Multiple sequence alignment - TraesCS1B01G217400

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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 TraesCS1B01G217400 chr1B 100.000 4521 0 0 1 4521 394372090 394376610 0.000000e+00 8349.0
1 TraesCS1B01G217400 chr1B 96.920 2890 87 2 960 3849 388172151 388169264 0.000000e+00 4843.0
2 TraesCS1B01G217400 chr1B 96.160 677 26 0 3845 4521 489611658 489612334 0.000000e+00 1107.0
3 TraesCS1B01G217400 chr1B 96.399 361 13 0 1 361 489611306 489611666 3.010000e-166 595.0
4 TraesCS1B01G217400 chr1B 81.515 779 64 37 356 1072 327418626 327417866 6.560000e-158 568.0
5 TraesCS1B01G217400 chr1B 96.327 245 8 1 443 686 656528632 656528876 7.040000e-108 401.0
6 TraesCS1B01G217400 chr1B 83.565 432 33 20 361 770 388197605 388197190 1.990000e-98 370.0
7 TraesCS1B01G217400 chr1A 93.654 3530 159 39 362 3845 579645629 579649139 0.000000e+00 5217.0
8 TraesCS1B01G217400 chr6B 97.287 3023 78 4 823 3845 717062685 717065703 0.000000e+00 5125.0
9 TraesCS1B01G217400 chr6B 95.864 677 28 0 3845 4521 100646027 100645351 0.000000e+00 1096.0
10 TraesCS1B01G217400 chr6B 95.569 677 30 0 3845 4521 579978973 579979649 0.000000e+00 1085.0
11 TraesCS1B01G217400 chr6B 83.011 724 71 33 362 1050 27632396 27631690 3.870000e-170 608.0
12 TraesCS1B01G217400 chr6B 96.676 361 12 0 1 361 515005206 515005566 6.470000e-168 601.0
13 TraesCS1B01G217400 chr6B 96.676 361 12 0 1 361 579978621 579978981 6.470000e-168 601.0
14 TraesCS1B01G217400 chr2B 96.744 3071 80 10 784 3848 798713506 798710450 0.000000e+00 5099.0
15 TraesCS1B01G217400 chr2B 94.034 2028 92 18 600 2611 607250530 607252544 0.000000e+00 3048.0
16 TraesCS1B01G217400 chr2B 84.664 789 41 16 362 1094 200576893 200576129 0.000000e+00 713.0
17 TraesCS1B01G217400 chr2B 83.599 689 63 29 362 1017 733857870 733857199 6.470000e-168 601.0
18 TraesCS1B01G217400 chr2B 80.966 683 70 30 362 997 670509 671178 1.890000e-133 486.0
19 TraesCS1B01G217400 chr2B 93.043 230 9 3 764 993 459254354 459254576 3.370000e-86 329.0
20 TraesCS1B01G217400 chr7A 96.705 3065 85 6 784 3845 6754420 6751369 0.000000e+00 5086.0
21 TraesCS1B01G217400 chr7A 79.494 395 41 28 361 737 6754880 6754508 1.260000e-60 244.0
22 TraesCS1B01G217400 chr5B 95.443 3204 104 28 666 3845 123018597 123021782 0.000000e+00 5070.0
23 TraesCS1B01G217400 chr5B 95.421 677 31 0 3845 4521 570121316 570121992 0.000000e+00 1079.0
24 TraesCS1B01G217400 chr5B 95.273 677 32 0 3845 4521 40720939 40721615 0.000000e+00 1074.0
25 TraesCS1B01G217400 chr5B 96.399 361 13 0 1 361 467593008 467592648 3.010000e-166 595.0
26 TraesCS1B01G217400 chr5B 96.399 361 13 0 1 361 503201145 503201505 3.010000e-166 595.0
27 TraesCS1B01G217400 chr5B 96.399 361 13 0 1 361 570120964 570121324 3.010000e-166 595.0
28 TraesCS1B01G217400 chr5B 90.069 433 26 11 362 778 631596882 631597313 3.080000e-151 545.0
