Multiple sequence alignment - TraesCS2D01G353700

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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 TraesCS2D01G353700 chr2D 100.000 2688 0 0 1 2688 452407644 452404957 0.000000e+00 4964.0
1 TraesCS2D01G353700 chr2D 91.176 272 15 5 919 1189 545732040 545732303 7.070000e-96 361.0
2 TraesCS2D01G353700 chr2D 87.542 297 28 6 779 1073 294552667 294552378 4.290000e-88 335.0
3 TraesCS2D01G353700 chr2D 91.367 139 5 5 1 135 160389764 160389899 1.640000e-42 183.0
4 TraesCS2D01G353700 chr2D 84.615 143 6 4 639 777 294552832 294552702 7.810000e-26 128.0
5 TraesCS2D01G353700 chr2B 98.721 1407 16 2 1283 2688 532225076 532223671 0.000000e+00 2497.0
6 TraesCS2D01G353700 chr2B 96.530 634 15 3 770 1403 532225648 532225022 0.000000e+00 1042.0
7 TraesCS2D01G353700 chr2B 97.076 171 4 1 607 777 532226861 532226692 1.220000e-73 287.0
8 TraesCS2D01G353700 chr2B 95.808 167 7 0 1 167 532228217 532228051 1.230000e-68 270.0
9 TraesCS2D01G353700 chr2B 85.590 229 16 3 373 601 532228053 532227842 9.680000e-55 224.0
10 TraesCS2D01G353700 chr2B 96.522 115 4 0 1 115 570061355 570061241 9.820000e-45 191.0
11 TraesCS2D01G353700 chr2B 100.000 34 0 0 586 619 504248428 504248461 2.230000e-06 63.9
12 TraesCS2D01G353700 chr2B 78.095 105 14 3 626 729 175748603 175748699 1.040000e-04 58.4
13 TraesCS2D01G353700 chr2B 83.333 72 3 3 659 729 758094953 758095016 1.040000e-04 58.4
14 TraesCS2D01G353700 chr7D 90.050 1608 98 28 1109 2688 366749910 366751483 0.000000e+00 2026.0
15 TraesCS2D01G353700 chr7D 91.176 272 15 5 919 1189 488118261 488117998 7.070000e-96 361.0
16 TraesCS2D01G353700 chr7D 92.015 263 12 5 927 1189 613848687 613848940 7.070000e-96 361.0
17 TraesCS2D01G353700 chr7D 100.000 32 0 0 586 617 562258617 562258648 2.890000e-05 60.2
18 TraesCS2D01G353700 chr3D 89.925 1608 97 27 1109 2688 135170231 135168661 0.000000e+00 2012.0
19 TraesCS2D01G353700 chr3D 88.764 1602 118 26 1109 2688 159121661 159123222 0.000000e+00 1905.0
20 TraesCS2D01G353700 chr3D 88.998 409 31 6 787 1189 53826755 53826355 6.690000e-136 494.0
21 TraesCS2D01G353700 chr3D 95.161 124 6 0 1 124 505094840 505094717 2.110000e-46 196.0
22 TraesCS2D01G353700 chrUn 89.857 1607 99 24 1109 2688 291715584 291714015 0.000000e+00 2006.0
23 TraesCS2D01G353700 chrUn 89.857 1607 99 24 1109 2688 291933121 291931552 0.000000e+00 2006.0
24 TraesCS2D01G353700 chrUn 89.857 1607 99 24 1109 2688 302329480 302327911 0.000000e+00 2006.0
25 TraesCS2D01G353700 chr7A 89.428 1608 104 21 1109 2688 299410960 299409391 0.000000e+00 1967.0
26 TraesCS2D01G353700 chr7A 89.338 272 20 5 919 1189 648678978 648678715 1.540000e-87 333.0
27 TraesCS2D01G353700 chr5D 90.014 1382 89 23 1326 2688 22452337 22453688 0.000000e+00 1742.0
28 TraesCS2D01G353700 chr5D 94.309 123 7 0 1 123 479215716 479215594 3.530000e-44 189.0
29 TraesCS2D01G353700 chr5D 92.913 127 9 0 1 127 313105832 313105706 4.570000e-43 185.0
30 TraesCS2D01G353700 chr5D 85.345 116 17 0 283 398 355207266 355207151 1.310000e-23 121.0
31 TraesCS2D01G353700 chr3B 90.809 1001 83 3 1696 2688 295256845 295257844 0.000000e+00 1330.0
32 TraesCS2D01G353700 chr3B 96.610 59 2 0 727 785 295039965 295040023 6.120000e-17 99.0
33 TraesCS2D01G353700 chr3A 85.888 907 82 19 1113 1976 214466011 214465108 0.000000e+00 924.0
34 TraesCS2D01G353700 chr3A 89.706 272 18 6 919 1189 543675660 543675922 3.310000e-89 339.0
35 TraesCS2D01G353700 chr3A 90.299 134 13 0 1 134 538788721 538788854 2.750000e-40 176.0
