Multiple sequence alignment - TraesCS5D01G509600

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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 TraesCS5D01G509600 chr5D 100.000 5865 0 0 1 5865 534634783 534640647 0.000000e+00 10831.0
1 TraesCS5D01G509600 chr5D 96.894 2640 64 9 2240 4872 534856915 534859543 0.000000e+00 4405.0
2 TraesCS5D01G509600 chr5D 94.652 2487 130 3 2219 4703 534865016 534867501 0.000000e+00 3853.0
3 TraesCS5D01G509600 chr5D 82.374 278 34 10 1310 1585 534856097 534856361 1.640000e-55 228.0
4 TraesCS5D01G509600 chr5B 95.786 5529 160 30 1 5478 674889973 674895479 0.000000e+00 8852.0
5 TraesCS5D01G509600 chr5B 94.299 3052 137 15 2222 5245 675080189 675083231 0.000000e+00 4638.0
6 TraesCS5D01G509600 chr5B 94.974 2487 122 3 2219 4703 675423371 675425856 0.000000e+00 3897.0
7 TraesCS5D01G509600 chr5B 85.846 325 21 4 5557 5857 674895615 674895938 7.330000e-84 322.0
8 TraesCS5D01G509600 chr5B 82.734 278 33 10 1310 1585 675079085 675079349 3.530000e-57 233.0
9 TraesCS5D01G509600 chr5B 86.170 188 22 2 5556 5740 279028084 279027898 3.580000e-47 200.0
10 TraesCS5D01G509600 chr5B 84.324 185 26 2 5556 5739 566962262 566962080 1.680000e-40 178.0
11 TraesCS5D01G509600 chr5B 77.206 272 44 9 1315 1585 251567767 251567513 6.130000e-30 143.0
12 TraesCS5D01G509600 chr4A 95.900 2634 95 7 2240 4872 636687176 636684555 0.000000e+00 4253.0
13 TraesCS5D01G509600 chr4A 94.579 2472 132 2 2240 4710 636680085 636677615 0.000000e+00 3821.0
14 TraesCS5D01G509600 chr4A 85.046 1752 179 49 1 1711 636967287 636965578 0.000000e+00 1707.0
15 TraesCS5D01G509600 chr4A 84.078 358 35 10 238 590 638474683 638475023 5.670000e-85 326.0
16 TraesCS5D01G509600 chr4A 82.437 279 40 8 1310 1585 636687967 636687695 9.830000e-58 235.0
17 TraesCS5D01G509600 chr4A 86.471 170 23 0 5564 5733 705435789 705435958 2.790000e-43 187.0
18 TraesCS5D01G509600 chr4A 85.955 178 20 5 5559 5733 705244752 705244577 1.000000e-42 185.0
19 TraesCS5D01G509600 chr4A 91.489 47 2 2 1805 1849 650851198 650851244 4.910000e-06 63.9
20 TraesCS5D01G509600 chr4A 91.489 47 2 2 1805 1849 650861401 650861447 4.910000e-06 63.9
21 TraesCS5D01G509600 chr7B 93.397 2605 157 14 2240 4841 624351116 624353708 0.000000e+00 3843.0
22 TraesCS5D01G509600 chr7A 94.633 2478 132 1 2240 4717 657353214 657355690 0.000000e+00 3838.0
23 TraesCS5D01G509600 chr7A 85.042 361 32 10 238 593 668745830 668745487 1.210000e-91 348.0
24 TraesCS5D01G509600 chr7A 83.696 276 27 7 238 512 32211313 32211055 1.630000e-60 244.0
25 TraesCS5D01G509600 chr2B 87.088 364 40 6 236 593 104864520 104864158 7.080000e-109 405.0
26 TraesCS5D01G509600 chr2B 90.960 177 11 4 5563 5738 732640538 732640366 3.530000e-57 233.0
27 TraesCS5D01G509600 chr2B 93.333 45 1 2 1807 1849 221924886 221924842 1.360000e-06 65.8
28 TraesCS5D01G509600 chr6B 86.908 359 37 7 238 590 272620966 272620612 1.530000e-105 394.0
29 TraesCS5D01G509600 chr1B 87.156 327 24 2 5556 5865 561548034 561547709 7.230000e-94 355.0
