Multiple sequence alignment - TraesCS3D01G478500

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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 TraesCS3D01G478500 chr3D 100.000 2963 0 0 1 2963 578051783 578054745 0.000000e+00 5472.0
1 TraesCS3D01G478500 chr3D 91.584 1616 89 23 496 2092 577658496 577656909 0.000000e+00 2187.0
2 TraesCS3D01G478500 chr3D 88.795 946 106 0 1009 1954 579292678 579293623 0.000000e+00 1160.0
3 TraesCS3D01G478500 chr3D 83.300 503 79 4 1015 1514 579305617 579306117 2.690000e-125 459.0
4 TraesCS3D01G478500 chr3D 84.064 251 19 10 5 249 577658748 577658513 3.840000e-54 222.0
5 TraesCS3D01G478500 chr3B 91.380 1601 75 15 496 2094 771252611 771254150 0.000000e+00 2134.0
6 TraesCS3D01G478500 chr3B 91.678 1418 80 19 684 2085 770953862 770952467 0.000000e+00 1930.0
7 TraesCS3D01G478500 chr3B 89.054 941 101 2 1015 1954 773542558 773543497 0.000000e+00 1166.0
8 TraesCS3D01G478500 chr3B 86.458 960 125 4 1015 1973 773568649 773569604 0.000000e+00 1048.0
9 TraesCS3D01G478500 chr3B 88.475 833 40 13 509 1339 771194484 771195262 0.000000e+00 955.0
10 TraesCS3D01G478500 chr3B 93.316 389 25 1 1337 1725 771220742 771221129 9.210000e-160 573.0
11 TraesCS3D01G478500 chr3B 91.317 334 20 4 1771 2096 771221219 771221551 5.830000e-122 448.0
12 TraesCS3D01G478500 chr3B 83.937 442 42 9 2285 2700 746690588 746691026 2.140000e-106 396.0
13 TraesCS3D01G478500 chr3B 88.929 280 29 2 2096 2373 746690304 746690583 7.860000e-91 344.0
14 TraesCS3D01G478500 chr3B 86.911 191 10 5 46 230 771194304 771194485 1.800000e-47 200.0
15 TraesCS3D01G478500 chr3B 92.208 77 4 2 60 135 771252512 771252587 1.120000e-19 108.0
16 TraesCS3D01G478500 chr3B 87.500 56 6 1 46 101 770953953 770953899 2.470000e-06 63.9
17 TraesCS3D01G478500 chr3A 87.961 922 111 0 1009 1930 714535158 714536079 0.000000e+00 1088.0
18 TraesCS3D01G478500 chr3A 86.458 960 121 8 1015 1971 714541357 714542310 0.000000e+00 1044.0
19 TraesCS3D01G478500 chr3A 90.511 274 19 3 606 879 713216409 713216143 3.630000e-94 355.0
20 TraesCS3D01G478500 chr3A 85.375 253 21 6 20 265 713216733 713216490 6.340000e-62 248.0
21 TraesCS3D01G478500 chr3A 100.000 31 0 0 555 585 713216445 713216415 1.150000e-04 58.4
22 TraesCS3D01G478500 chr5B 89.054 740 50 15 2096 2810 380957356 380958089 0.000000e+00 889.0
23 TraesCS3D01G478500 chr5B 87.857 280 31 3 2096 2372 527838761 527838482 2.850000e-85 326.0
24 TraesCS3D01G478500 chr5B 80.682 264 38 10 243 497 426854906 426855165 3.010000e-45 193.0
25 TraesCS3D01G478500 chr5B 80.303 264 39 10 243 497 543674364 543674105 1.400000e-43 187.0
26 TraesCS3D01G478500 chr5B 79.848 263 42 9 243 497 435653974 435654233 6.520000e-42 182.0
27 TraesCS3D01G478500 chr7D 88.345 695 42 18 2096 2765 31117668 31116988 0.000000e+00 798.0
28 TraesCS3D01G478500 chr7D 82.937 252 36 7 260 505 2093457 2093207 1.380000e-53 220.0
29 TraesCS3D01G478500 chr7D 81.250 240 41 4 261 497 93733545 93733307 1.080000e-44 191.0
30 TraesCS3D01G478500 chr2B 95.385 325 13 1 2557 2881 703802032 703802354 1.570000e-142 516.0
31 TraesCS3D01G478500 chr2B 92.063 315 22 3 2088 2401 756557512 756557200 9.750000e-120 440.0
