Multiple sequence alignment - TraesCS2D01G103000

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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 TraesCS2D01G103000 chr2D 100.000 2720 0 0 1 2720 55601096 55603815 0.000000e+00 5024.0
1 TraesCS2D01G103000 chr2D 93.047 1539 86 10 188 1707 55412351 55413887 0.000000e+00 2230.0
2 TraesCS2D01G103000 chr2D 93.156 1315 66 9 456 1749 55405000 55406311 0.000000e+00 1908.0
3 TraesCS2D01G103000 chr2D 96.729 1009 31 2 765 1772 55435562 55436569 0.000000e+00 1679.0
4 TraesCS2D01G103000 chr2D 89.517 1345 110 13 456 1771 39438417 39437075 0.000000e+00 1674.0
5 TraesCS2D01G103000 chr2D 93.964 878 49 2 1840 2715 55436914 55437789 0.000000e+00 1325.0
6 TraesCS2D01G103000 chr2D 90.662 921 76 8 1797 2715 55406493 55407405 0.000000e+00 1216.0
7 TraesCS2D01G103000 chr2D 96.571 175 2 2 1 174 351412324 351412495 1.230000e-73 287.0
8 TraesCS2D01G103000 chr2D 89.950 199 18 2 277 473 55404781 55404979 3.480000e-64 255.0
9 TraesCS2D01G103000 chr2B 90.504 853 58 9 456 1297 88187664 88188504 0.000000e+00 1105.0
10 TraesCS2D01G103000 chr2B 89.787 235 24 0 1445 1679 88241317 88241551 4.400000e-78 302.0
11 TraesCS2D01G103000 chr2B 87.958 191 21 2 284 473 88187454 88187643 9.800000e-55 224.0
12 TraesCS2D01G103000 chr2B 90.741 108 9 1 1655 1762 88231610 88231716 2.820000e-30 143.0
13 TraesCS2D01G103000 chr2B 89.815 108 10 1 1655 1762 88241558 88241664 1.310000e-28 137.0
14 TraesCS2D01G103000 chr2B 78.626 131 26 2 2055 2184 135694639 135694768 4.830000e-13 86.1
15 TraesCS2D01G103000 chr2A 85.217 575 42 15 732 1306 56945205 56945736 3.960000e-153 551.0
16 TraesCS2D01G103000 chr2A 87.778 360 44 0 1304 1663 56990606 56990965 3.240000e-114 422.0
17 TraesCS2D01G103000 chr3D 98.795 166 2 0 1 166 178507871 178507706 2.050000e-76 296.0
18 TraesCS2D01G103000 chr3D 78.646 192 37 3 2324 2512 452407045 452406855 1.020000e-24 124.0
19 TraesCS2D01G103000 chr3D 80.769 156 29 1 2515 2669 8834958 8834803 1.320000e-23 121.0
20 TraesCS2D01G103000 chr3D 79.070 129 27 0 2057 2185 611536132 611536004 3.730000e-14 89.8
21 TraesCS2D01G103000 chr3D 83.721 86 6 5 1765 1843 390025 389941 1.040000e-09 75.0
22 TraesCS2D01G103000 chr4D 98.214 168 1 2 2 168 379587491 379587325 2.650000e-75 292.0
23 TraesCS2D01G103000 chr4D 95.604 182 5 3 1 180 456702259 456702079 3.430000e-74 289.0
24 TraesCS2D01G103000 chr4D 74.444 360 72 15 2324 2667 12032750 12033105 1.310000e-28 137.0
25 TraesCS2D01G103000 chr7D 98.780 164 1 1 1 164 197946361 197946523 9.530000e-75 291.0
26 TraesCS2D01G103000 chr7D 93.194 191 8 4 1 189 64419306 64419119 2.670000e-70 276.0
27 TraesCS2D01G103000 chr7D 84.483 58 8 1 2230 2286 453126840 453126783 3.780000e-04 56.5
28 TraesCS2D01G103000 chr5A 96.089 179 5 2 1 179 474245691 474245867 9.530000e-75 291.0
29 TraesCS2D01G103000 chr5A 96.067 178 5 2 2 179 473976870 473977045 3.430000e-74 289.0
30 TraesCS2D01G103000 chr5A 95.531 179 6 2 1 179 474120501 474120677 4.430000e-73 285.0
31 TraesCS2D01G103000 chr5A 79.121 91 17 2 2207 2295 338452299 338452389 8.130000e-06 62.1