30 TraesCS5D01G509600 chr1B 85.321 327 30 2 5556 5865 561546960 561546635 7.330000e-84 322.0
31 TraesCS5D01G509600 chr1B 77.007 274 41 15 1315 1585 197788455 197788709 2.850000e-28 137.0
32 TraesCS5D01G509600 chr1B 95.349 43 1 1 1808 1849 634510067 634510109 3.790000e-07 67.6
33 TraesCS5D01G509600 chr5A 84.211 361 35 10 238 593 135147720 135147377 1.220000e-86 331.0
34 TraesCS5D01G509600 chr7D 79.061 277 35 10 5573 5830 390933331 390933603 1.010000e-37 169.0
35 TraesCS5D01G509600 chr2A 83.721 172 26 2 5563 5733 674201649 674201819 1.690000e-35 161.0
36 TraesCS5D01G509600 chr2A 94.118 51 1 2 5431 5480 513247798 513247847 6.300000e-10 76.8
37 TraesCS5D01G509600 chr6D 77.206 272 45 11 1315 1585 248585096 248585351 6.130000e-30 143.0
38 TraesCS5D01G509600 chr3B 78.829 222 35 7 1365 1585 631814028 631813818 7.930000e-29 139.0
39 TraesCS5D01G509600 chr1D 95.745 47 0 2 1803 1848 436041618 436041573 2.270000e-09 75.0
40 TraesCS5D01G509600 chr1A 95.652 46 2 0 1803 1848 533221349 533221304 2.270000e-09 75.0
41 TraesCS5D01G509600 chr1A 95.349 43 0 2 1809 1849 121538529 121538571 3.790000e-07 67.6
42 TraesCS5D01G509600 chr1A 91.489 47 3 1 1804 1849 511009312 511009266 4.910000e-06 63.9


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 TraesCS5D01G509600 chr5D 534634783 534640647 5864 False 10831.0 10831 100.0000 1 5865 1 chr5D.!!$F1 5864
1 TraesCS5D01G509600 chr5D 534865016 534867501 2485 False 3853.0 3853 94.6520 2219 4703 1 chr5D.!!$F2 2484
2 TraesCS5D01G509600 chr5D 534856097 534859543 3446 False 2316.5 4405 89.6340 1310 4872 2 chr5D.!!$F3 3562
3 TraesCS5D01G509600 chr5B 674889973 674895938 5965 False 4587.0 8852 90.8160 1 5857 2 chr5B.!!$F2 5856
4 TraesCS5D01G509600 chr5B 675423371 675425856 2485 False 3897.0 3897 94.9740 2219 4703 1 chr5B.!!$F1 2484
5 TraesCS5D01G509600 chr5B 675079085 675083231 4146 False 2435.5 4638 88.5165 1310 5245 2 chr5B.!!$F3 3935
6 TraesCS5D01G509600 chr4A 636677615 636680085 2470 True 3821.0 3821 94.5790 2240 4710 1 chr4A.!!$R1 2470
7 TraesCS5D01G509600 chr4A 636684555 636687967 3412 True 2244.0 4253 89.1685 1310 4872 2 chr4A.!!$R4 3562
8 TraesCS5D01G509600 chr4A 636965578 636967287 1709 True 1707.0 1707 85.0460 1 1711 1 chr4A.!!$R2 1710
9 TraesCS5D01G509600 chr7B 624351116 624353708 2592 False 3843.0 3843 93.3970 2240 4841 1 chr7B.!!$F1 2601
10 TraesCS5D01G509600 chr7A 657353214 657355690 2476 False 3838.0 3838 94.6330 2240 4717 1 chr7A.!!$F1 2477
11 TraesCS5D01G509600 chr1B 561546635 561548034 1399 True 338.5 355 86.2385 5556 5865 2 chr1B.!!$R1 309

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
487 512 0.314935 TTGCTTACTTTGCTGCCTGC 59.685 50.000 0.00 0.0 43.25 4.85 F
557 588 1.015109 GAGATGCATGTCACTGCCTG 58.985 55.000 18.39 0.0 41.58 4.85 F
877 922 1.210931 CATGTGTGCTTGCTTCCCG 59.789 57.895 0.00 0.0 0.00 5.14 F
1877 1957 2.787035 ACTTGGGGTCCTAGGTTTCAAA 59.213 45.455 9.08 0.0 30.92 2.69 F