32 TraesCS3D01G478500 chr2B 88.968 281 27 4 2096 2373 703801599 703801878 7.860000e-91 344.0
33 TraesCS3D01G478500 chr7A 87.260 416 32 9 2409 2805 103049899 103050312 3.480000e-124 455.0
34 TraesCS3D01G478500 chr4B 83.559 444 40 14 2284 2700 73274620 73274183 4.630000e-103 385.0
35 TraesCS3D01G478500 chr4B 90.323 279 24 2 2096 2373 73274900 73274624 2.170000e-96 363.0
36 TraesCS3D01G478500 chr6B 83.333 444 44 18 2284 2700 11054014 11054454 1.670000e-102 383.0
37 TraesCS3D01G478500 chr6B 93.443 244 14 2 2557 2800 2932634 2932393 7.810000e-96 361.0
38 TraesCS3D01G478500 chr6B 88.693 283 28 4 2094 2373 11053729 11054010 2.830000e-90 342.0
39 TraesCS3D01G478500 chr2A 90.357 280 25 2 2095 2373 685630583 685630861 1.680000e-97 366.0
40 TraesCS3D01G478500 chr2A 96.528 144 5 0 2557 2700 685631138 685631281 3.820000e-59 239.0
41 TraesCS3D01G478500 chr5D 82.971 276 37 8 2092 2363 124208465 124208196 1.060000e-59 241.0
42 TraesCS3D01G478500 chr4A 82.083 240 41 2 261 498 673352182 673352421 1.390000e-48 204.0
43 TraesCS3D01G478500 chr7B 81.557 244 37 8 261 499 642478285 642478525 8.380000e-46 195.0
44 TraesCS3D01G478500 chr7B 81.172 239 43 2 261 497 28366207 28365969 1.080000e-44 191.0
45 TraesCS3D01G478500 chr6D 81.405 242 38 7 260 497 91526102 91526340 1.080000e-44 191.0


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 TraesCS3D01G478500 chr3D 578051783 578054745 2962 False 5472.000000 5472 100.0000 1 2963 1 chr3D.!!$F1 2962
1 TraesCS3D01G478500 chr3D 577656909 577658748 1839 True 1204.500000 2187 87.8240 5 2092 2 chr3D.!!$R1 2087
2 TraesCS3D01G478500 chr3D 579292678 579293623 945 False 1160.000000 1160 88.7950 1009 1954 1 chr3D.!!$F2 945
3 TraesCS3D01G478500 chr3D 579305617 579306117 500 False 459.000000 459 83.3000 1015 1514 1 chr3D.!!$F3 499
4 TraesCS3D01G478500 chr3B 773542558 773543497 939 False 1166.000000 1166 89.0540 1015 1954 1 chr3B.!!$F1 939
5 TraesCS3D01G478500 chr3B 771252512 771254150 1638 False 1121.000000 2134 91.7940 60 2094 2 chr3B.!!$F6 2034
6 TraesCS3D01G478500 chr3B 773568649 773569604 955 False 1048.000000 1048 86.4580 1015 1973 1 chr3B.!!$F2 958
7 TraesCS3D01G478500 chr3B 770952467 770953953 1486 True 996.950000 1930 89.5890 46 2085 2 chr3B.!!$R1 2039
8 TraesCS3D01G478500 chr3B 771194304 771195262 958 False 577.500000 955 87.6930 46 1339 2 chr3B.!!$F4 1293
9 TraesCS3D01G478500 chr3B 771220742 771221551 809 False 510.500000 573 92.3165 1337 2096 2 chr3B.!!$F5 759
10 TraesCS3D01G478500 chr3B 746690304 746691026 722 False 370.000000 396 86.4330 2096 2700 2 chr3B.!!$F3 604
11 TraesCS3D01G478500 chr3A 714535158 714536079 921 False 1088.000000 1088 87.9610 1009 1930 1 chr3A.!!$F1 921
12 TraesCS3D01G478500 chr3A 714541357 714542310 953 False 1044.000000 1044 86.4580 1015 1971 1 chr3A.!!$F2 956
13 TraesCS3D01G478500 chr3A 713216143 713216733 590 True 220.466667 355 91.9620 20 879 3 chr3A.!!$R1 859
14 TraesCS3D01G478500 chr5B 380957356 380958089 733 False 889.000000 889 89.0540 2096 2810 1 chr5B.!!$F1 714