32 TraesCS2D01G103000 chr5D 81.792 346 56 6 2322 2662 251938840 251938497 1.590000e-72 283.0
33 TraesCS2D01G103000 chr1D 75.630 357 60 13 2385 2715 16357448 16357093 4.690000e-33 152.0
34 TraesCS2D01G103000 chr7B 76.357 258 52 7 2057 2308 392641913 392641659 2.200000e-26 130.0
35 TraesCS2D01G103000 chr4B 80.667 150 25 3 2535 2682 659480532 659480385 2.210000e-21 113.0
36 TraesCS2D01G103000 chr6D 79.141 163 31 3 2507 2667 456639087 456639248 2.860000e-20 110.0
37 TraesCS2D01G103000 chr6D 93.443 61 2 2 1770 1828 158449042 158449102 3.730000e-14 89.8
38 TraesCS2D01G103000 chr4A 76.923 182 36 6 2515 2690 737746009 737746190 6.200000e-17 99.0


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 TraesCS2D01G103000 chr2D 55601096 55603815 2719 False 5024.000000 5024 100.0000 1 2720 1 chr2D.!!$F2 2719
1 TraesCS2D01G103000 chr2D 55412351 55413887 1536 False 2230.000000 2230 93.0470 188 1707 1 chr2D.!!$F1 1519
2 TraesCS2D01G103000 chr2D 39437075 39438417 1342 True 1674.000000 1674 89.5170 456 1771 1 chr2D.!!$R1 1315
3 TraesCS2D01G103000 chr2D 55435562 55437789 2227 False 1502.000000 1679 95.3465 765 2715 2 chr2D.!!$F5 1950
4 TraesCS2D01G103000 chr2D 55404781 55407405 2624 False 1126.333333 1908 91.2560 277 2715 3 chr2D.!!$F4 2438
5 TraesCS2D01G103000 chr2B 88187454 88188504 1050 False 664.500000 1105 89.2310 284 1297 2 chr2B.!!$F3 1013
6 TraesCS2D01G103000 chr2A 56945205 56945736 531 False 551.000000 551 85.2170 732 1306 1 chr2A.!!$F1 574

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
294 299 0.179004 TTTGAGCCGAGCTTTTGGGA 60.179 50.0 0.0 0.0 39.88 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 2476 0.179067 TGGCAAAACTCGTTCGGACT 60.179 50.0 0.0 0.0 0.0 3.85 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
21 22 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
22 23 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
23 24 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
24 25 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
25 26 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
26 27 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
27 28 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
28 29 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
29 30 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
30 31 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
31 32 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
32 33 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
33 34 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
34 35 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
35 36 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
36 37 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
37 38 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
38 39 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
39 40 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
40 41 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
41 42 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
42 43 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
