Alignment

overview

Window 8

Location 60 – 160
Length 100
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 82.11
Mean single sequence MFE -39.67
Consensus MFE -30.18
Energy contribution -30.30
Covariance contribution 0.12
Combinations/Pair 1.35
Mean z-score -1.32
Structure conservation index 0.76
SVM decision value 0.03
SVM RNA-class probability 0.550349
Prediction RNA

Download alignment: ClustalW | MAF

>Equus_caballus_9_1_1085/60-160
CAACCUCAUAUAGA-GGCACGUCCACCUACGUCAUCGCCCGCUGCGCCUCCGGAAGUUCCGCAAGCGGUGACGUGG-CACGCAAAG-CGCGCGGU
...((((.....))-)).......((((((((((((((....((((....(....)...)))).)))))))))))(-(.(((...)-)).))))) ( -34.60)
>Oryctolagus_cuniculus_23_1_1049/60-160
CAACCUCAUAUAGAGGGCACGUCCUUCUACGUCAUCGCCCGCUGCGCUCCCGGAAGCGCCGCAAGCAGUGACGUGG-CACGCAGAGCGGCGCGG-
...((((.....))))((.((..((.(((((((((.((..((.(((((......))))).))..)).)))))))))-.....))..))))....- ( -37.60)
>Mus_musculus_21_1_983/60-160
CAACCUCAUAUAGAGGGCACGCUCGGCUACGUCACCGUCCGCGGCUCCCCCGGAACUGUCGUCAGCGGUGACGUGA--ACGCAGGGCGGUGCGG-
...((((.....))))((((((((.(((((((((((((..((((((((...)))...)))))..))))))))))).--..)).)))).))))..- ( -45.40)
>Rattus_norvegicus_30_1_942/60-160
CAACCUCAUAUAGAGGGCACGCUCAUCUACGUCAUCGCCCGCUGCGCCCCCGGAACUGUCGUAAGCGGUGACGUGG-CACGCAGAGCCACGCGG-
...((((.....))))...(((........((((((((..((.((.((...))....)).))..))))))))((((-(.......)))))))).- ( -33.40)
>Cavia_porcellus_6_1_1053/60-160
CAACCUCAUAUAGAGGGCACACUC--UUACGUCACCGCGUGCUGCGCCUCCGGAAGCGCCGUAAGCGUUGGCGUGGGCACGUAGAGCCGCGCAG-
...((((.....))))((.(.(((--(.((((..((((((...((((...(((.....)))...))))..))))))..))))))))..).))..- ( -35.90)
>Canis_familiaris_5_1_1082/60-160
CAACCUCAUAUAGAGGGCACGUCCCCCUACGUCAUCGCCCGCGGCGCCUCCGGAAGCGCCGCGCGCGGUGACGUGG-CACGCACGGCCGCGCGGG
...((((.....)))).......(((((((((((((((.((((((((........)))))))).))))))))))))-..(((......))).))) ( -51.10)
>consensus
CAACCUCAUAUAGAGGGCACGCCCACCUACGUCAUCGCCCGCUGCGCCCCCGGAAGCGCCGCAAGCGGUGACGUGG_CACGCAGAGCCGCGCGG_
...((((.....))))((........((((((((((((..((.((((........)))).))..))))))))))))....((......))))... (-30.18 = -30.30 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Window 16

Location 140 – 240
Length 100
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 92.07
Mean single sequence MFE -46.85
Consensus MFE -38.97
Energy contribution -39.67
Covariance contribution 0.69
Combinations/Pair 1.04
Mean z-score -2.37
Structure conservation index 0.83
SVM decision value 0.92
SVM RNA-class probability 0.881731
Prediction RNA