15 TraesCS3D01G478500 chr7D 31116988 31117668 680 True 798.000000 798 88.3450 2096 2765 1 chr7D.!!$R2 669
16 TraesCS3D01G478500 chr2B 703801599 703802354 755 False 430.000000 516 92.1765 2096 2881 2 chr2B.!!$F1 785
17 TraesCS3D01G478500 chr4B 73274183 73274900 717 True 374.000000 385 86.9410 2096 2700 2 chr4B.!!$R1 604
18 TraesCS3D01G478500 chr6B 11053729 11054454 725 False 362.500000 383 86.0130 2094 2700 2 chr6B.!!$F1 606
19 TraesCS3D01G478500 chr2A 685630583 685631281 698 False 302.500000 366 93.4425 2095 2700 2 chr2A.!!$F1 605

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
796 812 0.248054 GCGATGCCAATGTTACGGTG 60.248 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2261 2370 0.111832 TCACTGACACTAGGTCCCGT 59.888 55.0 8.36 4.23 46.38 5.28 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
107 109 3.005155 AGAAAAGAAGTGCATTGTGCTCC 59.995 43.478 3.41 0.00 45.31 4.70
109 111 0.957395 AGAAGTGCATTGTGCTCCGG 60.957 55.000 0.00 0.00 45.31 5.14
131 133 2.112998 TGGGCCGTAAAGCACTAGTAT 58.887 47.619 0.00 0.00 36.97 2.12
152 154 8.830201 AGTATAGTGGTATAGTCAAGTAGTCG 57.170 38.462 0.00 0.00 0.00 4.18
155 157 5.743117 AGTGGTATAGTCAAGTAGTCGACT 58.257 41.667 23.66 23.66 44.51 4.18
230 238 9.807921 AACATTCCTCCATAAAGAAAAGTTAGA 57.192 29.630 0.00 0.00 0.00 2.10
258 267 9.770097 ATATGTACCAATCAAAGACACTATCAG 57.230 33.333 0.00 0.00 0.00 2.90
262 271 9.250624 GTACCAATCAAAGACACTATCAGATAC 57.749 37.037 0.00 0.00 0.00 2.24
265 274 9.469807 CCAATCAAAGACACTATCAGATACTAC 57.530 37.037 0.00 0.00 0.00 2.73
266 275 9.469807 CAATCAAAGACACTATCAGATACTACC 57.530 37.037 0.00 0.00 0.00 3.18
268 277 8.824756 TCAAAGACACTATCAGATACTACCTT 57.175 34.615 0.00 0.00 0.00 3.50
269 278 8.904834 TCAAAGACACTATCAGATACTACCTTC 58.095 37.037 0.00 0.00 0.00 3.46
270 279 7.499321 AAGACACTATCAGATACTACCTTCG 57.501 40.000 0.00 0.00 0.00 3.79
271 280 6.593807 AGACACTATCAGATACTACCTTCGT 58.406 40.000 0.00 0.00 0.00 3.85
272 281 6.707161 AGACACTATCAGATACTACCTTCGTC 59.293 42.308 0.00 0.00 0.00 4.20
273 282 6.593807 ACACTATCAGATACTACCTTCGTCT 58.406 40.000 0.00 0.00 0.00 4.18
274 283 7.055378 ACACTATCAGATACTACCTTCGTCTT 58.945 38.462 0.00 0.00 0.00 3.01
275 284 7.012515 ACACTATCAGATACTACCTTCGTCTTG 59.987 40.741 0.00 0.00 0.00 3.02
276 285 5.776173 ATCAGATACTACCTTCGTCTTGG 57.224 43.478 0.00 0.00 0.00 3.61
277 286 4.597004 TCAGATACTACCTTCGTCTTGGT 58.403 43.478 0.00 0.00 40.12 3.67
278 287 5.014858 TCAGATACTACCTTCGTCTTGGTT 58.985 41.667 0.00 0.00 37.74 3.67
279 288 5.479375 TCAGATACTACCTTCGTCTTGGTTT 59.521 40.000 0.00 0.00 37.74 3.27
280 289 6.660521 TCAGATACTACCTTCGTCTTGGTTTA 59.339 38.462 0.00 0.00 37.74 2.01
281 290 7.341256 TCAGATACTACCTTCGTCTTGGTTTAT 59.659 37.037 0.00 0.00 37.74 1.40
282 291 7.980099 CAGATACTACCTTCGTCTTGGTTTATT 59.020 37.037 0.00 0.00 37.74 1.40
283 292 7.980099 AGATACTACCTTCGTCTTGGTTTATTG 59.020 37.037 0.00 0.00 37.74 1.90
284 293 6.105397 ACTACCTTCGTCTTGGTTTATTGA 57.895 37.500 0.00 0.00 37.74 2.57
285 294 6.708285 ACTACCTTCGTCTTGGTTTATTGAT 58.292 36.000 0.00 0.00 37.74 2.57
286 295 6.817140 ACTACCTTCGTCTTGGTTTATTGATC 59.183 38.462 0.00 0.00 37.74 2.92