43 44 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
44 45 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
45 46 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
46 47 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
47 48 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
48 49 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
49 50 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
50 51 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
51 52 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
52 53 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
53 54 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
54 55 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
55 56 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
56 57 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
57 58 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
58 59 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
59 60 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
60 61 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
61 62 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
62 63 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
63 64 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
64 65 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
65 66 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
66 67 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
67 68 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
68 69 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
69 70 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
77 78 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
78 79 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
81 82 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
82 83 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
83 84 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
92 93 8.902540 ACAATTCTAGCATGGATAATAAACGA 57.097 30.769 0.00 0.00 0.00 3.85
93 94 9.507329 ACAATTCTAGCATGGATAATAAACGAT 57.493 29.630 0.00 0.00 0.00 3.73
157 158 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
158 159 4.792068 CCTCTAGGGCATATTTCCAACAA 58.208 43.478 0.00 0.00 0.00 2.83
159 160 4.823989 CCTCTAGGGCATATTTCCAACAAG 59.176 45.833 0.00 0.00 0.00 3.16
160 161 5.397899 CCTCTAGGGCATATTTCCAACAAGA 60.398 44.000 0.00 0.00 0.00 3.02
161 162 5.437060 TCTAGGGCATATTTCCAACAAGAC 58.563 41.667 0.00 0.00 0.00 3.01
162 163 4.322057 AGGGCATATTTCCAACAAGACT 57.678 40.909 0.00 0.00 0.00 3.24
163 164 4.677182 AGGGCATATTTCCAACAAGACTT 58.323 39.130 0.00 0.00 0.00 3.01
164 165 4.463891 AGGGCATATTTCCAACAAGACTTG 59.536 41.667 13.77 13.77 0.00 3.16
165 166 4.176271 GGCATATTTCCAACAAGACTTGC 58.824 43.478 15.24 0.00 0.00 4.01
166 167 4.176271 GCATATTTCCAACAAGACTTGCC 58.824 43.478 15.24 0.00 0.00 4.52
167 168 4.082026 GCATATTTCCAACAAGACTTGCCT 60.082 41.667 15.24 0.00 0.00 4.75
168 169 5.567423 GCATATTTCCAACAAGACTTGCCTT 60.567 40.000 15.24 0.12 0.00 4.35
169 170 6.458210 CATATTTCCAACAAGACTTGCCTTT 58.542 36.000 15.24 0.00 0.00 3.11