Download alignment: ClustalW | MAF

>Pan_troglodytes_25_1_1076/140-240
AGCGAGCGCGGUGCAGCCGGAGCAGCGCUCGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCAC
.((((((((..(((.......)))))))))..((((((.((.((((((.(......).))).)))..)).))))))..((((.....)))))).. ( -50.00)
>Microcebus_murinus_19_1_1098/140-240
AGCGAGCGCGGUGGAGCCGGAGCAGCGCUCGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGAUUCAGCCGCUCCCCAACCUCAUAUAGAGGGCAC
.((((((((.((.........)).))))))..((((((.((.((((((.(......).))).)))..)).))))))..((((.....)))))).. ( -46.30)
>Equus_caballus_9_1_1085/140-240
ACCGAGCGGGGUGCUUCCG-AGC-GCGCUCAGGGG--AGGGGGAGCGGGCGGAAAA-GCCGACUCAGCCGCUCCCCAACCUCAUAUAGA-GGCAC
.((....)).(((((((.(-((.-...))).((((--..(((((((((.(((....-.)))......)))))))))..)))).....))-))))) ( -44.10)
>Oryctolagus_cuniculus_23_1_1049/140-240
AGCGAGCGCGGUGCAGCCGGAGCGGCCCUCGGGGGUAGGGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCAC
..((..(.(((.....))))..))((((((.(((((...(((((((((.(((......)))......))))))))).))))).....)))))).. ( -49.70)
>Rattus_norvegicus_30_1_942/140-240
AGCGAGCGCGGUGCAGCCGGAGCGGCGCUCGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACUCGGGCGCUUCCCAACCUCAUAUAGAGGGCAC
.((((((((.((.(.....).)).))))))..((((((.(..((((((.(......).))).)))...).))))))..((((.....)))))).. ( -43.10)
>Cavia_porcellus_6_1_1053/140-240
GGCGAGCGCGGUGCAGCCGCAGCGGCACUCGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCAC
..((((.((.((((....))).).)).)))).((((((.((.((((((.(......).))).)))..)).))))))..((((.....)))).... ( -47.90)
>consensus
AGCGAGCGCGGUGCAGCCGGAGCGGCGCUCGGGGGGAGGGGGGAGCGGGCGGAAAAGGCCGACUCAGCCGCUCCCCAACCUCAUAUAGAGGGCAC
.((((((((.((.........)).)))))).((((....(((((((((.(((......)))......)))))))))..)))).........)).. (-38.97 = -39.67 +   0.69)

alignment

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secondary structure

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dotplot

Postscript

Window 59

Location 700 – 800
Length 100
Sequences 4
Columns 79
Reading direction forward
Mean pairwise identity 70.61
Mean single sequence MFE -39.08
Consensus MFE -23.04
Energy contribution -24.60
Covariance contribution 1.56
Combinations/Pair 1.28
Mean z-score -1.72
Structure conservation index 0.59
SVM decision value 0.95
SVM RNA-class probability 0.888919
Prediction RNA

Download alignment: ClustalW | MAF

>Homo_sapiens_14_1_1076/700-800
GGGCCUGCGCGUGGGGGAGUCCGGG------CCGAGCGGGCUCGGGUUUCCUCCGCUCCCCCGCCUGAGGUUGUGCAAU
.(((((.((.(((((((((((((((------((.....))))))).........)))))))))).)))))))....... ( -38.70)
>Pan_troglodytes_25_1_1076/700-800
AGGCCUGCGCGUGGGGGAGUCCGGG------CCGAGCAGGCUCGGGUUUCCGCCGCUCCCCCGCCUGAGGUUGUGCAAU
.(((((.((.((((((((((.((((------((.....))))))(((....))))))))))))).)))))))....... ( -40.10)
>Pongo_pygmaeus_28_1_1078/700-800
GGGCCUGCGCGUGGGGGAGUCCGGG------CCGAGCAGGCUCGGGUUUCCGCCGCUCCCCCGCCUGAGGUUGUGCAAU
.(((((.((.((((((((((.((((------((.....))))))(((....))))))))))))).)))))))....... ( -40.20)
>Rattus_norvegicus_30_1_942/700-800
GUCG----UGGGGAGGUUGGCCGGUCGCCGGCCGG-CCGGGCUGAGCU--UGCGGGGAGGCCGCUGGAGCUCGUGCAAU
....----......((((((((((...))))))))-))..((((((((--(((((.....))))..))))))).))... ( -37.30)
>consensus
GGGCCUGCGCGUGGGGGAGUCCGGG______CCGAGCAGGCUCGGGUUUCCGCCGCUCCCCCGCCUGAGGUUGUGCAAU
.(((((.((.(((((((((..((((......(((((....)))))......))))))))))))).)))))))....... (-23.04 = -24.60 +   1.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 62

