Locus 4662

Sequence ID	3L_DroMel_CAF1
Location	13,193,820 – 13,193,912
Length	92
Max. P	0.972232

overview

Window 2

Location	13,193,820 – 13,193,912
Length	92
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	73.49
Mean single sequence MFE	-32.77
Consensus MFE	-18.04
Energy contribution	-18.35
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.97
Structure conservation index	0.55
SVM decision value	0.82
SVM RNA-class probability	0.858365
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13193820 92 + 23771897
-GUUUUUAAG-----------------AGGUAUCUCUUAGGCGACCCUA-AGCCCUUUUUAAAUAAAAAGGCCUAGGGUGCUGUCAAUAGGAUUCCCUCGCAAAAGCGAAC---------
-((((((..(-----------------(((.((((....(((.((((((-.(((.(((((....)))))))).))))))))).......))))..))))..))))))....--------- ( -31.40)
>DroSec_CAF1 45121 117 + 1
-GUUUUUAAGAUCGCUCAGCAUUUACUAGGUAUCUGUGAGGCGACCCCU-AGCCCUUU-AAGAAAAAAACGCCUAGGGUGCUGUCAAUAGGAUUCCCUCGCAAAAGCGAACCGCUGGCAC
-............((.((((........((.((((.(((((((..((((-((.(.(((-.......))).).)))))))))).)))...)))).)).((((....))))...)))))).. ( -33.20)
>DroSim_CAF1 43562 117 + 1
-CUUUUUAAGAUCUCCCAGCAUUUACUAGGUAUCUGUUUGGCGACCCCU-AGCCCUUU-AAGAAAAAAAGGCCUAGGGUGCUGUCAAUAGGAUUCCCUCGUAAAAGCGAACCGCUGGCAC
-..............(((((........((.((((..((((((.(((((-((.(((((-.......))))).)))))).).))))))..)))).)).((((....))))...)))))... ( -38.30)
>DroEre_CAF1 48757 97 + 1
GUUUCCAA-------------------AGGUAUCUGAUAGGCGACCCCAGCGCGCUCU----UGGAAAAGGCCUAGGGUGCUGUCAAUAGGAUUCCCUCGCAAAAGCGAACCGCUGGCAC
........-------------------.(((..((....))..)))((((((((((((----.((......)).)))))))........((....))((((....))))...)))))... ( -28.20)
>consensus
_GUUUUUAAG_________________AGGUAUCUGUUAGGCGACCCCA_AGCCCUUU_AAGAAAAAAAGGCCUAGGGUGCUGUCAAUAGGAUUCCCUCGCAAAAGCGAACCGCUGGCAC
............................((.((((....(((.((((....((.((((........))))))...))))))).......)))).)).((((....))))........... (-18.04 = -18.35 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	13,193,820 – 13,193,912
Length	92
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.49
Mean single sequence MFE	-35.38
Consensus MFE	-19.93
Energy contribution	-21.06
Covariance contribution	1.13
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.56
SVM decision value	1.69
SVM RNA-class probability	0.972232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13193820 92 - 23771897
---------GUUCGCUUUUGCGAGGGAAUCCUAUUGACAGCACCCUAGGCCUUUUUAUUUAAAAAGGGCU-UAGGGUCGCCUAAGAGAUACCU-----------------CUUAAAAAC-
---------.(((((....)))))...............(((((((((((((((((.....)))))))))-)))))).)).((((((....))-----------------)))).....- ( -35.40)
>DroSec_CAF1 45121 117 - 1
GUGCCAGCGGUUCGCUUUUGCGAGGGAAUCCUAUUGACAGCACCCUAGGCGUUUUUUUCUU-AAAGGGCU-AGGGGUCGCCUCACAGAUACCUAGUAAAUGCUGAGCGAUCUUAAAAAC-
.((((((((..((((....))))(((.(((....(((..(((((((.(((.((((......-)))).)))-.))))).)).)))..))).)))......))))).)))...........- ( -36.20)
>DroSim_CAF1 43562 117 - 1
GUGCCAGCGGUUCGCUUUUACGAGGGAAUCCUAUUGACAGCACCCUAGGCCUUUUUUUCUU-AAAGGGCU-AGGGGUCGCCAAACAGAUACCUAGUAAAUGCUGGGAGAUCUUAAAAAG-
((....((((...(((.(((..(((....)))..))).))).((((((.(((((.......-))))).))-)))).))))...))((((.((((((....))))))..)))).......- ( -38.40)
>DroEre_CAF1 48757 97 - 1
GUGCCAGCGGUUCGCUUUUGCGAGGGAAUCCUAUUGACAGCACCCUAGGCCUUUUCCA----AGAGCGCGCUGGGGUCGCCUAUCAGAUACCU-------------------UUGGAAAC
...((((.(((((((....))))..........((((..(((((((((((((((....----)))).)).))))))).))...))))..))).-------------------)))).... ( -31.50)
>consensus
GUGCCAGCGGUUCGCUUUUGCGAGGGAAUCCUAUUGACAGCACCCUAGGCCUUUUUUUCUU_AAAGGGCU_AGGGGUCGCCUAACAGAUACCU_________________CUUAAAAAC_
...........((((....))))(((.(((.........((((((((((((((((.......)))))))).)))))).))......))).)))........................... (-19.93 = -21.06 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:59 2006