29 TraesCS1B01G217400 chr7B 96.052 3065 101 7 784 3845 211692939 211695986 0.000000e+00 4972.0
30 TraesCS1B01G217400 chr7B 90.452 1351 71 24 359 1682 710960200 710958881 0.000000e+00 1727.0
31 TraesCS1B01G217400 chr7B 95.273 677 32 0 3845 4521 174062836 174063512 0.000000e+00 1074.0
32 TraesCS1B01G217400 chr7B 85.425 789 35 21 362 1094 21660384 21659620 0.000000e+00 747.0
33 TraesCS1B01G217400 chr7B 92.706 425 18 4 362 778 592643274 592642855 6.470000e-168 601.0
34 TraesCS1B01G217400 chr7B 96.392 194 7 0 3652 3845 592642691 592642498 2.030000e-83 320.0
35 TraesCS1B01G217400 chr7B 99.138 116 1 0 767 882 592642824 592642709 4.580000e-50 209.0
36 TraesCS1B01G217400 chr3D 95.805 2908 108 10 904 3804 516531469 516528569 0.000000e+00 4682.0
37 TraesCS1B01G217400 chr6D 95.428 2909 125 5 835 3743 454965807 454962907 0.000000e+00 4628.0
38 TraesCS1B01G217400 chr4A 96.012 677 27 0 3845 4521 692819692 692820368 0.000000e+00 1101.0
39 TraesCS1B01G217400 chr4A 96.953 361 11 0 1 361 692819340 692819700 1.390000e-169 606.0
40 TraesCS1B01G217400 chr3B 95.428 678 31 0 3844 4521 103272144 103272821 0.000000e+00 1081.0
41 TraesCS1B01G217400 chr3B 95.421 677 31 0 3845 4521 159554267 159554943 0.000000e+00 1079.0
42 TraesCS1B01G217400 chr3B 97.230 361 10 0 1 361 528618590 528618230 2.990000e-171 612.0
43 TraesCS1B01G217400 chr3B 96.399 361 13 0 1 361 642977102 642976742 3.010000e-166 595.0
44 TraesCS1B01G217400 chr5A 82.648 657 69 31 362 991 704858286 704857648 1.430000e-149 540.0
45 TraesCS1B01G217400 chr4B 84.928 418 25 13 390 777 630346791 630346382 5.480000e-104 388.0
46 TraesCS1B01G217400 chr3A 98.182 55 1 0 767 821 670657646 670657592 3.720000e-16 97.1


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 TraesCS1B01G217400 chr1B 394372090 394376610 4520 False 8349.000000 8349 100.000000 1 4521 1 chr1B.!!$F1 4520
1 TraesCS1B01G217400 chr1B 388169264 388172151 2887 True 4843.000000 4843 96.920000 960 3849 1 chr1B.!!$R2 2889
2 TraesCS1B01G217400 chr1B 489611306 489612334 1028 False 851.000000 1107 96.279500 1 4521 2 chr1B.!!$F3 4520
3 TraesCS1B01G217400 chr1B 327417866 327418626 760 True 568.000000 568 81.515000 356 1072 1 chr1B.!!$R1 716
4 TraesCS1B01G217400 chr1A 579645629 579649139 3510 False 5217.000000 5217 93.654000 362 3845 1 chr1A.!!$F1 3483
5 TraesCS1B01G217400 chr6B 717062685 717065703 3018 False 5125.000000 5125 97.287000 823 3845 1 chr6B.!!$F2 3022
6 TraesCS1B01G217400 chr6B 100645351 100646027 676 True 1096.000000 1096 95.864000 3845 4521 1 chr6B.!!$R2 676
7 TraesCS1B01G217400 chr6B 579978621 579979649 1028 False 843.000000 1085 96.122500 1 4521 2 chr6B.!!$F3 4520
8 TraesCS1B01G217400 chr6B 27631690 27632396 706 True 608.000000 608 83.011000 362 1050 1 chr6B.!!$R1 688
9 TraesCS1B01G217400 chr2B 798710450 798713506 3056 True 5099.000000 5099 96.744000 784 3848 1 chr2B.!!$R3 3064