Location 720 – 820
Length 100
Sequences 2
Columns 73
Reading direction reverse
Mean pairwise identity 95.89
Mean single sequence MFE -34.80
Consensus MFE -34.55
Energy contribution -34.05
Covariance contribution -0.50
Combinations/Pair 1.09
Mean z-score -1.58
Structure conservation index 0.99
SVM decision value 0.73
SVM RNA-class probability 0.834102
Prediction RNA

Download alignment: ClustalW | MAF

>Equus_caballus_9_1_1085/720-820
GCCAGGAGGCAGCGGAGAGGAUUGCACAACCUCGGGCGGGGGAGCGGCGGAAACCCGAGCCUGCCCGGCCUCG
.....(((((......((((.((....))))))(((((((....(((.(....))))..))))))).))))). ( -36.50)
>Felis_catus_10_1_1097/720-820
GCCAGGAGGCAGCGGAGAGGAUUGCACAACUUCGGGCGGGGGUGCGGCGGAAACCCGAGCCUGCCCGGCCUUG
.....(((((.((((......)))).......((((((((....(((.(....))))..))))))))))))). ( -33.10)
>consensus
GCCAGGAGGCAGCGGAGAGGAUUGCACAACCUCGGGCGGGGGAGCGGCGGAAACCCGAGCCUGCCCGGCCUCG
.....(((((......((((.((....))))))(((((((....(((.(....))))..))))))).))))). (-34.55 = -34.05 +  -0.50)

alignment

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secondary structure

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dotplot

Postscript

Window 97

Location 1,080 – 1,180
Length 100
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 91.09
Mean single sequence MFE -20.83
Consensus MFE -18.19
Energy contribution -17.25
Covariance contribution -0.94
Combinations/Pair 1.28
Mean z-score -2.11
Structure conservation index 0.87
SVM decision value 1.39
SVM RNA-class probability 0.948806
Prediction RNA

Download alignment: ClustalW | MAF

>Macaca_mulatta_17_1_1076/1080-1180
AGCACAGUAAUCACUGGUGUCGAUAUUGUCAUGAACCAUCACCUGCAGGAAACAAGUUUCACGAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAU
......((((((..(((((((....((((..................(....)..(((((......)))))..))))...).))))))..)))))).. ( -20.20)
>Microcebus_murinus_19_1_1098/1080-1180
AGCACAGUAAUCACUGGUGUUGAUAUCGUCAUGAACCAUCAUUUGCAAGAAACCAGCUUCACAAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAU
......((((((..((((((.....((((.((((....))))..)).........(((((......)))))......))...))))))..)))))).. ( -19.90)
>Mus_musculus_21_1_983/1080-1180
AGCACAGUAGUCACCGGUGUUGACAUUGUCAUGAACCAUCACUUACAAGAAACCAGCUUCACAAAAGAGGCUUACAAAAAGUACAUCAAAGACUACAU
......((((((...(((..((((...))))...)))......(((........((((((......))))))........))).......)))))).. ( -22.69)
>Rattus_norvegicus_30_1_942/1080-1180
AGCACAGUAGUCACCGGUGUUGACAUUGUCAUGAACCAUCACUUACAAGAAACCAGCUUCACAAAAGAGGCCUACAAAAAGUAUAUCAAAGACUACAU
......((((((...(((..((((...))))...)))..................(((((......)))))...................)))))).. ( -21.60)
>Cavia_porcellus_6_1_1053/1080-1180
AGCACAGUAAUCACUGGUGUUGAUAUUGUCAUGAACCAUCACUUGCAGGAAACCAGUUUCACAAAAGAGGCCUACAAGAAGUACAUCAAAGAUUAUAU
......((((((..((((..((((...))))...))))...((((..(....)..(((((......)))))...))))............)))))).. ( -17.40)
>Felis_catus_10_1_1097/1080-1180
AGCACAGUAAUCACUGGUGUGGAUAUCGUCAUGAACCAUCACUUGCAGGAAACCAGCUUCACAAAGGAAGCCUACAAGAAGUACAUCAAAGAUUACAU
......((((((..(((((((..........(((....)))((((..(....)..(((((......)))))...))))...)))))))..)))))).. ( -23.20)
>consensus
AGCACAGUAAUCACUGGUGUUGAUAUUGUCAUGAACCAUCACUUGCAAGAAACCAGCUUCACAAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAU
......((((((...(((..((((...))))...)))..................(((((......)))))...................)))))).. (-18.19 = -17.25 +  -0.94)