36 TraesCS2D01G353700 chr3A 92.453 53 3 1 728 780 214466197 214466146 1.030000e-09 75.0
37 TraesCS2D01G353700 chr3A 97.368 38 1 0 586 623 26932792 26932829 6.210000e-07 65.8
38 TraesCS2D01G353700 chr3A 97.143 35 1 0 583 617 718655863 718655897 2.890000e-05 60.2
39 TraesCS2D01G353700 chr6D 86.099 705 67 14 1253 1942 15515439 15516127 0.000000e+00 730.0
40 TraesCS2D01G353700 chr6B 83.114 835 91 26 1202 2015 27328855 27329660 0.000000e+00 715.0
41 TraesCS2D01G353700 chr6B 79.439 107 13 3 624 729 579222256 579222158 1.730000e-07 67.6
42 TraesCS2D01G353700 chr6A 84.196 734 79 13 1253 1964 16226984 16227702 0.000000e+00 678.0
43 TraesCS2D01G353700 chr6A 87.500 56 7 0 1283 1338 16227065 16227120 6.210000e-07 65.8
44 TraesCS2D01G353700 chr4A 88.421 285 23 6 919 1202 23399018 23398743 4.290000e-88 335.0
45 TraesCS2D01G353700 chr4A 86.220 254 31 2 820 1073 419983138 419982889 3.410000e-69 272.0
46 TraesCS2D01G353700 chr4A 95.652 115 4 1 1 115 581099700 581099813 1.640000e-42 183.0
47 TraesCS2D01G353700 chr4A 77.326 344 44 18 638 959 23399342 23399011 3.560000e-39 172.0
48 TraesCS2D01G353700 chr2A 84.859 284 35 1 345 620 609509084 609508801 2.040000e-71 279.0
49 TraesCS2D01G353700 chr2A 91.603 131 10 1 1 131 378005464 378005335 2.130000e-41 180.0
50 TraesCS2D01G353700 chr2A 87.500 160 8 4 626 785 609505819 609505672 9.890000e-40 174.0
51 TraesCS2D01G353700 chr2A 92.500 40 3 0 577 616 700965503 700965542 1.040000e-04 58.4
52 TraesCS2D01G353700 chr5A 85.657 251 31 3 820 1070 219252117 219252362 2.650000e-65 259.0
53 TraesCS2D01G353700 chr4B 80.263 152 17 5 638 789 238089718 238089580 4.730000e-18 102.0
54 TraesCS2D01G353700 chr4B 96.970 33 1 0 697 729 223381592 223381624 3.740000e-04 56.5
55 TraesCS2D01G353700 chr5B 100.000 38 0 0 748 785 662813202 662813239 1.340000e-08 71.3
56 TraesCS2D01G353700 chr1B 90.909 44 1 3 598 640 550755055 550755096 3.740000e-04 56.5


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 TraesCS2D01G353700 chr2D 452404957 452407644 2687 True 4964.0 4964 100.0000 1 2688 1 chr2D.!!$R1 2687
1 TraesCS2D01G353700 chr2B 532223671 532228217 4546 True 864.0 2497 94.7450 1 2688 5 chr2B.!!$R2 2687
2 TraesCS2D01G353700 chr7D 366749910 366751483 1573 False 2026.0 2026 90.0500 1109 2688 1 chr7D.!!$F1 1579
3 TraesCS2D01G353700 chr3D 135168661 135170231 1570 True 2012.0 2012 89.9250 1109 2688 1 chr3D.!!$R2 1579
4 TraesCS2D01G353700 chr3D 159121661 159123222 1561 False 1905.0 1905 88.7640 1109 2688 1 chr3D.!!$F1 1579
5 TraesCS2D01G353700 chrUn 291714015 291715584 1569 True 2006.0 2006 89.8570 1109 2688 1 chrUn.!!$R1 1579
6 TraesCS2D01G353700 chrUn 291931552 291933121 1569 True 2006.0 2006 89.8570 1109 2688 1 chrUn.!!$R2 1579
7 TraesCS2D01G353700 chrUn 302327911 302329480 1569 True 2006.0 2006 89.8570 1109 2688 1 chrUn.!!$R3 1579
8 TraesCS2D01G353700 chr7A 299409391 299410960 1569 True 1967.0 1967 89.4280 1109 2688 1 chr7A.!!$R1 1579
9 TraesCS2D01G353700 chr5D 22452337 22453688 1351 False 1742.0 1742 90.0140 1326 2688 1 chr5D.!!$F1 1362
10 TraesCS2D01G353700 chr3B 295256845 295257844 999 False 1330.0 1330 90.8090 1696 2688 1 chr3B.!!$F2 992
11 TraesCS2D01G353700 chr3A 214465108 214466197 1089 True 499.5 924 89.1705 728 1976 2 chr3A.!!$R1 1248
12 TraesCS2D01G353700 chr6D 15515439 15516127 688 False 730.0 730 86.0990 1253 1942 1 chr6D.!!$F1 689
13 TraesCS2D01G353700 chr6B 27328855 27329660 805 False 715.0 715 83.1140 1202 2015 1 chr6B.!!$F1 813