2052 2134 7.829211 AGATTGTGTTTAGCCATGTTACTGTAT 59.171 33.333 0.00 0.0 0.00 2.29 F
4373 4756 2.308722 GGTTGAGATCCAGGCCCCA 61.309 63.158 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1457 8.295288 AGAATTGAACAAGAATGAGATGTGAAC 58.705 33.333 0.00 0.0 0.00 3.18 R
1877 1957 8.333235 TGATTATACACCAAACTGGGTAGATTT 58.667 33.333 0.00 0.0 43.37 2.17 R
2874 3257 1.685517 CAGCCTCTCCATCATCTTCGA 59.314 52.381 0.00 0.0 0.00 3.71 R
4373 4756 1.320344 TACCGCCGAGTGCATTCTCT 61.320 55.000 7.68 0.0 41.33 3.10 R
4496 4879 2.845363 GGGTACTTGAGAACCCGAAA 57.155 50.000 0.00 0.0 45.73 3.46 R
5352 5788 0.034337 CCCGAAAGTGGGTCGAGAAA 59.966 55.000 0.00 0.0 44.76 2.52 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
155 158 2.948134 GCCGGATTCGTCGTCGTC 60.948 66.667 5.05 0.00 38.33 4.20
229 232 4.489771 CTTGCTCCGGGGGCGATT 62.490 66.667 15.40 0.00 0.00 3.34
281 286 2.507102 CTGCGTGCGTCCACTAGG 60.507 66.667 0.00 0.00 39.86 3.02
487 512 0.314935 TTGCTTACTTTGCTGCCTGC 59.685 50.000 0.00 0.00 43.25 4.85
557 588 1.015109 GAGATGCATGTCACTGCCTG 58.985 55.000 18.39 0.00 41.58 4.85
582 613 7.652909 TGGCATGCTTAATCTAATTTAATGTGC 59.347 33.333 18.92 0.00 0.00 4.57
620 651 2.206750 TGTCGGTGTGTTTTGCTACTC 58.793 47.619 0.00 0.00 0.00 2.59
643 676 9.047947 ACTCCTCTATGTAATTTTAGTTCAGGT 57.952 33.333 0.00 0.00 0.00 4.00
674 707 6.484540 CATGAATTTTTCTCTGATCTGACCG 58.515 40.000 0.00 0.00 0.00 4.79
683 716 2.095212 TCTGATCTGACCGTTTCGTCTG 60.095 50.000 0.00 0.00 33.70 3.51
742 776 3.696051 GTGCTCACCATGTATGATTTGGT 59.304 43.478 0.00 0.00 44.49 3.67
766 800 3.328535 TCTCAGTGCTCCCCATGTATA 57.671 47.619 0.00 0.00 0.00 1.47
793 830 2.363680 CTCTGATCTGACCATTAGCCGT 59.636 50.000 0.00 0.00 0.00 5.68
829 866 4.522405 TGTACTTATGCACTGTTTTGCCAT 59.478 37.500 0.00 0.00 42.25 4.40
877 922 1.210931 CATGTGTGCTTGCTTCCCG 59.789 57.895 0.00 0.00 0.00 5.14
1084 1131 9.336171 AGCCTTTCTAACTTGATTAGATCAATC 57.664 33.333 4.03 3.42 46.96 2.67
1117 1164 5.049612 GCTTTACTATTATTCACCCCTTCGC 60.050 44.000 0.00 0.00 0.00 4.70
1146 1193 7.905604 TGTACAGATCTGGAAGTATTTTGTG 57.094 36.000 26.08 0.00 33.76 3.33
1166 1213 3.505680 GTGTAGTTGGTGAAATCCATGCA 59.494 43.478 0.00 0.00 37.33 3.96
1280 1327 6.442952 GTGATGTGTGTTTTTGCATTACCTA 58.557 36.000 0.00 0.00 0.00 3.08
1396 1457 6.603237 TTGCTGGATATTCATGTTTAGTCG 57.397 37.500 0.00 0.00 0.00 4.18
1406 1467 6.706055 TTCATGTTTAGTCGTTCACATCTC 57.294 37.500 0.00 0.00 0.00 2.75
1877 1957 2.787035 ACTTGGGGTCCTAGGTTTCAAA 59.213 45.455 9.08 0.00 30.92 2.69
1899 1979 8.164733 TCAAAAATCTACCCAGTTTGGTGTATA 58.835 33.333 0.00 0.00 39.53 1.47
2052 2134 7.829211 AGATTGTGTTTAGCCATGTTACTGTAT 59.171 33.333 0.00 0.00 0.00 2.29
4373 4756 2.308722 GGTTGAGATCCAGGCCCCA 61.309 63.158 0.00 0.00 0.00 4.96
4496 4879 1.454111 CCTCCCGGTCATCGAGTCT 60.454 63.158 0.00 0.00 42.43 3.24
4649 5032 3.357079 CGCAAGCGCAAGGGTCTT 61.357 61.111 11.47 0.00 38.40 3.01
4679 5062 3.848975 AGATGACCCCTCTGTCTGATTTT 59.151 43.478 0.00 0.00 36.21 1.82
