Multiple sequence alignment - TraesCS5B01G248300

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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 TraesCS5B01G248300 chr5B 100.000 5230 0 0 1 5230 430669025 430674254 0.000000e+00 9659.0
1 TraesCS5B01G248300 chr5B 86.923 1690 126 47 2770 4444 430751307 430749698 0.000000e+00 1808.0
2 TraesCS5B01G248300 chr5B 89.153 1134 97 14 1508 2627 430752430 430751309 0.000000e+00 1389.0
3 TraesCS5B01G248300 chr5B 87.867 783 42 19 736 1471 430753212 430752436 0.000000e+00 870.0
4 TraesCS5B01G248300 chr5A 94.777 3657 132 26 1597 5230 465992090 465995710 0.000000e+00 5640.0
5 TraesCS5B01G248300 chr5A 85.444 1800 156 54 2770 4551 466037521 466035810 0.000000e+00 1775.0
6 TraesCS5B01G248300 chr5A 90.787 1042 78 7 1597 2627 466038557 466037523 0.000000e+00 1376.0
7 TraesCS5B01G248300 chr5A 89.614 1011 64 15 555 1548 465990991 465991977 0.000000e+00 1247.0
8 TraesCS5B01G248300 chr5A 89.907 753 49 14 745 1479 466039740 466038997 0.000000e+00 944.0
9 TraesCS5B01G248300 chr5A 87.919 298 29 7 1251 1546 466038859 466038567 1.390000e-90 344.0
10 TraesCS5B01G248300 chr5A 80.919 283 39 9 233 502 635982125 635982405 5.310000e-50 209.0
11 TraesCS5B01G248300 chr5A 100.000 37 0 0 1225 1261 466038899 466038863 9.400000e-08 69.4
12 TraesCS5B01G248300 chr5D 93.116 2513 116 25 1597 4096 364666075 364668543 0.000000e+00 3629.0
13 TraesCS5B01G248300 chr5D 94.034 1123 37 13 4123 5228 364668531 364669640 0.000000e+00 1676.0
14 TraesCS5B01G248300 chr5D 90.691 1042 78 8 1597 2627 364765777 364764744 0.000000e+00 1369.0
15 TraesCS5B01G248300 chr5D 90.499 842 45 15 736 1548 364665232 364666067 0.000000e+00 1079.0
16 TraesCS5B01G248300 chr5D 85.756 1032 109 25 3422 4450 364764027 364763031 0.000000e+00 1057.0
17 TraesCS5B01G248300 chr5D 85.965 969 63 27 623 1548 364766723 364765785 0.000000e+00 968.0
18 TraesCS5B01G248300 chr5D 86.165 665 53 14 1 639 364664571 364665222 0.000000e+00 682.0
19 TraesCS5B01G248300 chr5D 89.154 544 57 2 3667 4208 30615835 30615292 0.000000e+00 676.0
20 TraesCS5B01G248300 chr5D 87.847 576 43 15 2770 3335 364764742 364764184 0.000000e+00 651.0
21 TraesCS5B01G248300 chr5D 83.575 414 50 9 2095 2495 30673524 30673116 6.400000e-99 372.0
22 TraesCS5B01G248300 chr5D 80.544 478 59 20 4276 4736 30613885 30613425 2.330000e-88 337.0
23 TraesCS5B01G248300 chr5D 76.837 449 66 17 211 623 441566704 441566258 8.820000e-53 219.0
24 TraesCS5B01G248300 chr5D 94.000 50 3 0 4945 4994 30613161 30613112 5.620000e-10 76.8
25 TraesCS5B01G248300 chr2D 81.019 432 40 16 232 623 71203503 71203074 6.580000e-79 305.0
26 TraesCS5B01G248300 chr2D 82.222 90 12 4 1381 1469 325752572 325752486 2.020000e-09 75.0
27 TraesCS5B01G248300 chr3A 81.127 408 51 16 234 622 699839872 699839472 2.370000e-78 303.0