14 TraesCS2D01G353700 chr6A 16226984 16227702 718 False 371.9 678 85.8480 1253 1964 2 chr6A.!!$F1 711
15 TraesCS2D01G353700 chr4A 23398743 23399342 599 True 253.5 335 82.8735 638 1202 2 chr4A.!!$R2 564
16 TraesCS2D01G353700 chr2A 609505672 609509084 3412 True 226.5 279 86.1795 345 785 2 chr2A.!!$R2 440

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
235 236 0.108377 TTGATCACGACCACCCGATG 60.108 55.0 0.0 0.0 0.0 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 4761 8.949421 ACAGAAAATATACTGGGATCCTACAAT 58.051 33.333 12.58 2.25 38.3 2.71 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
125 126 7.238723 TGTCCCTAGGGCATATATTTAACATCA 59.761 37.037 24.42 0.00 34.68 3.07
164 165 9.429109 AGGGAAAAAGTTACTGAAAGGAAATTA 57.571 29.630 0.00 0.00 45.69 1.40
178 179 9.679661 TGAAAGGAAATTATAGTATTGACAGCA 57.320 29.630 0.00 0.00 0.00 4.41
180 181 7.736447 AGGAAATTATAGTATTGACAGCAGC 57.264 36.000 0.00 0.00 0.00 5.25
181 182 7.282585 AGGAAATTATAGTATTGACAGCAGCA 58.717 34.615 0.00 0.00 0.00 4.41
182 183 7.941238 AGGAAATTATAGTATTGACAGCAGCAT 59.059 33.333 0.00 0.00 0.00 3.79
183 184 8.019669 GGAAATTATAGTATTGACAGCAGCATG 58.980 37.037 0.00 0.00 40.87 4.06
184 185 8.681486 AAATTATAGTATTGACAGCAGCATGA 57.319 30.769 0.00 0.00 39.69 3.07
185 186 7.902387 ATTATAGTATTGACAGCAGCATGAG 57.098 36.000 0.00 0.00 39.69 2.90
186 187 2.286872 AGTATTGACAGCAGCATGAGC 58.713 47.619 0.00 0.00 39.69 4.26
201 202 3.908382 GCATGAGCTGAAACAGTAAAACG 59.092 43.478 0.00 0.00 37.91 3.60
202 203 3.602390 TGAGCTGAAACAGTAAAACGC 57.398 42.857 0.00 0.00 33.43 4.84
203 204 2.033236 TGAGCTGAAACAGTAAAACGCG 60.033 45.455 3.53 3.53 33.43 6.01
204 205 2.206750 AGCTGAAACAGTAAAACGCGA 58.793 42.857 15.93 0.00 33.43 5.87
205 206 2.221055 AGCTGAAACAGTAAAACGCGAG 59.779 45.455 15.93 0.00 33.43 5.03
206 207 2.220133 GCTGAAACAGTAAAACGCGAGA 59.780 45.455 15.93 0.00 33.43 4.04
207 208 3.661936 GCTGAAACAGTAAAACGCGAGAG 60.662 47.826 15.93 0.00 33.43 3.20
231 232 2.107950 TGATTTGATCACGACCACCC 57.892 50.000 0.00 0.00 33.59 4.61
232 233 1.006832 GATTTGATCACGACCACCCG 58.993 55.000 0.00 0.00 0.00 5.28
233 234 0.611200 ATTTGATCACGACCACCCGA 59.389 50.000 0.00 0.00 0.00 5.14
234 235 0.611200 TTTGATCACGACCACCCGAT 59.389 50.000 0.00 0.00 0.00 4.18
235 236 0.108377 TTGATCACGACCACCCGATG 60.108 55.000 0.00 0.00 0.00 3.84
247 248 3.482156 CACCCGATGGAGATCAGATTT 57.518 47.619 0.00 0.00 34.81 2.17
248 249 3.397482 CACCCGATGGAGATCAGATTTC 58.603 50.000 0.00 0.00 34.81 2.17
249 250 2.370189 ACCCGATGGAGATCAGATTTCC 59.630 50.000 12.36 12.36 34.81 3.13
250 251 2.369860 CCCGATGGAGATCAGATTTCCA 59.630 50.000 22.01 22.01 44.52 3.53
256 257 6.705664 ATGGAGATCAGATTTCCATCAGAT 57.294 37.500 24.10 8.10 46.13 2.90
257 258 5.866207 TGGAGATCAGATTTCCATCAGATG 58.134 41.667 17.12 3.04 36.14 2.90
258 259 5.605488 TGGAGATCAGATTTCCATCAGATGA 59.395 40.000 17.12 0.00 36.14 2.92
259 260 5.933463 GGAGATCAGATTTCCATCAGATGAC 59.067 44.000 14.07 0.00 36.14 3.06
260 261 5.539979 AGATCAGATTTCCATCAGATGACG 58.460 41.667 12.41 0.00 36.14 4.35
261 262 3.461061 TCAGATTTCCATCAGATGACGC 58.539 45.455 12.41 0.00 0.00 5.19
262 263 2.547211 CAGATTTCCATCAGATGACGCC 59.453 50.000 12.41 0.00 0.00 5.68
263 264 2.437281 AGATTTCCATCAGATGACGCCT 59.563 45.455 12.41 0.00 0.00 5.52
264 265 2.315925 TTTCCATCAGATGACGCCTC 57.684 50.000 12.41 0.00 0.00 4.70
265 266 1.489481 TTCCATCAGATGACGCCTCT 58.511 50.000 12.41 0.00 0.00 3.69