170 171 4.385358 TTTCCAACAAGACTTGCCTTTC 57.615 40.909 15.24 0.00 0.00 2.62
171 172 3.011566 TCCAACAAGACTTGCCTTTCA 57.988 42.857 15.24 0.00 0.00 2.69
172 173 2.951642 TCCAACAAGACTTGCCTTTCAG 59.048 45.455 15.24 0.00 0.00 3.02
173 174 2.951642 CCAACAAGACTTGCCTTTCAGA 59.048 45.455 15.24 0.00 0.00 3.27
174 175 3.571401 CCAACAAGACTTGCCTTTCAGAT 59.429 43.478 15.24 0.00 0.00 2.90
175 176 4.761739 CCAACAAGACTTGCCTTTCAGATA 59.238 41.667 15.24 0.00 0.00 1.98
176 177 5.416952 CCAACAAGACTTGCCTTTCAGATAT 59.583 40.000 15.24 0.00 0.00 1.63
177 178 6.320171 CAACAAGACTTGCCTTTCAGATATG 58.680 40.000 15.24 0.00 0.00 1.78
178 179 5.564550 ACAAGACTTGCCTTTCAGATATGT 58.435 37.500 15.24 0.00 0.00 2.29
179 180 5.645497 ACAAGACTTGCCTTTCAGATATGTC 59.355 40.000 15.24 0.00 0.00 3.06
180 181 5.690464 AGACTTGCCTTTCAGATATGTCT 57.310 39.130 0.00 0.00 34.14 3.41
181 182 6.059787 AGACTTGCCTTTCAGATATGTCTT 57.940 37.500 0.00 0.00 30.42 3.01
182 183 5.879223 AGACTTGCCTTTCAGATATGTCTTG 59.121 40.000 0.00 0.00 30.42 3.02
183 184 5.809001 ACTTGCCTTTCAGATATGTCTTGA 58.191 37.500 0.00 0.00 30.42 3.02
184 185 5.879223 ACTTGCCTTTCAGATATGTCTTGAG 59.121 40.000 0.00 0.00 30.42 3.02
185 186 4.194640 TGCCTTTCAGATATGTCTTGAGC 58.805 43.478 0.00 0.00 30.42 4.26
186 187 4.080695 TGCCTTTCAGATATGTCTTGAGCT 60.081 41.667 0.00 0.00 30.42 4.09
242 247 3.627577 GCTCGGGCTTTCATTTTCTATCA 59.372 43.478 0.00 0.00 35.22 2.15
251 256 6.474140 TTTCATTTTCTATCAGGCATGCAT 57.526 33.333 21.36 10.32 0.00 3.96
294 299 0.179004 TTTGAGCCGAGCTTTTGGGA 60.179 50.000 0.00 0.00 39.88 4.37
303 308 2.098117 CGAGCTTTTGGGATTTAGGCTG 59.902 50.000 0.00 0.00 0.00 4.85
430 437 5.159209 ACGAGTCGAAAACGAGAATAACAT 58.841 37.500 21.50 0.00 0.00 2.71
533 593 3.323403 GGGTTAGGTGAGATCCTCAGATG 59.677 52.174 0.00 0.00 41.46 2.90
600 681 6.207417 CGAATAAATGCACCAATAGATTCCCT 59.793 38.462 0.00 0.00 0.00 4.20
608 689 4.402474 CACCAATAGATTCCCTTCCCAAAC 59.598 45.833 0.00 0.00 0.00 2.93
628 712 9.550406 CCCAAACGGTTTGAGATAGTATTTATA 57.450 33.333 29.82 0.00 43.26 0.98
781 870 7.540400 CGCAGATTCGTAAAGATATCTGATTCT 59.460 37.037 5.86 7.52 41.56 2.40
797 886 7.270757 TCTGATTCTCTACAAGTATGCTCTC 57.729 40.000 0.00 0.00 0.00 3.20
875 965 8.515473 TTGTTTTCTGTATCGGATATACATCG 57.485 34.615 0.29 0.00 34.42 3.84
910 1000 7.339732 ACGCGTAGATTTTTGATATCTCATC 57.660 36.000 11.67 0.89 34.35 2.92
990 1081 4.137543 CTGCTTTCTTGGTTCTTGGTACT 58.862 43.478 0.00 0.00 0.00 2.73
1015 1106 7.555306 AGAGAAATTCTATAAAAGCCGTTCC 57.445 36.000 0.00 0.00 33.23 3.62
1147 1238 0.179020 CACCACCTTGCTCTTCACCA 60.179 55.000 0.00 0.00 0.00 4.17
1189 1280 2.613026 TCCGTTAATGACCATCGCAT 57.387 45.000 0.00 0.00 0.00 4.73
1306 1397 3.473625 GCCAATATTGCTACGGGTACTT 58.526 45.455 10.11 0.00 0.00 2.24
1317 1408 5.361571 TGCTACGGGTACTTCTCAATATTCA 59.638 40.000 0.00 0.00 0.00 2.57
1601 1692 1.414181 CCGGGATCTGAGCACACTTAT 59.586 52.381 0.00 0.00 0.00 1.73
1829 2053 9.213777 TCCACCTGAATATATTACTCAAAGTCT 57.786 33.333 0.00 0.00 0.00 3.24
1833 2057 7.933577 CCTGAATATATTACTCAAAGTCTGCCA 59.066 37.037 0.00 0.00 0.00 4.92