28 TraesCS5B01G248300 chr3A 100.000 36 0 0 587 622 128301744 128301709 3.380000e-07 67.6
29 TraesCS5B01G248300 chr1A 95.028 181 7 2 742 921 439339842 439339663 3.080000e-72 283.0
30 TraesCS5B01G248300 chr6D 87.712 236 20 4 239 467 414434022 414434255 3.100000e-67 267.0
31 TraesCS5B01G248300 chr6D 87.395 119 8 4 505 618 299196402 299196286 4.250000e-26 130.0
32 TraesCS5B01G248300 chr1B 82.818 291 34 8 231 507 56620946 56621234 4.040000e-61 246.0
33 TraesCS5B01G248300 chr3D 82.699 289 37 7 231 507 345068903 345069190 1.450000e-60 244.0
34 TraesCS5B01G248300 chr7B 81.849 292 37 8 231 508 246018863 246018574 1.130000e-56 231.0
35 TraesCS5B01G248300 chr3B 79.088 373 42 15 272 619 727786029 727786390 1.900000e-54 224.0
36 TraesCS5B01G248300 chr6B 81.164 292 40 6 230 508 350203848 350204137 2.450000e-53 220.0
37 TraesCS5B01G248300 chr6B 78.272 382 45 17 248 624 633894845 633895193 1.480000e-50 211.0
38 TraesCS5B01G248300 chr4A 79.233 313 45 7 215 507 620262195 620262507 3.190000e-47 200.0
39 TraesCS5B01G248300 chr4A 94.915 59 3 0 564 622 616667848 616667790 5.580000e-15 93.5
40 TraesCS5B01G248300 chr6A 91.803 61 3 2 547 607 383587068 383587010 3.360000e-12 84.2
41 TraesCS5B01G248300 chr2B 82.292 96 13 4 1381 1475 394944239 394944147 4.340000e-11 80.5
42 TraesCS5B01G248300 chr2A 83.333 90 11 4 1381 1469 392456557 392456643 4.340000e-11 80.5
43 TraesCS5B01G248300 chr4B 100.000 33 0 0 3158 3190 666785481 666785449 1.570000e-05 62.1
44 TraesCS5B01G248300 chr4D 96.875 32 1 0 216 247 262650298 262650267 3.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G248300 chr5B 430669025 430674254 5229 False 9659.000000 9659 100.000000 1 5230 1 chr5B.!!$F1 5229
1 TraesCS5B01G248300 chr5B 430749698 430753212 3514 True 1355.666667 1808 87.981000 736 4444 3 chr5B.!!$R1 3708
2 TraesCS5B01G248300 chr5A 465990991 465995710 4719 False 3443.500000 5640 92.195500 555 5230 2 chr5A.!!$F2 4675
3 TraesCS5B01G248300 chr5A 466035810 466039740 3930 True 901.680000 1775 90.811400 745 4551 5 chr5A.!!$R1 3806
4 TraesCS5B01G248300 chr5D 364664571 364669640 5069 False 1766.500000 3629 90.953500 1 5228 4 chr5D.!!$F1 5227
5 TraesCS5B01G248300 chr5D 364763031 364766723 3692 True 1011.250000 1369 87.564750 623 4450 4 chr5D.!!$R4 3827
6 TraesCS5B01G248300 chr5D 30613112 30615835 2723 True 363.266667 676 87.899333 3667 4994 3 chr5D.!!$R3 1327

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
362 364 1.224592 CCCAACTGCTAATCGGGCT 59.775 57.895 0.00 0.00 0.00 5.19 F
364 366 1.718757 CCAACTGCTAATCGGGCTGC 61.719 60.000 0.00 0.00 33.04 5.25 F
414 417 1.996786 CTGCTATTTGGCGCACTGGG 61.997 60.000 10.83 0.00 34.52 4.45 F
1558 2006 2.136298 TGAACACAAGACCAAAGGCA 57.864 45.000 0.00 0.00 0.00 4.75 F