266 267 1.489481 TCCATCAGATGACGCCTCTT 58.511 50.000 12.41 0.00 0.00 2.85
267 268 1.137675 TCCATCAGATGACGCCTCTTG 59.862 52.381 12.41 0.00 0.00 3.02
268 269 1.137675 CCATCAGATGACGCCTCTTGA 59.862 52.381 12.41 0.00 0.00 3.02
269 270 2.224233 CCATCAGATGACGCCTCTTGAT 60.224 50.000 12.41 0.00 0.00 2.57
270 271 2.591571 TCAGATGACGCCTCTTGATG 57.408 50.000 0.00 0.00 0.00 3.07
271 272 2.102578 TCAGATGACGCCTCTTGATGA 58.897 47.619 0.00 0.00 0.00 2.92
272 273 2.159184 TCAGATGACGCCTCTTGATGAC 60.159 50.000 0.00 0.00 0.00 3.06
273 274 2.106566 AGATGACGCCTCTTGATGACT 58.893 47.619 0.00 0.00 0.00 3.41
274 275 2.499289 AGATGACGCCTCTTGATGACTT 59.501 45.455 0.00 0.00 0.00 3.01
275 276 2.084610 TGACGCCTCTTGATGACTTG 57.915 50.000 0.00 0.00 0.00 3.16
276 277 1.618343 TGACGCCTCTTGATGACTTGA 59.382 47.619 0.00 0.00 0.00 3.02
277 278 2.266554 GACGCCTCTTGATGACTTGAG 58.733 52.381 0.00 0.00 0.00 3.02
278 279 1.620819 ACGCCTCTTGATGACTTGAGT 59.379 47.619 0.00 0.00 0.00 3.41
279 280 1.998315 CGCCTCTTGATGACTTGAGTG 59.002 52.381 0.00 0.00 0.00 3.51
280 281 2.353109 CGCCTCTTGATGACTTGAGTGA 60.353 50.000 0.00 0.00 0.00 3.41
281 282 2.999355 GCCTCTTGATGACTTGAGTGAC 59.001 50.000 0.00 0.00 0.00 3.67
282 283 3.306641 GCCTCTTGATGACTTGAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
283 284 4.493547 CCTCTTGATGACTTGAGTGACTC 58.506 47.826 5.47 5.47 0.00 3.36
284 285 4.021632 CCTCTTGATGACTTGAGTGACTCA 60.022 45.833 11.93 11.93 38.87 3.41
285 286 5.131594 TCTTGATGACTTGAGTGACTCAG 57.868 43.478 15.60 12.04 41.75 3.35
286 287 3.309961 TGATGACTTGAGTGACTCAGC 57.690 47.619 15.60 9.83 41.75 4.26
287 288 2.257894 GATGACTTGAGTGACTCAGCG 58.742 52.381 15.60 12.94 41.75 5.18
288 289 1.032794 TGACTTGAGTGACTCAGCGT 58.967 50.000 15.60 15.90 41.75 5.07
289 290 2.227194 TGACTTGAGTGACTCAGCGTA 58.773 47.619 15.60 0.00 41.75 4.42
290 291 2.031069 TGACTTGAGTGACTCAGCGTAC 60.031 50.000 15.60 10.85 41.75 3.67
291 292 1.269998 ACTTGAGTGACTCAGCGTACC 59.730 52.381 15.60 0.00 41.75 3.34
292 293 1.542030 CTTGAGTGACTCAGCGTACCT 59.458 52.381 15.60 0.00 41.75 3.08
293 294 1.166129 TGAGTGACTCAGCGTACCTC 58.834 55.000 11.93 0.00 35.39 3.85
294 295 1.271434 TGAGTGACTCAGCGTACCTCT 60.271 52.381 11.93 0.00 35.39 3.69
295 296 1.813786 GAGTGACTCAGCGTACCTCTT 59.186 52.381 7.90 0.00 0.00 2.85
296 297 1.813786 AGTGACTCAGCGTACCTCTTC 59.186 52.381 0.00 0.00 0.00 2.87
297 298 0.803117 TGACTCAGCGTACCTCTTCG 59.197 55.000 0.00 0.00 0.00 3.79
298 299 1.085091 GACTCAGCGTACCTCTTCGA 58.915 55.000 0.00 0.00 0.00 3.71
299 300 1.062880 GACTCAGCGTACCTCTTCGAG 59.937 57.143 0.00 0.00 0.00 4.04
300 301 1.338864 ACTCAGCGTACCTCTTCGAGA 60.339 52.381 0.00 0.00 0.00 4.04
301 302 1.738350 CTCAGCGTACCTCTTCGAGAA 59.262 52.381 0.00 0.00 0.00 2.87
302 303 1.467734 TCAGCGTACCTCTTCGAGAAC 59.532 52.381 0.00 0.00 0.00 3.01
303 304 0.447011 AGCGTACCTCTTCGAGAACG 59.553 55.000 11.68 11.68 39.76 3.95
304 305 2.927437 CGTACCTCTTCGAGAACGC 58.073 57.895 6.03 0.00 39.58 4.84
305 306 0.167470 CGTACCTCTTCGAGAACGCA 59.833 55.000 6.03 0.00 39.58 5.24
306 307 1.202154 CGTACCTCTTCGAGAACGCAT 60.202 52.381 6.03 0.00 39.58 4.73
307 308 2.452105 GTACCTCTTCGAGAACGCATC 58.548 52.381 0.00 0.00 39.58 3.91
308 309 0.173708 ACCTCTTCGAGAACGCATCC 59.826 55.000 0.00 0.00 39.58 3.51
309 310 0.173481 CCTCTTCGAGAACGCATCCA 59.827 55.000 0.00 0.00 39.58 3.41
310 311 1.404181 CCTCTTCGAGAACGCATCCAA 60.404 52.381 0.00 0.00 39.58 3.53
311 312 2.337583 CTCTTCGAGAACGCATCCAAA 58.662 47.619 0.00 0.00 39.58 3.28