287 296 4.941873 ACCTTCGTCTTGGTTTATTGATCC 59.058 41.667 0.00 0.00 31.62 3.36
288 297 4.335594 CCTTCGTCTTGGTTTATTGATCCC 59.664 45.833 0.00 0.00 0.00 3.85
289 298 4.837093 TCGTCTTGGTTTATTGATCCCT 57.163 40.909 0.00 0.00 0.00 4.20
290 299 5.174037 TCGTCTTGGTTTATTGATCCCTT 57.826 39.130 0.00 0.00 0.00 3.95
291 300 6.302535 TCGTCTTGGTTTATTGATCCCTTA 57.697 37.500 0.00 0.00 0.00 2.69
292 301 6.713276 TCGTCTTGGTTTATTGATCCCTTAA 58.287 36.000 0.00 0.00 0.00 1.85
293 302 7.343357 TCGTCTTGGTTTATTGATCCCTTAAT 58.657 34.615 0.00 0.00 0.00 1.40
294 303 8.487848 TCGTCTTGGTTTATTGATCCCTTAATA 58.512 33.333 0.00 0.00 0.00 0.98
295 304 8.557029 CGTCTTGGTTTATTGATCCCTTAATAC 58.443 37.037 0.00 0.00 0.00 1.89
296 305 9.628500 GTCTTGGTTTATTGATCCCTTAATACT 57.372 33.333 0.00 0.00 0.00 2.12
300 309 9.762381 TGGTTTATTGATCCCTTAATACTTTGT 57.238 29.630 0.00 0.00 0.00 2.83
304 313 9.967451 TTATTGATCCCTTAATACTTTGTGTCA 57.033 29.630 0.00 0.00 0.00 3.58
305 314 8.877864 ATTGATCCCTTAATACTTTGTGTCAA 57.122 30.769 0.00 0.00 0.00 3.18
306 315 8.698973 TTGATCCCTTAATACTTTGTGTCAAA 57.301 30.769 0.00 0.00 0.00 2.69
307 316 8.877864 TGATCCCTTAATACTTTGTGTCAAAT 57.122 30.769 0.00 0.00 0.00 2.32
308 317 9.308000 TGATCCCTTAATACTTTGTGTCAAATT 57.692 29.630 0.00 0.00 0.00 1.82
311 320 9.757227 TCCCTTAATACTTTGTGTCAAATTTTG 57.243 29.630 2.59 2.59 0.00 2.44
312 321 8.987890 CCCTTAATACTTTGTGTCAAATTTTGG 58.012 33.333 9.18 0.00 0.00 3.28
313 322 9.757227 CCTTAATACTTTGTGTCAAATTTTGGA 57.243 29.630 9.18 0.00 0.00 3.53
315 324 7.692908 AATACTTTGTGTCAAATTTTGGACG 57.307 32.000 9.18 0.00 36.83 4.79
316 325 5.066968 ACTTTGTGTCAAATTTTGGACGT 57.933 34.783 9.18 0.00 36.83 4.34
317 326 4.862018 ACTTTGTGTCAAATTTTGGACGTG 59.138 37.500 9.18 4.30 36.83 4.49
318 327 3.428746 TGTGTCAAATTTTGGACGTGG 57.571 42.857 9.18 0.00 36.83 4.94
319 328 3.017442 TGTGTCAAATTTTGGACGTGGA 58.983 40.909 9.18 0.00 36.83 4.02
320 329 3.634448 TGTGTCAAATTTTGGACGTGGAT 59.366 39.130 9.18 0.00 36.83 3.41
321 330 4.098654 TGTGTCAAATTTTGGACGTGGATT 59.901 37.500 9.18 0.00 36.83 3.01
322 331 5.047188 GTGTCAAATTTTGGACGTGGATTT 58.953 37.500 9.18 0.00 36.83 2.17
323 332 6.183360 TGTGTCAAATTTTGGACGTGGATTTA 60.183 34.615 9.18 0.00 36.83 1.40
324 333 6.697892 GTGTCAAATTTTGGACGTGGATTTAA 59.302 34.615 9.18 0.00 36.83 1.52
325 334 7.383843 GTGTCAAATTTTGGACGTGGATTTAAT 59.616 33.333 9.18 0.00 36.83 1.40
326 335 7.928706 TGTCAAATTTTGGACGTGGATTTAATT 59.071 29.630 9.18 0.00 36.83 1.40
327 336 9.413048 GTCAAATTTTGGACGTGGATTTAATTA 57.587 29.630 9.18 0.00 0.00 1.40
328 337 9.982651 TCAAATTTTGGACGTGGATTTAATTAA 57.017 25.926 9.18 0.00 0.00 1.40
363 372 8.846943 AATACATGTCACACAGAAAAGTATCA 57.153 30.769 0.00 0.00 0.00 2.15
364 373 9.453572 AATACATGTCACACAGAAAAGTATCAT 57.546 29.630 0.00 0.00 0.00 2.45
365 374 7.750229 ACATGTCACACAGAAAAGTATCATT 57.250 32.000 0.00 0.00 0.00 2.57
366 375 7.587629 ACATGTCACACAGAAAAGTATCATTG 58.412 34.615 0.00 0.00 0.00 2.82
367 376 7.445096 ACATGTCACACAGAAAAGTATCATTGA 59.555 33.333 0.00 0.00 0.00 2.57
368 377 7.800155 TGTCACACAGAAAAGTATCATTGAA 57.200 32.000 0.00 0.00 0.00 2.69
369 378 8.219546 TGTCACACAGAAAAGTATCATTGAAA 57.780 30.769 0.00 0.00 0.00 2.69