1560 2008 2.297701 GAACACAAGACCAAAGGCAGA 58.702 47.619 0.00 0.00 0.00 4.26 F
1561 2009 2.664402 ACACAAGACCAAAGGCAGAT 57.336 45.000 0.00 0.00 0.00 2.90 F
1562 2010 2.949447 ACACAAGACCAAAGGCAGATT 58.051 42.857 0.00 0.00 0.00 2.40 F
1610 2177 3.119531 TGCAACCAAGTTGTGAAGTTGAG 60.120 43.478 20.28 2.77 44.40 3.02 F
2240 2820 3.125316 GGAGCATGAACAGAAGGTAAACG 59.875 47.826 0.00 0.00 0.00 3.60 F
3190 3788 2.825836 CAAGAGCCATGGGTCCGC 60.826 66.667 34.70 15.85 42.97 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2618 0.251742 TCAATTTGGCCCTGAGGTGG 60.252 55.000 0.00 0.0 34.57 4.61 R
2175 2751 6.569226 GCACATGAGAATGCAAAGAACTTACT 60.569 38.462 0.00 0.0 41.65 2.24 R
2403 2988 3.740115 GGCGAAAAGAATGGCCTATCTA 58.260 45.455 3.32 0.0 42.29 1.98 R
2423 3008 1.160137 GCAACTGCTACAAGACCAGG 58.840 55.000 0.00 0.0 38.21 4.45 R
2909 3500 2.551270 TCAACCCTGCCTCTACAATCT 58.449 47.619 0.00 0.0 0.00 2.40 R
2910 3501 3.567478 ATCAACCCTGCCTCTACAATC 57.433 47.619 0.00 0.0 0.00 2.67 R
2912 3503 3.806949 AAATCAACCCTGCCTCTACAA 57.193 42.857 0.00 0.0 0.00 2.41 R
3156 3754 5.504830 GGCTCTTGACTTCTTGTTGAAACTC 60.505 44.000 0.00 0.0 33.79 3.01 R
3733 4431 1.151668 GCTGCTGTACCAGTGTTCAG 58.848 55.000 0.00 0.0 41.38 3.02 R
4684 6798 1.270305 GGGAAAGGAAAAGGCAAGTGC 60.270 52.381 0.00 0.0 41.14 4.40 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
66 67 1.521423 GAATACACGCATACACCTCGC 59.479 52.381 0.00 0.00 0.00 5.03
69 70 1.446099 CACGCATACACCTCGCTGT 60.446 57.895 0.00 0.00 0.00 4.40
88 89 5.163953 CGCTGTCACTTTACTCTTTACCATG 60.164 44.000 0.00 0.00 0.00 3.66
92 93 7.728148 TGTCACTTTACTCTTTACCATGTACA 58.272 34.615 0.00 0.00 0.00 2.90
96 97 6.534079 ACTTTACTCTTTACCATGTACATCGC 59.466 38.462 5.07 0.00 0.00 4.58
99 100 4.051922 CTCTTTACCATGTACATCGCTCC 58.948 47.826 5.07 0.00 0.00 4.70
147 149 6.391227 ACGTCATTGGAAACAGAAAGAAAT 57.609 33.333 0.00 0.00 44.54 2.17
149 151 6.183360 ACGTCATTGGAAACAGAAAGAAATGT 60.183 34.615 0.00 0.00 44.54 2.71
161 163 6.718454 ACAGAAAGAAATGTGACCTCATTGAT 59.282 34.615 0.00 0.00 37.96 2.57
163 165 5.909621 AAGAAATGTGACCTCATTGATGG 57.090 39.130 0.00 0.00 37.96 3.51
202 204 4.823989 CAGAAGGGCCCACTAAATTCATAG 59.176 45.833 27.56 8.08 0.00 2.23
214 216 3.914426 AATTCATAGAGGGTCAAGCGT 57.086 42.857 0.00 0.00 0.00 5.07
299 301 1.993370 GCCGAGGCACGATGATTATAC 59.007 52.381 9.58 0.00 45.77 1.47
305 307 1.346365 CACGATGATTATACGGGCCG 58.654 55.000 27.06 27.06 0.00 6.13
339 341 3.042560 GCAACCTGCAACCCAGAC 58.957 61.111 0.00 0.00 44.64 3.51
340 342 1.827789 GCAACCTGCAACCCAGACA 60.828 57.895 0.00 0.00 44.64 3.41
341 343 2.032981 CAACCTGCAACCCAGACAC 58.967 57.895 0.00 0.00 44.64 3.67
342 344 1.525995 AACCTGCAACCCAGACACG 60.526 57.895 0.00 0.00 44.64 4.49
343 345 2.669569 CCTGCAACCCAGACACGG 60.670 66.667 0.00 0.00 44.64 4.94