4774 5157 8.616076 GCTGCACTATTATTTTCTGTCTATTGT 58.384 33.333 0.00 0.00 0.00 2.71
4808 5212 6.501805 TGTATTGCTATTGGGATGTCCTATCT 59.498 38.462 0.00 0.00 33.19 1.98
4809 5213 4.897509 TGCTATTGGGATGTCCTATCTG 57.102 45.455 0.00 0.00 33.19 2.90
4810 5214 4.234550 TGCTATTGGGATGTCCTATCTGT 58.765 43.478 0.00 0.00 33.19 3.41
4811 5215 4.284490 TGCTATTGGGATGTCCTATCTGTC 59.716 45.833 0.00 0.00 33.19 3.51
4812 5216 4.619394 GCTATTGGGATGTCCTATCTGTCG 60.619 50.000 0.00 0.00 33.19 4.35
4815 5219 2.307768 GGGATGTCCTATCTGTCGTGA 58.692 52.381 0.00 0.00 35.95 4.35
4816 5220 2.894126 GGGATGTCCTATCTGTCGTGAT 59.106 50.000 0.00 0.00 35.95 3.06
4817 5221 4.079970 GGGATGTCCTATCTGTCGTGATA 58.920 47.826 0.00 0.00 35.95 2.15
4818 5222 4.082679 GGGATGTCCTATCTGTCGTGATAC 60.083 50.000 0.00 0.00 35.95 2.24
4819 5223 4.762765 GGATGTCCTATCTGTCGTGATACT 59.237 45.833 0.00 0.00 0.00 2.12
4820 5224 5.335269 GGATGTCCTATCTGTCGTGATACTG 60.335 48.000 0.00 0.00 0.00 2.74
4821 5225 3.883489 TGTCCTATCTGTCGTGATACTGG 59.117 47.826 0.00 0.00 0.00 4.00
4822 5226 2.885266 TCCTATCTGTCGTGATACTGGC 59.115 50.000 0.00 0.00 0.00 4.85
4823 5227 2.623416 CCTATCTGTCGTGATACTGGCA 59.377 50.000 0.00 0.00 0.00 4.92
4824 5228 2.586258 ATCTGTCGTGATACTGGCAC 57.414 50.000 0.00 0.00 0.00 5.01
4825 5229 1.545841 TCTGTCGTGATACTGGCACT 58.454 50.000 0.00 0.00 34.18 4.40
4826 5230 1.893137 TCTGTCGTGATACTGGCACTT 59.107 47.619 0.00 0.00 34.18 3.16
4827 5231 2.299013 TCTGTCGTGATACTGGCACTTT 59.701 45.455 0.00 0.00 34.18 2.66
4828 5232 2.412870 TGTCGTGATACTGGCACTTTG 58.587 47.619 0.00 0.00 34.18 2.77
4829 5233 2.224185 TGTCGTGATACTGGCACTTTGT 60.224 45.455 0.00 0.00 34.18 2.83
5029 5453 6.899089 TCCCTGCTCTTATCATCATTTTACA 58.101 36.000 0.00 0.00 0.00 2.41
5084 5508 2.821378 TCGAAATGTGTTCCCTCGTCTA 59.179 45.455 0.00 0.00 0.00 2.59
5170 5599 3.378742 ACAGTACATAGCTCTCCAGTTCG 59.621 47.826 0.00 0.00 0.00 3.95
5182 5611 5.731126 GCTCTCCAGTTCGTACTCTACAATC 60.731 48.000 0.00 0.00 30.26 2.67
5297 5733 3.609853 TCTGTTGGTGCTGACAATATCC 58.390 45.455 0.00 0.00 0.00 2.59
5309 5745 5.029807 TGACAATATCCGAACTTGGCATA 57.970 39.130 0.00 0.00 33.09 3.14
5335 5771 6.588719 TTCTTTGGAATAATGAAGGGTGTG 57.411 37.500 0.00 0.00 0.00 3.82
5360 5796 5.363979 AGAGCAAAAATTCCTTTCTCGAC 57.636 39.130 0.00 0.00 0.00 4.20
5368 5804 2.833631 TCCTTTCTCGACCCACTTTC 57.166 50.000 0.00 0.00 0.00 2.62
5370 5806 1.429463 CTTTCTCGACCCACTTTCGG 58.571 55.000 0.00 0.00 37.09 4.30
5387 5825 3.322211 TCGGGTGTTTGGTAGTGTATG 57.678 47.619 0.00 0.00 0.00 2.39
5392 5830 4.506095 GGGTGTTTGGTAGTGTATGAAGGT 60.506 45.833 0.00 0.00 0.00 3.50
5396 5834 4.634012 TTGGTAGTGTATGAAGGTTGCT 57.366 40.909 0.00 0.00 0.00 3.91
5405 5843 1.967319 TGAAGGTTGCTTGAGTCCAC 58.033 50.000 0.00 0.00 0.00 4.02
5409 5847 2.047061 AGGTTGCTTGAGTCCACACTA 58.953 47.619 0.00 0.00 30.63 2.74
5424 5862 8.603242 AGTCCACACTAGTTTAACACAAATAG 57.397 34.615 0.00 0.00 0.00 1.73
