCUGUGCUAUCC-U
(((((..((((((.........))))))..))))).......((.((((((....--..(((((((....)))))))....(((((....))))))))))).))..............-. ( -34.20)
>DroSec_CAF1 5730 100 - 1
GGCCACCCAUGGGCC-CCCAU-----------------UCCCGCCAGCGACCAUU--GUGGUCAUUCUUAAAUGGCCUUUUACUUAAAGCUAAGUGUCGUUUGACUGCUGUGCUGCCCCA
(((.....((((...-.))))-----------------....((((((((((...--..))))....(((((((((.....(((((....))))))))))))))..)))).)).)))... ( -30.50)
>DroSim_CAF1 4964 100 - 1
GGCCACCCAUGGGCC-CCCAU-----------------UCCCGCCAGCGACCAUU--GUGGUCAUUCUUAAAUGGCCUUUUACUUAAUGCUAAGUGUCGUUUGACUGCUGUGCUGCCCCA
(((.....((((...-.))))-----------------....((((((((((...--..))))....(((((((((.....(((((....))))))))))))))..)))).)).)))... ( -30.50)
>DroEre_CAF1 10973 113 - 1
GGCCACCCAGGGGCC-CCCCUCCCCGUGAAUGCCCC---UCCUCCGACGACCAUU--GUGGUCAUUCUUAAAUGGCCUUUUACUUAAUGCUAAGUGUCGUUUGACUGCUGUGCUGCCCC-
((((((..((((((.-...............)))))---)..((.((((((....--..(((((((....)))))))....(((((....))))))))))).)).....)))..)))..- ( -31.39)
>DroAna_CAF1 33142 101 - 1
GGUGGCCGA--GACC-CCUCUCUGCG------------UCUC-UCUGCCACCAUUCUGUGACCAUUCUUAAAUGGCCUUUUACUUAAUGCUAAGUGUCGUUUGACGGCUGCC--UCCUC-
((((((.((--((..-((.....).)------------..))-)).)))))).....((..((....(((((((((.....(((((....)))))))))))))).))..)).--.....- ( -27.90)
>consensus
GGCCACCCAUGGGCC_CCCAU___CG____________UCCCGCCAGCGACCAUU__GUGGUCAUUCUUAAAUGGCCUUUUACUUAAUGCUAAGUGUCGUUUGACUGCUGUGCUGCCCC_
((((((..((((.....))))......................(.((((((........(((((((....)))))))....(((((....))))))))))).)......)))..)))... (-20.16 = -19.84 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	14,811,818 – 14,811,934
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.36
Mean single sequence MFE	-38.34
Consensus MFE	-20.59
Energy contribution	-20.35
Covariance contribution	-0.24
Combinations/Pair	1.30
Mean z-score	-2.16
Structure conservation index	0.54
SVM decision value	0.98
SVM RNA-class probability	0.894205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14811818 116 + 22224390
AAAGGCCAUUUAAGAAUGACCAC--AAUGGUCGUUGGAGGGAUGGGGCCAUUCACGGGUAUGGGUGGCCCAUGGGUGGCCAAGUCC-AAGUUUCGCCUC-CAUCCAGUCAAAUUGGAUUA
..((((........(((((((..--...)))))))....((((..(((((((((.((((.......)))).)))))))))..))))-.......)))).-.(((((((...))))))).. ( -47.30)
>DroSec_CAF1 5770 98 + 1
AAAGGCCAUUUAAGAAUGACCAC--AAUGGUCGCUGGCGGGA-----------------AUGGG-GGCCCAUGGGUGGCCAAGUCC-AAGUUUCGCCUC-CGUCCAGUCAAAUUGGAUUA
...(((((((.............--)))))))(..((((..(-----------------.((((-(((((....).))))...)))-)..)..))))..-)(((((((...))))))).. ( -31.22)
>DroSim_CAF1 5004 98 + 1
AAAGGCCAUUUAAGAAUGACCAC--AAUGGUCGCUGGCGGGA-----------------AUGGG-GGCCCAUGGGUGGCCAAGUCC-AAGUUUCGCCUC-CGUCCAGUCAAAUUGGAUUA
