Alignment

overview

Window 1

Location 0 – 120
Length 120
RNAz 1.0 Sequences 2
Columns 120
Reading direction forward
Mean pairwise identity 74.17
Mean single sequence MFE -58.45
Consensus MFE -38.15
Energy contribution -39.40
Covariance contribution 1.25
Combinations/Pair 1.03
Mean z-score -2.07
Structure conservation index 0.65
SVM decision value 1.13
SVM RNA-class probability 0.919978
Prediction RNA

Download alignment: ClustalW | MAF

>Mus_1_466/0-120
-----------------AGUUCCGGGGGAGCCGCGGACGGUGACGUAGCCGAGCGUGCCCUCUAUAUGAGGUUGGGGAGCGCCCGCGUCGGCCUUUUCCGCCCGCUCCCCCCUCCCCCCG
-----------------......((((((((.(((((((....))).(((((.(((..((((.....))))..(((.....))))))))))).....))))..))))))))......... ( -51.30)
>Homo_1_499/0-120
ACGUCACCGCCUGCGUCGCUUCCGGAGGCGCAGCGGGCGAUGACGUAGAGGGACGUGCCCUCUAUAUGAGGUUGGGGAGCGGCUGAGUCGGCCUUUUCCGCCCGCUCCCCCCUCCCCCCG
((((((.(((((((..(((((....)))))..))))))).))))))((((((.....))))))....((((..((((((((((.(((........))).).)))))))))))))...... ( -65.60)
>consensus
_________________ACUUCCGGAGGAGCAGCGGACGAUGACGUAGACGAACGUGCCCUCUAUAUGAGGUUGGGGAGCGCCCGAGUCGGCCUUUUCCGCCCGCUCCCCCCUCCCCCCG
......................((((((......((((....((((......)))))))).......((((..(((((((((....(.(((......))))))))))))))))))))))) (-38.15 = -39.40 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 0 – 120
Length 120
Sequences 2
Columns 120
Reading direction reverse
Mean pairwise identity 74.17
Mean single sequence MFE -61.15
Consensus MFE -45.30
Energy contribution -45.30
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.66
Structure conservation index 0.74
SVM decision value 2.91
SVM RNA-class probability 0.997696
Prediction RNA

Download alignment: ClustalW | MAF

>Mus_1_466/0-120
CGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACGCGGGCGCUCCCCAACCUCAUAUAGAGGGCACGCUCGGCUACGUCACCGUCCGCGGCUCCCCCGGAACU-----------------
(.(((((((......((((((((....((((((.(((((.....)))..((((.....))))....))))))))......))))))))..))))))).)....----------------- ( -53.50)
>Homo_1_499/0-120
CGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCACGUCCCUCUACGUCAUCGCCCGCUGCGCCUCCGGAAGCGACGCAGGCGGUGACGU
.(((((((.((((((((((.(((......)))......)))))))))..((((.....))))...).)))))))(((((((((((.((..(((........)))..)).))))))))))) ( -68.80)
>consensus
CGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACGCAGCCGCUCCCCAACCUCAUAUAGAGGGCACGCCCCGCUACGUCACCGCCCGCGGCGCCCCCGGAACC_________________
(((((((((((((((((((.(((......)))......)))))))))..)))).......(((((((........)))....))))......))))))...................... (-45.30 = -45.30 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

These windows have a probability below the cutoff.


WindowLocationStrandNLengthMean pairwise IDzSCIP
3 40 – 160 + 2 120 85.00 -0.90 0.80 0.126295
4 40 – 160 - 2 120 85.00 -1.13 0.84 0.244517
5 120 – 240 + 6 120 80.24 1.07 0.65 0.000003
6 120 – 240 - 6 120 80.24 0.51 0.69 0.006145
7 160 – 280 + 6 120 85.29 0.56 0.64 0.059107
8 160 – 280 - 6 120 85.29 0.51 0.64 0.060730
9 200 – 320 + 6 120 73.17 -0.80 0.38 0.000001
10 200 – 320 - 6 120 73.17 -0.30 0.30 0.000000
11 240 – 360 + 6 120 81.61 -1.72 0.51 0.184281
12 240 – 360 - 6 120 81.61 -1.33 0.32 0.000004
13 280 – 400 + 6 120 84.83 -2.13 0.65 0.356793
14 280 – 400 - 6 120 84.83 -0.68 0.43 0.005290
15 320 – 440 + 6 120 84.50 -1.05 0.56 0.093609
16 320 – 440 - 6 120 84.50 -1.32 0.51 0.050108
17 360 – 480 + 6 120 77.78 -0.43 0.27 0.000000
18 360 – 480 - 6 120 77.78 -0.80 0.40 0.000001
19 382 – 502 + 6 120 85.44 -0.51 0.53 0.053838
20 382 – 502 - 6 120 85.44 0.47 0.59 0.069272