Locus 454

Sequence ID	X_DroMel_CAF1
Location	1,339,078 – 1,339,217
Length	139
Max. P	0.999168

overview

Window 4

Location	1,339,078 – 1,339,198
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.92
Mean single sequence MFE	-47.50
Consensus MFE	-39.70
Energy contribution	-41.46
Covariance contribution	1.76
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.84
SVM decision value	0.38
SVM RNA-class probability	0.714022
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1339078 120 + 22224390
UGAAGGCAAUCACGGGGAUGUUCACGUAGCUGGCCUCCAUGAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGA
....(((.((((.((((..(((.....)))...)).)).))))..)))(((((((((........)))))))))(((((((((..((((((((.....))))))))..))).)))))).. ( -51.10)
>DroGri_CAF1 16758 120 + 1
UGAACGCAAUAACGGGUAUGUUCACAUACGAUGCUUCCAUAAUUGGCUGAUGAUCGGUAUUGGGAUCGGUGACCACCAACAGACGAGGCUCGCGAAAAGCGGGCUGAAUCUGAUUGGUGA
.((.(.(((((.((((((((....)))))....(..(((....)))..)....))).))))).).))(....)((((((((((...(((((((.....)))))))...)))).)))))). ( -42.60)
>DroSec_CAF1 4933 120 + 1
UGAAGGCAAUCACGGGGAUGUUCACGUAGCUGGCCUCCAUGAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCAGGCUGGAUCUGGUUGGUGA
....(((.((((.((((..(((.....)))...)).)).))))..)))(((((((((........)))))))))(((((((((..((((..((.....))..))))..))).)))))).. ( -46.20)
>DroEre_CAF1 5987 120 + 1
UGAAGGCAAUCACGGGGAUGUUCACGUAGCUGGCCUCCAUGAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGAGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGA
....(((.((((.((((..(((.....)))...)).)).))))..)))(((((((((........)))))))))(((((((((...(((((((.....)))))))...))).)))))).. ( -48.90)
>DroYak_CAF1 4935 120 + 1
UGAAAGCGAUCACGGGGAUGUUCACGUAGCUGGCCUCCAUGAUGGGCUGGUGAUCGGUGUUGGGGUCAGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGA
......((((((((..(.....).))).((..((((.......))))..)))))))((((((....))).)))((((((((((..((((((((.....))))))))..))).))))))). ( -48.70)
>consensus
UGAAGGCAAUCACGGGGAUGUUCACGUAGCUGGCCUCCAUGAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGA
....(((.((((.((((..(((.....)))...)).)).))))..)))(((((((((........)))))))))(((((((((..((((((((.....))))))))..)))).))))).. (-39.70 = -41.46 +   1.76)

alignment

secondary structure

dotplot

Window 5

Location	1,339,118 – 1,339,217
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	92.32
Mean single sequence MFE	-42.84
Consensus MFE	-38.12
Energy contribution	-38.08
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-2.36
Structure conservation index	0.89
SVM decision value	3.41
SVM RNA-class probability	0.999168
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1339118 99 + 22224390
GAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGAAGGCACCGGGCGUGAAGCG
..(((((((((((((((........)))))))))(((((((((..((((((((.....))))))))..))).))))))...))).))).((.....)). ( -46.60)
>DroGri_CAF1 16798 99 + 1
AAUUGGCUGAUGAUCGGUAUUGGGAUCGGUGACCACCAACAGACGAGGCUCGCGAAAAGCGGGCUGAAUCUGAUUGGUGAACGCGCCGGGCGUAAAGCG
..(((((...(((((........)))))(((..((((((((((...(((((((.....)))))))...)))).))))))..))))))))((.....)). ( -40.90)
>DroSec_CAF1 4973 99 + 1
GAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCAGGCUGGAUCUGGUUGGUGAAGGCACCGGGCGUGAAGCG
..(((((((((((((((........)))))))))(((((((((..((((..((.....))..))))..))).))))))...))).))).((.....)). ( -41.70)
>DroEre_CAF1 6027 99 + 1
GAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGAGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGAAGGCACCGGGAGUGAAGCG
..(((((((((((((((........)))))))))(((((((((...(((((((.....)))))))...))).))))))...))).)))........... ( -42.70)
>DroYak_CAF1 4975 99 + 1
GAUGGGCUGGUGAUCGGUGUUGGGGUCAGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGAAGGCACCGGGAGUGAAUCG
(((...((((((.(((((((((....))).))))(((((((((..((((((((.....))))))))..))).))))))...))))))))......))). ( -42.30)
>consensus
GAUGGGCUGGUGAUCGGUGUUGGGGUCGGUCACCACCAGCAGACGCGGCUCGCGGAAAGCGGGCUGGAUCUGGUUGGUGAAGGCACCGGGCGUGAAGCG
......(((((((((........)))).(((..((((((((((..((((((((.....))))))))..)))).))))))..))))))))((.....)). (-38.12 = -38.08 +  -0.04)

