Multiple sequence alignment - TraesCS3A01G451400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G451400 chr3A 100.000 2559 0 0 1 2559 689523023 689525581 0.000000e+00 4726.0
1 TraesCS3A01G451400 chr3A 98.213 1399 22 2 274 1672 689608205 689609600 0.000000e+00 2442.0
2 TraesCS3A01G451400 chr3A 97.713 1399 29 2 274 1672 689578427 689579822 0.000000e+00 2403.0
3 TraesCS3A01G451400 chr3A 98.870 885 10 0 1675 2559 689580435 689581319 0.000000e+00 1580.0
4 TraesCS3A01G451400 chr3A 98.305 885 14 1 1675 2559 689610213 689611096 0.000000e+00 1550.0
5 TraesCS3A01G451400 chr3A 87.853 1276 127 17 370 1627 689659666 689660931 0.000000e+00 1472.0
6 TraesCS3A01G451400 chr3A 87.893 1272 127 16 373 1627 689662507 689663768 0.000000e+00 1471.0
7 TraesCS3A01G451400 chr3A 86.782 1271 136 17 373 1627 689666322 689667576 0.000000e+00 1402.0
8 TraesCS3A01G451400 chr3A 85.819 818 99 8 822 1627 686281128 686280316 0.000000e+00 852.0
9 TraesCS3A01G451400 chr3A 86.073 797 91 9 662 1438 689867182 689867978 0.000000e+00 839.0
10 TraesCS3A01G451400 chr3A 85.571 797 95 9 662 1438 689846868 689847664 0.000000e+00 817.0
11 TraesCS3A01G451400 chr3A 87.963 540 54 6 373 906 689866848 689867382 6.010000e-176 627.0
12 TraesCS3A01G451400 chr3A 87.970 532 60 3 233 763 686281571 686281043 2.160000e-175 625.0
13 TraesCS3A01G451400 chr3A 88.889 117 13 0 1678 1794 686278307 686278191 7.380000e-31 145.0
14 TraesCS3A01G451400 chr3A 81.215 181 18 10 1859 2023 47273907 47274087 5.740000e-27 132.0
15 TraesCS3A01G451400 chr3A 88.000 100 12 0 232 331 689866746 689866845 4.470000e-23 119.0
16 TraesCS3A01G451400 chr3A 87.879 99 12 0 232 330 689846432 689846530 1.610000e-22 117.0
17 TraesCS3A01G451400 chr3D 91.053 1263 94 8 373 1624 553357146 553358400 0.000000e+00 1688.0
18 TraesCS3A01G451400 chr3D 86.061 947 101 10 712 1627 553405894 553406840 0.000000e+00 989.0
19 TraesCS3A01G451400 chr3D 94.805 539 23 2 2023 2559 553372471 553373006 0.000000e+00 835.0
20 TraesCS3A01G451400 chr3D 89.700 534 49 5 232 763 549000025 548999496 0.000000e+00 676.0
21 TraesCS3A01G451400 chr3D 96.035 227 8 1 1785 2010 553372169 553372395 4.020000e-98 368.0
22 TraesCS3A01G451400 chr3D 81.220 410 47 16 2089 2491 553419159 553419545 1.150000e-78 303.0
23 TraesCS3A01G451400 chr3D 85.050 301 34 6 1331 1627 548999104 548998811 1.930000e-76 296.0
24 TraesCS3A01G451400 chr3D 95.575 113 5 0 1677 1789 553362441 553362553 5.620000e-42 182.0
25 TraesCS3A01G451400 chr3B 92.308 234 18 0 1 234 734595218 734595451 1.470000e-87 333.0
26 TraesCS3A01G451400 chr3B 85.473 296 33 5 1331 1623 728294962 728294674 1.490000e-77 300.0
27 TraesCS3A01G451400 chr3B 88.793 232 19 3 1 232 734543096 734543320 6.970000e-71 278.0
28 TraesCS3A01G451400 chr3B 94.017 117 7 0 1678 1794 728293144 728293028 7.280000e-41 178.0
29 TraesCS3A01G451400 chr3B 77.049 122 13 8 2075 2196 771130859 771130965 3.560000e-04 56.5
30 TraesCS3A01G451400 chr2A 86.032 315 29 9 2247 2559 81690632 81690331 8.830000e-85 324.0
31 TraesCS3A01G451400 chr2A 85.079 315 31 9 2247 2559 16896881 16897181 8.890000e-80 307.0
32 TraesCS3A01G451400 chr2A 82.320 181 16 10 1859 2023 16896446 16896626 2.650000e-30 143.0
33 TraesCS3A01G451400 chr2A 82.320 181 16 5 1859 2023 81691066 81690886 2.650000e-30 143.0
34 TraesCS3A01G451400 chr2A 81.955 133 16 7 233 365 114865400 114865524 3.480000e-19 106.0
35 TraesCS3A01G451400 chr7D 85.397 315 31 9 2247 2559 580802145 580802446 1.910000e-81 313.0
36 TraesCS3A01G451400 chr7D 84.127 315 34 9 2247 2559 105223139 105223439 8.960000e-75 291.0
