Locus 7386

Sequence ID	2L_DroMel_CAF1
Location	20,548,744 – 20,548,840
Length	96
Max. P	0.997280

overview

Window 4

Location	20,548,744 – 20,548,840
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.06
Mean single sequence MFE	-37.01
Consensus MFE	-14.68
Energy contribution	-14.85
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-2.46
Structure conservation index	0.40
SVM decision value	0.66
SVM RNA-class probability	0.816098
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20548744 96 + 22407834
UGGGUCGUUGU------UG-GUUUUAAUGCGACUCGCUUGCCAC-------------UUUUGCUGUUAUCAGCAG---CGUCAAUGUUUGGUGAUAACAGCCAGCGGCAGCG-CAGCAGC
.(((((((...------..-........)))))))(((((((.(-------------(...((((((((((.(((---((....)).))).)))))))))).)).))))).)-)...... ( -37.12)
>DroPse_CAF1 113637 117 + 1
UGGGUCGUUGUUGUUGUUG-GUUUUAAUGUGCCUCCAUUGGCACACUCUGCCACACGCUUUGCUGUUAUCAGCAGCGGCGUCAAUGUUUGGUGAUAACAGCUCAAGGCAGCG-CAGCAG-
......(((((.(((((((-((.....((((((......))))))....)))).))(((((((((((((((.(((((.......)).))).))))))))))..)))))))))-))))..- ( -43.40)
>DroEre_CAF1 62857 95 + 1
UGGGUCGUUGU------UG-CUUUUAAUGCGACUCGCUUGCCAC-------------UUUUGCUGUUAUCAGCUG---CGCCAAUGUUUGCUGAUAACAGCCAGCGGCAUCG-CAGCUG-
.(((((((...------..-........)))))))((.((((.(-------------(...((((((((((((.(---((....)))..)))))))))))).)).))))..)-).....- ( -39.12)
>DroYak_CAF1 65733 86 + 1
UGGGUCGUUGU------UG-GUUUUAAUGCGACUCGCUUGCCAC-------------UUUUGCUGUUAUCAGCUG---CGCCAAUGUUUGGUGAUAACAGCCAGCGGCA-----------
.(((((((...------..-........)))))))...((((.(-------------(...((((((((((.(.(---((....)))..).)))))))))).)).))))----------- ( -31.42)
>DroAna_CAF1 63673 98 + 1
UGGGUCGUUGU------UGGGUUUUAAUGUGCCUCGGUUGCCAC-------------UUUUUCUGUUAUCAGCAG---CGUCAAUGUUUGGUGAUAACAGCUACAGGCAGAGGCUGUGGC
.(((((((((.------.......))))).)))).....(((((-------------..((((((((((((.(((---((....)).))).))))))).((.....)))))))..))))) ( -28.90)
>DroPer_CAF1 119170 114 + 1
UGGGUCGUUGU---UGUUG-GUUUUAAUGUGCCUCCAUUGGCACACUCUGCCACACGCUUUGCUGUUAUCAGCAGCGGCGUCAAUGUUUGGUGAUAACAGCUCAAGGCAGCG-CAGCAG-
......(((((---.((((-((.....((((((......))))))....)))).))(((((((((((((((.(((((.......)).))).))))))))))..)))))...)-))))..- ( -42.10)
>consensus
UGGGUCGUUGU______UG_GUUUUAAUGCGACUCGCUUGCCAC_____________UUUUGCUGUUAUCAGCAG___CGUCAAUGUUUGGUGAUAACAGCCAGAGGCAGCG_CAGCAG_
.(((.(((((..............)))))...)))..........................((((((((((.(................).))))))))))................... (-14.68 = -14.85 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	20,548,744 – 20,548,840
Length	96
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.06
Mean single sequence MFE	-35.14
Consensus MFE	-18.41
Energy contribution	-18.16
Covariance contribution	-0.25
Combinations/Pair	1.12
Mean z-score	-3.80
Structure conservation index	0.52
SVM decision value	2.83
SVM RNA-class probability	0.997280
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20548744 96 - 22407834
GCUGCUG-CGCUGCCGCUGGCUGUUAUCACCAAACAUUGACG---CUGCUGAUAACAGCAAAA-------------GUGGCAAGCGAGUCGCAUUAAAAC-CA------ACAACGACCCA
((.(((.-((((((((((.((((((((((.((..........---.)).))))))))))...)-------------))))).))))))).))........-..------........... ( -37.40)
>DroPse_CAF1 113637 117 - 1
-CUGCUG-CGCUGCCUUGAGCUGUUAUCACCAAACAUUGACGCCGCUGCUGAUAACAGCAAAGCGUGUGGCAGAGUGUGCCAAUGGAGGCACAUUAAAAC-CAACAACAACAACGACCCA
-((((..-(((.((.((..((((((((((.((..............)).)))))))))).)))))))..))))((((((((......)))))))).....-................... ( -40.44)
>DroEre_CAF1 62857 95 - 1
-CAGCUG-CGAUGCCGCUGGCUGUUAUCAGCAAACAUUGGCG---CAGCUGAUAACAGCAAAA-------------GUGGCAAGCGAGUCGCAUUAAAAG-CA------ACAACGACCCA
-..(.((-(..(((((((.((((((((((((...........---..))))))))))))...)-------------)))))).(((...))).......)-))------.)......... ( -37.62)
>DroYak_CAF1 65733 86 - 1
-----------UGCCGCUGGCUGUUAUCACCAAACAUUGGCG---CAGCUGAUAACAGCAAAA-------------GUGGCAAGCGAGUCGCAUUAAAAC-CA------ACAACGACCCA
-----------(((((((.(((((((((((((.....)))..---....))))))))))...)-------------))))))...(.((((.........-..------....)))).). ( -29.56)
>DroAna_CAF1 63673 98 - 1
GCCACAGCCUCUGCCUGUAGCUGUUAUCACCAAACAUUGACG---CUGCUGAUAACAGAAAAA-------------GUGGCAACCGAGGCACAUUAAAACCCA------ACAACGACCCA
......(((((((((.....(((((((((.((..........---.)).))))))))).....-------------..))))...))))).............------........... ( -25.40)
>DroPer_CAF1 119170 114 - 1
-CUGCUG-CGCUGCCUUGAGCUGUUAUCACCAAACAUUGACGCCGCUGCUGAUAACAGCAAAGCGUGUGGCAGAGUGUGCCAAUGGAGGCACAUUAAAAC-CAACA---ACAACGACCCA
-((((..-(((.((.((..((((((((((.((..............)).)))))))))).)))))))..))))((((((((......)))))))).....-.....---........... ( -40.44)
>consensus
_CUGCUG_CGCUGCCGCUAGCUGUUAUCACCAAACAUUGACG___CUGCUGAUAACAGCAAAA_____________GUGGCAAGCGAGGCACAUUAAAAC_CA______ACAACGACCCA
...................((((((((((.(................).)))))))))).................(((((......)))))............................ (-18.41 = -18.16 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:27 2006