Alignment

overview

Window 6

Location 80 – 200
Length 120
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 82.48
Mean single sequence MFE -52.08
Consensus MFE -35.85
Energy contribution -39.05
Covariance contribution 3.20
Combinations/Pair 1.24
Mean z-score -1.82
Structure conservation index 0.69
SVM decision value 0.24
SVM RNA-class probability 0.647134
Prediction RNA

Download alignment: ClustalW | MAF

>Equus_caballus_9_1_1085/80-200
GGGGGAGCGGGCGGAAAA-GCCGACUCAGCCGCUCCCCAACCUCAUAUAGA-GGCACGUCCACCUACGUCAUCGCCCGCUGCGCCUCCGGAAGUUCCGCAAGCGGUGACGUGG
.(((((((((.(((....-.)))......)))))))))..((((.....))-)).........((((((((((((....((((....(....)...)))).)))))))))))) ( -51.80)
>Oryctolagus_cuniculus_23_1_1049/80-200
GGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCACGUCCUUCUACGUCAUCGCCCGCUGCGCUCCCGGAAGCGCCGCAAGCAGUGACGUGG
.(((((((((.(((......)))......)))))))))..((((.....))))..........(((((((((.((..((.(((((......))))).))..)).))))))))) ( -54.50)
>Mus_musculus_21_1_983/80-200
GGGGGAGCGGGCGGAAAAGGCCGACGCGGGCGCUCCCCAACCUCAUAUAGAGGGCACGCUCGGCUACGUCACCGUCCGCGGCUCCCCCGGAACUGUCGUCAGCGGUGACGUGA
((((((((((((((....((((((.(((((.....)))..((((.....))))....))))))))......))))))...))))))))(..(((((.....)))))..).... ( -56.00)
>Rattus_norvegicus_30_1_942/80-200
GGGGGAGCGGGCGGAAAAGGCCGACUCGGGCGCUUCCCAACCUCAUAUAGAGGGCACGCUCAUCUACGUCAUCGCCCGCUGCGCCCCCGGAACUGUCGUAAGCGGUGACGUGG
((((((((((((((((..(.(((...))).)..))))...((((.....))))....................)))))))...)))))(..((((.(....)))))..).... ( -47.70)
>Cavia_porcellus_6_1_1053/80-200
GGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCACACUC--UUACGUCACCGCGUGCUGCGCCUCCGGAAGCGCCGUAAGCGUUGGCGUGG
.(((((((((.(((......)))......)))))))))..((((.....))))........--.(((((((.(((.(((.((((........)))).))).))).))))))). ( -52.20)
>Mus_1_466/80-200
GGGGGAGCGGGCGGAAAAGGCCGACGCGGGCGCUCCCCAACCUCAUAUAGAGGGCACGCUCGGCUACGUCACCGUCCGCGGCUCCCCCGGAACU-------------------
((((((((((((((....((((((.(((((.....)))..((((.....))))....))))))))......))))))...))))))))......------------------- ( -50.30)
>consensus
GGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCACGCUCAGCUACGUCACCGCCCGCUGCGCCCCCGGAACUGCCGUAAGCGGUGACGUGG
.(((((((((((((......))).))....))))))))..((((.....))))..........((((((((((((..((.(((..........))).))..)))))))))))) (-35.85 = -39.05 +   3.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 34

Location 720 – 840
Length 120
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 91.88
Mean single sequence MFE -46.03
Consensus MFE -40.49
Energy contribution -40.55
Covariance contribution 0.06
Combinations/Pair 1.19
Mean z-score -1.76
Structure conservation index 0.88
SVM decision value 0.97
SVM RNA-class probability 0.891835
Prediction RNA

Download alignment: ClustalW | MAF

>Homo_sapiens_14_1_1076/720-840
CGGAAAGAGCGUCUCCUCCGCCAGGAGGCGGCGGGGAGGAUUGCACAACCUCAGGCGGGGGAGCGGAGGAAACCCGAGCCCGCUCGGCCCGG
(((...(((((.((((((((((..((((..((((......))))....)))).))))))))))(((.(....))))....)))))...))). ( -48.40)
>Macaca_mulatta_17_1_1076/720-840
CGGAAAGAGCGUCUCCUCCGCCAGGAGGCGGCGGGGAGGAUUGCACAACCUCAGGUGGGGGAGCGGCGGAAACCCGAGCCCGCUCGGCCCGG
(((...(((((.((((((((((..((((..((((......))))....)))).))))))))))(((.(....))))....)))))...))). ( -46.50)
>Microcebus_murinus_19_1_1098/720-840
CGGAAAGA--GUCUCCUCCGCCAGGAGGUGGCGGAGAGGAUUGCACAACCUCGGGCGGGGGAGCGGCGGAAACCCGAGCCCGCCCGGCCUCG
.((....(--(((..((((((((.....))))))))..))))........(((((((((....(((.(....))))..)))))))))))... ( -47.80)
>Equus_caballus_9_1_1085/720-840
CGGAAAGUGCGUCUCCUCCGCCAGGAGGCAGCGGAGAGGAUUGCACAACCUCGGGCGGGGGAGCGGCGGAAACCCGAGCCUGCCCGGCCUCG
.((...(((((((..((((((.........))))))..)).)))))....(((((((((....(((.(....))))..)))))))))))... ( -46.20)
>Oryctolagus_cuniculus_23_1_1049/720-840
CGGAAAGAGCGUCUCCUCCGCCAGGAGGCGGCGGGGAGGAUUGCACAACCUCGGGAGGGGGUGCGGCGGAAACCCGAGCCCGCCCGGCCUCG
......(((.(((.(((((....))))).((((((.......((((..(((....)))..))))((.(....)))...)))))).)))))). ( -45.30)
>Felis_catus_10_1_1097/720-840
CGGAAAAAGCGUCUCCUCCGCCAGGAGGCAGCGGAGAGGAUUGCACAACUUCGGGCGGGGGUGCGGCGGAAACCCGAGCCUGCCCGGCCUUG
.((.....(((((..((((((.........))))))..)).)))......(((((((((....(((.(....))))..)))))))))))... ( -42.00)
>consensus
CGGAAAGAGCGUCUCCUCCGCCAGGAGGCGGCGGAGAGGAUUGCACAACCUCGGGCGGGGGAGCGGCGGAAACCCGAGCCCGCCCGGCCUCG
.((......(.(((((.(((((....))))).))))).)...........(((((((((....(((.(....))))..)))))))))))... (-40.49 = -40.55 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