37 TraesCS3A01G451400 chr7D 82.873 181 15 9 1859 2023 580801707 580801887 5.700000e-32 148.0
38 TraesCS3A01G451400 chr7D 96.875 32 1 0 2209 2240 471054679 471054648 1.000000e-03 54.7
39 TraesCS3A01G451400 chr2B 84.494 316 33 11 2247 2559 757859486 757859788 5.350000e-77 298.0
40 TraesCS3A01G451400 chr2B 83.978 181 13 10 1859 2023 757859051 757859231 2.640000e-35 159.0
41 TraesCS3A01G451400 chr1A 83.438 320 33 11 2247 2559 215941324 215941018 1.940000e-71 279.0
42 TraesCS3A01G451400 chr1A 82.624 282 34 8 2249 2527 14803304 14803573 4.260000e-58 235.0
43 TraesCS3A01G451400 chr1A 86.466 133 13 4 2074 2203 436397447 436397577 9.550000e-30 141.0
44 TraesCS3A01G451400 chr1A 81.215 181 18 10 1859 2023 14802912 14803092 5.740000e-27 132.0
45 TraesCS3A01G451400 chr1A 80.460 174 26 6 232 403 500921611 500921778 2.670000e-25 126.0
46 TraesCS3A01G451400 chr5D 86.861 137 14 3 2074 2207 260429326 260429191 1.590000e-32 150.0
47 TraesCS3A01G451400 chr5A 90.667 75 7 0 2248 2322 529787402 529787476 1.620000e-17 100.0
48 TraesCS3A01G451400 chr5A 78.698 169 22 7 232 400 652653565 652653411 1.620000e-17 100.0
49 TraesCS3A01G451400 chr4B 92.647 68 5 0 2248 2315 223394906 223394973 5.830000e-17 99.0
50 TraesCS3A01G451400 chr7B 96.875 32 1 0 2209 2240 494742511 494742480 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G451400 chr3A 689523023 689525581 2558 False 4726.000000 4726 100.000000 1 2559 1 chr3A.!!$F2 2558
1 TraesCS3A01G451400 chr3A 689608205 689611096 2891 False 1996.000000 2442 98.259000 274 2559 2 chr3A.!!$F4 2285
2 TraesCS3A01G451400 chr3A 689578427 689581319 2892 False 1991.500000 2403 98.291500 274 2559 2 chr3A.!!$F3 2285
3 TraesCS3A01G451400 chr3A 689659666 689667576 7910 False 1448.333333 1472 87.509333 370 1627 3 chr3A.!!$F5 1257
4 TraesCS3A01G451400 chr3A 686278191 686281571 3380 True 540.666667 852 87.559333 233 1794 3 chr3A.!!$R1 1561
5 TraesCS3A01G451400 chr3A 689866746 689867978 1232 False 528.333333 839 87.345333 232 1438 3 chr3A.!!$F7 1206
6 TraesCS3A01G451400 chr3A 689846432 689847664 1232 False 467.000000 817 86.725000 232 1438 2 chr3A.!!$F6 1206
7 TraesCS3A01G451400 chr3D 553357146 553358400 1254 False 1688.000000 1688 91.053000 373 1624 1 chr3D.!!$F1 1251
8 TraesCS3A01G451400 chr3D 553405894 553406840 946 False 989.000000 989 86.061000 712 1627 1 chr3D.!!$F3 915
9 TraesCS3A01G451400 chr3D 553372169 553373006 837 False 601.500000 835 95.420000 1785 2559 2 chr3D.!!$F5 774
10 TraesCS3A01G451400 chr3D 548998811 549000025 1214 True 486.000000 676 87.375000 232 1627 2 chr3D.!!$R1 1395
11 TraesCS3A01G451400 chr3B 728293028 728294962 1934 True 239.000000 300 89.745000 1331 1794 2 chr3B.!!$R1 463
12 TraesCS3A01G451400 chr2A 81690331 81691066 735 True 233.500000 324 84.176000 1859 2559 2 chr2A.!!$R1 700
13 TraesCS3A01G451400 chr2A 16896446 16897181 735 False 225.000000 307 83.699500 1859 2559 2 chr2A.!!$F2 700
14 TraesCS3A01G451400 chr7D 580801707 580802446 739 False 230.500000 313 84.135000 1859 2559 2 chr7D.!!$F2 700
15 TraesCS3A01G451400 chr2B 757859051 757859788 737 False 228.500000 298 84.236000 1859 2559 2 chr2B.!!$F1 700

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
136 137 0.604073 GCTCGGGCTTAGATACTCCC 59.396 60.0 0.00 0.00 35.22 4.30 F
242 243 0.609681 AGGTGACCTCTCAGTCGACC 60.610 60.0 13.01 0.00 39.77 4.79 F
368 369 0.667792 GTCACTTGACTGAGACGCCC 60.668 60.0 1.92 0.00 41.65 6.13 F
1327 4179 0.737367 TTGGCGATGAGCTCAACGAG 60.737 55.0 39.89 23.32 43.47 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 4023 2.815211 CGACCATCCACACCTGCG 60.815 66.667 0.0 0.0 0.00 5.18 R