5425 5863 7.660208 AGTCCACACTAGTTTAACACAAATAGG 59.340 37.037 0.00 0.00 0.00 2.57
5426 5864 7.658575 GTCCACACTAGTTTAACACAAATAGGA 59.341 37.037 0.00 0.00 0.00 2.94
5427 5865 7.658575 TCCACACTAGTTTAACACAAATAGGAC 59.341 37.037 0.00 0.00 0.00 3.85
5428 5866 7.359765 CCACACTAGTTTAACACAAATAGGACG 60.360 40.741 0.00 0.00 0.00 4.79
5429 5867 6.146673 ACACTAGTTTAACACAAATAGGACGC 59.853 38.462 0.00 0.00 0.00 5.19
5431 5869 4.060205 AGTTTAACACAAATAGGACGCGT 58.940 39.130 13.85 13.85 0.00 6.01
5432 5870 4.512571 AGTTTAACACAAATAGGACGCGTT 59.487 37.500 15.53 0.00 0.00 4.84
5433 5871 5.007921 AGTTTAACACAAATAGGACGCGTTT 59.992 36.000 15.53 7.94 0.00 3.60
5435 5873 1.533731 ACACAAATAGGACGCGTTTGG 59.466 47.619 15.53 3.27 37.20 3.28
5436 5874 1.533731 CACAAATAGGACGCGTTTGGT 59.466 47.619 15.53 4.05 37.20 3.67
5438 5876 2.031508 ACAAATAGGACGCGTTTGGTTG 60.032 45.455 15.53 16.37 37.20 3.77
5439 5877 0.519961 AATAGGACGCGTTTGGTTGC 59.480 50.000 15.53 0.00 0.00 4.17
5440 5878 1.303091 ATAGGACGCGTTTGGTTGCC 61.303 55.000 15.53 8.18 0.00 4.52
5441 5879 2.386064 TAGGACGCGTTTGGTTGCCT 62.386 55.000 15.53 16.05 0.00 4.75
5442 5880 2.051345 GACGCGTTTGGTTGCCTG 60.051 61.111 15.53 0.00 0.00 4.85
5443 5881 4.264638 ACGCGTTTGGTTGCCTGC 62.265 61.111 5.58 0.00 0.00 4.85
5444 5882 4.263209 CGCGTTTGGTTGCCTGCA 62.263 61.111 0.00 0.00 0.00 4.41
5445 5883 2.339712 GCGTTTGGTTGCCTGCAT 59.660 55.556 0.00 0.00 0.00 3.96
5446 5884 1.300853 GCGTTTGGTTGCCTGCATT 60.301 52.632 0.00 0.00 0.00 3.56
5447 5885 0.038709 GCGTTTGGTTGCCTGCATTA 60.039 50.000 0.00 0.00 0.00 1.90
5449 5887 1.539388 CGTTTGGTTGCCTGCATTAGA 59.461 47.619 0.00 0.00 0.00 2.10
5450 5888 2.668279 CGTTTGGTTGCCTGCATTAGAC 60.668 50.000 0.00 0.00 0.00 2.59
5451 5889 1.544724 TTGGTTGCCTGCATTAGACC 58.455 50.000 4.18 4.18 0.00 3.85
5452 5890 0.323360 TGGTTGCCTGCATTAGACCC 60.323 55.000 7.95 0.00 0.00 4.46
5454 5892 1.544724 GTTGCCTGCATTAGACCCAA 58.455 50.000 0.00 0.00 0.00 4.12
5455 5893 2.102578 GTTGCCTGCATTAGACCCAAT 58.897 47.619 0.00 0.00 0.00 3.16
5457 5895 1.284491 TGCCTGCATTAGACCCAATCA 59.716 47.619 0.00 0.00 0.00 2.57
5458 5896 1.952296 GCCTGCATTAGACCCAATCAG 59.048 52.381 0.00 0.00 0.00 2.90
5459 5897 2.579873 CCTGCATTAGACCCAATCAGG 58.420 52.381 0.00 0.00 32.22 3.86
5460 5898 1.952296 CTGCATTAGACCCAATCAGGC 59.048 52.381 0.00 0.00 35.39 4.85
5463 5901 0.474184 ATTAGACCCAATCAGGCCCG 59.526 55.000 0.00 0.00 35.39 6.13
5464 5902 0.912487 TTAGACCCAATCAGGCCCGT 60.912 55.000 0.00 0.00 35.39 5.28
5479 5917 1.506262 CCGTGCGGGAAGAAAATGG 59.494 57.895 2.15 0.00 38.47 3.16
5480 5918 1.506262 CGTGCGGGAAGAAAATGGG 59.494 57.895 0.00 0.00 0.00 4.00
5481 5919 1.215382 GTGCGGGAAGAAAATGGGC 59.785 57.895 0.00 0.00 0.00 5.36
5483 5921 1.215382 GCGGGAAGAAAATGGGCAC 59.785 57.895 0.00 0.00 0.00 5.01
5528 5966 0.658368 GACGAGCTAGATCGAGCACA 59.342 55.000 34.72 0.00 45.56 4.57
5530 5968 1.064803 ACGAGCTAGATCGAGCACAAG 59.935 52.381 34.72 16.98 45.56 3.16