370 379 8.681806 TGTCACACAGAAAAGTATCATTGAAAA 58.318 29.630 0.00 0.00 0.00 2.29
371 380 8.958043 GTCACACAGAAAAGTATCATTGAAAAC 58.042 33.333 0.00 0.00 0.00 2.43
372 381 8.902806 TCACACAGAAAAGTATCATTGAAAACT 58.097 29.630 0.00 0.00 0.00 2.66
395 404 9.524106 AACTATGTTCAAATACGAATCATACGA 57.476 29.630 0.00 0.00 34.70 3.43
396 405 9.692749 ACTATGTTCAAATACGAATCATACGAT 57.307 29.630 0.00 0.00 34.70 3.73
484 493 9.774413 AAATACGAATAGGACTAATAAACCAGG 57.226 33.333 0.00 0.00 0.00 4.45
485 494 8.716674 ATACGAATAGGACTAATAAACCAGGA 57.283 34.615 0.00 0.00 0.00 3.86
486 495 6.814043 ACGAATAGGACTAATAAACCAGGAC 58.186 40.000 0.00 0.00 0.00 3.85
487 496 6.381994 ACGAATAGGACTAATAAACCAGGACA 59.618 38.462 0.00 0.00 0.00 4.02
488 497 6.924060 CGAATAGGACTAATAAACCAGGACAG 59.076 42.308 0.00 0.00 0.00 3.51
489 498 7.201884 CGAATAGGACTAATAAACCAGGACAGA 60.202 40.741 0.00 0.00 0.00 3.41
490 499 5.678955 AGGACTAATAAACCAGGACAGAC 57.321 43.478 0.00 0.00 0.00 3.51
491 500 4.159879 AGGACTAATAAACCAGGACAGACG 59.840 45.833 0.00 0.00 0.00 4.18
492 501 4.081807 GGACTAATAAACCAGGACAGACGT 60.082 45.833 0.00 0.00 0.00 4.34
493 502 5.126061 GGACTAATAAACCAGGACAGACGTA 59.874 44.000 0.00 0.00 0.00 3.57
494 503 6.205101 ACTAATAAACCAGGACAGACGTAG 57.795 41.667 0.00 0.00 0.00 3.51
594 603 4.389374 CTGCCTCCAAACTAAGACAAGAA 58.611 43.478 0.00 0.00 0.00 2.52
595 604 4.985538 TGCCTCCAAACTAAGACAAGAAT 58.014 39.130 0.00 0.00 0.00 2.40
596 605 6.121776 TGCCTCCAAACTAAGACAAGAATA 57.878 37.500 0.00 0.00 0.00 1.75
597 606 6.173339 TGCCTCCAAACTAAGACAAGAATAG 58.827 40.000 0.00 0.00 0.00 1.73
598 607 5.586643 GCCTCCAAACTAAGACAAGAATAGG 59.413 44.000 0.00 0.00 0.00 2.57
599 608 6.116126 CCTCCAAACTAAGACAAGAATAGGG 58.884 44.000 0.00 0.00 0.00 3.53
600 609 6.296489 CCTCCAAACTAAGACAAGAATAGGGT 60.296 42.308 0.00 0.00 0.00 4.34
601 610 6.708285 TCCAAACTAAGACAAGAATAGGGTC 58.292 40.000 0.00 0.00 0.00 4.46
721 737 2.363359 ACCGTCCGTATCCTACCATTTC 59.637 50.000 0.00 0.00 0.00 2.17
796 812 0.248054 GCGATGCCAATGTTACGGTG 60.248 55.000 0.00 0.00 0.00 4.94
847 863 3.870274 TCTCTCTGCACGCTACTACTAA 58.130 45.455 0.00 0.00 0.00 2.24
884 908 3.975670 GGTCTGTATAAATCGACTGAGCG 59.024 47.826 0.00 0.00 34.05 5.03
885 909 3.975670 GTCTGTATAAATCGACTGAGCGG 59.024 47.826 0.00 0.00 0.00 5.52
973 1018 4.214545 TGGTTACAATTTGGCACGTTCTAG 59.785 41.667 0.78 0.00 0.00 2.43
977 1022 3.003275 ACAATTTGGCACGTTCTAGTGTG 59.997 43.478 0.78 7.76 43.61 3.82
1116 1168 0.250338 GGGACAACGGCTTCAACTCT 60.250 55.000 0.00 0.00 0.00 3.24
1191 1244 4.796231 GGCGTCATCGTCGGTGCT 62.796 66.667 0.00 0.00 39.49 4.40
1213 1266 1.303888 AACTACGTGCTCCCCGAGA 60.304 57.895 0.00 0.00 0.00 4.04
1354 1407 1.596934 GTCCCAGCGATGGAGAACA 59.403 57.895 24.05 0.00 30.98 3.18
1911 2008 2.583441 CGTGGAGCAGAACTGGGGA 61.583 63.158 3.99 0.00 0.00 4.81
1914 2011 1.298014 GGAGCAGAACTGGGGACTG 59.702 63.158 3.99 0.00 35.14 3.51
2003 2108 2.108976 CCATCCATGTACGCGGCT 59.891 61.111 12.47 0.00 0.00 5.52
2014 2119 1.538512 GTACGCGGCTATGGTCATAGA 59.461 52.381 18.94 0.00 42.55 1.98
2157 2266 7.399245 AAAGTCAGTTTGGTGCTAAAACTTA 57.601 32.000 8.61 0.99 43.60 2.24
