Locus 105

Sequence ID	Eco_1
Location	4,173,495 – 4,173,580
Length	85
Max. P	0.909301

overview

Window 4

Location	4,173,495 – 4,173,580
Length	85
Sequences	6
Columns	85
Reading direction	forward
Mean pairwise identity	91.51
Mean single sequence MFE	-29.03
Consensus MFE	-27.16
Energy contribution	-27.05
Covariance contribution	-0.11
Combinations/Pair	1.21
Mean z-score	-1.37
Structure conservation index	0.94
SVM decision value	1.06
SVM RNA-class probability	0.909301
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4173495 85 + 1
GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUGUAAAUCUGCCGUCACAGACUUCGAAGGUUCGAAUCCUUCCCCCACCACCA
((((((((((((...........)))))).(((.(((....))).))).........(((((.......))))).)))))).... ( -31.80)
>Hin_1 1 82 + 1
---GGGGUUCCCGAGCGGCCAAAGGGGGCAGACUGUAAAUCUGUUGGCUCAGCCUUCGAAGGUUCGAAUCCUUCUCCCUCCACCA
---(((((((..((((..((....))((((((.......)))))).))))(((((....))))).)))))))............. ( -22.80)
>Lpn_1 1 82 + 1
---GGGGUUCCCGAGCGGUCAAAGGGAUCAGACUGUAAAUCUGACGGCUCAGCCUUCGAAGGUUCGAAUCCUUCCCCCUCCACCA
---((((.....((((.((((..((.......)).......)))).)))).......(((((.......)))))))))....... ( -24.20)
>Sfl_1 1 85 + 1
GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUGUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCACCA
((((((((((((...........)))))).(((.(((....))).))).........(((((.......))))).)))))).... ( -31.80)
>Sty_1 1 85 + 1
GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUGUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCACCA
((((((((((((...........)))))).(((.(((....))).))).........(((((.......))))).)))))).... ( -31.80)
>Ype_1 1 85 + 1
GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUGUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCACCA
((((((((((((...........)))))).(((.(((....))).))).........(((((.......))))).)))))).... ( -31.80)
>consensus
GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUGUAAAUCUGCCGUCACAGACUUCGAAGGUUCGAAUCCUUCCCCCACCACCA
(((((((.((((...........))))(((((.......))))).(((...)))...(((((.......)))))))))))).... (-27.16 = -27.05 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	4,173,495 – 4,173,580
Length	85
Sequences	6
Columns	85
Reading direction	reverse
Mean pairwise identity	91.51
Mean single sequence MFE	-31.88
Consensus MFE	-28.10
Energy contribution	-28.93
Covariance contribution	0.83
Combinations/Pair	1.07
Mean z-score	-1.38
Structure conservation index	0.88
SVM decision value	0.22
SVM RNA-class probability	0.640954
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4173495 85 - 1
UGGUGGUGGGGGAAGGAUUCGAACCUUCGAAGUCUGUGACGGCAGAUUUACAGUCUGCUCCCUUUGGCCGCUCGGGAACCCCACC
....((((((((((((.(((((....)))))(((...)))(((((((.....))))))).)))))..((....))...))))))) ( -33.10)
>Hin_1 1 82 - 1
UGGUGGAGGGAGAAGGAUUCGAACCUUCGAAGGCUGAGCCAACAGAUUUACAGUCUGCCCCCUUUGGCCGCUCGGGAACCCC---
.(((.(((((.(((((.......)))))...(((...)))..(((((.....)))))...))))).)))....((....)).--- ( -25.90)
>Lpn_1 1 82 - 1
UGGUGGAGGGGGAAGGAUUCGAACCUUCGAAGGCUGAGCCGUCAGAUUUACAGUCUGAUCCCUUUGACCGCUCGGGAACCCC---
.(((.(((((((((((.......)))))...(((...)))(((((((.....))))))))))))).)))....((....)).--- ( -31.50)
>Sfl_1 1 85 - 1
UGGUGGUGGGGGAAGGAUUCGAACCUUCGAAGUCGAUGACGGCAGAUUUACAGUCUGCUCCCUUUGGCCGCUCGGGAACCCCACC
....((((((((((((.......)))))...(((((.(..(((((((.....)))))))..).)))))..........))))))) ( -33.60)
>Sty_1 1 85 - 1
UGGUGGUGGGGGAAGGAUUCGAACCUUCGAAGUCGAUGACGGCAGAUUUACAGUCUGCUCCCUUUGGCCGCUCGGGAACCCCACC
....((((((((((((.......)))))...(((((.(..(((((((.....)))))))..).)))))..........))))))) ( -33.60)
>Ype_1 1 85 - 1
UGGUGGUGGGGGAAGGAUUCGAACCUUCGAAGUCGAUGACGGCAGAUUUACAGUCUGCUCCCUUUGGCCGCUCGGGAACCCCACC
....((((((((((((.......)))))...(((((.(..(((((((.....)))))))..).)))))..........))))))) ( -33.60)
>consensus
UGGUGGUGGGGGAAGGAUUCGAACCUUCGAAGUCGAUGACGGCAGAUUUACAGUCUGCUCCCUUUGGCCGCUCGGGAACCCCACC
....((((((((((((.(((((....)))))(((...)))(((((((.....))))))).)))))..((....))...))))))) (-28.10 = -28.93 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:07:18 2006