...(((((((.............--)))))))(..((((..(-----------------.((((-(((((....).))))...)))-)..)..))))..-)(((((((...))))))).. ( -31.22)
>DroEre_CAF1 11012 113 + 1
AAAGGCCAUUUAAGAAUGACCAC--AAUGGUCGUCGGAGGA---GGGGCAUUCACGGGGAGGGG-GGCCCCUGGGUGGCCAAGUCCCAUAUUUCGCCUC-CGUCCAGUCAAAUUGGAUUA
.....(((.....((.(((((..--...)))))))(((.(.---(((((.......((((....-(((((....).))))...)))).......)))))-).)))........))).... ( -40.04)
>DroAna_CAF1 33179 103 + 1
AAAGGCCAUUUAAGAAUGGUCACAGAAUGGUGGCAGA-GAGA------------CGCAGAGAGG-GGUC--UCGGCCACCAAGUCC-AAGUUUCGCCUUUUGGCCACUCAAAUUGGAUUA
...(((((((....)))))))......(((((((...-((((------------(.(......)-.)))--)).)))))))(((((-((.....(((....)))........))))))). ( -41.92)
>consensus
AAAGGCCAUUUAAGAAUGACCAC__AAUGGUCGCUGGAGGGA____________CG___AUGGG_GGCCCAUGGGUGGCCAAGUCC_AAGUUUCGCCUC_CGUCCAGUCAAAUUGGAUUA
..((((((((....)))).........((((((((.(.(((..........................))).).)))))))).............))))...(((((((...))))))).. (-20.59 = -20.35 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	14,811,818 – 14,811,934
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.36
Mean single sequence MFE	-33.32
Consensus MFE	-19.06
Energy contribution	-19.42
Covariance contribution	0.36
Combinations/Pair	1.14
Mean z-score	-1.88
Structure conservation index	0.57
SVM decision value	0.40
SVM RNA-class probability	0.722537
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14811818 116 - 22224390
UAAUCCAAUUUGACUGGAUG-GAGGCGAAACUU-GGACUUGGCCACCCAUGGGCCACCCAUACCCGUGAAUGGCCCCAUCCCUCCAACGACCAUU--GUGGUCAUUCUUAAAUGGCCUUU
..(((((.......)))))(-((((.((....(-((....(((((..((((((.........))))))..)))))))))))))))..........--..(((((((....)))))))... ( -39.80)
>DroSec_CAF1 5770 98 - 1
UAAUCCAAUUUGACUGGACG-GAGGCGAAACUU-GGACUUGGCCACCCAUGGGCC-CCCAU-----------------UCCCGCCAGCGACCAUU--GUGGUCAUUCUUAAAUGGCCUUU
.....(((((((.((((.((-(.(((.((....-....)).)))....((((...-.))))-----------------..))))))))))..)))--).(((((((....)))))))... ( -29.40)
>DroSim_CAF1 5004 98 - 1
UAAUCCAAUUUGACUGGACG-GAGGCGAAACUU-GGACUUGGCCACCCAUGGGCC-CCCAU-----------------UCCCGCCAGCGACCAUU--GUGGUCAUUCUUAAAUGGCCUUU
.....(((((((.((((.((-(.(((.((....-....)).)))....((((...-.))))-----------------..))))))))))..)))--).(((((((....)))))))... ( -29.40)
>DroEre_CAF1 11012 113 - 1
UAAUCCAAUUUGACUGGACG-GAGGCGAAAUAUGGGACUUGGCCACCCAGGGGCC-CCCCUCCCCGUGAAUGCCCC---UCCUCCGACGACCAUU--GUGGUCAUUCUUAAAUGGCCUUU
....(((.(((((.((((.(-((((.(...((((((....((((.(....)))))-......))))))....).))---)))))))..((((...--..))))....))))))))..... ( -36.70)
>DroAna_CAF1 33179 103 - 1