312 313 2.066262 TCTTCGAGAACGCATCCAAAC 58.934 47.619 0.00 0.00 39.58 2.93
313 314 1.798223 CTTCGAGAACGCATCCAAACA 59.202 47.619 0.00 0.00 39.58 2.83
314 315 1.428448 TCGAGAACGCATCCAAACAG 58.572 50.000 0.00 0.00 39.58 3.16
315 316 1.148310 CGAGAACGCATCCAAACAGT 58.852 50.000 0.00 0.00 0.00 3.55
316 317 2.029739 TCGAGAACGCATCCAAACAGTA 60.030 45.455 0.00 0.00 39.58 2.74
317 318 2.734606 CGAGAACGCATCCAAACAGTAA 59.265 45.455 0.00 0.00 0.00 2.24
318 319 3.181530 CGAGAACGCATCCAAACAGTAAG 60.182 47.826 0.00 0.00 0.00 2.34
319 320 2.484264 AGAACGCATCCAAACAGTAAGC 59.516 45.455 0.00 0.00 0.00 3.09
320 321 2.185004 ACGCATCCAAACAGTAAGCT 57.815 45.000 0.00 0.00 0.00 3.74
322 323 1.131126 CGCATCCAAACAGTAAGCTGG 59.869 52.381 0.00 0.00 46.62 4.85
323 324 2.436417 GCATCCAAACAGTAAGCTGGA 58.564 47.619 0.00 0.00 46.62 3.86
324 325 2.421424 GCATCCAAACAGTAAGCTGGAG 59.579 50.000 0.00 0.00 46.62 3.86
325 326 3.869912 GCATCCAAACAGTAAGCTGGAGA 60.870 47.826 0.00 0.00 46.62 3.71
326 327 4.521146 CATCCAAACAGTAAGCTGGAGAT 58.479 43.478 0.00 0.00 46.62 2.75
327 328 4.207891 TCCAAACAGTAAGCTGGAGATC 57.792 45.455 0.00 0.00 46.62 2.75
328 329 3.055094 TCCAAACAGTAAGCTGGAGATCC 60.055 47.826 0.00 0.00 46.62 3.36
329 330 3.307691 CCAAACAGTAAGCTGGAGATCCA 60.308 47.826 0.79 0.79 46.62 3.41
330 331 4.326826 CAAACAGTAAGCTGGAGATCCAA 58.673 43.478 2.65 0.00 46.97 3.53
331 332 4.851639 AACAGTAAGCTGGAGATCCAAT 57.148 40.909 2.65 0.00 46.97 3.16
332 333 4.148128 ACAGTAAGCTGGAGATCCAATG 57.852 45.455 2.65 0.00 46.97 2.82
333 334 3.118112 ACAGTAAGCTGGAGATCCAATGG 60.118 47.826 2.65 0.00 46.97 3.16
334 335 2.158696 AGTAAGCTGGAGATCCAATGGC 60.159 50.000 2.65 3.38 46.97 4.40
335 336 0.924823 AAGCTGGAGATCCAATGGCT 59.075 50.000 7.98 7.98 46.97 4.75
336 337 0.924823 AGCTGGAGATCCAATGGCTT 59.075 50.000 7.98 0.00 46.97 4.35
337 338 1.030457 GCTGGAGATCCAATGGCTTG 58.970 55.000 2.65 0.00 46.97 4.01
338 339 1.409241 GCTGGAGATCCAATGGCTTGA 60.409 52.381 2.65 0.00 46.97 3.02
339 340 2.947243 GCTGGAGATCCAATGGCTTGAA 60.947 50.000 2.65 0.00 46.97 2.69
340 341 2.950309 CTGGAGATCCAATGGCTTGAAG 59.050 50.000 2.65 0.00 46.97 3.02
341 342 1.680207 GGAGATCCAATGGCTTGAAGC 59.320 52.381 9.04 9.04 36.84 3.86
342 343 2.652590 GAGATCCAATGGCTTGAAGCT 58.347 47.619 17.59 0.00 41.99 3.74
343 344 3.434167 GGAGATCCAATGGCTTGAAGCTA 60.434 47.826 17.59 11.97 37.40 3.32
351 352 0.748005 GGCTTGAAGCTATTGCCGGA 60.748 55.000 17.59 0.00 41.99 5.14
359 360 0.651031 GCTATTGCCGGACGAAGAAC 59.349 55.000 5.05 0.00 0.00 3.01
366 367 1.334054 CCGGACGAAGAACAGTAACG 58.666 55.000 0.00 0.00 0.00 3.18
713 1697 3.070446 AGTCATTAAGTGGTCAACGGTGA 59.930 43.478 0.00 0.00 0.00 4.02
943 3010 2.423947 CCTCCTGCAATATTCAAGCCCT 60.424 50.000 0.00 0.00 0.00 5.19
2021 4761 9.219603 CACATTTTCTTTCTACATTCCTCTGTA 57.780 33.333 0.00 0.00 0.00 2.74
2470 6088 3.176411 TGACCCAGATGTCATCAGAAGT 58.824 45.455 15.20 7.86 40.22 3.01
2569 6191 7.444183 TGCATTTTAGGCTGTATAGGAATACAC 59.556 37.037 0.00 0.00 42.40 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.106475 TGACCGGAAACTTAAATACATGTGC 60.106 40.000 9.46 0.00 0.00 4.57
103 104 8.109634 ACCTTGATGTTAAATATATGCCCTAGG 58.890 37.037 0.06 0.06 0.00 3.02
107 108 6.948309 AGGACCTTGATGTTAAATATATGCCC 59.052 38.462 0.00 0.00 0.00 5.36
164 165 4.063689 GCTCATGCTGCTGTCAATACTAT 58.936 43.478 0.00 0.00 36.03 2.12
165 166 3.461061 GCTCATGCTGCTGTCAATACTA 58.539 45.455 0.00 0.00 36.03 1.82
166 167 2.286872 GCTCATGCTGCTGTCAATACT 58.713 47.619 0.00 0.00 36.03 2.12