These windows have a probability below the cutoff.


WindowLocationStrandNLengthMean pairwise IDzSCIP
1 0 – 120 + 6 120 72.08 0.40 0.46 0.000000
2 0 – 120 - 6 120 72.08 0.13 0.43 0.000000
3 40 – 160 + 6 120 79.66 -0.23 0.55 0.003969
4 40 – 160 - 6 120 79.66 -0.97 0.73 0.474261
5 80 – 200 + 6 120 82.48 -1.34 0.55 0.145823
7 120 – 240 + 6 120 86.68 -0.59 0.71 0.113574
8 120 – 240 - 6 120 86.68 -1.01 0.72 0.150117
9 160 – 280 + 6 120 86.11 -0.48 0.76 0.074647
10 160 – 280 - 6 120 86.11 -0.79 0.64 0.144259
11 200 – 320 + 6 120 85.49 -0.20 0.71 0.084988
12 200 – 320 - 6 120 85.49 -0.33 0.72 0.089235
13 240 – 360 + 6 120 84.15 1.32 0.55 0.008851
14 240 – 360 - 6 120 84.15 0.50 0.53 0.015067
15 280 – 400 + 6 120 74.88 -0.24 0.26 0.000000
16 280 – 400 - 6 120 74.88 1.68 0.39 0.000000
17 320 – 440 + 6 120 80.61 0.69 0.56 0.000002
18 320 – 440 - 6 120 80.61 1.78 0.49 0.000000
19 360 – 480 + 2 120 54.78 -0.42 0.47 0.000000
20 360 – 480 - 2 120 54.78 0.39 0.47 0.000000
21 440 – 560 + 2 120 83.19 -0.36 0.76 0.055207
22 440 – 560 - 2 120 83.19 0.47 0.81 0.028617
23 520 – 640 + 6 120 74.60 -0.18 0.45 0.000000
24 520 – 640 - 6 120 74.60 -0.50 0.41 0.000000
25 560 – 680 + 6 120 81.30 -0.52 0.48 0.004076
26 560 – 680 - 6 120 81.30 -0.32 0.56 0.014577
27 600 – 720 + 6 120 80.66 0.22 0.47 0.000000
28 600 – 720 - 6 120 80.66 0.18 0.46 0.000000
29 640 – 760 + 6 120 78.42 -0.28 0.39 0.000000
30 640 – 760 - 6 120 78.42 0.02 0.21 0.000000
31 680 – 800 + 6 120 84.91 0.19 0.60 0.072917
32 680 – 800 - 6 120 84.91 -0.85 0.59 0.129229
33 720 – 840 + 6 120 91.88 -0.69 0.78 0.027538
35 760 – 880 + 6 120 81.07 -1.15 0.49 0.032073
36 760 – 880 - 6 120 81.07 -1.22 0.52 0.064611
37 800 – 920 + 6 120 85.98 -1.36 0.57 0.087232
38 800 – 920 - 6 120 85.98 -0.84 0.53 0.055267
39 840 – 960 + 6 120 81.89 -0.63 0.61 0.091427
40 840 – 960 - 6 120 81.89 -1.27 0.68 0.466952
41 880 – 1000 + 6 120 76.47 -0.44 0.49 0.000001
42 880 – 1000 - 6 120 76.47 -0.84 0.59 0.063718
43 920 – 1040 + 6 120 73.77 -0.25 0.51 0.000000
44 920 – 1040 - 6 120 73.77 0.14 0.46 0.000000
45 960 – 1080 + 6 120 81.08 -0.26 0.67 0.062385
46 960 – 1080 - 6 120 81.08 0.31 0.66 0.012981
47 1000 – 1120 + 6 120 87.05 -0.93 0.71 0.128093
48 1000 – 1120 - 6 120 87.05 -0.78 0.54 0.061687
49 1040 – 1160 + 6 120 87.46 -0.05 0.60 0.128939
50 1040 – 1160 - 6 120 87.46 -0.16 0.71 0.068865
51 1080 – 1200 + 6 120 83.60 -1.20 0.70 0.343656
52 1080 – 1200 - 6 120 83.60 0.01 0.56 0.032916
53 1096 – 1216 + 6 120 89.30 -0.80 0.82 0.068678
54 1096 – 1216 - 6 120 89.30 -0.12 0.82 0.010667