10 TraesCS1B01G217400 chr2B 607250530 607252544 2014 False 3048.000000 3048 94.034000 600 2611 1 chr2B.!!$F3 2011
11 TraesCS1B01G217400 chr2B 200576129 200576893 764 True 713.000000 713 84.664000 362 1094 1 chr2B.!!$R1 732
12 TraesCS1B01G217400 chr2B 733857199 733857870 671 True 601.000000 601 83.599000 362 1017 1 chr2B.!!$R2 655
13 TraesCS1B01G217400 chr2B 670509 671178 669 False 486.000000 486 80.966000 362 997 1 chr2B.!!$F1 635
14 TraesCS1B01G217400 chr7A 6751369 6754880 3511 True 2665.000000 5086 88.099500 361 3845 2 chr7A.!!$R1 3484
15 TraesCS1B01G217400 chr5B 123018597 123021782 3185 False 5070.000000 5070 95.443000 666 3845 1 chr5B.!!$F2 3179
16 TraesCS1B01G217400 chr5B 40720939 40721615 676 False 1074.000000 1074 95.273000 3845 4521 1 chr5B.!!$F1 676
17 TraesCS1B01G217400 chr5B 570120964 570121992 1028 False 837.000000 1079 95.910000 1 4521 2 chr5B.!!$F5 4520
18 TraesCS1B01G217400 chr7B 211692939 211695986 3047 False 4972.000000 4972 96.052000 784 3845 1 chr7B.!!$F2 3061
19 TraesCS1B01G217400 chr7B 710958881 710960200 1319 True 1727.000000 1727 90.452000 359 1682 1 chr7B.!!$R2 1323
20 TraesCS1B01G217400 chr7B 174062836 174063512 676 False 1074.000000 1074 95.273000 3845 4521 1 chr7B.!!$F1 676
21 TraesCS1B01G217400 chr7B 21659620 21660384 764 True 747.000000 747 85.425000 362 1094 1 chr7B.!!$R1 732
22 TraesCS1B01G217400 chr7B 592642498 592643274 776 True 376.666667 601 96.078667 362 3845 3 chr7B.!!$R3 3483
23 TraesCS1B01G217400 chr3D 516528569 516531469 2900 True 4682.000000 4682 95.805000 904 3804 1 chr3D.!!$R1 2900
24 TraesCS1B01G217400 chr6D 454962907 454965807 2900 True 4628.000000 4628 95.428000 835 3743 1 chr6D.!!$R1 2908
25 TraesCS1B01G217400 chr4A 692819340 692820368 1028 False 853.500000 1101 96.482500 1 4521 2 chr4A.!!$F1 4520
26 TraesCS1B01G217400 chr3B 103272144 103272821 677 False 1081.000000 1081 95.428000 3844 4521 1 chr3B.!!$F1 677
27 TraesCS1B01G217400 chr3B 159554267 159554943 676 False 1079.000000 1079 95.421000 3845 4521 1 chr3B.!!$F2 676
28 TraesCS1B01G217400 chr5A 704857648 704858286 638 True 540.000000 540 82.648000 362 991 1 chr5A.!!$R1 629

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
346 347 0.038166 TGCCCATCCCTTTCAGTGTC 59.962 55.000 0.00 0.00 0.00 3.67 F
347 348 0.329596 GCCCATCCCTTTCAGTGTCT 59.670 55.000 0.00 0.00 0.00 3.41 F
582 652 0.527817 GGATACGCCGTGACTCAAGG 60.528 60.000 0.00 6.64 36.14 3.61 F
1201 1484 1.297893 GTGAATGAAGATGGCGCGC 60.298 57.895 25.94 25.94 0.00 6.86 F
1736 2023 2.440409 GATTGCAAAGGAGAAGGAGCA 58.560 47.619 1.71 0.00 0.00 4.26 F
3433 3726 1.929860 ATGGCCTGGCTATGTGCTGT 61.930 55.000 17.39 0.00 42.39 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2257 0.108186 CACGGCATCAGCAAGGACTA 60.108 55.000 0.00 0.00 44.61 2.59 R
2043 2330 1.762957 CTCACATCCGGGGTACAATCT 59.237 52.381 0.00 0.00 0.00 2.40 R
2312 2601 2.299867 GGCATATACAATGCTTTGGGGG 59.700 50.000 15.92 3.19 44.02 5.40 R