5531 5969 1.599171 CGAGCTAGATCGAGCACAAGG 60.599 57.143 25.49 7.29 45.56 3.61
5532 5970 1.678627 GAGCTAGATCGAGCACAAGGA 59.321 52.381 26.72 0.00 45.43 3.36
5533 5971 1.680735 AGCTAGATCGAGCACAAGGAG 59.319 52.381 26.72 0.00 45.43 3.69
5542 5980 4.722700 CACAAGGAGTGGGCCCCG 62.723 72.222 22.27 0.88 44.69 5.73
5544 5982 3.966543 CAAGGAGTGGGCCCCGTT 61.967 66.667 22.27 9.13 0.00 4.44
5545 5983 3.966543 AAGGAGTGGGCCCCGTTG 61.967 66.667 22.27 0.00 0.00 4.10
5548 5986 4.740822 GAGTGGGCCCCGTTGCAT 62.741 66.667 22.27 0.00 0.00 3.96
5551 5989 4.738998 TGGGCCCCGTTGCATGAG 62.739 66.667 22.27 0.00 0.00 2.90
5552 5990 4.424711 GGGCCCCGTTGCATGAGA 62.425 66.667 12.23 0.00 0.00 3.27
5554 5992 2.825836 GCCCCGTTGCATGAGAGG 60.826 66.667 0.00 0.00 0.00 3.69
5555 5993 2.989639 CCCCGTTGCATGAGAGGA 59.010 61.111 0.00 0.00 0.00 3.71
5557 5995 1.450312 CCCGTTGCATGAGAGGACC 60.450 63.158 0.00 0.00 0.00 4.46
5558 5996 1.599047 CCGTTGCATGAGAGGACCT 59.401 57.895 0.00 0.00 0.00 3.85
5559 5997 0.460987 CCGTTGCATGAGAGGACCTC 60.461 60.000 14.15 14.15 42.30 3.85
5560 5998 0.534412 CGTTGCATGAGAGGACCTCT 59.466 55.000 24.56 24.56 44.28 3.69
5660 6248 4.993584 AGATGCACATCGATCTTATGGTTC 59.006 41.667 0.00 0.00 42.48 3.62
5689 6277 5.803461 CAGACGATCGGTTTGTAGTTTCATA 59.197 40.000 20.98 0.00 0.00 2.15
5693 6281 7.039882 ACGATCGGTTTGTAGTTTCATAGATT 58.960 34.615 20.98 0.00 0.00 2.40
5759 6364 3.102972 CTCTTGAGGAACATGAGGGAGA 58.897 50.000 0.00 0.00 42.97 3.71
5831 6443 1.776710 AGGTACTTGGTTGGGGGCA 60.777 57.895 0.00 0.00 27.25 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 179 3.120105 CAGCAGATCTACCGCGGA 58.880 61.111 35.90 14.96 0.00 5.54
229 232 1.750018 CATCCATCCACGCCAGCAA 60.750 57.895 0.00 0.00 0.00 3.91
281 286 2.277084 CACCTAAGCAACCACCGATAC 58.723 52.381 0.00 0.00 0.00 2.24
292 297 2.582436 GCGCCTACCACCTAAGCA 59.418 61.111 0.00 0.00 0.00 3.91
354 367 2.900546 ACACGAACTCCTCTCTGGAATT 59.099 45.455 0.00 0.00 45.63 2.17
355 368 2.530701 ACACGAACTCCTCTCTGGAAT 58.469 47.619 0.00 0.00 45.63 3.01
366 379 3.979495 ACACGATAACAGAACACGAACTC 59.021 43.478 0.00 0.00 0.00 3.01
509 537 1.155889 CACGCTGAACATGGTAGCAA 58.844 50.000 15.34 0.00 37.29 3.91
531 559 4.096833 GCAGTGACATGCATCTCCATTTTA 59.903 41.667 0.00 0.00 45.77 1.52
557 588 7.652909 TGCACATTAAATTAGATTAAGCATGCC 59.347 33.333 15.66 0.00 33.88 4.40
620 651 9.449719 AACACCTGAACTAAAATTACATAGAGG 57.550 33.333 0.00 0.00 0.00 3.69
643 676 6.146601 TCAGAGAAAAATTCATGCACAACA 57.853 33.333 0.00 0.00 0.00 3.33
647 680 6.746364 GTCAGATCAGAGAAAAATTCATGCAC 59.254 38.462 0.00 0.00 0.00 4.57
674 707 6.183360 CCCACACATAATAGTTCAGACGAAAC 60.183 42.308 0.00 0.00 31.43 2.78
683 716 6.017605 CAGAAGATGCCCACACATAATAGTTC 60.018 42.308 0.00 0.00 0.00 3.01
742 776 2.158475 ACATGGGGAGCACTGAGAAAAA 60.158 45.455 0.00 0.00 0.00 1.94
766 800 6.112058 GCTAATGGTCAGATCAGAGAAACTT 58.888 40.000 0.00 0.00 0.00 2.66
788 824 1.152756 AGCCCAAAACAAGACGGCT 60.153 52.632 0.00 0.00 45.12 5.52