167 168 2.752144 GCTCATGCTGCTGTCAATAC 57.248 50.000 0.00 0.00 36.03 1.89
179 180 3.908382 CGTTTTACTGTTTCAGCTCATGC 59.092 43.478 0.00 0.00 34.37 4.06
180 181 3.908382 GCGTTTTACTGTTTCAGCTCATG 59.092 43.478 0.00 0.00 34.37 3.07
181 182 3.363970 CGCGTTTTACTGTTTCAGCTCAT 60.364 43.478 0.00 0.00 34.37 2.90
182 183 2.033236 CGCGTTTTACTGTTTCAGCTCA 60.033 45.455 0.00 0.00 34.37 4.26
183 184 2.220133 TCGCGTTTTACTGTTTCAGCTC 59.780 45.455 5.77 0.00 34.37 4.09
184 185 2.206750 TCGCGTTTTACTGTTTCAGCT 58.793 42.857 5.77 0.00 34.37 4.24
185 186 2.220133 TCTCGCGTTTTACTGTTTCAGC 59.780 45.455 5.77 0.00 34.37 4.26
186 187 3.661936 GCTCTCGCGTTTTACTGTTTCAG 60.662 47.826 5.77 0.00 37.52 3.02
187 188 2.220133 GCTCTCGCGTTTTACTGTTTCA 59.780 45.455 5.77 0.00 0.00 2.69
188 189 2.475487 AGCTCTCGCGTTTTACTGTTTC 59.525 45.455 5.77 0.00 42.32 2.78
189 190 2.480845 AGCTCTCGCGTTTTACTGTTT 58.519 42.857 5.77 0.00 42.32 2.83
190 191 2.150397 AGCTCTCGCGTTTTACTGTT 57.850 45.000 5.77 0.00 42.32 3.16
191 192 2.228343 ACTAGCTCTCGCGTTTTACTGT 59.772 45.455 5.77 0.00 42.32 3.55
192 193 2.594654 CACTAGCTCTCGCGTTTTACTG 59.405 50.000 5.77 0.00 42.32 2.74
193 194 2.486982 TCACTAGCTCTCGCGTTTTACT 59.513 45.455 5.77 1.12 42.32 2.24
194 195 2.860062 TCACTAGCTCTCGCGTTTTAC 58.140 47.619 5.77 0.00 42.32 2.01
195 196 3.777465 ATCACTAGCTCTCGCGTTTTA 57.223 42.857 5.77 0.00 42.32 1.52
196 197 2.656560 ATCACTAGCTCTCGCGTTTT 57.343 45.000 5.77 0.00 42.32 2.43
197 198 2.656560 AATCACTAGCTCTCGCGTTT 57.343 45.000 5.77 0.00 42.32 3.60
198 199 2.094700 TCAAATCACTAGCTCTCGCGTT 60.095 45.455 5.77 0.00 42.32 4.84
199 200 1.472878 TCAAATCACTAGCTCTCGCGT 59.527 47.619 5.77 0.00 42.32 6.01
200 201 2.194800 TCAAATCACTAGCTCTCGCG 57.805 50.000 0.00 0.00 42.32 5.87
201 202 3.711086 TGATCAAATCACTAGCTCTCGC 58.289 45.455 0.00 0.00 33.59 5.03
212 213 1.674519 CGGGTGGTCGTGATCAAATCA 60.675 52.381 0.00 0.00 36.84 2.57
213 214 1.006832 CGGGTGGTCGTGATCAAATC 58.993 55.000 0.00 0.00 0.00 2.17
214 215 0.611200 TCGGGTGGTCGTGATCAAAT 59.389 50.000 0.00 0.00 0.00 2.32
215 216 0.611200 ATCGGGTGGTCGTGATCAAA 59.389 50.000 0.00 0.00 0.00 2.69
216 217 0.108377 CATCGGGTGGTCGTGATCAA 60.108 55.000 0.00 0.00 0.00 2.57
217 218 1.515487 CATCGGGTGGTCGTGATCA 59.485 57.895 0.00 0.00 0.00 2.92
218 219 1.227263 CCATCGGGTGGTCGTGATC 60.227 63.158 0.00 0.00 43.44 2.92
219 220 2.900273 CCATCGGGTGGTCGTGAT 59.100 61.111 0.00 0.00 43.44 3.06
227 228 3.397482 GAAATCTGATCTCCATCGGGTG 58.603 50.000 0.00 0.00 36.19 4.61
228 229 2.370189 GGAAATCTGATCTCCATCGGGT 59.630 50.000 5.12 0.00 36.19 5.28
229 230 2.369860 TGGAAATCTGATCTCCATCGGG 59.630 50.000 8.63 0.00 36.19 5.14
230 231 3.758755 TGGAAATCTGATCTCCATCGG 57.241 47.619 8.63 0.00 34.26 4.18
234 235 5.605488 TCATCTGATGGAAATCTGATCTCCA 59.395 40.000 14.73 14.73 43.26 3.86
235 236 5.933463 GTCATCTGATGGAAATCTGATCTCC 59.067 44.000 17.06 2.94 37.20 3.71
236 237 5.634439 CGTCATCTGATGGAAATCTGATCTC 59.366 44.000 17.06 0.00 37.20 2.75
237 238 5.539979 CGTCATCTGATGGAAATCTGATCT 58.460 41.667 17.06 0.00 37.20 2.75
238 239 4.152045 GCGTCATCTGATGGAAATCTGATC 59.848 45.833 17.06 0.00 37.20 2.92
239 240 4.063689 GCGTCATCTGATGGAAATCTGAT 58.936 43.478 17.06 3.15 39.00 2.90
240 241 3.461061 GCGTCATCTGATGGAAATCTGA 58.539 45.455 17.06 0.00 33.96 3.27
241 242 2.547211 GGCGTCATCTGATGGAAATCTG 59.453 50.000 17.06 2.09 0.00 2.90
242 243 2.437281 AGGCGTCATCTGATGGAAATCT 59.563 45.455 17.06 6.69 0.00 2.40
243 244 2.805099 GAGGCGTCATCTGATGGAAATC 59.195 50.000 17.06 6.46 0.00 2.17