1327 4179 4.142773 TGAAAGAAGTTGTCGTTGTTGTCC 60.143 41.667 0.0 0.0 0.00 4.02 R
1334 4186 4.152759 TCGTTTGTGAAAGAAGTTGTCGTT 59.847 37.500 0.0 0.0 0.00 3.85 R
2233 9705 5.888724 TCACAAGGTAGTTTGGTGATCAAAA 59.111 36.000 0.0 0.0 45.74 2.44 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.969816 ACTACAAAAATGCATAGTCGTGC 58.030 39.130 0.00 0.00 45.25 5.34
28 29 3.216147 ACAAAAATGCATAGTCGTGCC 57.784 42.857 0.00 0.00 44.43 5.01
29 30 2.819608 ACAAAAATGCATAGTCGTGCCT 59.180 40.909 0.00 0.00 44.43 4.75
30 31 3.255642 ACAAAAATGCATAGTCGTGCCTT 59.744 39.130 0.00 0.00 44.43 4.35
31 32 4.457603 ACAAAAATGCATAGTCGTGCCTTA 59.542 37.500 0.00 0.00 44.43 2.69
32 33 4.882671 AAAATGCATAGTCGTGCCTTAG 57.117 40.909 0.00 0.00 44.43 2.18
33 34 3.543680 AATGCATAGTCGTGCCTTAGT 57.456 42.857 0.00 0.00 44.43 2.24
34 35 3.543680 ATGCATAGTCGTGCCTTAGTT 57.456 42.857 0.00 0.00 44.43 2.24
35 36 2.888594 TGCATAGTCGTGCCTTAGTTC 58.111 47.619 0.00 0.00 44.43 3.01
36 37 2.232696 TGCATAGTCGTGCCTTAGTTCA 59.767 45.455 0.00 0.00 44.43 3.18
37 38 3.259064 GCATAGTCGTGCCTTAGTTCAA 58.741 45.455 0.00 0.00 39.18 2.69
38 39 3.871594 GCATAGTCGTGCCTTAGTTCAAT 59.128 43.478 0.00 0.00 39.18 2.57
39 40 4.332819 GCATAGTCGTGCCTTAGTTCAATT 59.667 41.667 0.00 0.00 39.18 2.32
40 41 5.163754 GCATAGTCGTGCCTTAGTTCAATTT 60.164 40.000 0.00 0.00 39.18 1.82
41 42 6.622896 GCATAGTCGTGCCTTAGTTCAATTTT 60.623 38.462 0.00 0.00 39.18 1.82
42 43 5.108385 AGTCGTGCCTTAGTTCAATTTTG 57.892 39.130 0.00 0.00 0.00 2.44
43 44 3.668656 GTCGTGCCTTAGTTCAATTTTGC 59.331 43.478 0.00 0.00 0.00 3.68
44 45 3.316588 TCGTGCCTTAGTTCAATTTTGCA 59.683 39.130 0.00 0.00 0.00 4.08
45 46 4.047822 CGTGCCTTAGTTCAATTTTGCAA 58.952 39.130 0.00 0.00 0.00 4.08
46 47 4.505922 CGTGCCTTAGTTCAATTTTGCAAA 59.494 37.500 8.05 8.05 0.00 3.68
47 48 5.006165 CGTGCCTTAGTTCAATTTTGCAAAA 59.994 36.000 25.76 25.76 0.00 2.44
48 49 6.292811 CGTGCCTTAGTTCAATTTTGCAAAAT 60.293 34.615 27.73 27.73 40.15 1.82
49 50 6.852345 GTGCCTTAGTTCAATTTTGCAAAATG 59.148 34.615 32.23 25.04 38.53 2.32
50 51 6.541641 TGCCTTAGTTCAATTTTGCAAAATGT 59.458 30.769 32.23 20.86 38.53 2.71
51 52 7.712639 TGCCTTAGTTCAATTTTGCAAAATGTA 59.287 29.630 32.23 21.98 38.53 2.29
52 53 8.555361 GCCTTAGTTCAATTTTGCAAAATGTAA 58.445 29.630 32.23 25.45 38.53 2.41
64 65 8.902040 TTTGCAAAATGTAAAATTTGACAACC 57.098 26.923 12.46 1.09 38.50 3.77
65 66 7.856145 TGCAAAATGTAAAATTTGACAACCT 57.144 28.000 12.46 0.00 38.50 3.50
66 67 8.948631 TGCAAAATGTAAAATTTGACAACCTA 57.051 26.923 12.46 0.00 38.50 3.08
67 68 9.553064 TGCAAAATGTAAAATTTGACAACCTAT 57.447 25.926 12.46 0.00 38.50 2.57
83 84 9.226606 TGACAACCTATTAGTCTTTTATGTTGG 57.773 33.333 0.00 0.00 35.95 3.77
84 85 9.444600 GACAACCTATTAGTCTTTTATGTTGGA 57.555 33.333 0.00 0.00 35.95 3.53
85 86 9.975218 ACAACCTATTAGTCTTTTATGTTGGAT 57.025 29.630 0.00 0.00 35.95 3.41
93 94 7.716799 AGTCTTTTATGTTGGATAATTGGCA 57.283 32.000 0.00 0.00 0.00 4.92
94 95 8.310122 AGTCTTTTATGTTGGATAATTGGCAT 57.690 30.769 0.00 0.00 0.00 4.40
95 96 9.420118 AGTCTTTTATGTTGGATAATTGGCATA 57.580 29.630 0.00 0.00 0.00 3.14
96 97 9.683069 GTCTTTTATGTTGGATAATTGGCATAG 57.317 33.333 0.00 0.00 0.00 2.23
97 98 9.420118 TCTTTTATGTTGGATAATTGGCATAGT 57.580 29.630 0.00 0.00 0.00 2.12
98 99 9.467258 CTTTTATGTTGGATAATTGGCATAGTG 57.533 33.333 0.00 0.00 0.00 2.74
99 100 7.523293 TTATGTTGGATAATTGGCATAGTGG 57.477 36.000 0.00 0.00 0.00 4.00
100 101 3.636300 TGTTGGATAATTGGCATAGTGGC 59.364 43.478 0.00 0.00 44.03 5.01
112 113 5.376854 GGCATAGTGGCGAATATTCATTT 57.623 39.130 15.57 0.00 31.79 2.32