UAAUCCAAUUUGAGUGGCCAAAAGGCGAAACUU-GGACUUGGUGGCCGA--GACC-CCUCUCUGCG------------UCUC-UCUGCCACCAUUCUGUGACCAUUCUUAAAUGGCCUUU
....(((.((.((((((.((.(((......)))-(((..(((((((.((--((..-((.....).)------------..))-)).))))))).))).)).))))))..)).)))..... ( -31.30)
>consensus
UAAUCCAAUUUGACUGGACG_GAGGCGAAACUU_GGACUUGGCCACCCAUGGGCC_CCCAU___CG____________UCCCGCCAGCGACCAUU__GUGGUCAUUCUUAAAUGGCCUUU
...((((.......))))...(((((........((....((((.......))))..)).............................((((((...))))))...........))))). (-19.06 = -19.42 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	14,811,934 – 14,812,032
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.07
Mean single sequence MFE	-34.90
Consensus MFE	-12.58
Energy contribution	-13.90
Covariance contribution	1.32
Combinations/Pair	1.12
Mean z-score	-1.81
Structure conservation index	0.36
SVM decision value	0.39
SVM RNA-class probability	0.716267
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14811934 98 - 22224390
---UCUGUCACUU--UCAGUUGGCCCCUGUUU--------------UGUGCCCCCCGCCCA-GGCACACCUG-CCAGGCACUUCACACUGACAUGGGC-GAUGGGAAUGGGGCAACAACU
---..........--..((((((((((.....--------------....(((..((((((-((((....))-)).......((.....))..)))))-)..)))...)))))..))))) ( -33.80)
>DroSec_CAF1 5868 98 - 1
---UCUGCCACUU--UCAGUAGGCCCCUGUUU--------------UGUGCCCCCCGCCCA-GGCACACCUG-CCAGGCACUUCACACUGACAUGGGC-GAUGGGGAUGGGGCAACAACU
---.((((.....--...))))(((((.....--------------....((((.((((((-((((....))-)).......((.....))..)))))-)..))))..)))))....... ( -35.90)
>DroSim_CAF1 5102 98 - 1
---UCUGCCACUU--UCGGUAGGCCCCUGUUU--------------CGUGCCCCCCGGCCA-GGCACACCUG-CCAGGCACUUCACACUGACAUGGGC-GAUGGGGAUGGGGCAACAACU
---.(((((....--..)))))(((((..(..--------------(((((((....(((.-((((....))-)).)))...((.....))...))))-.)))..)..)))))....... ( -39.90)
>DroEre_CAF1 11125 112 - 1
---UCUGCCACUU--UCAGUGGGUCCCCGUUUACAGACCCCCACUUUCAGCCCCCCACACA-GGCACACCUG-CCAGGCACUUCACAGUGACAUGGAA-GAUGGGGAUGGGACAACAACU
---....((((..--...))))(((((.(((....)))(((((((((((............-((((....))-)).(.((((....)))).).)))))-).)))))..)))))....... ( -37.30)
>DroAna_CAF1 33282 91 - 1
CAUUCUCUCAUUUCGUCAGUUGGCCAAGCGAG--------------UG--------GGCCAGAGAACACCUGGCCAGAAAC-------CGACAACCAAAAGAGGAGAAGGGGCAACAACU
.....((((.((((.((..((((.....((.(--------------(.--------((((((.......))))))....))-------))....))))..)).)))).))))........ ( -27.60)
>consensus
___UCUGCCACUU__UCAGUAGGCCCCUGUUU______________UGUGCCCCCCGCCCA_GGCACACCUG_CCAGGCACUUCACACUGACAUGGGC_GAUGGGGAUGGGGCAACAACU
.................(((..(((((....................(((((..........))))).(((....)))..............................)))))....))) (-12.58 = -13.90 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:48 2006