2896 3185 4.214310 TGCCTCTTTCTTTTCCATTGACA 58.786 39.130 0.00 0.00 0.00 3.58 R
3482 3775 3.057315 CGGGCATTTCTTGATGTGAAGTT 60.057 43.478 0.00 0.00 0.00 2.66 R
4436 4739 0.761323 TCAGTCACCCAGGAAACCGA 60.761 55.000 0.00 0.00 0.00 4.69 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
276 277 3.121030 CGCGACCTTCTTGCCAGG 61.121 66.667 0.00 0.00 37.45 4.45
277 278 2.347490 GCGACCTTCTTGCCAGGA 59.653 61.111 0.00 0.00 35.14 3.86
278 279 1.302511 GCGACCTTCTTGCCAGGAA 60.303 57.895 0.00 0.00 35.14 3.36
279 280 0.678048 GCGACCTTCTTGCCAGGAAT 60.678 55.000 0.00 0.00 35.14 3.01
280 281 1.089920 CGACCTTCTTGCCAGGAATG 58.910 55.000 0.00 0.00 35.14 2.67
281 282 1.339055 CGACCTTCTTGCCAGGAATGA 60.339 52.381 0.00 0.00 35.14 2.57
282 283 2.087646 GACCTTCTTGCCAGGAATGAC 58.912 52.381 0.00 0.00 35.14 3.06
283 284 1.707427 ACCTTCTTGCCAGGAATGACT 59.293 47.619 0.00 0.00 35.14 3.41
284 285 2.290577 ACCTTCTTGCCAGGAATGACTC 60.291 50.000 0.00 0.00 35.14 3.36
285 286 2.363683 CTTCTTGCCAGGAATGACTCC 58.636 52.381 0.00 0.00 45.81 3.85
296 297 3.531538 GGAATGACTCCATAGAAACGCA 58.468 45.455 0.00 0.00 44.67 5.24
297 298 4.130118 GGAATGACTCCATAGAAACGCAT 58.870 43.478 0.00 0.00 44.67 4.73
298 299 4.024556 GGAATGACTCCATAGAAACGCATG 60.025 45.833 0.00 0.00 44.67 4.06
299 300 3.610040 TGACTCCATAGAAACGCATGT 57.390 42.857 0.00 0.00 0.00 3.21
300 301 3.937814 TGACTCCATAGAAACGCATGTT 58.062 40.909 0.00 0.00 40.98 2.71
301 302 3.684305 TGACTCCATAGAAACGCATGTTG 59.316 43.478 0.00 0.00 38.62 3.33
302 303 2.420022 ACTCCATAGAAACGCATGTTGC 59.580 45.455 0.00 0.00 38.62 4.17
303 304 2.679837 CTCCATAGAAACGCATGTTGCT 59.320 45.455 0.00 0.00 46.17 3.91
304 305 3.081061 TCCATAGAAACGCATGTTGCTT 58.919 40.909 0.00 0.00 41.46 3.91
305 306 3.119884 TCCATAGAAACGCATGTTGCTTG 60.120 43.478 0.00 0.00 41.46 4.01
306 307 3.366273 CCATAGAAACGCATGTTGCTTGT 60.366 43.478 0.00 0.00 41.46 3.16
307 308 2.124011 AGAAACGCATGTTGCTTGTG 57.876 45.000 0.00 0.00 41.46 3.33
308 309 0.503961 GAAACGCATGTTGCTTGTGC 59.496 50.000 0.00 0.00 42.25 4.57
309 310 0.102844 AAACGCATGTTGCTTGTGCT 59.897 45.000 0.00 0.00 42.25 4.40
310 311 0.595567 AACGCATGTTGCTTGTGCTG 60.596 50.000 0.00 0.00 42.25 4.41
311 312 1.283487 CGCATGTTGCTTGTGCTGA 59.717 52.632 0.00 0.00 42.25 4.26
312 313 0.728129 CGCATGTTGCTTGTGCTGAG 60.728 55.000 0.00 0.00 42.25 3.35
313 314 0.313043 GCATGTTGCTTGTGCTGAGT 59.687 50.000 0.00 0.00 40.96 3.41
314 315 1.665161 GCATGTTGCTTGTGCTGAGTC 60.665 52.381 0.00 0.00 40.96 3.36
315 316 1.878088 CATGTTGCTTGTGCTGAGTCT 59.122 47.619 0.00 0.00 40.48 3.24
316 317 1.302366 TGTTGCTTGTGCTGAGTCTG 58.698 50.000 0.00 0.00 40.48 3.51
317 318 0.590195 GTTGCTTGTGCTGAGTCTGG 59.410 55.000 0.00 0.00 40.48 3.86
318 319 0.469494 TTGCTTGTGCTGAGTCTGGA 59.531 50.000 0.00 0.00 40.48 3.86
319 320 0.250038 TGCTTGTGCTGAGTCTGGAC 60.250 55.000 13.67 13.67 40.48 4.02
320 321 0.250038 GCTTGTGCTGAGTCTGGACA 60.250 55.000 18.26 18.26 32.77 4.02