113 114 5.393962 GGCATAGTGGCGAATATTCATTTC 58.606 41.667 15.57 3.50 31.79 2.17
114 115 5.393962 GCATAGTGGCGAATATTCATTTCC 58.606 41.667 15.57 10.25 0.00 3.13
115 116 5.621422 CATAGTGGCGAATATTCATTTCCG 58.379 41.667 15.57 2.20 0.00 4.30
116 117 3.804036 AGTGGCGAATATTCATTTCCGA 58.196 40.909 15.57 0.60 0.00 4.55
117 118 3.809832 AGTGGCGAATATTCATTTCCGAG 59.190 43.478 15.57 0.00 0.00 4.63
118 119 2.548057 TGGCGAATATTCATTTCCGAGC 59.452 45.455 15.57 7.55 0.00 5.03
119 120 2.808543 GGCGAATATTCATTTCCGAGCT 59.191 45.455 15.57 0.00 0.00 4.09
120 121 3.120511 GGCGAATATTCATTTCCGAGCTC 60.121 47.826 15.57 2.73 0.00 4.09
121 122 3.422343 GCGAATATTCATTTCCGAGCTCG 60.422 47.826 29.06 29.06 39.44 5.03
136 137 0.604073 GCTCGGGCTTAGATACTCCC 59.396 60.000 0.00 0.00 35.22 4.30
142 143 3.927854 GGGCTTAGATACTCCCGAAATC 58.072 50.000 0.00 0.00 0.00 2.17
143 144 3.323979 GGGCTTAGATACTCCCGAAATCA 59.676 47.826 0.00 0.00 0.00 2.57
144 145 4.561105 GGCTTAGATACTCCCGAAATCAG 58.439 47.826 0.00 0.00 0.00 2.90
145 146 4.281182 GGCTTAGATACTCCCGAAATCAGA 59.719 45.833 0.00 0.00 0.00 3.27
146 147 5.465935 GCTTAGATACTCCCGAAATCAGAG 58.534 45.833 0.00 0.00 0.00 3.35
147 148 5.010213 GCTTAGATACTCCCGAAATCAGAGT 59.990 44.000 7.86 7.86 43.17 3.24
148 149 6.636562 TTAGATACTCCCGAAATCAGAGTC 57.363 41.667 6.42 0.00 41.09 3.36
149 150 3.566322 AGATACTCCCGAAATCAGAGTCG 59.434 47.826 6.42 0.18 41.09 4.18
150 151 1.546961 ACTCCCGAAATCAGAGTCGT 58.453 50.000 5.75 0.00 36.06 4.34
151 152 2.719739 ACTCCCGAAATCAGAGTCGTA 58.280 47.619 5.75 0.00 36.06 3.43
152 153 3.288964 ACTCCCGAAATCAGAGTCGTAT 58.711 45.455 5.75 0.00 36.06 3.06
153 154 3.066900 ACTCCCGAAATCAGAGTCGTATG 59.933 47.826 5.75 0.00 36.06 2.39
154 155 2.128035 CCCGAAATCAGAGTCGTATGC 58.872 52.381 5.75 0.00 35.48 3.14
155 156 2.223829 CCCGAAATCAGAGTCGTATGCT 60.224 50.000 5.75 0.00 35.48 3.79
156 157 3.004419 CCCGAAATCAGAGTCGTATGCTA 59.996 47.826 5.75 0.00 35.48 3.49
157 158 4.222886 CCGAAATCAGAGTCGTATGCTAG 58.777 47.826 5.75 0.00 35.48 3.42
158 159 4.023963 CCGAAATCAGAGTCGTATGCTAGA 60.024 45.833 0.00 0.00 35.48 2.43
159 160 5.505819 CCGAAATCAGAGTCGTATGCTAGAA 60.506 44.000 0.00 0.00 35.48 2.10
160 161 6.146216 CGAAATCAGAGTCGTATGCTAGAAT 58.854 40.000 0.00 0.00 32.61 2.40
161 162 6.087423 CGAAATCAGAGTCGTATGCTAGAATG 59.913 42.308 0.00 0.00 32.61 2.67
162 163 6.398234 AATCAGAGTCGTATGCTAGAATGT 57.602 37.500 0.00 0.00 0.00 2.71
163 164 5.175090 TCAGAGTCGTATGCTAGAATGTG 57.825 43.478 0.00 0.00 0.00 3.21
164 165 4.036852 TCAGAGTCGTATGCTAGAATGTGG 59.963 45.833 0.00 0.00 0.00 4.17
165 166 4.036852 CAGAGTCGTATGCTAGAATGTGGA 59.963 45.833 0.00 0.00 0.00 4.02
166 167 4.830046 AGAGTCGTATGCTAGAATGTGGAT 59.170 41.667 0.00 0.00 0.00 3.41
167 168 5.048364 AGAGTCGTATGCTAGAATGTGGATC 60.048 44.000 0.00 0.00 0.00 3.36
168 169 4.830046 AGTCGTATGCTAGAATGTGGATCT 59.170 41.667 0.00 0.00 0.00 2.75
169 170 4.920340 GTCGTATGCTAGAATGTGGATCTG 59.080 45.833 0.00 0.00 0.00 2.90
170 171 4.584743 TCGTATGCTAGAATGTGGATCTGT 59.415 41.667 0.00 0.00 0.00 3.41
171 172 4.683320 CGTATGCTAGAATGTGGATCTGTG 59.317 45.833 0.00 0.00 0.00 3.66
172 173 2.910199 TGCTAGAATGTGGATCTGTGC 58.090 47.619 0.00 0.00 0.00 4.57
173 174 2.236893 TGCTAGAATGTGGATCTGTGCA 59.763 45.455 0.00 0.00 36.27 4.57
174 175 2.611292 GCTAGAATGTGGATCTGTGCAC 59.389 50.000 10.75 10.75 45.82 4.57
178 179 3.566261 GTGGATCTGTGCACGTGG 58.434 61.111 18.88 5.15 36.94 4.94
179 180 2.358615 TGGATCTGTGCACGTGGC 60.359 61.111 18.88 10.30 45.13 5.01
180 181 2.046892 GGATCTGTGCACGTGGCT 60.047 61.111 18.88 0.00 45.15 4.75