244 245 2.437281 AGAGGCGTCATCTGATGGAAAT 59.563 45.455 17.06 1.08 0.00 2.17
245 246 1.833630 AGAGGCGTCATCTGATGGAAA 59.166 47.619 17.06 0.00 0.00 3.13
246 247 1.489481 AGAGGCGTCATCTGATGGAA 58.511 50.000 17.06 0.00 0.00 3.53
247 248 1.137675 CAAGAGGCGTCATCTGATGGA 59.862 52.381 17.06 2.19 0.00 3.41
248 249 1.137675 TCAAGAGGCGTCATCTGATGG 59.862 52.381 17.06 3.89 0.00 3.51
249 250 2.591571 TCAAGAGGCGTCATCTGATG 57.408 50.000 11.42 11.42 0.00 3.07
250 251 2.697229 TCATCAAGAGGCGTCATCTGAT 59.303 45.455 9.41 10.33 0.00 2.90
251 252 2.102578 TCATCAAGAGGCGTCATCTGA 58.897 47.619 9.41 8.51 0.00 3.27
252 253 2.159128 AGTCATCAAGAGGCGTCATCTG 60.159 50.000 9.41 3.25 0.00 2.90
253 254 2.106566 AGTCATCAAGAGGCGTCATCT 58.893 47.619 9.41 0.00 0.00 2.90
254 255 2.593346 AGTCATCAAGAGGCGTCATC 57.407 50.000 9.41 0.00 0.00 2.92
255 256 2.234661 TCAAGTCATCAAGAGGCGTCAT 59.765 45.455 9.41 0.00 0.00 3.06
256 257 1.618343 TCAAGTCATCAAGAGGCGTCA 59.382 47.619 9.41 0.00 0.00 4.35
257 258 2.266554 CTCAAGTCATCAAGAGGCGTC 58.733 52.381 0.00 0.00 0.00 5.19
258 259 1.620819 ACTCAAGTCATCAAGAGGCGT 59.379 47.619 0.00 0.00 32.52 5.68
259 260 1.998315 CACTCAAGTCATCAAGAGGCG 59.002 52.381 0.00 0.00 32.52 5.52
260 261 2.999355 GTCACTCAAGTCATCAAGAGGC 59.001 50.000 0.00 0.00 32.52 4.70
261 262 4.021632 TGAGTCACTCAAGTCATCAAGAGG 60.022 45.833 4.55 0.00 37.57 3.69
262 263 5.131594 TGAGTCACTCAAGTCATCAAGAG 57.868 43.478 4.55 0.00 37.57 2.85
263 264 4.560311 GCTGAGTCACTCAAGTCATCAAGA 60.560 45.833 9.30 0.00 40.18 3.02
264 265 3.679025 GCTGAGTCACTCAAGTCATCAAG 59.321 47.826 9.30 0.00 40.18 3.02
265 266 3.657634 GCTGAGTCACTCAAGTCATCAA 58.342 45.455 9.30 0.00 40.18 2.57
266 267 2.352127 CGCTGAGTCACTCAAGTCATCA 60.352 50.000 9.30 0.00 40.18 3.07
267 268 2.257894 CGCTGAGTCACTCAAGTCATC 58.742 52.381 9.30 0.00 40.18 2.92
268 269 1.615883 ACGCTGAGTCACTCAAGTCAT 59.384 47.619 9.30 0.00 40.18 3.06
269 270 1.032794 ACGCTGAGTCACTCAAGTCA 58.967 50.000 9.30 0.00 40.18 3.41
270 271 2.586900 GTACGCTGAGTCACTCAAGTC 58.413 52.381 16.34 5.36 40.18 3.01
271 272 1.269998 GGTACGCTGAGTCACTCAAGT 59.730 52.381 9.30 13.95 40.18 3.16
272 273 1.542030 AGGTACGCTGAGTCACTCAAG 59.458 52.381 9.30 8.58 40.18 3.02
273 274 1.540267 GAGGTACGCTGAGTCACTCAA 59.460 52.381 9.30 0.00 40.18 3.02
274 275 1.166129 GAGGTACGCTGAGTCACTCA 58.834 55.000 7.44 7.44 38.25 3.41
275 276 1.455248 AGAGGTACGCTGAGTCACTC 58.545 55.000 0.00 0.00 36.88 3.51
276 277 1.813786 GAAGAGGTACGCTGAGTCACT 59.186 52.381 0.00 0.00 37.64 3.41
277 278 1.466024 CGAAGAGGTACGCTGAGTCAC 60.466 57.143 0.00 0.00 37.64 3.67
278 279 0.803117 CGAAGAGGTACGCTGAGTCA 59.197 55.000 0.00 0.00 37.64 3.41
279 280 1.085091 TCGAAGAGGTACGCTGAGTC 58.915 55.000 0.00 0.00 37.64 3.36
280 281 3.244764 TCGAAGAGGTACGCTGAGT 57.755 52.632 0.00 0.00 37.64 3.41
292 293 2.066262 GTTTGGATGCGTTCTCGAAGA 58.934 47.619 0.00 0.00 39.71 2.87
293 294 1.798223 TGTTTGGATGCGTTCTCGAAG 59.202 47.619 0.00 0.00 39.71 3.79
294 295 1.798223 CTGTTTGGATGCGTTCTCGAA 59.202 47.619 0.00 0.00 39.71 3.71
295 296 1.270094 ACTGTTTGGATGCGTTCTCGA 60.270 47.619 0.00 0.00 39.71 4.04
296 297 1.148310 ACTGTTTGGATGCGTTCTCG 58.852 50.000 0.00 0.00 40.37 4.04
297 298 3.424962 GCTTACTGTTTGGATGCGTTCTC 60.425 47.826 0.00 0.00 0.00 2.87
298 299 2.484264 GCTTACTGTTTGGATGCGTTCT 59.516 45.455 0.00 0.00 0.00 3.01
299 300 2.484264 AGCTTACTGTTTGGATGCGTTC 59.516 45.455 0.00 0.00 0.00 3.95
300 301 2.226437 CAGCTTACTGTTTGGATGCGTT 59.774 45.455 0.00 0.00 39.22 4.84