344 346 3.357079 CTGCAACCCAGACACGGC 61.357 66.667 0.00 0.00 44.64 5.68
345 347 4.947147 TGCAACCCAGACACGGCC 62.947 66.667 0.00 0.00 0.00 6.13
347 349 4.263572 CAACCCAGACACGGCCCA 62.264 66.667 0.00 0.00 0.00 5.36
348 350 3.494254 AACCCAGACACGGCCCAA 61.494 61.111 0.00 0.00 0.00 4.12
351 353 2.669569 CCAGACACGGCCCAACTG 60.670 66.667 0.00 1.90 0.00 3.16
362 364 1.224592 CCCAACTGCTAATCGGGCT 59.775 57.895 0.00 0.00 0.00 5.19
364 366 1.718757 CCAACTGCTAATCGGGCTGC 61.719 60.000 0.00 0.00 33.04 5.25
414 417 1.996786 CTGCTATTTGGCGCACTGGG 61.997 60.000 10.83 0.00 34.52 4.45
424 427 4.552278 GCACTGGGCGTTTTTAGC 57.448 55.556 0.00 0.00 0.00 3.09
1052 1115 2.439156 GGATGCAGTGGGGTGAGC 60.439 66.667 0.00 0.00 0.00 4.26
1173 1252 5.700183 TCAGCATATGGAGTTCTCTAGAGT 58.300 41.667 19.21 0.00 0.00 3.24
1335 1780 6.608405 TGGTGAATGAGGATAGAATGCATTTT 59.392 34.615 14.33 10.78 30.06 1.82
1342 1787 8.158169 TGAGGATAGAATGCATTTTATGTCAC 57.842 34.615 23.13 14.72 0.00 3.67
1363 1808 3.380637 ACTTGTAACGAGTGTCTGTCAGT 59.619 43.478 0.00 0.00 0.00 3.41
1416 1861 2.532843 TGTTTCGGCCTACTCTTAGGT 58.467 47.619 0.00 0.00 46.33 3.08
1477 1925 2.824341 AGCTTTGCATTTTCTGGGAGAG 59.176 45.455 0.00 0.00 0.00 3.20
1506 1954 3.562557 AGAGTAACGCGGTGAATTGTTTT 59.437 39.130 7.07 0.00 0.00 2.43
1558 2006 2.136298 TGAACACAAGACCAAAGGCA 57.864 45.000 0.00 0.00 0.00 4.75
1560 2008 2.297701 GAACACAAGACCAAAGGCAGA 58.702 47.619 0.00 0.00 0.00 4.26
1561 2009 2.664402 ACACAAGACCAAAGGCAGAT 57.336 45.000 0.00 0.00 0.00 2.90
1562 2010 2.949447 ACACAAGACCAAAGGCAGATT 58.051 42.857 0.00 0.00 0.00 2.40
1563 2011 4.098914 ACACAAGACCAAAGGCAGATTA 57.901 40.909 0.00 0.00 0.00 1.75
1564 2012 4.469657 ACACAAGACCAAAGGCAGATTAA 58.530 39.130 0.00 0.00 0.00 1.40
1565 2013 4.892934 ACACAAGACCAAAGGCAGATTAAA 59.107 37.500 0.00 0.00 0.00 1.52
1566 2014 5.539955 ACACAAGACCAAAGGCAGATTAAAT 59.460 36.000 0.00 0.00 0.00 1.40
1567 2015 6.041979 ACACAAGACCAAAGGCAGATTAAATT 59.958 34.615 0.00 0.00 0.00 1.82
1576 2024 7.707893 CCAAAGGCAGATTAAATTGTTCCATAG 59.292 37.037 0.00 0.00 0.00 2.23
1593 2055 9.542462 TGTTCCATAGATATAGTACTTTGCAAC 57.458 33.333 0.00 0.00 0.00 4.17
1594 2056 8.989980 GTTCCATAGATATAGTACTTTGCAACC 58.010 37.037 0.00 0.00 0.00 3.77
1595 2162 8.257602 TCCATAGATATAGTACTTTGCAACCA 57.742 34.615 0.00 0.00 0.00 3.67
1610 2177 3.119531 TGCAACCAAGTTGTGAAGTTGAG 60.120 43.478 20.28 2.77 44.40 3.02
1876 2452 7.293745 GTTCTTATGTTTCAGACAGTCATGTG 58.706 38.462 2.66 0.00 42.62 3.21
1958 2534 9.651913 TCTTTGCCATAAATATTTGAACCTTTC 57.348 29.630 11.05 0.00 0.00 2.62
2041 2617 7.504924 AAAAAGACAAATCGATACTTCCACA 57.495 32.000 0.00 0.00 0.00 4.17
2042 2618 6.481954 AAAGACAAATCGATACTTCCACAC 57.518 37.500 0.00 0.00 0.00 3.82
2172 2748 8.400186 TGTTGCTGTAAGATATCATGAAACATG 58.600 33.333 5.32 5.51 34.07 3.21