2099 2467 1.234615 AAACCGTCTGCAACCATCCG 61.235 55.000 0.00 0.00 0.00 4.18
2108 2476 3.632080 AACCATCCGGACCGCACA 61.632 61.111 6.12 0.00 35.59 4.57
2118 2486 3.547249 GACCGCACAGTCCGAACGA 62.547 63.158 0.00 0.00 0.00 3.85
2197 2565 0.574922 CCGCAAACCGAAAGCAAAAC 59.425 50.000 0.00 0.00 40.02 2.43
2199 2567 1.656095 CGCAAACCGAAAGCAAAACAA 59.344 42.857 0.00 0.00 40.02 2.83
2205 2573 3.020984 ACCGAAAGCAAAACAAGGAGAA 58.979 40.909 0.00 0.00 0.00 2.87
2213 2581 0.405973 AAACAAGGAGAAGGGGGCTC 59.594 55.000 0.00 0.00 0.00 4.70
2241 2609 2.440796 CGGACCATTGCCATGCCT 60.441 61.111 0.00 0.00 0.00 4.75
2242 2610 1.152984 CGGACCATTGCCATGCCTA 60.153 57.895 0.00 0.00 0.00 3.93
2253 2621 2.168521 TGCCATGCCTACTTCTGACTAC 59.831 50.000 0.00 0.00 0.00 2.73
2277 2645 1.974543 CCCACCCAAACCATTCTGC 59.025 57.895 0.00 0.00 0.00 4.26
2278 2646 0.831288 CCCACCCAAACCATTCTGCA 60.831 55.000 0.00 0.00 0.00 4.41
2295 2663 3.717294 ATCGCCCGCACCCTTTCT 61.717 61.111 0.00 0.00 0.00 2.52
2339 2707 2.280524 TGCCGGACTTGAACGTGG 60.281 61.111 5.05 0.00 0.00 4.94
2349 2717 1.466025 TTGAACGTGGCCGAGTAGGT 61.466 55.000 0.00 0.00 43.70 3.08
2354 2722 2.203728 TGGCCGAGTAGGTGGTGT 60.204 61.111 0.00 0.00 43.70 4.16
2371 2739 1.218316 GTGGCTGGACTCTTACCGG 59.782 63.158 0.00 0.00 36.91 5.28
2383 2751 1.171308 CTTACCGGTCCTCTCGTGAA 58.829 55.000 12.40 0.00 0.00 3.18
2410 2778 4.065281 GACCGCTGGCAGTACCGT 62.065 66.667 17.16 6.97 43.94 4.83
2433 2803 1.592400 CGTCAGACGGACTTAGGCCA 61.592 60.000 15.64 0.00 44.68 5.36
2526 2896 2.548295 GCCAAAACCACGAAGCCGA 61.548 57.895 0.00 0.00 39.50 5.54
2567 2937 1.040339 CAGCGAGGAAGGGTAGAGCT 61.040 60.000 0.00 0.00 0.00 4.09
2619 2989 3.181967 CACCGCTCTTTCGCTCCG 61.182 66.667 0.00 0.00 0.00 4.63
2649 3019 0.112995 AGCTTGGCAGGGTCAAATCA 59.887 50.000 0.00 0.00 0.00 2.57
2700 3070 2.391389 CGAAGCTTCAGTTCCCGGC 61.391 63.158 25.47 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
1 2 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
2 3 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
3 4 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
4 5 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
5 6 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
6 7 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
7 8 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
8 9 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
9 10 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
15 16 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
16 17 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
17 18 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
18 19 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
34 35 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
35 36 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
36 37 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
37 38 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
38 39 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
39 40 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
40 41 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