321 322 1.610102 GCTTGTGCTGAGTCTGGACAT 60.610 52.381 21.76 0.00 34.34 3.06
322 323 2.775890 CTTGTGCTGAGTCTGGACATT 58.224 47.619 21.76 0.00 34.34 2.71
323 324 2.174363 TGTGCTGAGTCTGGACATTG 57.826 50.000 18.26 0.00 30.16 2.82
324 325 1.271001 TGTGCTGAGTCTGGACATTGG 60.271 52.381 18.26 0.00 30.16 3.16
325 326 1.002430 GTGCTGAGTCTGGACATTGGA 59.998 52.381 15.30 0.00 0.00 3.53
326 327 1.699083 TGCTGAGTCTGGACATTGGAA 59.301 47.619 3.51 0.00 0.00 3.53
327 328 2.306805 TGCTGAGTCTGGACATTGGAAT 59.693 45.455 3.51 0.00 0.00 3.01
328 329 2.681848 GCTGAGTCTGGACATTGGAATG 59.318 50.000 3.51 0.00 42.10 2.67
329 330 2.681848 CTGAGTCTGGACATTGGAATGC 59.318 50.000 3.51 0.00 40.04 3.56
330 331 2.019984 GAGTCTGGACATTGGAATGCC 58.980 52.381 3.51 3.25 40.04 4.40
331 332 1.106285 GTCTGGACATTGGAATGCCC 58.894 55.000 0.00 0.00 39.16 5.36
332 333 0.703488 TCTGGACATTGGAATGCCCA 59.297 50.000 7.14 7.14 45.08 5.36
333 334 1.288633 TCTGGACATTGGAATGCCCAT 59.711 47.619 7.74 0.00 45.89 4.00
334 335 1.684983 CTGGACATTGGAATGCCCATC 59.315 52.381 7.74 0.00 45.89 3.51
335 336 1.043022 GGACATTGGAATGCCCATCC 58.957 55.000 0.18 0.00 46.10 3.51
336 337 1.043022 GACATTGGAATGCCCATCCC 58.957 55.000 0.00 0.00 46.10 3.85
337 338 0.638292 ACATTGGAATGCCCATCCCT 59.362 50.000 0.00 0.00 46.10 4.20
338 339 1.008693 ACATTGGAATGCCCATCCCTT 59.991 47.619 0.00 0.00 46.10 3.95
339 340 2.121129 CATTGGAATGCCCATCCCTTT 58.879 47.619 0.00 0.00 46.10 3.11
340 341 1.864669 TTGGAATGCCCATCCCTTTC 58.135 50.000 0.00 0.00 46.10 2.62
341 342 0.709397 TGGAATGCCCATCCCTTTCA 59.291 50.000 0.00 0.00 40.82 2.69
342 343 1.342275 TGGAATGCCCATCCCTTTCAG 60.342 52.381 0.00 0.00 40.82 3.02
343 344 1.342374 GGAATGCCCATCCCTTTCAGT 60.342 52.381 0.00 0.00 34.14 3.41
344 345 1.753073 GAATGCCCATCCCTTTCAGTG 59.247 52.381 0.00 0.00 0.00 3.66
345 346 0.706433 ATGCCCATCCCTTTCAGTGT 59.294 50.000 0.00 0.00 0.00 3.55
346 347 0.038166 TGCCCATCCCTTTCAGTGTC 59.962 55.000 0.00 0.00 0.00 3.67
347 348 0.329596 GCCCATCCCTTTCAGTGTCT 59.670 55.000 0.00 0.00 0.00 3.41
348 349 1.680249 GCCCATCCCTTTCAGTGTCTC 60.680 57.143 0.00 0.00 0.00 3.36
349 350 1.630369 CCCATCCCTTTCAGTGTCTCA 59.370 52.381 0.00 0.00 0.00 3.27
350 351 2.355513 CCCATCCCTTTCAGTGTCTCAG 60.356 54.545 0.00 0.00 0.00 3.35
351 352 2.354259 CATCCCTTTCAGTGTCTCAGC 58.646 52.381 0.00 0.00 0.00 4.26
352 353 1.423584 TCCCTTTCAGTGTCTCAGCA 58.576 50.000 0.00 0.00 0.00 4.41
353 354 1.980765 TCCCTTTCAGTGTCTCAGCAT 59.019 47.619 0.00 0.00 0.00 3.79
354 355 3.173151 TCCCTTTCAGTGTCTCAGCATA 58.827 45.455 0.00 0.00 0.00 3.14
355 356 3.582647 TCCCTTTCAGTGTCTCAGCATAA 59.417 43.478 0.00 0.00 0.00 1.90
356 357 4.041567 TCCCTTTCAGTGTCTCAGCATAAA 59.958 41.667 0.00 0.00 0.00 1.40
357 358 4.394300 CCCTTTCAGTGTCTCAGCATAAAG 59.606 45.833 0.00 0.00 0.00 1.85
538 557 2.625617 GGAGGCCCAGATATAGCTAGCT 60.626 54.545 23.12 23.12 0.00 3.32