2173 2749 8.615211 GTTGCTGTAAGATATCATGAAACATGA 58.385 33.333 15.14 15.14 34.07 3.07
2174 2750 8.913487 TGCTGTAAGATATCATGAAACATGAT 57.087 30.769 23.98 23.98 38.16 2.45
2240 2820 3.125316 GGAGCATGAACAGAAGGTAAACG 59.875 47.826 0.00 0.00 0.00 3.60
2423 3008 4.574828 TGTTAGATAGGCCATTCTTTTCGC 59.425 41.667 5.01 0.00 0.00 4.70
2632 3220 4.688021 TCTGTTGCAAATTTTACGCCTTT 58.312 34.783 0.00 0.00 0.00 3.11
2634 3222 6.273825 TCTGTTGCAAATTTTACGCCTTTTA 58.726 32.000 0.00 0.00 0.00 1.52
2677 3266 5.964958 ATAAAGTGGACAACAGACATTGG 57.035 39.130 0.00 0.00 33.63 3.16
2718 3307 4.582701 AAAACATTCAGGTTTCATCGCA 57.417 36.364 0.00 0.00 39.93 5.10
2724 3313 4.359971 TTCAGGTTTCATCGCATCAATG 57.640 40.909 0.00 0.00 0.00 2.82
2857 3448 9.777297 TTGATGGTTGATCTCGAAATATAATGA 57.223 29.630 0.00 0.00 31.55 2.57
2858 3449 9.948964 TGATGGTTGATCTCGAAATATAATGAT 57.051 29.630 0.00 0.00 31.55 2.45
2860 3451 9.730705 ATGGTTGATCTCGAAATATAATGATGT 57.269 29.630 0.00 0.00 0.00 3.06
2861 3452 9.559732 TGGTTGATCTCGAAATATAATGATGTT 57.440 29.630 0.00 0.00 0.00 2.71
2906 3497 9.886132 ATTTTCTAATGTACGACTTCCAAGTAT 57.114 29.630 0.00 0.00 39.88 2.12
2907 3498 8.697846 TTTCTAATGTACGACTTCCAAGTATG 57.302 34.615 0.00 0.00 39.88 2.39
2908 3499 7.400599 TCTAATGTACGACTTCCAAGTATGT 57.599 36.000 0.00 0.00 39.88 2.29
2909 3500 8.510243 TCTAATGTACGACTTCCAAGTATGTA 57.490 34.615 0.00 0.00 39.88 2.29
2910 3501 8.618677 TCTAATGTACGACTTCCAAGTATGTAG 58.381 37.037 0.00 0.00 39.88 2.74
2911 3502 7.400599 AATGTACGACTTCCAAGTATGTAGA 57.599 36.000 0.00 4.75 39.88 2.59
2912 3503 7.584122 ATGTACGACTTCCAAGTATGTAGAT 57.416 36.000 0.00 7.58 39.88 1.98
2972 3563 8.058667 TCGAGTGAGTTACTTGGTTCATATTA 57.941 34.615 2.62 0.00 40.53 0.98
2973 3564 8.525316 TCGAGTGAGTTACTTGGTTCATATTAA 58.475 33.333 2.62 0.00 40.53 1.40
3156 3754 5.421374 AGCTAACTTACTACCAGTAACCCTG 59.579 44.000 0.00 0.00 35.89 4.45
3190 3788 2.825836 CAAGAGCCATGGGTCCGC 60.826 66.667 34.70 15.85 42.97 5.54
3211 3810 3.181397 CGGCTATGTTTTTGCCAATGAG 58.819 45.455 0.00 0.00 46.39 2.90
3634 4330 6.064717 CCTACTTAAATGAATTCTCAGGGGG 58.935 44.000 7.05 0.00 34.23 5.40
3733 4431 5.751243 TTGCCTTTTTCAGAACTCAGTAC 57.249 39.130 0.00 0.00 0.00 2.73
3769 4467 3.802722 CAGCTAGTCTGCAAACTTGTC 57.197 47.619 0.00 0.00 35.78 3.18
3777 4475 6.942532 AGTCTGCAAACTTGTCTAAATGAA 57.057 33.333 0.00 0.00 0.00 2.57
3827 4525 9.907229 GATTATTATTAAGTATAAGCTGGCCCT 57.093 33.333 0.00 0.00 32.40 5.19
3829 4527 9.734984 TTATTATTAAGTATAAGCTGGCCCTTC 57.265 33.333 0.00 0.00 32.40 3.46
3918 4619 8.519799 TTGAAGAAGAAACTATTGTTGAAGGT 57.480 30.769 0.00 0.00 36.39 3.50
3976 4678 8.905702 GTGTGCTTTTGTGTAAATATCTCAAAG 58.094 33.333 0.00 0.00 32.59 2.77
4001 4703 8.141909 AGTTGAATATTGCATTCATCTCCATTG 58.858 33.333 2.22 0.00 37.79 2.82