181 182 2.393768 GGATCTGTGCACGTGGCTG 61.394 63.158 18.88 5.09 45.15 4.85
182 183 3.031964 GATCTGTGCACGTGGCTGC 62.032 63.158 18.88 2.77 45.15 5.25
183 184 3.830464 ATCTGTGCACGTGGCTGCA 62.830 57.895 18.88 5.93 45.06 4.41
187 188 3.127451 TGCACGTGGCTGCATTTT 58.873 50.000 18.88 0.00 42.36 1.82
188 189 1.440893 TGCACGTGGCTGCATTTTT 59.559 47.368 18.88 0.00 42.36 1.94
211 212 9.451002 TTTTTCTGTCCGTATATTCCATGTAAA 57.549 29.630 0.00 0.00 0.00 2.01
212 213 8.657074 TTTCTGTCCGTATATTCCATGTAAAG 57.343 34.615 0.00 0.00 0.00 1.85
213 214 7.356089 TCTGTCCGTATATTCCATGTAAAGT 57.644 36.000 0.00 0.00 0.00 2.66
214 215 8.467963 TCTGTCCGTATATTCCATGTAAAGTA 57.532 34.615 0.00 0.00 0.00 2.24
215 216 8.916062 TCTGTCCGTATATTCCATGTAAAGTAA 58.084 33.333 0.00 0.00 0.00 2.24
216 217 9.706691 CTGTCCGTATATTCCATGTAAAGTAAT 57.293 33.333 0.00 0.00 0.00 1.89
228 229 9.575868 TCCATGTAAAGTAATAAAAACAGGTGA 57.424 29.630 0.00 0.00 0.00 4.02
229 230 9.620660 CCATGTAAAGTAATAAAAACAGGTGAC 57.379 33.333 0.00 0.00 0.00 3.67
230 231 9.620660 CATGTAAAGTAATAAAAACAGGTGACC 57.379 33.333 0.00 0.00 0.00 4.02
242 243 0.609681 AGGTGACCTCTCAGTCGACC 60.610 60.000 13.01 0.00 39.77 4.79
253 254 2.683867 CTCAGTCGACCGAGGACTTAAT 59.316 50.000 19.19 0.00 42.63 1.40
366 367 1.852942 TTGTCACTTGACTGAGACGC 58.147 50.000 10.63 0.00 44.99 5.19
368 369 0.667792 GTCACTTGACTGAGACGCCC 60.668 60.000 1.92 0.00 41.65 6.13
405 407 1.833630 TGAGATCTAGCCACACCCTTG 59.166 52.381 0.00 0.00 0.00 3.61
456 458 7.523380 GCATTTTGCATGAGAGATAGCCTTAAT 60.523 37.037 0.00 0.00 44.26 1.40
590 594 2.294512 CCAAGAGCCAACAGAAGGTTTC 59.705 50.000 0.00 0.00 37.72 2.78
631 635 6.741500 GCACAAGCTTTTATTTTGATACACG 58.258 36.000 0.00 0.00 37.91 4.49
1171 4023 6.898041 TGCACACATTAATTCTAACTCACAC 58.102 36.000 0.00 0.00 0.00 3.82
1327 4179 0.737367 TTGGCGATGAGCTCAACGAG 60.737 55.000 39.89 23.32 43.47 4.18
1334 4186 0.750249 TGAGCTCAACGAGGACAACA 59.250 50.000 15.67 0.00 0.00 3.33
1493 4375 2.434185 CGCCGCCGCCATATGTAT 60.434 61.111 1.24 0.00 0.00 2.29
1660 5282 6.206829 CGAAACCTTCCATCCCTAATTAATCC 59.793 42.308 0.00 0.00 0.00 3.01
1672 6456 2.864639 ATTAATCCCCTCCCCCTGAT 57.135 50.000 0.00 0.00 0.00 2.90
2029 9017 6.434028 TGCATGCTATGGAGTTTCTAGTTTTT 59.566 34.615 20.33 0.00 0.00 1.94
2233 9705 7.072076 ACCCCCTGTAAAGAAATATAAGATCGT 59.928 37.037 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.696453 GCACGACTATGCATTTTTGTAGTATTT 59.304 33.333 3.54 0.00 45.39 1.40
3 4 6.715464 GCACGACTATGCATTTTTGTAGTAT 58.285 36.000 3.54 0.00 45.39 2.12
4 5 6.102006 GCACGACTATGCATTTTTGTAGTA 57.898 37.500 3.54 0.00 45.39 1.82
5 6 4.969816 GCACGACTATGCATTTTTGTAGT 58.030 39.130 3.54 0.00 45.39 2.73
6 7 5.391950 AAGGCACGACTATGCATTTTTGTAG 60.392 40.000 3.54 0.00 46.79 2.74
7 8 4.457603 AAGGCACGACTATGCATTTTTGTA 59.542 37.500 3.54 0.00 46.79 2.41
8 9 3.255642 AAGGCACGACTATGCATTTTTGT 59.744 39.130 3.54 0.00 46.79 2.83
9 10 3.836949 AAGGCACGACTATGCATTTTTG 58.163 40.909 3.54 0.00 46.79 2.44
10 11 4.700213 ACTAAGGCACGACTATGCATTTTT 59.300 37.500 3.54 0.00 46.79 1.94
11 12 4.261801 ACTAAGGCACGACTATGCATTTT 58.738 39.130 3.54 0.00 46.79 1.82
12 13 3.873910 ACTAAGGCACGACTATGCATTT 58.126 40.909 3.54 0.00 46.79 2.32
16 17 2.888594 TGAACTAAGGCACGACTATGC 58.111 47.619 0.00 0.00 45.34 3.14
17 18 6.422776 AAATTGAACTAAGGCACGACTATG 57.577 37.500 0.00 0.00 0.00 2.23
18 19 6.622896 GCAAAATTGAACTAAGGCACGACTAT 60.623 38.462 0.00 0.00 0.00 2.12
19 20 5.334569 GCAAAATTGAACTAAGGCACGACTA 60.335 40.000 0.00 0.00 0.00 2.59
20 21 4.556699 GCAAAATTGAACTAAGGCACGACT 60.557 41.667 0.00 0.00 0.00 4.18