539 558 3.373220 GGAGGCCCAGATATAGCTAGCTA 60.373 52.174 26.09 26.09 0.00 3.32
540 559 3.634910 GAGGCCCAGATATAGCTAGCTAC 59.365 52.174 26.41 14.07 0.00 3.58
541 560 2.696187 GGCCCAGATATAGCTAGCTACC 59.304 54.545 26.41 16.02 0.00 3.18
542 561 3.628769 GGCCCAGATATAGCTAGCTACCT 60.629 52.174 26.41 19.19 0.00 3.08
543 562 4.386536 GGCCCAGATATAGCTAGCTACCTA 60.387 50.000 26.41 16.09 0.00 3.08
544 563 4.825085 GCCCAGATATAGCTAGCTACCTAG 59.175 50.000 26.41 15.43 43.23 3.02
580 650 0.821517 ATGGATACGCCGTGACTCAA 59.178 50.000 0.00 0.00 40.66 3.02
582 652 0.527817 GGATACGCCGTGACTCAAGG 60.528 60.000 0.00 6.64 36.14 3.61
833 1106 9.140874 TGACAATCTCACTAATCACTATCTCAT 57.859 33.333 0.00 0.00 0.00 2.90
1058 1341 6.985188 AAAAAGGAGGAAAAAGAAAGCAAC 57.015 33.333 0.00 0.00 0.00 4.17
1197 1480 3.084039 TGTTGAGGTGAATGAAGATGGC 58.916 45.455 0.00 0.00 0.00 4.40
1201 1484 1.297893 GTGAATGAAGATGGCGCGC 60.298 57.895 25.94 25.94 0.00 6.86
1471 1758 9.059260 GGAAGTTAAGTAATGGTGAGTTTGTTA 57.941 33.333 0.00 0.00 0.00 2.41
1474 1761 8.843262 AGTTAAGTAATGGTGAGTTTGTTAACC 58.157 33.333 2.48 0.00 34.71 2.85
1736 2023 2.440409 GATTGCAAAGGAGAAGGAGCA 58.560 47.619 1.71 0.00 0.00 4.26
1970 2257 5.765182 ACAAAATCCAGAACGAGTTGATCTT 59.235 36.000 0.00 0.00 0.00 2.40
2093 2380 4.823442 AGAACAAATGACTCTCATTGTGCA 59.177 37.500 0.00 0.00 45.57 4.57
2312 2601 4.152580 CCAGAGTCGCTTCCTTAAAGAAAC 59.847 45.833 0.00 0.00 37.12 2.78
2896 3185 7.398332 ACATAGAGCCAGAATTTCCTTCAAAAT 59.602 33.333 0.00 0.00 36.24 1.82
2902 3191 6.652062 GCCAGAATTTCCTTCAAAATGTCAAT 59.348 34.615 0.00 0.00 36.24 2.57
2920 3209 5.166398 GTCAATGGAAAAGAAAGAGGCATG 58.834 41.667 0.00 0.00 0.00 4.06
3433 3726 1.929860 ATGGCCTGGCTATGTGCTGT 61.930 55.000 17.39 0.00 42.39 4.40
3482 3775 6.889177 TGTTGATCTTGATTGTGCCCTTAATA 59.111 34.615 0.00 0.00 0.00 0.98
3953 4256 2.676608 CAGGGGTGGCTATGTGCA 59.323 61.111 0.00 0.00 45.15 4.57
4128 4431 3.187700 GCGGATATTCTTCGTCACTGTT 58.812 45.455 0.00 0.00 0.00 3.16
4137 4440 3.887110 TCTTCGTCACTGTTCTCCTTGTA 59.113 43.478 0.00 0.00 0.00 2.41
4212 4515 4.329392 TGTTGTATCAGGAGTCGACACTA 58.671 43.478 19.50 2.14 30.63 2.74
4408 4711 1.613836 CAGCTGGCTTGACTTTCCTT 58.386 50.000 5.57 0.00 0.00 3.36
4436 4739 1.639628 TCCGACTAGAGTTCCCTCCTT 59.360 52.381 0.00 0.00 38.58 3.36
4449 4752 1.489560 CCTCCTTCGGTTTCCTGGGT 61.490 60.000 0.00 0.00 0.00 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 1.707427 AGTCATTCCTGGCAAGAAGGT 59.293 47.619 9.99 0.00 36.14 3.50
276 277 4.572389 ACATGCGTTTCTATGGAGTCATTC 59.428 41.667 0.00 0.00 34.96 2.67
277 278 4.517285 ACATGCGTTTCTATGGAGTCATT 58.483 39.130 0.00 0.00 34.96 2.57
278 279 4.142609 ACATGCGTTTCTATGGAGTCAT 57.857 40.909 0.00 0.00 37.40 3.06
279 280 3.610040 ACATGCGTTTCTATGGAGTCA 57.390 42.857 0.00 0.00 0.00 3.41
280 281 3.485877 GCAACATGCGTTTCTATGGAGTC 60.486 47.826 0.00 0.00 31.71 3.36
281 282 2.420022 GCAACATGCGTTTCTATGGAGT 59.580 45.455 0.00 0.00 31.71 3.85
