Locus 23

Sequence ID	Eco_1
Location	3,426,585 – 3,426,705
Length	120
Max. P	0.933681

overview

Window 9

Location	3,426,585 – 3,426,705
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	88.06
Mean single sequence MFE	-34.52
Consensus MFE	-27.21
Energy contribution	-27.99
Covariance contribution	0.79
Combinations/Pair	1.15
Mean z-score	-3.16
Structure conservation index	0.79
SVM decision value	1.23
SVM RNA-class probability	0.933681
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3426585 120 + 1
CAGGGUAGAAAGUAGUGAGCUCUCUAUUACCUUUCUAGCUUAUGACUUUCUCCCAGCCUGCUGUUGGGCCCGGGCUAUAACACUCUCAGCCCAGCUCCCUCACCCUACAGUCGACUAUCC
..(((.(((((((.(((((((...............))))))).))))))))))((.(.(((((.(((...(((((...........)))))((....))..))).))))).).)).... ( -37.06)
>Hin_1 241 120 + 1
CCGGGUCCAAAGAAGUAGACUUUCUAUUACCUUGCUGGCUUAUCACAUUCUCCCAGCCUGCUCUUAGGCACGGGCUACAACACUCUCAGCCCAGCUCCCUCACCCUAAAAAAGACUAUCC
..((((((.(((((((((.....))))).....((.((((..............)))).)))))).))...(((((...........))))).........))))............... ( -25.94)
>Sty_1 241 120 + 1
CAGGGUAGAAAGUAGUGAGCUCUCUAUUACCUUCCUAGCUUAUGACUUUCUCCCAGCCUGCUGUUGGGCCCGGGCUGUAACACUCUCAGCCCAGCUCCCUCACCCUACAGUCGACUAUCC
..(((.(((((((.(((((((...............))))))).))))))))))((.(.(((((.(((...((((((.........))))))((....))..))).))))).).)).... ( -40.56)
>consensus
CAGGGUAGAAAGUAGUGAGCUCUCUAUUACCUUCCUAGCUUAUGACUUUCUCCCAGCCUGCUGUUGGGCCCGGGCUAUAACACUCUCAGCCCAGCUCCCUCACCCUACAGUCGACUAUCC
..(((.(((((((.(((((((...............))))))).)))))))))).((((......))))..(((((...........)))))............................ (-27.21 = -27.99 +   0.79)

alignment

secondary structure

dotplot

Window 0

Location	3,426,585 – 3,426,705
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.06
Mean single sequence MFE	-40.28
Consensus MFE	-33.74
Energy contribution	-32.87
Covariance contribution	-0.88
Combinations/Pair	1.18
Mean z-score	-1.74
Structure conservation index	0.84
SVM decision value	0.04
SVM RNA-class probability	0.554774
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 3426585 120 - 1
GGAUAGUCGACUGUAGGGUGAGGGAGCUGGGCUGAGAGUGUUAUAGCCCGGGCCCAACAGCAGGCUGGGAGAAAGUCAUAAGCUAGAAAGGUAAUAGAGAGCUCACUACUUUCUACCCUG
....((((..((((.((((.......((((((((.........)))))))))))).))))..))))((((((((((....((((...............))))....))))))).))).. ( -40.77)
>Hin_1 241 120 - 1
GGAUAGUCUUUUUUAGGGUGAGGGAGCUGGGCUGAGAGUGUUGUAGCCCGUGCCUAAGAGCAGGCUGGGAGAAUGUGAUAAGCCAGCAAGGUAAUAGAAAGUCUACUUCUUUGGACCCGG
...............(((((((((((((..((((.(..(((..((.((((.((((......))))))))....))..)))..)))))..))...(((.....))))))))))..)))).. ( -36.90)
>Sty_1 241 120 - 1
GGAUAGUCGACUGUAGGGUGAGGGAGCUGGGCUGAGAGUGUUACAGCCCGGGCCCAACAGCAGGCUGGGAGAAAGUCAUAAGCUAGGAAGGUAAUAGAGAGCUCACUACUUUCUACCCUG
....((((..((((.((((.......((((((((.........)))))))))))).))))..))))((((((((((....((((...............))))....))))))).))).. ( -43.17)
>consensus
GGAUAGUCGACUGUAGGGUGAGGGAGCUGGGCUGAGAGUGUUAUAGCCCGGGCCCAACAGCAGGCUGGGAGAAAGUCAUAAGCUAGAAAGGUAAUAGAGAGCUCACUACUUUCUACCCUG
....((((..((((.((((.((....))((((((.........))))))..)))).))))..))))(((............(((.....)))..(((((((.......)))))))))).. (-33.74 = -32.87 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Dec 7 14:11:28 2006