21 22 3.668656 GCAAAATTGAACTAAGGCACGAC 59.331 43.478 0.00 0.00 0.00 4.34
22 23 3.316588 TGCAAAATTGAACTAAGGCACGA 59.683 39.130 0.00 0.00 0.00 4.35
23 24 3.637432 TGCAAAATTGAACTAAGGCACG 58.363 40.909 0.00 0.00 0.00 5.34
24 25 5.982465 TTTGCAAAATTGAACTAAGGCAC 57.018 34.783 10.02 0.00 0.00 5.01
25 26 6.541641 ACATTTTGCAAAATTGAACTAAGGCA 59.458 30.769 30.13 3.89 36.52 4.75
26 27 6.958255 ACATTTTGCAAAATTGAACTAAGGC 58.042 32.000 30.13 0.00 36.52 4.35
38 39 9.346725 GGTTGTCAAATTTTACATTTTGCAAAA 57.653 25.926 25.76 25.76 34.19 2.44
39 40 8.734386 AGGTTGTCAAATTTTACATTTTGCAAA 58.266 25.926 8.05 8.05 34.19 3.68
40 41 8.273780 AGGTTGTCAAATTTTACATTTTGCAA 57.726 26.923 6.05 0.00 33.77 4.08
41 42 7.856145 AGGTTGTCAAATTTTACATTTTGCA 57.144 28.000 6.05 0.00 33.77 4.08
57 58 9.226606 CCAACATAAAAGACTAATAGGTTGTCA 57.773 33.333 16.93 0.00 38.79 3.58
58 59 9.444600 TCCAACATAAAAGACTAATAGGTTGTC 57.555 33.333 16.93 0.00 38.79 3.18
59 60 9.975218 ATCCAACATAAAAGACTAATAGGTTGT 57.025 29.630 16.93 4.48 38.79 3.32
67 68 9.249053 TGCCAATTATCCAACATAAAAGACTAA 57.751 29.630 0.00 0.00 0.00 2.24
68 69 8.815565 TGCCAATTATCCAACATAAAAGACTA 57.184 30.769 0.00 0.00 0.00 2.59
69 70 7.716799 TGCCAATTATCCAACATAAAAGACT 57.283 32.000 0.00 0.00 0.00 3.24
70 71 9.683069 CTATGCCAATTATCCAACATAAAAGAC 57.317 33.333 0.00 0.00 0.00 3.01
71 72 9.420118 ACTATGCCAATTATCCAACATAAAAGA 57.580 29.630 0.00 0.00 0.00 2.52
72 73 9.467258 CACTATGCCAATTATCCAACATAAAAG 57.533 33.333 0.00 0.00 0.00 2.27
73 74 8.420222 CCACTATGCCAATTATCCAACATAAAA 58.580 33.333 0.00 0.00 0.00 1.52
74 75 7.471260 GCCACTATGCCAATTATCCAACATAAA 60.471 37.037 0.00 0.00 0.00 1.40
75 76 6.015519 GCCACTATGCCAATTATCCAACATAA 60.016 38.462 0.00 0.00 0.00 1.90
76 77 5.476599 GCCACTATGCCAATTATCCAACATA 59.523 40.000 0.00 0.00 0.00 2.29
77 78 4.281688 GCCACTATGCCAATTATCCAACAT 59.718 41.667 0.00 0.00 0.00 2.71
78 79 3.636300 GCCACTATGCCAATTATCCAACA 59.364 43.478 0.00 0.00 0.00 3.33
79 80 3.304659 CGCCACTATGCCAATTATCCAAC 60.305 47.826 0.00 0.00 0.00 3.77
80 81 2.884012 CGCCACTATGCCAATTATCCAA 59.116 45.455 0.00 0.00 0.00 3.53
81 82 2.105649 TCGCCACTATGCCAATTATCCA 59.894 45.455 0.00 0.00 0.00 3.41
82 83 2.778299 TCGCCACTATGCCAATTATCC 58.222 47.619 0.00 0.00 0.00 2.59
83 84 6.683974 ATATTCGCCACTATGCCAATTATC 57.316 37.500 0.00 0.00 0.00 1.75
84 85 6.658816 TGAATATTCGCCACTATGCCAATTAT 59.341 34.615 10.80 0.00 0.00 1.28
85 86 6.000840 TGAATATTCGCCACTATGCCAATTA 58.999 36.000 10.80 0.00 0.00 1.40
86 87 4.826733 TGAATATTCGCCACTATGCCAATT 59.173 37.500 10.80 0.00 0.00 2.32
87 88 4.397420 TGAATATTCGCCACTATGCCAAT 58.603 39.130 10.80 0.00 0.00 3.16
88 89 3.814625 TGAATATTCGCCACTATGCCAA 58.185 40.909 10.80 0.00 0.00 4.52
89 90 3.483808 TGAATATTCGCCACTATGCCA 57.516 42.857 10.80 0.00 0.00 4.92
90 91 5.376854 AAATGAATATTCGCCACTATGCC 57.623 39.130 10.80 0.00 0.00 4.40
91 92 5.393962 GGAAATGAATATTCGCCACTATGC 58.606 41.667 10.80 0.00 0.00 3.14
92 93 5.408299 TCGGAAATGAATATTCGCCACTATG 59.592 40.000 10.80 0.00 0.00 2.23
93 94 5.547465 TCGGAAATGAATATTCGCCACTAT 58.453 37.500 10.80 0.00 0.00 2.12
94 95 4.951254 TCGGAAATGAATATTCGCCACTA 58.049 39.130 10.80 0.00 0.00 2.74
95 96 3.804036 TCGGAAATGAATATTCGCCACT 58.196 40.909 10.80 0.00 0.00 4.00
96 97 3.607078 GCTCGGAAATGAATATTCGCCAC 60.607 47.826 10.80 3.12 0.00 5.01
97 98 2.548057 GCTCGGAAATGAATATTCGCCA 59.452 45.455 10.80 0.00 0.00 5.69
98 99 2.808543 AGCTCGGAAATGAATATTCGCC 59.191 45.455 10.80 8.29 0.00 5.54
99 100 3.422343 CGAGCTCGGAAATGAATATTCGC 60.422 47.826 28.40 5.45 35.37 4.70
100 101 4.299352 CGAGCTCGGAAATGAATATTCG 57.701 45.455 28.40 0.00 35.37 3.34