2165 2274 4.519213 TGGTGCTAAAACTTACGGCATAT 58.481 39.130 0.00 0.00 35.37 1.78
2169 2278 7.932491 TGGTGCTAAAACTTACGGCATATATTA 59.068 33.333 0.00 0.00 35.37 0.98
2190 2299 1.765230 ACCGGTAACAAAAGTTGGCA 58.235 45.000 4.49 0.00 34.12 4.92
2192 2301 3.488363 ACCGGTAACAAAAGTTGGCATA 58.512 40.909 4.49 0.00 34.12 3.14
2207 2316 0.318699 GCATAGGCGTGCATCTACGA 60.319 55.000 12.07 0.00 46.46 3.43
2222 2331 6.928492 TGCATCTACGATGCTAATCATGTTTA 59.072 34.615 24.13 0.00 44.79 2.01
2258 2367 0.608856 TGATGAGGCACGCCAACATT 60.609 50.000 11.35 1.37 36.26 2.71
2261 2370 2.911509 AGGCACGCCAACATTGCA 60.912 55.556 11.35 0.00 38.04 4.08
2266 2375 3.361158 CGCCAACATTGCACGGGA 61.361 61.111 0.00 0.00 0.00 5.14
2427 2638 1.696314 TCTATGACCCTTGGGCCCC 60.696 63.158 22.27 2.17 0.00 5.80
2454 2665 5.468746 CGATCAGGAAACAGTACAAAAGGAA 59.531 40.000 0.00 0.00 0.00 3.36
2510 2724 2.477375 GCGACCTCACGACAATAAAACA 59.523 45.455 0.00 0.00 35.09 2.83
2535 2749 0.598065 GCTAGCCACAACACCAAAGG 59.402 55.000 2.29 0.00 0.00 3.11
2546 2760 3.280334 ACACCAAAGGCACGTTGATGC 62.280 52.381 0.00 0.00 45.24 3.91
2555 2769 1.805120 GCACGTTGATGCCTATACGGT 60.805 52.381 0.00 0.00 39.86 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.199327 CACTCAGCATGCACTTCTTGG 59.801 52.381 21.98 5.07 34.76 3.61
109 111 0.743345 CTAGTGCTTTACGGCCCACC 60.743 60.000 0.00 0.00 0.00 4.61
131 133 6.882656 AGTCGACTACTTGACTATACCACTA 58.117 40.000 18.46 0.00 43.36 2.74
140 142 8.508883 AGAACATAATAGTCGACTACTTGACT 57.491 34.615 26.87 20.85 46.60 3.41
141 143 7.856894 GGAGAACATAATAGTCGACTACTTGAC 59.143 40.741 26.87 19.46 39.80 3.18
142 144 7.555195 TGGAGAACATAATAGTCGACTACTTGA 59.445 37.037 26.87 12.79 39.80 3.02
152 154 6.742559 TTAGGGGTGGAGAACATAATAGTC 57.257 41.667 0.00 0.00 0.00 2.59
179 187 9.979578 TTCTGCACATTGTTAGAAAACATAATT 57.020 25.926 9.62 0.00 44.85 1.40
201 209 8.115490 ACTTTTCTTTATGGAGGAATGTTCTG 57.885 34.615 0.00 0.00 0.00 3.02
249 257 6.593807 AGACGAAGGTAGTATCTGATAGTGT 58.406 40.000 13.95 3.57 0.00 3.55
256 265 4.985538 ACCAAGACGAAGGTAGTATCTG 57.014 45.455 0.00 0.00 36.07 2.90
258 267 7.977853 TCAATAAACCAAGACGAAGGTAGTATC 59.022 37.037 0.00 0.00 37.07 2.24
262 271 6.258068 GGATCAATAAACCAAGACGAAGGTAG 59.742 42.308 0.00 0.00 37.07 3.18
265 274 4.335594 GGGATCAATAAACCAAGACGAAGG 59.664 45.833 0.00 0.00 0.00 3.46
266 275 5.186198 AGGGATCAATAAACCAAGACGAAG 58.814 41.667 0.00 0.00 0.00 3.79
268 277 4.837093 AGGGATCAATAAACCAAGACGA 57.163 40.909 0.00 0.00 0.00 4.20
269 278 6.995511 TTAAGGGATCAATAAACCAAGACG 57.004 37.500 0.00 0.00 0.00 4.18
270 279 9.628500 AGTATTAAGGGATCAATAAACCAAGAC 57.372 33.333 0.00 0.00 0.00 3.01
274 283 9.762381 ACAAAGTATTAAGGGATCAATAAACCA 57.238 29.630 0.00 0.00 0.00 3.67
278 287 9.967451 TGACACAAAGTATTAAGGGATCAATAA 57.033 29.630 0.00 0.00 0.00 1.40
279 288 9.967451 TTGACACAAAGTATTAAGGGATCAATA 57.033 29.630 0.00 0.00 0.00 1.90
280 289 8.877864 TTGACACAAAGTATTAAGGGATCAAT 57.122 30.769 0.00 0.00 0.00 2.57
281 290 8.698973 TTTGACACAAAGTATTAAGGGATCAA 57.301 30.769 0.00 0.00 0.00 2.57
282 291 8.877864 ATTTGACACAAAGTATTAAGGGATCA 57.122 30.769 0.00 0.00 0.00 2.92