alignment

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secondary structure

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dotplot

Postscript

Window 101

Location 1,116 – 1,216
Length 100
Sequences 6
Columns 80
Reading direction forward
Mean pairwise identity 90.06
Mean single sequence MFE -15.92
Consensus MFE -15.22
Energy contribution -15.13
Covariance contribution -0.08
Combinations/Pair 1.35
Mean z-score -2.89
Structure conservation index 0.96
SVM decision value 4.08
SVM RNA-class probability 0.999786
Prediction RNA

Download alignment: ClustalW | MAF

>Microcebus_murinus_19_1_1098/1116-1216
ACCAUCAUUUGCAAGAAACCAGCUUCACAAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAUGAAGUCGUAAGUA---
......((((((.........(((((......)))))...................((((......)))))))))).--- ( -11.60)
>Mus_musculus_21_1_983/1116-1216
ACCAUCACUUACAAGAAACCAGCUUCACAAAAGAGGCUUACAAAAAGUACAUCAAAGACUACAUGAAAUCGUAAGUGACA
....((((((((........((((((......))))))(((.....))).....................)))))))).. ( -17.10)
>Rattus_norvegicus_30_1_942/1116-1216
ACCAUCACUUACAAGAAACCAGCUUCACAAAAGAGGCCUACAAAAAGUAUAUCAAAGACUACAUGAAAUCGUAAGUGACG
....((((((((.........(((((......))))).(((.....))).....................)))))))).. ( -16.10)
>Cavia_porcellus_6_1_1053/1116-1216
ACCAUCACUUGCAGGAAACCAGUUUCACAAAAGAGGCCUACAAGAAGUACAUCAAAGAUUAUAUGAAAUCGUAAGUG---
.....(((((((.(....)..(((((......)))))...................((((......)))))))))))--- ( -13.20)
>Canis_familiaris_5_1_1082/1116-1216
ACCAUCACUUGCAGGAAACCAGCUUCACAAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAUGAAAUCGUAAGUGGUC
...(((((((((.(....)..(((((......)))))...................((((......))))))))))))). ( -18.70)
>Felis_catus_10_1_1097/1116-1216
ACCAUCACUUGCAGGAAACCAGCUUCACAAAGGAAGCCUACAAGAAGUACAUCAAAGAUUACAUGAAAUCGUAAGUGAAC
....((((((((.(....)..(((((......)))))...................((((......)))))))))))).. ( -18.80)
>consensus
ACCAUCACUUGCAAGAAACCAGCUUCACAAAAGAAGCCUACAAGAAGUACAUCAAAGAUUACAUGAAAUCGUAAGUGA__
....((((((((.........(((((......)))))...................((((......)))))))))))).. (-15.22 = -15.13 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

These windows have a probability below the cutoff.