41 42 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
42 43 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
43 44 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
51 52 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
52 53 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
55 56 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
56 57 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
57 58 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
66 67 9.990360 TCGTTTATTATCCATGCTAGAATTGTA 57.010 29.630 0.00 0.00 0.00 2.41
67 68 8.902540 TCGTTTATTATCCATGCTAGAATTGT 57.097 30.769 0.00 0.00 0.00 2.71
136 137 4.437682 TGTTGGAAATATGCCCTAGAGG 57.562 45.455 0.00 0.00 39.47 3.69
137 138 5.529060 GTCTTGTTGGAAATATGCCCTAGAG 59.471 44.000 0.00 0.00 0.00 2.43
138 139 5.191722 AGTCTTGTTGGAAATATGCCCTAGA 59.808 40.000 0.00 0.00 0.00 2.43
139 140 5.440610 AGTCTTGTTGGAAATATGCCCTAG 58.559 41.667 0.00 0.00 0.00 3.02
140 141 5.450818 AGTCTTGTTGGAAATATGCCCTA 57.549 39.130 0.00 0.00 0.00 3.53
141 142 4.322057 AGTCTTGTTGGAAATATGCCCT 57.678 40.909 0.00 0.00 0.00 5.19
142 143 4.747810 CAAGTCTTGTTGGAAATATGCCC 58.252 43.478 4.27 0.00 0.00 5.36
143 144 4.176271 GCAAGTCTTGTTGGAAATATGCC 58.824 43.478 14.03 0.00 0.00 4.40
144 145 4.082026 AGGCAAGTCTTGTTGGAAATATGC 60.082 41.667 14.03 0.00 0.00 3.14
145 146 5.649782 AGGCAAGTCTTGTTGGAAATATG 57.350 39.130 14.03 0.00 0.00 1.78
146 147 6.267471 TGAAAGGCAAGTCTTGTTGGAAATAT 59.733 34.615 14.03 0.00 0.00 1.28
147 148 5.596361 TGAAAGGCAAGTCTTGTTGGAAATA 59.404 36.000 14.03 0.00 0.00 1.40
148 149 4.405358 TGAAAGGCAAGTCTTGTTGGAAAT 59.595 37.500 14.03 0.00 0.00 2.17
149 150 3.766591 TGAAAGGCAAGTCTTGTTGGAAA 59.233 39.130 14.03 0.00 0.00 3.13
150 151 3.360867 TGAAAGGCAAGTCTTGTTGGAA 58.639 40.909 14.03 0.00 0.00 3.53
151 152 2.951642 CTGAAAGGCAAGTCTTGTTGGA 59.048 45.455 14.03 0.00 0.00 3.53
152 153 2.951642 TCTGAAAGGCAAGTCTTGTTGG 59.048 45.455 14.03 0.00 0.00 3.77
153 154 4.843220 ATCTGAAAGGCAAGTCTTGTTG 57.157 40.909 14.03 0.00 0.00 3.33
154 155 6.006449 ACATATCTGAAAGGCAAGTCTTGTT 58.994 36.000 14.03 0.72 0.00 2.83
155 156 5.564550 ACATATCTGAAAGGCAAGTCTTGT 58.435 37.500 14.03 0.00 0.00 3.16
156 157 5.879223 AGACATATCTGAAAGGCAAGTCTTG 59.121 40.000 8.31 8.31 32.53 3.02
157 158 6.059787 AGACATATCTGAAAGGCAAGTCTT 57.940 37.500 0.00 0.00 32.53 3.01
158 159 5.690464 AGACATATCTGAAAGGCAAGTCT 57.310 39.130 0.00 0.00 32.29 3.24
159 160 5.877012 TCAAGACATATCTGAAAGGCAAGTC 59.123 40.000 0.00 0.00 34.48 3.01
160 161 5.809001 TCAAGACATATCTGAAAGGCAAGT 58.191 37.500 0.00 0.00 34.48 3.16
161 162 5.220815 GCTCAAGACATATCTGAAAGGCAAG 60.221 44.000 0.00 0.00 34.48 4.01
162 163 4.637534 GCTCAAGACATATCTGAAAGGCAA 59.362 41.667 0.00 0.00 34.48 4.52
163 164 4.080695 AGCTCAAGACATATCTGAAAGGCA 60.081 41.667 0.00 0.00 34.48 4.75
164 165 4.450053 AGCTCAAGACATATCTGAAAGGC 58.550 43.478 0.00 0.00 34.48 4.35
165 166 6.111382 TGAAGCTCAAGACATATCTGAAAGG 58.889 40.000 0.00 0.00 34.48 3.11
166 167 7.789273 ATGAAGCTCAAGACATATCTGAAAG 57.211 36.000 0.00 0.00 34.48 2.62