282 283 3.056952 GCAACATGCGTTTCTATGGAG 57.943 47.619 0.00 0.00 31.71 3.86
294 295 0.313043 ACTCAGCACAAGCAACATGC 59.687 50.000 0.00 0.00 45.49 4.06
295 296 1.878088 AGACTCAGCACAAGCAACATG 59.122 47.619 0.00 0.00 45.49 3.21
296 297 1.878088 CAGACTCAGCACAAGCAACAT 59.122 47.619 0.00 0.00 45.49 2.71
297 298 1.302366 CAGACTCAGCACAAGCAACA 58.698 50.000 0.00 0.00 45.49 3.33
298 299 0.590195 CCAGACTCAGCACAAGCAAC 59.410 55.000 0.00 0.00 45.49 4.17
299 300 0.469494 TCCAGACTCAGCACAAGCAA 59.531 50.000 0.00 0.00 45.49 3.91
300 301 0.250038 GTCCAGACTCAGCACAAGCA 60.250 55.000 0.00 0.00 45.49 3.91
301 302 0.250038 TGTCCAGACTCAGCACAAGC 60.250 55.000 0.00 0.00 42.56 4.01
302 303 2.469274 ATGTCCAGACTCAGCACAAG 57.531 50.000 0.00 0.00 0.00 3.16
303 304 2.497138 CAATGTCCAGACTCAGCACAA 58.503 47.619 0.00 0.00 0.00 3.33
304 305 1.271001 CCAATGTCCAGACTCAGCACA 60.271 52.381 0.00 0.00 0.00 4.57
305 306 1.002430 TCCAATGTCCAGACTCAGCAC 59.998 52.381 0.00 0.00 0.00 4.40
306 307 1.351076 TCCAATGTCCAGACTCAGCA 58.649 50.000 0.00 0.00 0.00 4.41
307 308 2.479566 TTCCAATGTCCAGACTCAGC 57.520 50.000 0.00 0.00 0.00 4.26
308 309 2.681848 GCATTCCAATGTCCAGACTCAG 59.318 50.000 0.00 0.00 38.65 3.35
309 310 2.618816 GGCATTCCAATGTCCAGACTCA 60.619 50.000 0.00 0.00 38.65 3.41
310 311 2.019984 GGCATTCCAATGTCCAGACTC 58.980 52.381 0.00 0.00 38.65 3.36
311 312 2.134789 GGCATTCCAATGTCCAGACT 57.865 50.000 0.00 0.00 38.65 3.24
320 321 6.676592 ACTGAAAGGGATGGGCATTCCAAT 62.677 45.833 7.19 0.00 44.71 3.16
321 322 5.434091 ACTGAAAGGGATGGGCATTCCAA 62.434 47.826 7.19 0.00 44.71 3.53
322 323 3.976248 ACTGAAAGGGATGGGCATTCCA 61.976 50.000 7.19 0.00 45.40 3.53
323 324 1.342374 ACTGAAAGGGATGGGCATTCC 60.342 52.381 0.00 0.00 39.30 3.01
324 325 1.753073 CACTGAAAGGGATGGGCATTC 59.247 52.381 0.00 0.00 43.23 2.67
325 326 1.077663 ACACTGAAAGGGATGGGCATT 59.922 47.619 0.00 0.00 43.23 3.56
326 327 0.706433 ACACTGAAAGGGATGGGCAT 59.294 50.000 0.00 0.00 43.23 4.40
327 328 0.038166 GACACTGAAAGGGATGGGCA 59.962 55.000 0.00 0.00 43.23 5.36
328 329 0.329596 AGACACTGAAAGGGATGGGC 59.670 55.000 0.00 0.00 43.23 5.36
329 330 1.630369 TGAGACACTGAAAGGGATGGG 59.370 52.381 0.00 0.00 43.23 4.00
330 331 2.938756 GCTGAGACACTGAAAGGGATGG 60.939 54.545 0.00 0.00 43.23 3.51
331 332 2.289882 TGCTGAGACACTGAAAGGGATG 60.290 50.000 0.00 0.00 43.23 3.51
332 333 1.980765 TGCTGAGACACTGAAAGGGAT 59.019 47.619 0.00 0.00 43.23 3.85
333 334 1.423584 TGCTGAGACACTGAAAGGGA 58.576 50.000 0.00 0.00 43.23 4.20
335 336 4.999950 ACTTTATGCTGAGACACTGAAAGG 59.000 41.667 0.00 0.00 39.30 3.11
336 337 7.547019 TGATACTTTATGCTGAGACACTGAAAG 59.453 37.037 0.00 0.00 42.29 2.62
337 338 7.386059 TGATACTTTATGCTGAGACACTGAAA 58.614 34.615 0.00 0.00 0.00 2.69
338 339 6.935167 TGATACTTTATGCTGAGACACTGAA 58.065 36.000 0.00 0.00 0.00 3.02
339 340 6.406288 CCTGATACTTTATGCTGAGACACTGA 60.406 42.308 0.00 0.00 0.00 3.41