4038 4740 1.319374 CATGTACAAGTTCGTACGCGG 59.681 52.381 12.47 0.20 43.89 6.46
4106 4808 4.558226 TTCTCCATCTTAAGCAGCAGAA 57.442 40.909 0.00 0.00 0.00 3.02
4165 4867 6.349611 GCTGAAGCTTCACCAAAGAATAATGA 60.350 38.462 25.16 0.00 37.12 2.57
4209 4911 3.902881 ATCTAACACCTGGCAAGAGAG 57.097 47.619 0.00 0.00 0.00 3.20
4272 6337 4.819630 TGGGTTGTTGTATGTTCTTCTCAC 59.180 41.667 0.00 0.00 0.00 3.51
4402 6470 2.428171 AGTTTCAGCAGCATGTGTTGTT 59.572 40.909 0.00 0.00 38.48 2.83
4403 6471 3.119029 AGTTTCAGCAGCATGTGTTGTTT 60.119 39.130 0.00 0.00 38.48 2.83
4511 6583 5.200734 CGATGCTAGATTCATTTCATCGG 57.799 43.478 13.84 1.24 45.27 4.18
4598 6696 6.728089 TTATATCAAAATGGGAAGCATGCA 57.272 33.333 21.98 0.00 0.00 3.96
4600 6698 1.551430 TCAAAATGGGAAGCATGCAGG 59.449 47.619 21.98 0.00 0.00 4.85
4602 6700 2.496871 CAAAATGGGAAGCATGCAGGTA 59.503 45.455 21.98 2.10 0.00 3.08
4603 6701 2.530460 AATGGGAAGCATGCAGGTAA 57.470 45.000 21.98 2.37 0.00 2.85
4616 6726 5.674569 GCATGCAGGTAATGTTTCACTGTAG 60.675 44.000 14.21 0.00 0.00 2.74
4734 6957 1.267533 TGTGCACTGTGCTAGCAATTG 59.732 47.619 30.43 17.01 45.31 2.32
4782 7029 6.425114 CAGAACTGGATATACATAGGCAACAC 59.575 42.308 0.00 0.00 41.41 3.32
4920 7167 2.197324 GCTGTCCACCCAACCCAA 59.803 61.111 0.00 0.00 0.00 4.12
4937 7184 7.040686 CCCAACCCAAGTAAGTATATTATGTGC 60.041 40.741 0.00 0.00 0.00 4.57
5203 7456 6.072175 TGGCACCTACATACAAATTTGACTTC 60.072 38.462 24.64 2.71 0.00 3.01
5206 7459 7.308589 GCACCTACATACAAATTTGACTTCTGT 60.309 37.037 24.64 18.47 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.994432 TTTGTTTAAACTGGCAATTTGTTATTG 57.006 25.926 18.72 0.00 0.00 1.90
51 52 1.413767 GACAGCGAGGTGTATGCGTG 61.414 60.000 7.98 0.00 0.00 5.34
52 53 1.153823 GACAGCGAGGTGTATGCGT 60.154 57.895 7.98 0.00 0.00 5.24
66 67 7.870954 TGTACATGGTAAAGAGTAAAGTGACAG 59.129 37.037 0.00 0.00 0.00 3.51
69 70 7.758076 CGATGTACATGGTAAAGAGTAAAGTGA 59.242 37.037 14.43 0.00 0.00 3.41
147 149 1.352017 AGCACCATCAATGAGGTCACA 59.648 47.619 2.17 0.00 35.52 3.58
149 151 1.951895 GCAGCACCATCAATGAGGTCA 60.952 52.381 2.17 0.00 35.52 4.02
192 194 5.353394 ACGCTTGACCCTCTATGAATTTA 57.647 39.130 0.00 0.00 0.00 1.40
292 294 3.961729 GGCACGGCCCGTATAATC 58.038 61.111 9.25 0.00 44.06 1.75
325 327 2.111043 CGTGTCTGGGTTGCAGGT 59.889 61.111 0.00 0.00 0.00 4.00
332 334 4.265056 GTTGGGCCGTGTCTGGGT 62.265 66.667 0.00 0.00 0.00 4.51
338 340 0.676782 GATTAGCAGTTGGGCCGTGT 60.677 55.000 0.00 0.00 0.00 4.49
339 341 1.705337 CGATTAGCAGTTGGGCCGTG 61.705 60.000 0.00 0.00 0.00 4.94
340 342 1.449601 CGATTAGCAGTTGGGCCGT 60.450 57.895 0.00 0.00 0.00 5.68
341 343 2.180204 CCGATTAGCAGTTGGGCCG 61.180 63.158 0.00 0.00 0.00 6.13
342 344 1.823899 CCCGATTAGCAGTTGGGCC 60.824 63.158 0.00 0.00 33.56 5.80
343 345 3.827634 CCCGATTAGCAGTTGGGC 58.172 61.111 0.00 0.00 33.56 5.36
