Locus 123

Sequence ID	3L_DroMel_CAF1
Location	405,343 – 405,434
Length	91
Max. P	0.579001

overview

Window 4

Location	405,343 – 405,434
Length	91
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	77.68
Mean single sequence MFE	-21.75
Consensus MFE	-13.24
Energy contribution	-14.82
Covariance contribution	1.57
Combinations/Pair	1.25
Mean z-score	-1.39
Structure conservation index	0.61
SVM decision value	0.01
SVM RNA-class probability	0.540088
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 405343 91 + 23771897
-----------UUGGUUUUUAUUGCUAAUGAGAGAACACGUCAUAAAAUAGCCUGUUCGGGGCUGGCUGACC-AGCGCAAAUCUCUCAAUUAGCUUAUACGAA
-----------............((((((((((((................(((....)))(((((....))-))).....)))))).))))))......... ( -26.30)
>DroGri_CAF1 62170 97 + 1
UGUGUGUGUUAUUCGUUUUAAUUGCUAAUGAGAG-ACACAUCAUAAAAUAACACAU-CAU----GCCUGGCCAGGCGCAAAUCUCUCAAUUAGUUUAUACAAA
((((((((((.((((((.........)))))).)-))))).))))...........-...----((((....))))........................... ( -18.60)
>DroSec_CAF1 52306 91 + 1
-----------UUGGUUUUUAUUGCUAAUGAGAGAACACGUCAUAAAAUAGCCCAGUCGGGGCUGGCUGACC-AGCGCAAAUCUCUCAAUUAGCUUAUACGAA
-----------............((((((((((((.............((((((.....))))))(((....-))).....)))))).))))))......... ( -28.00)
>DroEre_CAF1 56703 90 + 1
-----------UUGGUUUUUAUUGCUAAUGAGAGAACACGUCAUAAAGCAGUCUGUGCG-GGCUGGCUGAUC-AGCGCAAAUCUCCCAAUUAGCUUAUGCGAA
-----------............((((((..((((...(((.....((((((((....)-)))).)))....-.)))....))))...))))))......... ( -21.30)
>DroYak_CAF1 56636 91 + 1
-----------UUGGUUUUUAUUGCUAAUGAGAGAACACGUCAUAAAAUAGCCUGUUCGGGGCUGGCUGAUC-AGCGCAAAUCUCGCAAUUAGCUUAUACAAA
-----------............((((((..((((.............((((((.....))))))(((....-))).....))))...))))))......... ( -22.10)
>DroAna_CAF1 46471 80 + 1
-----------UUGGCU-UUAUUGCUAAUGAAGGAACACAUCAUAAAGUUUC------CG----GGCUGACC-AGCACAAAUAUCUCAAUUAGCUCGAACAAA
-----------(((((.-.....)))))....((((.((........)))))------)(----((((((..-................)))))))....... ( -14.17)
>consensus
___________UUGGUUUUUAUUGCUAAUGAGAGAACACGUCAUAAAAUAGCCUGUUCGGGGCUGGCUGACC_AGCGCAAAUCUCUCAAUUAGCUUAUACAAA
.......................((((((((((((.............(((((.......)))))(((.....))).....)))))).))))))......... (-13.24 = -14.82 +   1.57)

alignment

secondary structure

dotplot

Window 5

Location	405,343 – 405,434
Length	91
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	77.68
Mean single sequence MFE	-22.07
Consensus MFE	-12.37
Energy contribution	-13.21
Covariance contribution	0.84
Combinations/Pair	1.20
Mean z-score	-1.64
Structure conservation index	0.56
SVM decision value	0.09
SVM RNA-class probability	0.579001
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 405343 91 - 23771897
UUCGUAUAAGCUAAUUGAGAGAUUUGCGCU-GGUCAGCCAGCCCCGAACAGGCUAUUUUAUGACGUGUUCUCUCAUUAGCAAUAAAAACCAA-----------
.........((((((.((((((..((((((-((....))))).((.....))............))).))))))))))))............----------- ( -26.50)
>DroGri_CAF1 62170 97 - 1
UUUGUAUAAACUAAUUGAGAGAUUUGCGCCUGGCCAGGC----AUG-AUGUGUUAUUUUAUGAUGUGU-CUCUCAUUAGCAAUUAAAACGAAUAACACACACA
(((((.....(((((.(((((((..((((((....))))----((.-(((........))).))))))-))))))))))........)))))........... ( -19.22)
>DroSec_CAF1 52306 91 - 1
UUCGUAUAAGCUAAUUGAGAGAUUUGCGCU-GGUCAGCCAGCCCCGACUGGGCUAUUUUAUGACGUGUUCUCUCAUUAGCAAUAAAAACCAA-----------
.........((((((.((((((...((((.-.((((...(((((.....)))))......))))))))))))))))))))............----------- ( -29.60)
>DroEre_CAF1 56703 90 - 1
UUCGCAUAAGCUAAUUGGGAGAUUUGCGCU-GAUCAGCCAGCC-CGCACAGACUGCUUUAUGACGUGUUCUCUCAUUAGCAAUAAAAACCAA-----------
.........((((((.((((((..((((((-(......)))).-.(((.....)))........))).))))))))))))............----------- ( -22.80)
>DroYak_CAF1 56636 91 - 1
UUUGUAUAAGCUAAUUGCGAGAUUUGCGCU-GAUCAGCCAGCCCCGAACAGGCUAUUUUAUGACGUGUUCUCUCAUUAGCAAUAAAAACCAA-----------
.........((((((...((((.....(((-(......))))...(((((.((........).).)))))))))))))))............----------- ( -20.40)
>DroAna_CAF1 46471 80 - 1
UUUGUUCGAGCUAAUUGAGAUAUUUGUGCU-GGUCAGCC----CG------GAAACUUUAUGAUGUGUUCCUUCAUUAGCAAUAA-AGCCAA-----------
.........((((((.(((......(.(((-....))).----)(------(((((........)).))))))))))))).....-......----------- ( -13.90)
>consensus
UUCGUAUAAGCUAAUUGAGAGAUUUGCGCU_GGUCAGCCAGCCCCGAACAGGCUAUUUUAUGACGUGUUCUCUCAUUAGCAAUAAAAACCAA___________
.........((((((.((((((...((((...((((........................))))))))))))))))))))....................... (-12.37 = -13.21 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:04 2006