301 302 1.806542 CAGCTTACTGTTTGGATGCGT 59.193 47.619 0.00 0.00 39.22 5.24
302 303 1.131126 CCAGCTTACTGTTTGGATGCG 59.869 52.381 0.00 0.00 42.81 4.73
303 304 2.421424 CTCCAGCTTACTGTTTGGATGC 59.579 50.000 0.00 0.00 42.81 3.91
304 305 3.942829 TCTCCAGCTTACTGTTTGGATG 58.057 45.455 0.00 0.00 42.81 3.51
305 306 4.384647 GGATCTCCAGCTTACTGTTTGGAT 60.385 45.833 0.00 0.00 42.81 3.41
306 307 3.055094 GGATCTCCAGCTTACTGTTTGGA 60.055 47.826 0.00 0.00 42.81 3.53
307 308 3.274288 GGATCTCCAGCTTACTGTTTGG 58.726 50.000 0.00 0.00 42.81 3.28
308 309 3.942829 TGGATCTCCAGCTTACTGTTTG 58.057 45.455 0.00 0.00 42.81 2.93
312 313 7.898316 AAGCCATTGGATCTCCAGCTTACTG 62.898 48.000 17.75 4.24 46.56 2.74
313 314 5.922815 AAGCCATTGGATCTCCAGCTTACT 61.923 45.833 17.75 4.45 46.56 2.24
314 315 3.686691 AAGCCATTGGATCTCCAGCTTAC 60.687 47.826 17.75 2.59 46.56 2.34
315 316 2.511218 AAGCCATTGGATCTCCAGCTTA 59.489 45.455 17.75 0.00 46.56 3.09
319 320 4.798689 GCTTCAAGCCATTGGATCTCCAG 61.799 52.174 6.95 0.00 40.56 3.86
320 321 2.947243 GCTTCAAGCCATTGGATCTCCA 60.947 50.000 6.95 0.00 38.79 3.86
321 322 1.680207 GCTTCAAGCCATTGGATCTCC 59.320 52.381 6.95 0.00 37.02 3.71
322 323 2.652590 AGCTTCAAGCCATTGGATCTC 58.347 47.619 5.53 0.00 43.77 2.75
323 324 2.822707 AGCTTCAAGCCATTGGATCT 57.177 45.000 5.53 0.00 43.77 2.75
324 325 4.795308 GCAATAGCTTCAAGCCATTGGATC 60.795 45.833 25.81 10.60 45.93 3.36
325 326 3.069158 GCAATAGCTTCAAGCCATTGGAT 59.931 43.478 25.81 0.00 45.93 3.41
326 327 2.428171 GCAATAGCTTCAAGCCATTGGA 59.572 45.455 25.81 0.00 45.93 3.53
327 328 2.482490 GGCAATAGCTTCAAGCCATTGG 60.482 50.000 25.81 12.13 45.93 3.16
329 330 1.406539 CGGCAATAGCTTCAAGCCATT 59.593 47.619 5.53 0.48 43.77 3.16
330 331 1.027357 CGGCAATAGCTTCAAGCCAT 58.973 50.000 5.53 0.00 43.77 4.40
331 332 1.031571 CCGGCAATAGCTTCAAGCCA 61.032 55.000 5.53 0.00 43.77 4.75
332 333 0.748005 TCCGGCAATAGCTTCAAGCC 60.748 55.000 5.53 0.00 43.77 4.35
333 334 0.378610 GTCCGGCAATAGCTTCAAGC 59.621 55.000 0.00 0.00 42.84 4.01
334 335 0.652592 CGTCCGGCAATAGCTTCAAG 59.347 55.000 0.00 0.00 41.70 3.02
335 336 0.248012 TCGTCCGGCAATAGCTTCAA 59.752 50.000 0.00 0.00 41.70 2.69
336 337 0.248012 TTCGTCCGGCAATAGCTTCA 59.752 50.000 0.00 0.00 41.70 3.02
337 338 0.931005 CTTCGTCCGGCAATAGCTTC 59.069 55.000 0.00 0.00 41.70 3.86
338 339 0.535335 TCTTCGTCCGGCAATAGCTT 59.465 50.000 0.00 0.00 41.70 3.74
339 340 0.535335 TTCTTCGTCCGGCAATAGCT 59.465 50.000 0.00 0.00 41.70 3.32
340 341 0.651031 GTTCTTCGTCCGGCAATAGC 59.349 55.000 0.00 0.00 41.10 2.97
341 342 1.927174 CTGTTCTTCGTCCGGCAATAG 59.073 52.381 0.00 0.00 0.00 1.73
342 343 1.274167 ACTGTTCTTCGTCCGGCAATA 59.726 47.619 0.00 0.00 0.00 1.90
343 344 0.034896 ACTGTTCTTCGTCCGGCAAT 59.965 50.000 0.00 0.00 0.00 3.56
351 352 3.996150 TCTTCCGTTACTGTTCTTCGT 57.004 42.857 0.00 0.00 0.00 3.85
359 360 5.962433 TCCTCTGTTATTCTTCCGTTACTG 58.038 41.667 0.00 0.00 0.00 2.74
366 367 3.389656 CCCCTCTCCTCTGTTATTCTTCC 59.610 52.174 0.00 0.00 0.00 3.46
420 429 2.359975 CACCGCCCCACCTTCTTC 60.360 66.667 0.00 0.00 0.00 2.87
421 430 3.175710 ACACCGCCCCACCTTCTT 61.176 61.111 0.00 0.00 0.00 2.52
658 1642 3.688673 CCGCGGGTTAATTACCTAAAACA 59.311 43.478 20.10 0.00 46.86 2.83
2021 4761 8.949421 ACAGAAAATATACTGGGATCCTACAAT 58.051 33.333 12.58 2.25 38.30 2.71
2470 6088 9.474313 AGAATAGTTTGGGTATTCAATTGCTAA 57.526 29.630 0.00 0.00 38.75 3.09
2569 6191 7.421613 GTGCTAAGTATTGTAAAATCAACGTCG 59.578 37.037 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.