WindowLocationStrandNLengthMean pairwise IDzSCIP
1 0 – 100 + 6 100 76.62 0.75 0.46 0.000000
2 0 – 100 - 6 100 76.62 0.56 0.50 0.000000
3 20 – 120 + 5 100 54.31 -0.81 0.24 0.002836
4 20 – 120 - 5 100 54.31 -1.14 0.29 0.051918
5 40 – 140 + 6 100 78.87 -0.24 0.61 0.010620
6 40 – 140 - 6 100 78.87 -0.16 0.71 0.044367
7 60 – 160 + 6 100 82.11 -1.01 0.59 0.158480
9 80 – 180 + 6 100 85.02 -0.85 0.48 0.023597
10 80 – 180 - 6 100 85.02 -1.33 0.77 0.336243
11 100 – 200 + 6 100 87.59 -0.85 0.69 0.107807
12 100 – 200 - 6 100 87.59 -0.84 0.79 0.095466
13 120 – 220 + 6 100 87.59 -0.77 0.69 0.106263
14 120 – 220 - 6 100 87.59 -1.34 0.76 0.179914
15 140 – 240 + 6 100 92.07 -1.50 0.84 0.458848
17 160 – 260 + 4 100 59.45 -0.89 0.38 0.011875
18 160 – 260 - 4 100 59.45 -0.61 0.43 0.017191
19 180 – 280 + 6 100 85.87 -0.57 0.67 0.141851
20 180 – 280 - 6 100 85.87 -0.56 0.64 0.142497
21 200 – 300 + 6 100 84.91 0.07 0.69 0.069570
22 200 – 300 - 6 100 84.91 -0.00 0.67 0.085556
23 220 – 320 + 6 100 86.11 0.30 0.74 0.026692
24 220 – 320 - 6 100 86.11 0.27 0.73 0.034383
25 240 – 340 + 6 100 83.47 1.19 0.57 0.006726
26 240 – 340 - 6 100 83.47 0.78 0.56 0.009848
27 260 – 360 + 6 100 80.63 1.04 0.40 0.000000
28 260 – 360 - 6 100 80.63 -0.01 0.54 0.002744
29 280 – 380 + 6 100 77.72 0.66 0.29 0.000000
30 280 – 380 - 6 100 77.72 1.31 0.38 0.000000
31 300 – 400 + 6 100 86.98 -0.27 0.67 0.109552
32 300 – 400 - 6 100 86.98 1.45 0.63 0.042342
33 320 – 420 + 6 100 83.18 -0.08 0.61 0.053573
34 320 – 420 - 6 100 83.18 1.43 0.52 0.000014
35 340 – 440 + 6 100 83.83 0.44 0.72 0.022652
36 340 – 440 - 6 100 83.83 1.16 0.35 0.000000
37 360 – 460 + 2 100 53.12 -0.40 0.36 0.000000
38 360 – 460 - 2 100 53.12 0.58 0.32 0.000000
39 380 – 480 + 3 100 56.18 -0.60 0.21 0.000000
40 380 – 480 - 3 100 56.18 -0.16 0.21 0.000000
41 500 – 600 + 4 100 91.30 -0.14 0.80 0.019092
42 500 – 600 - 4 100 91.30 -0.10 0.79 0.018776
43 520 – 620 + 6 100 78.05 -0.21 0.50 0.000000
44 520 – 620 - 6 100 78.05 0.00 0.41 0.000000
45 540 – 640 + 6 100 74.73 -0.17 0.38 0.000000
46 540 – 640 - 6 100 74.73 -0.07 0.49 0.000000
47 560 – 660 + 6 100 78.44 0.25 0.44 0.000000
48 560 – 660 - 6 100 78.44 0.14 0.54 0.000000
49 580 – 680 + 6 100 81.27 0.53 0.48 0.000000
50 580 – 680 - 6 100 81.27 0.03 0.50 0.000007