167 168 8.571461 AAATGAAGCTCAAGACATATCTGAAA 57.429 30.769 0.00 0.00 34.48 2.69
168 169 8.456471 CAAAATGAAGCTCAAGACATATCTGAA 58.544 33.333 0.00 0.00 34.48 3.02
169 170 7.609146 ACAAAATGAAGCTCAAGACATATCTGA 59.391 33.333 0.00 0.00 34.48 3.27
170 171 7.759465 ACAAAATGAAGCTCAAGACATATCTG 58.241 34.615 0.00 0.00 34.48 2.90
171 172 7.934855 ACAAAATGAAGCTCAAGACATATCT 57.065 32.000 0.00 0.00 36.42 1.98
172 173 9.102757 TCTACAAAATGAAGCTCAAGACATATC 57.897 33.333 0.00 0.00 0.00 1.63
173 174 8.887717 GTCTACAAAATGAAGCTCAAGACATAT 58.112 33.333 0.00 0.00 32.91 1.78
174 175 7.334421 GGTCTACAAAATGAAGCTCAAGACATA 59.666 37.037 0.00 0.00 34.03 2.29
175 176 6.150140 GGTCTACAAAATGAAGCTCAAGACAT 59.850 38.462 0.00 0.00 34.03 3.06
176 177 5.470098 GGTCTACAAAATGAAGCTCAAGACA 59.530 40.000 0.00 0.00 34.03 3.41
177 178 5.389935 CGGTCTACAAAATGAAGCTCAAGAC 60.390 44.000 0.00 0.00 0.00 3.01
178 179 4.690748 CGGTCTACAAAATGAAGCTCAAGA 59.309 41.667 0.00 0.00 0.00 3.02
179 180 4.690748 TCGGTCTACAAAATGAAGCTCAAG 59.309 41.667 0.00 0.00 0.00 3.02
180 181 4.637276 TCGGTCTACAAAATGAAGCTCAA 58.363 39.130 0.00 0.00 0.00 3.02
181 182 4.265904 TCGGTCTACAAAATGAAGCTCA 57.734 40.909 0.00 0.00 0.00 4.26
182 183 5.390991 CCTTTCGGTCTACAAAATGAAGCTC 60.391 44.000 0.00 0.00 0.00 4.09
183 184 4.455877 CCTTTCGGTCTACAAAATGAAGCT 59.544 41.667 0.00 0.00 0.00 3.74
184 185 4.379499 CCCTTTCGGTCTACAAAATGAAGC 60.379 45.833 0.00 0.00 0.00 3.86
185 186 4.760204 ACCCTTTCGGTCTACAAAATGAAG 59.240 41.667 0.00 0.00 43.58 3.02
186 187 4.721132 ACCCTTTCGGTCTACAAAATGAA 58.279 39.130 0.00 0.00 43.58 2.57
251 256 1.155889 ATCTTTCAATGCGCACACGA 58.844 45.000 14.90 6.70 43.93 4.35
258 263 4.790140 GCTCAAACACTATCTTTCAATGCG 59.210 41.667 0.00 0.00 0.00 4.73
294 299 2.624293 GCCCCTTTTCTCCAGCCTAAAT 60.624 50.000 0.00 0.00 0.00 1.40
303 308 1.204704 CCGAAAATGCCCCTTTTCTCC 59.795 52.381 11.89 0.00 41.07 3.71
447 454 2.692041 CCCCTACCTAGTTTTCGATCGT 59.308 50.000 15.94 0.00 0.00 3.73
576 657 7.530426 AGGGAATCTATTGGTGCATTTATTC 57.470 36.000 0.00 0.00 0.00 1.75
588 669 3.632145 CCGTTTGGGAAGGGAATCTATTG 59.368 47.826 0.00 0.00 42.16 1.90
684 773 8.567285 TTATCTCCTCCTCAAAAGAAACATTC 57.433 34.615 0.00 0.00 0.00 2.67
688 777 7.987750 AACTTATCTCCTCCTCAAAAGAAAC 57.012 36.000 0.00 0.00 0.00 2.78
810 899 7.201291 CGAAATCACAACATAAATTGCTCACTG 60.201 37.037 0.00 0.00 32.47 3.66
811 900 6.803320 CGAAATCACAACATAAATTGCTCACT 59.197 34.615 0.00 0.00 32.47 3.41
825 914 6.142817 AGTTTTAGATGCACGAAATCACAAC 58.857 36.000 0.00 0.00 0.00 3.32
875 965 7.849026 TCAAAAATCTACGCGTATCTTTTATGC 59.151 33.333 26.01 0.00 0.00 3.14
950 1040 6.389830 AAGCAGTGTGAATGTGTGATAAAA 57.610 33.333 0.00 0.00 0.00 1.52
959 1050 3.290710 ACCAAGAAAGCAGTGTGAATGT 58.709 40.909 0.00 0.00 0.00 2.71
990 1081 8.483758 AGGAACGGCTTTTATAGAATTTCTCTA 58.516 33.333 1.27 0.00 41.00 2.43
1015 1106 1.271325 TGTGGCCATGTAGAACACCAG 60.271 52.381 9.72 0.00 0.00 4.00
1189 1280 4.720902 CACCTGGTGGCATGCGGA 62.721 66.667 19.23 0.00 36.63 5.54
1218 1309 2.743928 CAGAGCTCCAACACGGGC 60.744 66.667 10.93 0.00 34.36 6.13
1222 1313 1.527034 TTCATGCAGAGCTCCAACAC 58.473 50.000 10.93 0.00 0.00 3.32