114 115 4.018253 GGAGTATCTAAGCCCGAGCTCG 62.018 59.091 29.06 29.06 42.36 5.03
115 116 1.542472 GGAGTATCTAAGCCCGAGCTC 59.458 57.143 2.73 2.73 42.36 4.09
116 117 1.623163 GGAGTATCTAAGCCCGAGCT 58.377 55.000 0.00 0.00 44.45 4.09
117 118 0.604073 GGGAGTATCTAAGCCCGAGC 59.396 60.000 0.00 0.00 35.12 5.03
121 122 3.323979 TGATTTCGGGAGTATCTAAGCCC 59.676 47.826 0.00 0.00 37.21 5.19
122 123 4.281182 TCTGATTTCGGGAGTATCTAAGCC 59.719 45.833 0.00 0.00 33.73 4.35
123 124 5.010213 ACTCTGATTTCGGGAGTATCTAAGC 59.990 44.000 0.00 0.00 38.37 3.09
124 125 6.566942 CGACTCTGATTTCGGGAGTATCTAAG 60.567 46.154 0.00 0.00 39.95 2.18
125 126 5.238868 CGACTCTGATTTCGGGAGTATCTAA 59.761 44.000 0.00 0.00 39.95 2.10
126 127 4.755629 CGACTCTGATTTCGGGAGTATCTA 59.244 45.833 0.00 0.00 39.95 1.98
127 128 3.566322 CGACTCTGATTTCGGGAGTATCT 59.434 47.826 0.00 0.00 39.95 1.98
128 129 3.315749 ACGACTCTGATTTCGGGAGTATC 59.684 47.826 11.93 0.00 39.95 2.24
129 130 3.288964 ACGACTCTGATTTCGGGAGTAT 58.711 45.455 11.93 0.00 39.95 2.12
130 131 2.719739 ACGACTCTGATTTCGGGAGTA 58.280 47.619 11.93 0.00 39.95 2.59
131 132 1.546961 ACGACTCTGATTTCGGGAGT 58.453 50.000 11.93 0.00 42.15 3.85
132 133 3.633235 CATACGACTCTGATTTCGGGAG 58.367 50.000 11.93 0.00 39.63 4.30
133 134 2.223735 GCATACGACTCTGATTTCGGGA 60.224 50.000 11.93 2.42 39.63 5.14
134 135 2.128035 GCATACGACTCTGATTTCGGG 58.872 52.381 11.93 4.38 39.63 5.14
135 136 3.085443 AGCATACGACTCTGATTTCGG 57.915 47.619 11.93 0.00 39.63 4.30
136 137 5.096954 TCTAGCATACGACTCTGATTTCG 57.903 43.478 7.14 7.14 41.14 3.46
137 138 6.920758 ACATTCTAGCATACGACTCTGATTTC 59.079 38.462 0.00 0.00 0.00 2.17
138 139 6.699204 CACATTCTAGCATACGACTCTGATTT 59.301 38.462 0.00 0.00 0.00 2.17
139 140 6.212235 CACATTCTAGCATACGACTCTGATT 58.788 40.000 0.00 0.00 0.00 2.57
140 141 5.278709 CCACATTCTAGCATACGACTCTGAT 60.279 44.000 0.00 0.00 0.00 2.90
141 142 4.036852 CCACATTCTAGCATACGACTCTGA 59.963 45.833 0.00 0.00 0.00 3.27
142 143 4.036852 TCCACATTCTAGCATACGACTCTG 59.963 45.833 0.00 0.00 0.00 3.35
143 144 4.207955 TCCACATTCTAGCATACGACTCT 58.792 43.478 0.00 0.00 0.00 3.24
144 145 4.569761 TCCACATTCTAGCATACGACTC 57.430 45.455 0.00 0.00 0.00 3.36
145 146 4.830046 AGATCCACATTCTAGCATACGACT 59.170 41.667 0.00 0.00 0.00 4.18
146 147 4.920340 CAGATCCACATTCTAGCATACGAC 59.080 45.833 0.00 0.00 0.00 4.34
147 148 4.584743 ACAGATCCACATTCTAGCATACGA 59.415 41.667 0.00 0.00 0.00 3.43
148 149 4.683320 CACAGATCCACATTCTAGCATACG 59.317 45.833 0.00 0.00 0.00 3.06
149 150 4.450419 GCACAGATCCACATTCTAGCATAC 59.550 45.833 0.00 0.00 0.00 2.39
150 151 4.101430 TGCACAGATCCACATTCTAGCATA 59.899 41.667 0.00 0.00 32.10 3.14
151 152 3.118149 TGCACAGATCCACATTCTAGCAT 60.118 43.478 0.00 0.00 32.10 3.79
152 153 2.236893 TGCACAGATCCACATTCTAGCA 59.763 45.455 0.00 0.00 33.61 3.49
153 154 2.611292 GTGCACAGATCCACATTCTAGC 59.389 50.000 13.17 0.00 32.37 3.42
154 155 2.862536 CGTGCACAGATCCACATTCTAG 59.137 50.000 18.64 0.00 32.37 2.43
155 156 2.233676 ACGTGCACAGATCCACATTCTA 59.766 45.455 18.64 0.00 32.37 2.10
156 157 1.002430 ACGTGCACAGATCCACATTCT 59.998 47.619 18.64 0.00 32.37 2.40
157 158 1.129251 CACGTGCACAGATCCACATTC 59.871 52.381 18.64 0.00 32.37 2.67
158 159 1.159285 CACGTGCACAGATCCACATT 58.841 50.000 18.64 0.00 32.37 2.71
159 160 0.674581 CCACGTGCACAGATCCACAT 60.675 55.000 18.64 0.00 32.37 3.21
160 161 1.301637 CCACGTGCACAGATCCACA 60.302 57.895 18.64 0.00 32.37 4.17
161 162 2.680913 GCCACGTGCACAGATCCAC 61.681 63.158 18.64 0.00 40.77 4.02
162 163 2.358615 GCCACGTGCACAGATCCA 60.359 61.111 18.64 0.00 40.77 3.41