344 346 1.097547 CAGCCCGATTAGCAGTTGGG 61.098 60.000 4.38 4.38 42.40 4.12
345 347 1.718757 GCAGCCCGATTAGCAGTTGG 61.719 60.000 0.00 0.00 0.00 3.77
346 348 1.718757 GGCAGCCCGATTAGCAGTTG 61.719 60.000 0.00 0.00 0.00 3.16
347 349 1.452108 GGCAGCCCGATTAGCAGTT 60.452 57.895 0.00 0.00 0.00 3.16
348 350 2.190578 GGCAGCCCGATTAGCAGT 59.809 61.111 0.00 0.00 0.00 4.40
351 353 4.956932 GGGGGCAGCCCGATTAGC 62.957 72.222 25.18 9.09 46.66 3.09
383 385 4.454678 CCAAATAGCAGGCAGACTAATGA 58.545 43.478 0.00 0.00 0.00 2.57
465 468 4.174009 CACGACACGACCTGATTATCTTT 58.826 43.478 0.00 0.00 0.00 2.52
466 469 3.770666 CACGACACGACCTGATTATCTT 58.229 45.455 0.00 0.00 0.00 2.40
531 553 2.359975 GCACAGGCTAAACGGGCT 60.360 61.111 0.00 0.00 42.97 5.19
952 1010 1.880027 CCGGAAACTCTTGGAAGGTTG 59.120 52.381 0.00 0.00 0.00 3.77
1052 1115 7.727331 TTCAGACATTAAAAGGCAAAATTGG 57.273 32.000 0.00 0.00 0.00 3.16
1173 1252 6.721318 AGTCTAAAATGGCATCCTTCTTGTA 58.279 36.000 0.00 0.00 0.00 2.41
1335 1780 5.009310 ACAGACACTCGTTACAAGTGACATA 59.991 40.000 10.67 0.00 45.64 2.29
1342 1787 3.966154 ACTGACAGACACTCGTTACAAG 58.034 45.455 10.08 0.00 0.00 3.16
1363 1808 1.810221 GACAAAACCGCGTCGAACGA 61.810 55.000 4.92 0.00 46.05 3.85
1535 1983 4.081198 TGCCTTTGGTCTTGTGTTCAAATT 60.081 37.500 0.00 0.00 32.87 1.82
1536 1984 3.450457 TGCCTTTGGTCTTGTGTTCAAAT 59.550 39.130 0.00 0.00 32.87 2.32
1576 2024 7.962918 CACAACTTGGTTGCAAAGTACTATATC 59.037 37.037 0.00 0.00 46.20 1.63
1588 2050 2.822561 TCAACTTCACAACTTGGTTGCA 59.177 40.909 9.89 0.00 46.20 4.08
1593 2055 6.226787 AGATAGACTCAACTTCACAACTTGG 58.773 40.000 0.00 0.00 0.00 3.61
1594 2056 7.655328 AGAAGATAGACTCAACTTCACAACTTG 59.345 37.037 0.00 0.00 40.47 3.16
1595 2162 7.655328 CAGAAGATAGACTCAACTTCACAACTT 59.345 37.037 0.00 0.00 40.47 2.66
1610 2177 5.352846 GGCTGTCCTTTTTCAGAAGATAGAC 59.647 44.000 0.00 0.00 34.02 2.59
1755 2323 4.391830 TCGCAAAAAGAAGTAGTATGGCAG 59.608 41.667 0.00 0.00 0.00 4.85
1770 2338 2.020720 TGCCACTTCTTCTCGCAAAAA 58.979 42.857 0.00 0.00 0.00 1.94
1958 2534 2.849942 TGGTGCGAGATTCCCAATATG 58.150 47.619 0.00 0.00 0.00 1.78
1963 2539 3.358111 TTTAATGGTGCGAGATTCCCA 57.642 42.857 0.00 0.00 0.00 4.37
2041 2617 0.542702 CAATTTGGCCCTGAGGTGGT 60.543 55.000 0.00 0.00 34.57 4.16
2042 2618 0.251742 TCAATTTGGCCCTGAGGTGG 60.252 55.000 0.00 0.00 34.57 4.61
2172 2748 8.887717 ACATGAGAATGCAAAGAACTTACTATC 58.112 33.333 0.00 0.00 0.00 2.08
2173 2749 8.671921 CACATGAGAATGCAAAGAACTTACTAT 58.328 33.333 0.00 0.00 0.00 2.12
2174 2750 7.361201 GCACATGAGAATGCAAAGAACTTACTA 60.361 37.037 0.00 0.00 41.65 1.82
2175 2751 6.569226 GCACATGAGAATGCAAAGAACTTACT 60.569 38.462 0.00 0.00 41.65 2.24
2387 2971 7.094377 TGGCCTATCTAACATCAAAACAAGTTC 60.094 37.037 3.32 0.00 0.00 3.01