1306 1397 7.174413 TGGGTTTCTTGACATGAATATTGAGA 58.826 34.615 0.00 0.00 0.00 3.27
1317 1408 0.537143 TGCGCTGGGTTTCTTGACAT 60.537 50.000 9.73 0.00 0.00 3.06
1601 1692 2.669569 GGAGTGCCAGCGAGCAAA 60.670 61.111 5.21 0.00 46.19 3.68
1772 1863 4.038642 CCCCCGTTGATTCTCAAAGAAAAA 59.961 41.667 4.68 0.00 38.22 1.94
1773 1864 3.572255 CCCCCGTTGATTCTCAAAGAAAA 59.428 43.478 4.68 0.00 38.22 2.29
1774 1865 3.153919 CCCCCGTTGATTCTCAAAGAAA 58.846 45.455 4.68 0.00 38.22 2.52
1775 1866 2.790433 CCCCCGTTGATTCTCAAAGAA 58.210 47.619 4.68 0.00 38.22 2.52
1776 1867 2.489938 CCCCCGTTGATTCTCAAAGA 57.510 50.000 4.68 0.00 38.22 2.52
1797 1888 8.861086 TGAGTAATATATTCAGGTGGAGAACTC 58.139 37.037 0.00 6.08 0.00 3.01
1798 1889 8.783660 TGAGTAATATATTCAGGTGGAGAACT 57.216 34.615 0.00 0.00 0.00 3.01
1799 1890 9.832445 TTTGAGTAATATATTCAGGTGGAGAAC 57.168 33.333 0.00 0.00 0.00 3.01
1803 2027 9.213777 AGACTTTGAGTAATATATTCAGGTGGA 57.786 33.333 0.00 0.00 0.00 4.02
1833 2057 1.328279 GTAACACCCCTTGCTGCTTT 58.672 50.000 0.00 0.00 0.00 3.51
2023 2391 2.151502 TGGGAGGAACTTTGCAACAA 57.848 45.000 0.00 0.00 41.55 2.83
2108 2476 0.179067 TGGCAAAACTCGTTCGGACT 60.179 50.000 0.00 0.00 0.00 3.85
2114 2482 1.613437 CCTTGGATGGCAAAACTCGTT 59.387 47.619 0.00 0.00 0.00 3.85
2115 2483 1.247567 CCTTGGATGGCAAAACTCGT 58.752 50.000 0.00 0.00 0.00 4.18
2197 2565 1.606531 CAGAGCCCCCTTCTCCTTG 59.393 63.158 0.00 0.00 0.00 3.61
2199 2567 2.690510 GCAGAGCCCCCTTCTCCT 60.691 66.667 0.00 0.00 0.00 3.69
2230 2598 2.240667 AGTCAGAAGTAGGCATGGCAAT 59.759 45.455 22.64 3.93 0.00 3.56
2241 2609 1.621622 GGGCCAGGGTAGTCAGAAGTA 60.622 57.143 4.39 0.00 0.00 2.24
2242 2610 0.910088 GGGCCAGGGTAGTCAGAAGT 60.910 60.000 4.39 0.00 0.00 3.01
2277 2645 3.508840 GAAAGGGTGCGGGCGATG 61.509 66.667 0.00 0.00 0.00 3.84
2278 2646 3.682292 GAGAAAGGGTGCGGGCGAT 62.682 63.158 0.00 0.00 0.00 4.58
2314 2682 3.241530 AAGTCCGGCACTGGAGCA 61.242 61.111 0.00 0.00 39.14 4.26
2315 2683 2.731691 TTCAAGTCCGGCACTGGAGC 62.732 60.000 0.00 0.00 36.33 4.70
2326 2694 2.027625 CTCGGCCACGTTCAAGTCC 61.028 63.158 2.24 0.00 41.85 3.85
2339 2707 2.264794 CCACACCACCTACTCGGC 59.735 66.667 0.00 0.00 35.61 5.54
2349 2717 0.685097 GTAAGAGTCCAGCCACACCA 59.315 55.000 0.00 0.00 0.00 4.17
2354 2722 1.229082 ACCGGTAAGAGTCCAGCCA 60.229 57.895 4.49 0.00 0.00 4.75
2371 2739 0.806492 GGCGGATTTCACGAGAGGAC 60.806 60.000 0.00 0.00 0.00 3.85
2403 2771 1.572085 CGTCTGACGGACACGGTACT 61.572 60.000 21.78 0.00 44.70 2.73
2425 2793 4.640364 GATCTCCTTGAAGATGGCCTAAG 58.360 47.826 3.32 0.00 36.13 2.18
2433 2803 2.621055 CCTCGTCGATCTCCTTGAAGAT 59.379 50.000 0.00 0.00 38.72 2.40
2546 2916 1.304962 TCTACCCTTCCTCGCTGCA 60.305 57.895 0.00 0.00 0.00 4.41
2547 2917 1.439644 CTCTACCCTTCCTCGCTGC 59.560 63.158 0.00 0.00 0.00 5.25
2567 2937 4.467084 GCACCGGCGATCTCCCAA 62.467 66.667 9.30 0.00 0.00 4.12
2684 3054 2.358737 CGCCGGGAACTGAAGCTT 60.359 61.111 2.18 0.00 36.31 3.74
2700 3070 3.063704 TTTGGCAGGCCATGAGCG 61.064 61.111 14.71 0.00 46.64 5.03


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

AutoCloner maintained by Alex Coulton.