163 164 2.046892 AGCCACGTGCACAGATCC 60.047 61.111 18.64 0.42 44.83 3.36
164 165 3.031964 GCAGCCACGTGCACAGATC 62.032 63.158 18.64 2.81 43.41 2.75
165 166 3.052082 GCAGCCACGTGCACAGAT 61.052 61.111 18.64 0.00 43.41 2.90
171 172 4.341827 AAAAATGCAGCCACGTGC 57.658 50.000 10.91 5.91 44.27 5.34
185 186 9.451002 TTTACATGGAATATACGGACAGAAAAA 57.549 29.630 0.00 0.00 0.00 1.94
186 187 9.104965 CTTTACATGGAATATACGGACAGAAAA 57.895 33.333 0.00 0.00 0.00 2.29
187 188 8.262227 ACTTTACATGGAATATACGGACAGAAA 58.738 33.333 0.00 0.00 0.00 2.52
188 189 7.788026 ACTTTACATGGAATATACGGACAGAA 58.212 34.615 0.00 0.00 0.00 3.02
189 190 7.356089 ACTTTACATGGAATATACGGACAGA 57.644 36.000 0.00 0.00 0.00 3.41
190 191 9.706691 ATTACTTTACATGGAATATACGGACAG 57.293 33.333 0.00 0.00 0.00 3.51
202 203 9.575868 TCACCTGTTTTTATTACTTTACATGGA 57.424 29.630 0.00 0.00 0.00 3.41
203 204 9.620660 GTCACCTGTTTTTATTACTTTACATGG 57.379 33.333 0.00 0.00 0.00 3.66
204 205 9.620660 GGTCACCTGTTTTTATTACTTTACATG 57.379 33.333 0.00 0.00 0.00 3.21
205 206 9.582648 AGGTCACCTGTTTTTATTACTTTACAT 57.417 29.630 0.00 0.00 29.57 2.29
206 207 8.983702 AGGTCACCTGTTTTTATTACTTTACA 57.016 30.769 0.00 0.00 29.57 2.41
207 208 9.281371 AGAGGTCACCTGTTTTTATTACTTTAC 57.719 33.333 0.00 0.00 31.76 2.01
208 209 9.498176 GAGAGGTCACCTGTTTTTATTACTTTA 57.502 33.333 0.00 0.00 31.76 1.85
209 210 7.996644 TGAGAGGTCACCTGTTTTTATTACTTT 59.003 33.333 0.00 0.00 31.76 2.66
210 211 7.514721 TGAGAGGTCACCTGTTTTTATTACTT 58.485 34.615 0.00 0.00 31.76 2.24
211 212 7.074653 TGAGAGGTCACCTGTTTTTATTACT 57.925 36.000 0.00 0.00 31.76 2.24
212 213 6.935208 ACTGAGAGGTCACCTGTTTTTATTAC 59.065 38.462 0.00 0.00 31.76 1.89
213 214 7.074653 ACTGAGAGGTCACCTGTTTTTATTA 57.925 36.000 0.00 0.00 31.76 0.98
214 215 5.941788 ACTGAGAGGTCACCTGTTTTTATT 58.058 37.500 0.00 0.00 31.76 1.40
215 216 5.552178 GACTGAGAGGTCACCTGTTTTTAT 58.448 41.667 0.00 0.00 36.35 1.40
216 217 4.500887 CGACTGAGAGGTCACCTGTTTTTA 60.501 45.833 0.00 0.00 36.12 1.52
217 218 3.741388 CGACTGAGAGGTCACCTGTTTTT 60.741 47.826 0.00 0.00 36.12 1.94
218 219 2.224066 CGACTGAGAGGTCACCTGTTTT 60.224 50.000 0.00 0.00 36.12 2.43
219 220 1.341531 CGACTGAGAGGTCACCTGTTT 59.658 52.381 0.00 0.00 36.12 2.83
220 221 0.962489 CGACTGAGAGGTCACCTGTT 59.038 55.000 0.00 0.00 36.12 3.16
221 222 0.110678 TCGACTGAGAGGTCACCTGT 59.889 55.000 0.00 0.00 36.12 4.00
222 223 0.523966 GTCGACTGAGAGGTCACCTG 59.476 60.000 0.00 0.00 36.12 4.00
223 224 0.609681 GGTCGACTGAGAGGTCACCT 60.610 60.000 16.46 0.00 36.00 4.00
224 225 1.884444 GGTCGACTGAGAGGTCACC 59.116 63.158 16.46 0.00 36.12 4.02
225 226 0.954449 TCGGTCGACTGAGAGGTCAC 60.954 60.000 23.11 0.00 36.12 3.67
226 227 1.373812 TCGGTCGACTGAGAGGTCA 59.626 57.895 23.11 0.00 36.12 4.02
227 228 4.298009 TCGGTCGACTGAGAGGTC 57.702 61.111 23.11 0.00 0.00 3.85
366 367 2.758979 TCAGCCGACTAAGACTTAAGGG 59.241 50.000 7.53 7.12 0.00 3.95
368 369 4.966965 TCTCAGCCGACTAAGACTTAAG 57.033 45.455 0.00 0.00 0.00 1.85
405 407 7.387122 GCCTATACAGGTGCTAAGGTAAATAAC 59.613 40.741 0.00 0.00 44.68 1.89
1146 3998 7.359595 GTGTGAGTTAGAATTAATGTGTGCAA 58.640 34.615 0.00 0.00 0.00 4.08
1171 4023 2.815211 CGACCATCCACACCTGCG 60.815 66.667 0.00 0.00 0.00 5.18
1327 4179 4.142773 TGAAAGAAGTTGTCGTTGTTGTCC 60.143 41.667 0.00 0.00 0.00 4.02
1334 4186 4.152759 TCGTTTGTGAAAGAAGTTGTCGTT 59.847 37.500 0.00 0.00 0.00 3.85
1493 4375 4.758251 CGGCTCCGGCACATCACA 62.758 66.667 0.00 0.00 40.87 3.58
2233 9705 5.888724 TCACAAGGTAGTTTGGTGATCAAAA 59.111 36.000 0.00 0.00 45.74 2.44


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.