Locus 8326

Sequence ID	X_DroMel_CAF1
Location	20,674,417 – 20,674,540
Length	123
Max. P	0.993921

overview

Window 7

Location	20,674,417 – 20,674,508
Length	91
Sequences	3
Columns	92
Reading direction	forward
Mean pairwise identity	83.15
Mean single sequence MFE	-15.58
Consensus MFE	-12.05
Energy contribution	-11.83
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-2.00
Structure conservation index	0.77
SVM decision value	0.63
SVM RNA-class probability	0.805503
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20674417 91 + 22224390
CCAGUCUGCUCAGGCAUAUUGGCAAAUGCAAACAAGCAAACAAAGUUAAGGCUGGCUUCUUUGCACUCAAAAAA-CAAAAAAAAAAAAAUAC
(((((.(((....))).)))))....((((((.((((......(((....))).)))).)))))).........-................. ( -18.60)
>DroEre_CAF1 70865 83 + 1
ACAGUCUGCUCAGGCAUAUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCUGUGCACUCGAAAAAAUGAAAUAU---------
...((.(((...(((.....)))....))).))..(((....((((((....))))))...)))...................--------- ( -15.10)
>DroYak_CAF1 72411 83 + 1
CCAGUCUGCUCAGACAUAUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCAGUGCACUCGAAAAAAUAUAAAAC---------
...((((....))))(((((......((((...((((......(((....))).))))...))))........))))).....--------- ( -13.04)
>consensus
CCAGUCUGCUCAGGCAUAUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCUGUGCACUCGAAAAAAUAAAAAAA_________
...((((....))))...........((((...((((......(((....))).))))...))))........................... (-12.05 = -11.83 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	20,674,417 – 20,674,508
Length	91
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	83.15
Mean single sequence MFE	-19.63
Consensus MFE	-16.26
Energy contribution	-16.27
Covariance contribution	0.01
Combinations/Pair	1.14
Mean z-score	-1.58
Structure conservation index	0.83
SVM decision value	0.28
SVM RNA-class probability	0.665478
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20674417 91 - 22224390
GUAUUUUUUUUUUUUUG-UUUUUUGAGUGCAAAGAAGCCAGCCUUAACUUUGUUUGCUUGUUUGCAUUUGCCAAUAUGCCUGAGCAGACUGG
.................-......(((((((((.((((.(((.........))).)))).))))))))).(((...(((....)))...))) ( -20.50)
>DroEre_CAF1 70865 83 - 1
---------AUAUUUCAUUUUUUCGAGUGCACAGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAUAUGCCUGAGCAGACUGU
---------..............((((((((.(.((((.(((.........))).)))).).))))))))(((...(((....)))...))) ( -19.50)
>DroYak_CAF1 72411 83 - 1
---------GUUUUAUAUUUUUUCGAGUGCACUGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAUAUGUCUGAGCAGACUGG
---------((((.((((.((.(((((((((...((((.(((.........))).))))...))))))))).)).))))..))))....... ( -18.90)
>consensus
_________AUUUUUUAUUUUUUCGAGUGCACAGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAUAUGCCUGAGCAGACUGG
.......................((((((((.(.((((.(((.........))).)))).).))))))))(((...(((....)))...))) (-16.26 = -16.27 +   0.01)

alignment

secondary structure

dotplot

Window 9

Location	20,674,434 – 20,674,540
Length	106
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	70.75
Mean single sequence MFE	-13.55
Consensus MFE	-8.03
Energy contribution	-8.03
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.59
SVM decision value	0.47
SVM RNA-class probability	0.748104
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20674434 106 + 22224390
AUUGGCAAAUGCAAACAAGCAAACAAAGUUAAGGCUGGCUUCUUUGCACUCAAAAAA-CAAAAAAAAAAAAAUACAAGUAUCUGCGGUAUUUAUAAAUUUCAAAAAA----
.((((....((((((.((((......(((....))).)))).)))))).........-...........((((((..((....)).)))))).......))))....---- ( -14.10)
>DroEre_CAF1 70882 91 + 1
AUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCUGUGCACUCGAAAAAAUGAAAUAU---------------AUCAGGUAUAACU-AAUUCC----AAAUUA
..((((...((((...((((......(((....))).))))...))))..........(((.....---------------.))))))).....-......----...... ( -12.80)
>DroYak_CAF1 72428 96 + 1
AUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCAGUGCACUCGAAAAAAUAUAAAAC---------------CUGAAGUAUAACUUAAAUGCAGAAAAAUAA
.((((....(((......)))....((((((......(((((((......................---------------))))))).))))))....))))........ ( -13.75)
>consensus
AUUGCCAAAUGCAAACAAGCAAACAAAGUUAAAGCUGGCUUCUGUGCACUCGAAAAAAUAAAAAAA_______________CUGAGGUAUAACU_AAUUCCA_AAAAAU_A
.........((((...((((......(((....))).))))...))))............................................................... ( -8.03 =  -8.03 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	20,674,434 – 20,674,540
Length	106
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	70.75
Mean single sequence MFE	-17.97
Consensus MFE	-14.22
Energy contribution	-14.33
Covariance contribution	0.11
Combinations/Pair	1.06
Mean z-score	-1.48
Structure conservation index	0.79
SVM decision value	2.44
SVM RNA-class probability	0.993921
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20674434 106 - 22224390
----UUUUUUGAAAUUUAUAAAUACCGCAGAUACUUGUAUUUUUUUUUUUUUG-UUUUUUGAGUGCAAAGAAGCCAGCCUUAACUUUGUUUGCUUGUUUGCAUUUGCCAAU
----......................(((((((....)))))...........-......(((((((((.((((.(((.........))).)))).))))))))))).... ( -18.00)
>DroEre_CAF1 70882 91 - 1
UAAUUU----GGAAUU-AGUUAUACCUGAU---------------AUAUUUCAUUUUUUCGAGUGCACAGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAU
.....(----(((((.-.((((....))))---------------..)))))).....(((((((((.(.((((.(((.........))).)))).).))))))))).... ( -19.40)
>DroYak_CAF1 72428 96 - 1
UUAUUUUUCUGCAUUUAAGUUAUACUUCAG---------------GUUUUAUAUUUUUUCGAGUGCACUGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAU
.........((((((((((.....))).))---------------))............((((((((...((((.(((.........))).))))...))))))))))).. ( -16.50)
>consensus
U_AUUUUU_UGAAAUU_AGUUAUACCUCAG_______________AUUUUUUAUUUUUUCGAGUGCACAGAAGCCAGCUUUAACUUUGUUUGCUUGUUUGCAUUUGGCAAU
...........................................................((((((((.(.((((.(((.........))).)))).).))))))))..... (-14.22 = -14.33 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:01:19 2006