285 294 9.757227 CAAAATTTGACACAAAGTATTAAGGGA 57.243 29.630 0.00 0.00 0.00 4.20
286 295 8.987890 CCAAAATTTGACACAAAGTATTAAGGG 58.012 33.333 7.37 0.00 0.00 3.95
287 296 9.757227 TCCAAAATTTGACACAAAGTATTAAGG 57.243 29.630 7.37 0.00 0.00 2.69
289 298 9.239002 CGTCCAAAATTTGACACAAAGTATTAA 57.761 29.630 7.37 0.00 0.00 1.40
290 299 8.407064 ACGTCCAAAATTTGACACAAAGTATTA 58.593 29.630 7.37 0.00 0.00 0.98
291 300 7.221838 CACGTCCAAAATTTGACACAAAGTATT 59.778 33.333 7.37 0.00 0.00 1.89
292 301 6.695278 CACGTCCAAAATTTGACACAAAGTAT 59.305 34.615 7.37 0.00 0.00 2.12
293 302 6.030849 CACGTCCAAAATTTGACACAAAGTA 58.969 36.000 7.37 0.00 0.00 2.24
294 303 4.862018 CACGTCCAAAATTTGACACAAAGT 59.138 37.500 7.37 0.00 0.00 2.66
295 304 4.267452 CCACGTCCAAAATTTGACACAAAG 59.733 41.667 7.37 0.00 0.00 2.77
296 305 4.082190 TCCACGTCCAAAATTTGACACAAA 60.082 37.500 7.37 0.00 0.00 2.83
297 306 3.444034 TCCACGTCCAAAATTTGACACAA 59.556 39.130 7.37 0.00 0.00 3.33
298 307 3.017442 TCCACGTCCAAAATTTGACACA 58.983 40.909 7.37 0.00 0.00 3.72
299 308 3.701532 TCCACGTCCAAAATTTGACAC 57.298 42.857 7.37 2.81 0.00 3.67
300 309 4.927978 AATCCACGTCCAAAATTTGACA 57.072 36.364 7.37 0.00 0.00 3.58
301 310 7.883229 ATTAAATCCACGTCCAAAATTTGAC 57.117 32.000 7.37 3.18 0.00 3.18
302 311 9.982651 TTAATTAAATCCACGTCCAAAATTTGA 57.017 25.926 7.37 0.00 0.00 2.69
337 346 9.936759 TGATACTTTTCTGTGTGACATGTATTA 57.063 29.630 0.00 0.00 30.68 0.98
338 347 8.846943 TGATACTTTTCTGTGTGACATGTATT 57.153 30.769 0.00 0.00 30.68 1.89
339 348 9.453572 AATGATACTTTTCTGTGTGACATGTAT 57.546 29.630 0.00 0.00 32.15 2.29
340 349 8.720562 CAATGATACTTTTCTGTGTGACATGTA 58.279 33.333 0.00 0.00 0.00 2.29
341 350 7.445096 TCAATGATACTTTTCTGTGTGACATGT 59.555 33.333 0.00 0.00 0.00 3.21
342 351 7.809665 TCAATGATACTTTTCTGTGTGACATG 58.190 34.615 0.00 0.00 0.00 3.21
343 352 7.984422 TCAATGATACTTTTCTGTGTGACAT 57.016 32.000 0.00 0.00 0.00 3.06
344 353 7.800155 TTCAATGATACTTTTCTGTGTGACA 57.200 32.000 0.00 0.00 0.00 3.58
345 354 8.958043 GTTTTCAATGATACTTTTCTGTGTGAC 58.042 33.333 0.00 0.00 0.00 3.67
346 355 8.902806 AGTTTTCAATGATACTTTTCTGTGTGA 58.097 29.630 0.00 0.00 0.00 3.58
369 378 9.524106 TCGTATGATTCGTATTTGAACATAGTT 57.476 29.630 0.00 0.00 30.17 2.24
370 379 9.692749 ATCGTATGATTCGTATTTGAACATAGT 57.307 29.630 0.00 0.00 30.17 2.12
458 467 9.774413 CCTGGTTTATTAGTCCTATTCGTATTT 57.226 33.333 0.00 0.00 0.00 1.40
459 468 9.151177 TCCTGGTTTATTAGTCCTATTCGTATT 57.849 33.333 0.00 0.00 0.00 1.89
460 469 8.583296 GTCCTGGTTTATTAGTCCTATTCGTAT 58.417 37.037 0.00 0.00 0.00 3.06
461 470 7.560991 TGTCCTGGTTTATTAGTCCTATTCGTA 59.439 37.037 0.00 0.00 0.00 3.43
462 471 6.381994 TGTCCTGGTTTATTAGTCCTATTCGT 59.618 38.462 0.00 0.00 0.00 3.85
463 472 6.812998 TGTCCTGGTTTATTAGTCCTATTCG 58.187 40.000 0.00 0.00 0.00 3.34
464 473 7.927092 GTCTGTCCTGGTTTATTAGTCCTATTC 59.073 40.741 0.00 0.00 0.00 1.75
465 474 7.417570 CGTCTGTCCTGGTTTATTAGTCCTATT 60.418 40.741 0.00 0.00 0.00 1.73
466 475 6.040616 CGTCTGTCCTGGTTTATTAGTCCTAT 59.959 42.308 0.00 0.00 0.00 2.57
467 476 5.359009 CGTCTGTCCTGGTTTATTAGTCCTA 59.641 44.000 0.00 0.00 0.00 2.94