51 600 – 700 + 6 100 86.40 0.35 0.62 0.103226
52 600 – 700 - 6 100 86.40 0.33 0.57 0.098108
53 620 – 720 + 6 100 82.75 -0.32 0.55 0.027319
54 620 – 720 - 6 100 82.75 0.17 0.55 0.011178
55 640 – 740 + 6 100 79.09 -0.33 0.46 0.000001
56 640 – 740 - 6 100 79.09 -0.71 0.24 0.000000
57 660 – 760 + 5 100 75.06 0.38 0.36 0.000000
58 660 – 760 - 5 100 75.06 0.16 0.23 0.000000
60 700 – 800 - 4 100 70.61 -0.99 0.58 0.058343
61 720 – 820 + 2 100 95.89 0.27 0.95 0.015985
63 740 – 840 + 6 100 84.15 -0.95 0.67 0.231923
64 740 – 840 - 6 100 84.15 -1.38 0.65 0.292415
65 760 – 860 + 6 100 82.54 -0.87 0.58 0.099388
66 760 – 860 - 6 100 82.54 -1.42 0.51 0.084635
67 780 – 880 + 6 100 86.39 -0.49 0.65 0.134175
68 780 – 880 - 6 100 86.39 -0.38 0.61 0.128955
69 800 – 900 + 6 100 88.53 -2.17 0.58 0.022207
70 800 – 900 - 6 100 88.53 -0.97 0.59 0.056816
71 820 – 920 + 6 100 86.39 -1.38 0.52 0.037077
72 820 – 920 - 6 100 86.39 -0.93 0.38 0.000017
73 840 – 940 + 6 100 82.40 -0.40 0.45 0.000018
74 840 – 940 - 6 100 82.40 -1.10 0.49 0.026245
75 860 – 960 + 6 100 77.11 -0.69 0.63 0.079966
76 860 – 960 - 6 100 77.11 -1.13 0.59 0.205110
77 880 – 980 + 6 100 72.89 -0.65 0.58 0.020256
78 880 – 980 - 6 100 72.89 -0.81 0.62 0.141225
79 900 – 1000 + 6 100 78.91 -0.72 0.47 0.002640
80 900 – 1000 - 6 100 78.91 -0.94 0.59 0.116871
81 920 – 1020 + 6 100 76.69 -0.26 0.43 0.000000
82 920 – 1020 - 6 100 76.69 -0.28 0.60 0.005035
83 940 – 1040 + 6 100 72.00 0.00 0.51 0.000000
84 940 – 1040 - 6 100 72.00 -0.03 0.13 0.000000
85 960 – 1060 + 6 100 78.80 -0.21 0.69 0.046193
86 960 – 1060 - 6 100 78.80 0.07 0.49 0.000000
87 980 – 1080 + 6 100 89.83 -0.70 0.82 0.048954
88 980 – 1080 - 6 100 89.83 -0.33 0.61 0.072400
89 1000 – 1100 + 6 100 90.32 -0.24 0.72 0.030052
90 1000 – 1100 - 6 100 90.32 -0.31 0.62 0.061090
91 1020 – 1120 + 6 100 91.97 -0.95 0.80 0.052992
92 1020 – 1120 - 6 100 91.97 -0.58 0.69 0.019557
93 1040 – 1140 + 6 100 91.16 0.60 0.76 0.004156
94 1040 – 1140 - 6 100 91.16 0.08 0.87 0.002988
95 1060 – 1160 + 6 100 90.41 -0.09 0.74 0.020928
96 1060 – 1160 - 6 100 90.41 0.79 0.77 0.003348
98 1080 – 1180 - 6 100 91.09 -0.17 0.87 0.008136
99 1100 – 1200 + 6 100 89.07 -1.08 0.81 0.137530
100 1100 – 1200 - 6 100 89.07 -0.29 0.82 0.017564
102 1116 – 1216 - 6 100 90.06 -0.93 0.54 0.022160