alignment

secondary structure

dotplot

Window 6

Location	1,339,118 – 1,339,217
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	92.32
Mean single sequence MFE	-28.52
Consensus MFE	-24.80
Energy contribution	-24.76
Covariance contribution	-0.04
Combinations/Pair	1.16
Mean z-score	-1.42
Structure conservation index	0.87
SVM decision value	0.69
SVM RNA-class probability	0.823454
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1339118 99 - 22224390
CGCUUCACGCCCGGUGCCUUCACCAACCAGAUCCAGCCCGCUUUCCGCGAGCCGCGUCUGCUGGUGGUGACCGACCCCAACACCGAUCACCAGCCCAUC
.((.....))..((.((....((((..(((((.(.((.(((.....))).)).).))))).))))(((((.((..........)).))))).))))... ( -29.20)
>DroGri_CAF1 16798 99 - 1
CGCUUUACGCCCGGCGCGUUCACCAAUCAGAUUCAGCCCGCUUUUCGCGAGCCUCGUCUGUUGGUGGUCACCGAUCCCAAUACCGAUCAUCAGCCAAUU
.((.....))..(((..(..((((((.(((((...((.(((.....))).))...)))))))))))..)...((((........))))....))).... ( -31.00)
>DroSec_CAF1 4973 99 - 1
CGCUUCACGCCCGGUGCCUUCACCAACCAGAUCCAGCCUGCUUUCCGCGAGCCGCGUCUGCUGGUGGUGACCGACCCCAACACCGAUCACCAGCCCAUC
.((.....))..((.((....((((..(((((.(.((.(((.....))).)).).))))).))))(((((.((..........)).))))).))))... ( -27.40)
>DroEre_CAF1 6027 99 - 1
CGCUUCACUCCCGGUGCCUUCACCAACCAGAUCCAGCCCGCUUUCCGCGAGCCUCGUCUGCUGGUGGUGACCGACCCCAACACCGAUCACCAGCCCAUC
............((.((....((((..(((((...((.(((.....))).))...))))).))))(((((.((..........)).))))).))))... ( -27.70)
>DroYak_CAF1 4975 99 - 1
CGAUUCACUCCCGGUGCCUUCACCAACCAGAUCCAGCCCGCUUUCCGCGAGCCGCGUCUGCUGGUGGUGACUGACCCCAACACCGAUCACCAGCCCAUC
............((((...((((((..(((((.(.((.(((.....))).)).).))))).))))((((..((....)).)))))).))))........ ( -27.30)
>consensus
CGCUUCACGCCCGGUGCCUUCACCAACCAGAUCCAGCCCGCUUUCCGCGAGCCGCGUCUGCUGGUGGUGACCGACCCCAACACCGAUCACCAGCCCAUC
............(((......((((..(((((.(.((.(((.....))).)).).))))).))))(((((.((..........)).))))).))).... (-24.80 = -24.76 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:56 2006