468 477 4.159879 CGTCTGTCCTGGTTTATTAGTCCT 59.840 45.833 0.00 0.00 0.00 3.85
469 478 4.081807 ACGTCTGTCCTGGTTTATTAGTCC 60.082 45.833 0.00 0.00 0.00 3.85
470 479 5.069501 ACGTCTGTCCTGGTTTATTAGTC 57.930 43.478 0.00 0.00 0.00 2.59
471 480 5.713861 ACTACGTCTGTCCTGGTTTATTAGT 59.286 40.000 0.00 0.00 0.00 2.24
472 481 6.205101 ACTACGTCTGTCCTGGTTTATTAG 57.795 41.667 0.00 0.00 0.00 1.73
473 482 7.701539 TTACTACGTCTGTCCTGGTTTATTA 57.298 36.000 0.00 0.00 0.00 0.98
474 483 6.594788 TTACTACGTCTGTCCTGGTTTATT 57.405 37.500 0.00 0.00 0.00 1.40
475 484 6.379133 TCATTACTACGTCTGTCCTGGTTTAT 59.621 38.462 0.00 0.00 0.00 1.40
476 485 5.711506 TCATTACTACGTCTGTCCTGGTTTA 59.288 40.000 0.00 0.00 0.00 2.01
477 486 4.525487 TCATTACTACGTCTGTCCTGGTTT 59.475 41.667 0.00 0.00 0.00 3.27
478 487 4.084287 TCATTACTACGTCTGTCCTGGTT 58.916 43.478 0.00 0.00 0.00 3.67
479 488 3.693807 TCATTACTACGTCTGTCCTGGT 58.306 45.455 0.00 0.00 0.00 4.00
480 489 4.713824 TTCATTACTACGTCTGTCCTGG 57.286 45.455 0.00 0.00 0.00 4.45
721 737 0.597568 TTCTGTTGGCGGCAATTGAG 59.402 50.000 28.07 21.55 0.00 3.02
847 863 2.438795 ACCCAAACCGTGCGTGTT 60.439 55.556 0.00 0.00 0.00 3.32
884 908 0.514691 GGATGAATTGCTCGATCGCC 59.485 55.000 11.09 4.37 0.00 5.54
885 909 1.070309 GTGGATGAATTGCTCGATCGC 60.070 52.381 11.09 0.00 0.00 4.58
1191 1244 2.288025 GGGGAGCACGTAGTTGGGA 61.288 63.158 0.00 0.00 41.61 4.37
1464 1517 1.006571 GAACGGCTTGGACTCGTCA 60.007 57.895 0.00 0.00 36.01 4.35
1911 2008 1.827399 CGGTGCTGGGGTAGAACAGT 61.827 60.000 0.00 0.00 36.59 3.55
1914 2011 1.068741 CTATCGGTGCTGGGGTAGAAC 59.931 57.143 0.00 0.00 33.79 3.01
2157 2266 5.609423 TGTTACCGGTTTAATATATGCCGT 58.391 37.500 15.04 0.00 40.70 5.68
2165 2274 6.040166 TGCCAACTTTTGTTACCGGTTTAATA 59.960 34.615 15.04 0.00 41.35 0.98
2169 2278 2.496470 TGCCAACTTTTGTTACCGGTTT 59.504 40.909 15.04 0.00 41.35 3.27
2190 2299 1.670087 GCATCGTAGATGCACGCCTAT 60.670 52.381 24.79 0.00 45.12 2.57
2192 2301 1.592669 GCATCGTAGATGCACGCCT 60.593 57.895 24.79 0.00 45.12 5.52
2207 2316 8.615211 CCATGCGTATATAAACATGATTAGCAT 58.385 33.333 20.28 11.30 41.93 3.79
2258 2367 1.532078 TGACACTAGGTCCCGTGCA 60.532 57.895 8.44 5.71 46.38 4.57
2261 2370 0.111832 TCACTGACACTAGGTCCCGT 59.888 55.000 8.36 4.23 46.38 5.28
2266 2375 0.111832 TCCGGTCACTGACACTAGGT 59.888 55.000 11.34 0.00 33.68 3.08
2427 2638 3.313012 TGTACTGTTTCCTGATCGGTG 57.687 47.619 0.00 0.00 0.00 4.94
2431 2642 6.877611 TTCCTTTTGTACTGTTTCCTGATC 57.122 37.500 0.00 0.00 0.00 2.92
2454 2665 6.127842 ACGGCACTTCGTTTTGGATATTAATT 60.128 34.615 0.00 0.00 40.85 1.40
2487 2701 2.736144 TTATTGTCGTGAGGTCGCTT 57.264 45.000 0.00 0.00 0.00 4.68
2488 2702 2.735134 GTTTTATTGTCGTGAGGTCGCT 59.265 45.455 0.00 0.00 0.00 4.93
2510 2724 2.094675 GGTGTTGTGGCTAGCATGATT 58.905 47.619 18.24 0.00 0.00 2.57
2535 2749 0.859232 CCGTATAGGCATCAACGTGC 59.141 55.000 0.00 0.00 44.31 5.34
2547 2761 1.257936 GCATGTGCGTGAACCGTATAG 59.742 52.381 0.00 0.00 39.32 1.31
2555 2769 1.233919 TTAAGCTGCATGTGCGTGAA 58.766 45.000 1.02 3.54 45.83 3.18
2568 2805 1.555075 TCGCTCCAGGTCATTTAAGCT 59.445 47.619 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.