789 825 1.007387 CAGCCCAAAACAAGACGGC 60.007 57.895 0.00 0.00 40.03 5.68
793 830 4.217550 GCATAAGTACAGCCCAAAACAAGA 59.782 41.667 0.00 0.00 0.00 3.02
829 866 7.966246 ATTTCTTTTGCAAGCAATGTATGAA 57.034 28.000 8.46 5.46 35.70 2.57
877 922 2.629051 AGCTTGACGCCTAATTACACC 58.371 47.619 0.00 0.00 40.39 4.16
1084 1131 7.442666 GGTGAATAATAGTAAAGCTTCTCAGGG 59.557 40.741 0.00 0.00 0.00 4.45
1117 1164 9.877178 AAAATACTTCCAGATCTGTACAACTAG 57.123 33.333 21.11 9.41 0.00 2.57
1146 1193 4.158394 ACATGCATGGATTTCACCAACTAC 59.842 41.667 29.41 0.00 43.47 2.73
1166 1213 7.121315 GGCTGTAAAACTATGAGGAAGAAACAT 59.879 37.037 0.00 0.00 0.00 2.71
1396 1457 8.295288 AGAATTGAACAAGAATGAGATGTGAAC 58.705 33.333 0.00 0.00 0.00 3.18
1877 1957 8.333235 TGATTATACACCAAACTGGGTAGATTT 58.667 33.333 0.00 0.00 43.37 2.17
2675 3058 4.942852 AGAAAGTCTGATATGCTTCCTCG 58.057 43.478 0.00 0.00 0.00 4.63
2874 3257 1.685517 CAGCCTCTCCATCATCTTCGA 59.314 52.381 0.00 0.00 0.00 3.71
4373 4756 1.320344 TACCGCCGAGTGCATTCTCT 61.320 55.000 7.68 0.00 41.33 3.10
4496 4879 2.845363 GGGTACTTGAGAACCCGAAA 57.155 50.000 0.00 0.00 45.73 3.46
4523 4906 4.479993 GCCTGGCCAGATGTCGCT 62.480 66.667 34.91 0.00 0.00 4.93
4649 5032 3.107601 CAGAGGGGTCATCTGTTCCTTA 58.892 50.000 1.91 0.00 39.48 2.69
4679 5062 4.821805 CCAAAAGTTTAGAGCTTGTCCTCA 59.178 41.667 0.00 0.00 34.26 3.86
4774 5157 2.935849 CAATAGCAATACAGCCACGACA 59.064 45.455 0.00 0.00 34.23 4.35
4808 5212 2.224185 ACAAAGTGCCAGTATCACGACA 60.224 45.455 0.00 0.00 39.31 4.35
4809 5213 2.413837 ACAAAGTGCCAGTATCACGAC 58.586 47.619 0.00 0.00 39.31 4.34
4810 5214 2.831685 ACAAAGTGCCAGTATCACGA 57.168 45.000 0.00 0.00 39.31 4.35
4811 5215 3.896648 AAACAAAGTGCCAGTATCACG 57.103 42.857 0.00 0.00 39.31 4.35
4812 5216 5.587289 TCAAAAACAAAGTGCCAGTATCAC 58.413 37.500 0.00 0.00 34.80 3.06
4815 5219 6.040842 AGACATCAAAAACAAAGTGCCAGTAT 59.959 34.615 0.00 0.00 0.00 2.12
4816 5220 5.359576 AGACATCAAAAACAAAGTGCCAGTA 59.640 36.000 0.00 0.00 0.00 2.74
4817 5221 4.160252 AGACATCAAAAACAAAGTGCCAGT 59.840 37.500 0.00 0.00 0.00 4.00
4818 5222 4.685924 AGACATCAAAAACAAAGTGCCAG 58.314 39.130 0.00 0.00 0.00 4.85
4819 5223 4.734398 AGACATCAAAAACAAAGTGCCA 57.266 36.364 0.00 0.00 0.00 4.92
4820 5224 5.569059 CGATAGACATCAAAAACAAAGTGCC 59.431 40.000 0.00 0.00 39.76 5.01
4821 5225 6.370593 TCGATAGACATCAAAAACAAAGTGC 58.629 36.000 0.00 0.00 42.67 4.40
4874 5278 1.589803 AACAACGAACTACCAGTGGC 58.410 50.000 9.78 0.00 0.00 5.01
5029 5453 2.941064 CTGGACGAGTGCATCAATCAAT 59.059 45.455 0.00 0.00 0.00 2.57
5084 5508 8.814038 AGGATAAATTGAAAGATACAACTGCT 57.186 30.769 0.00 0.00 0.00 4.24
5114 5538 4.157656 TGACAAACTGCAGCTTAAACAAGT 59.842 37.500 15.27 0.36 0.00 3.16
5158 5587 3.008330 TGTAGAGTACGAACTGGAGAGC 58.992 50.000 0.00 0.00 35.56 4.09
5159 5588 5.587043 AGATTGTAGAGTACGAACTGGAGAG 59.413 44.000 0.00 0.00 35.56 3.20
5182 5611 5.402398 TCATCATCAGTTTGTGTCTACGAG 58.598 41.667 0.00 0.00 0.00 4.18
5257 5686 7.981789 CCAACAGATGCTTCTACTACAGAATAA 59.018 37.037 1.16 0.00 42.44 1.40