2403 2988 3.740115 GGCGAAAAGAATGGCCTATCTA 58.260 45.455 3.32 0.00 42.29 1.98
2423 3008 1.160137 GCAACTGCTACAAGACCAGG 58.840 55.000 0.00 0.00 38.21 4.45
2677 3266 9.691362 ATGTTTTTCAATTCAACATGTACTACC 57.309 29.630 0.00 0.00 39.22 3.18
2906 3497 3.116096 ACCCTGCCTCTACAATCTACA 57.884 47.619 0.00 0.00 0.00 2.74
2907 3498 3.451178 TCAACCCTGCCTCTACAATCTAC 59.549 47.826 0.00 0.00 0.00 2.59
2908 3499 3.719871 TCAACCCTGCCTCTACAATCTA 58.280 45.455 0.00 0.00 0.00 1.98
2909 3500 2.551270 TCAACCCTGCCTCTACAATCT 58.449 47.619 0.00 0.00 0.00 2.40
2910 3501 3.567478 ATCAACCCTGCCTCTACAATC 57.433 47.619 0.00 0.00 0.00 2.67
2911 3502 4.322057 AAATCAACCCTGCCTCTACAAT 57.678 40.909 0.00 0.00 0.00 2.71
2912 3503 3.806949 AAATCAACCCTGCCTCTACAA 57.193 42.857 0.00 0.00 0.00 2.41
3156 3754 5.504830 GGCTCTTGACTTCTTGTTGAAACTC 60.505 44.000 0.00 0.00 33.79 3.01
3211 3810 7.175467 TGCAAAATATCATGTGGGAGATATCAC 59.825 37.037 5.32 0.00 36.65 3.06
3273 3872 8.777413 TGAAGATCAAATATAGCATGTACTTGC 58.223 33.333 22.56 22.56 43.09 4.01
3733 4431 1.151668 GCTGCTGTACCAGTGTTCAG 58.848 55.000 0.00 0.00 41.38 3.02
3827 4525 7.360861 CGTTGACATGGTCTAATAGCAAAAGAA 60.361 37.037 0.00 0.00 39.48 2.52
3829 4527 6.128282 ACGTTGACATGGTCTAATAGCAAAAG 60.128 38.462 0.00 0.00 39.48 2.27
3918 4619 3.071892 ACCTACTTGAACGGATGGTTTCA 59.928 43.478 0.00 0.00 39.50 2.69
3976 4678 7.924412 ACAATGGAGATGAATGCAATATTCAAC 59.076 33.333 5.38 3.41 40.84 3.18
3985 4687 5.925506 AATGAACAATGGAGATGAATGCA 57.074 34.783 0.00 0.00 0.00 3.96
4001 4703 2.825532 ACATGGCCACCTACAAATGAAC 59.174 45.455 8.16 0.00 0.00 3.18
4038 4740 2.934553 CTCGGAGAAAATTTACCGGGTC 59.065 50.000 22.04 4.84 44.57 4.46
4067 4769 3.900601 GAGAATCCCTCTTCTCATGGCTA 59.099 47.826 8.55 0.00 46.81 3.93
4106 4808 4.038642 GGAGAATCGTTCTTAGCAGAGGAT 59.961 45.833 2.51 0.00 40.87 3.24
4165 4867 3.971245 TTTCTGTTGCCAAAACACCTT 57.029 38.095 0.00 0.00 0.00 3.50
4209 4911 1.556911 TCAGGTCTCCTTTGATGCCTC 59.443 52.381 0.00 0.00 0.00 4.70
4244 6309 5.818678 AGAACATACAACAACCCACTAGA 57.181 39.130 0.00 0.00 0.00 2.43
4402 6470 9.959749 CTTAAGACTTAAGGCAACAAATTGTAA 57.040 29.630 22.36 0.00 39.11 2.41
4574 6672 7.122138 TGCATGCTTCCCATTTTGATATAAA 57.878 32.000 20.33 0.00 29.71 1.40
4576 6674 5.244402 CCTGCATGCTTCCCATTTTGATATA 59.756 40.000 20.33 0.00 29.71 0.86
4582 6680 1.648116 ACCTGCATGCTTCCCATTTT 58.352 45.000 20.33 0.00 29.71 1.82
4616 6726 5.416947 ACCGAGATGACCAATAGTAAACAC 58.583 41.667 0.00 0.00 0.00 3.32
4684 6798 1.270305 GGGAAAGGAAAAGGCAAGTGC 60.270 52.381 0.00 0.00 41.14 4.40
4782 7029 7.961283 GCTGTTTAAATAGAGTTAACTTTCGGG 59.039 37.037 15.41 0.00 0.00 5.14
4920 7167 8.432805 AGAGCTTTGGCACATAATATACTTACT 58.567 33.333 0.00 0.00 39.30 2.24


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

AutoCloner maintained by Alex Coulton.