340 341 5.752472 CCTGATACTTTATGCTGAGACACTG 59.248 44.000 0.00 0.00 0.00 3.66
341 342 5.163364 CCCTGATACTTTATGCTGAGACACT 60.163 44.000 0.00 0.00 0.00 3.55
342 343 5.053145 CCCTGATACTTTATGCTGAGACAC 58.947 45.833 0.00 0.00 0.00 3.67
343 344 4.443457 GCCCTGATACTTTATGCTGAGACA 60.443 45.833 0.00 0.00 0.00 3.41
344 345 4.061596 GCCCTGATACTTTATGCTGAGAC 58.938 47.826 0.00 0.00 0.00 3.36
345 346 3.071602 GGCCCTGATACTTTATGCTGAGA 59.928 47.826 0.00 0.00 0.00 3.27
346 347 3.406764 GGCCCTGATACTTTATGCTGAG 58.593 50.000 0.00 0.00 0.00 3.35
347 348 2.224281 CGGCCCTGATACTTTATGCTGA 60.224 50.000 0.00 0.00 0.00 4.26
348 349 2.146342 CGGCCCTGATACTTTATGCTG 58.854 52.381 0.00 0.00 0.00 4.41
349 350 2.047061 TCGGCCCTGATACTTTATGCT 58.953 47.619 0.00 0.00 0.00 3.79
350 351 2.143925 GTCGGCCCTGATACTTTATGC 58.856 52.381 0.00 0.00 0.00 3.14
351 352 2.767505 GGTCGGCCCTGATACTTTATG 58.232 52.381 0.00 0.00 0.00 1.90
582 652 3.121227 CGACGAGGAAAGGTAAAAACGAC 60.121 47.826 0.00 0.00 0.00 4.34
622 716 4.856607 GAGCGAGAAGGCCGACGG 62.857 72.222 10.29 10.29 0.00 4.79
624 718 4.117661 ACGAGCGAGAAGGCCGAC 62.118 66.667 0.00 0.00 33.07 4.79
898 1180 9.654663 GATTGGAACCCTAGACATGTTATATAC 57.345 37.037 0.00 0.00 0.00 1.47
1055 1338 7.118825 TCAGTGCTAGAATTTTCAGATCAGTTG 59.881 37.037 0.00 0.00 0.00 3.16
1058 1341 7.201626 CCTTCAGTGCTAGAATTTTCAGATCAG 60.202 40.741 0.00 0.00 0.00 2.90
1201 1484 4.718940 AATTTATTTTCTCCCCTGTGCG 57.281 40.909 0.00 0.00 0.00 5.34
1303 1588 7.839907 TCCCATGTTCTTGGATCAAAAATAAG 58.160 34.615 6.34 0.00 39.25 1.73
1736 2023 5.825593 TCTTACCAGAACTTGTCTCCAAT 57.174 39.130 0.00 0.00 32.70 3.16
1970 2257 0.108186 CACGGCATCAGCAAGGACTA 60.108 55.000 0.00 0.00 44.61 2.59
2043 2330 1.762957 CTCACATCCGGGGTACAATCT 59.237 52.381 0.00 0.00 0.00 2.40
2093 2380 5.477984 AGGTTGCTTGACATATTGACACAAT 59.522 36.000 0.00 0.00 0.00 2.71
2312 2601 2.299867 GGCATATACAATGCTTTGGGGG 59.700 50.000 15.92 3.19 44.02 5.40
2896 3185 4.214310 TGCCTCTTTCTTTTCCATTGACA 58.786 39.130 0.00 0.00 0.00 3.58
2902 3191 4.665451 TCATCATGCCTCTTTCTTTTCCA 58.335 39.130 0.00 0.00 0.00 3.53
3433 3726 8.717717 ACATTGTCCAAGATATCCTTCTCAATA 58.282 33.333 0.00 0.00 31.57 1.90
3482 3775 3.057315 CGGGCATTTCTTGATGTGAAGTT 60.057 43.478 0.00 0.00 0.00 2.66
3866 4169 5.221823 TGACTAAAGTGTTGATGGATGGTGA 60.222 40.000 0.00 0.00 0.00 4.02
3868 4171 5.221925 ACTGACTAAAGTGTTGATGGATGGT 60.222 40.000 0.00 0.00 0.00 3.55
3953 4256 1.115467 GACCAGTCTGATCACCCGAT 58.885 55.000 0.00 0.00 33.31 4.18
4128 4431 3.255149 GGACAAAGTCGAGTACAAGGAGA 59.745 47.826 0.00 0.00 32.65 3.71
4137 4440 1.606903 AGAGTCGGACAAAGTCGAGT 58.393 50.000 11.27 0.00 41.10 4.18
4408 4711 4.062991 GGAACTCTAGTCGGAAGCAAAAA 58.937 43.478 0.00 0.00 0.00 1.94
4436 4739 0.761323 TCAGTCACCCAGGAAACCGA 60.761 55.000 0.00 0.00 0.00 4.69
4449 4752 1.725641 CGGCAAGCATAAGTCAGTCA 58.274 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.