5297 5733 6.618287 TCCAAAGAATATATGCCAAGTTCG 57.382 37.500 0.00 0.00 0.00 3.95
5309 5745 8.917088 CACACCCTTCATTATTCCAAAGAATAT 58.083 33.333 0.00 0.00 43.01 1.28
5334 5770 3.569701 AGAAAGGAATTTTTGCTCTCGCA 59.430 39.130 0.00 0.00 46.24 5.10
5335 5771 4.162072 GAGAAAGGAATTTTTGCTCTCGC 58.838 43.478 4.98 0.00 0.00 5.03
5347 5783 3.676093 GAAAGTGGGTCGAGAAAGGAAT 58.324 45.455 0.00 0.00 0.00 3.01
5352 5788 0.034337 CCCGAAAGTGGGTCGAGAAA 59.966 55.000 0.00 0.00 44.76 2.52
5368 5804 3.322211 TCATACACTACCAAACACCCG 57.678 47.619 0.00 0.00 0.00 5.28
5370 5806 4.648651 ACCTTCATACACTACCAAACACC 58.351 43.478 0.00 0.00 0.00 4.16
5387 5825 1.604278 GTGTGGACTCAAGCAACCTTC 59.396 52.381 0.00 0.00 0.00 3.46
5392 5830 3.838244 AACTAGTGTGGACTCAAGCAA 57.162 42.857 0.00 0.00 33.21 3.91
5396 5834 5.979993 TGTGTTAAACTAGTGTGGACTCAA 58.020 37.500 0.00 0.00 33.21 3.02
5405 5843 6.531439 GCGTCCTATTTGTGTTAAACTAGTG 58.469 40.000 0.00 0.00 0.00 2.74
5409 5847 4.060205 ACGCGTCCTATTTGTGTTAAACT 58.940 39.130 5.58 0.00 0.00 2.66
5424 5862 3.284449 AGGCAACCAAACGCGTCC 61.284 61.111 14.44 7.63 37.17 4.79
5425 5863 2.051345 CAGGCAACCAAACGCGTC 60.051 61.111 14.44 0.00 37.17 5.19
5426 5864 4.264638 GCAGGCAACCAAACGCGT 62.265 61.111 5.58 5.58 37.17 6.01
5427 5865 3.556543 ATGCAGGCAACCAAACGCG 62.557 57.895 3.53 3.53 37.17 6.01
5428 5866 0.038709 TAATGCAGGCAACCAAACGC 60.039 50.000 0.00 0.00 37.17 4.84
5429 5867 1.539388 TCTAATGCAGGCAACCAAACG 59.461 47.619 0.00 0.00 37.17 3.60
5431 5869 1.892474 GGTCTAATGCAGGCAACCAAA 59.108 47.619 7.74 0.00 37.17 3.28
5432 5870 1.544724 GGTCTAATGCAGGCAACCAA 58.455 50.000 7.74 0.00 37.17 3.67
5433 5871 0.323360 GGGTCTAATGCAGGCAACCA 60.323 55.000 13.21 0.00 37.17 3.67
5435 5873 1.544724 TTGGGTCTAATGCAGGCAAC 58.455 50.000 0.00 0.00 0.00 4.17
5436 5874 2.291475 TGATTGGGTCTAATGCAGGCAA 60.291 45.455 0.00 0.00 0.00 4.52
5438 5876 1.952296 CTGATTGGGTCTAATGCAGGC 59.048 52.381 0.00 0.00 0.00 4.85
5439 5877 2.579873 CCTGATTGGGTCTAATGCAGG 58.420 52.381 0.00 0.00 33.38 4.85
5440 5878 1.952296 GCCTGATTGGGTCTAATGCAG 59.048 52.381 0.00 0.00 36.00 4.41
5441 5879 1.410083 GGCCTGATTGGGTCTAATGCA 60.410 52.381 0.00 0.00 36.00 3.96
5442 5880 1.322442 GGCCTGATTGGGTCTAATGC 58.678 55.000 0.00 0.00 36.00 3.56
5443 5881 1.815408 CGGGCCTGATTGGGTCTAATG 60.815 57.143 5.28 0.00 36.00 1.90
5444 5882 0.474184 CGGGCCTGATTGGGTCTAAT 59.526 55.000 5.28 0.00 36.00 1.73
5445 5883 0.912487 ACGGGCCTGATTGGGTCTAA 60.912 55.000 21.41 0.00 36.00 2.10
5446 5884 1.306654 ACGGGCCTGATTGGGTCTA 60.307 57.895 21.41 0.00 36.00 2.59
5447 5885 2.610859 ACGGGCCTGATTGGGTCT 60.611 61.111 21.41 0.00 36.00 3.85
5449 5887 4.740822 GCACGGGCCTGATTGGGT 62.741 66.667 21.41 0.00 36.00 4.51
5463 5901 1.215382 GCCCATTTTCTTCCCGCAC 59.785 57.895 0.00 0.00 0.00 5.34
5464 5902 1.228706 TGCCCATTTTCTTCCCGCA 60.229 52.632 0.00 0.00 0.00 5.69
5467 5905 0.610785 TCGGTGCCCATTTTCTTCCC 60.611 55.000 0.00 0.00 0.00 3.97
5468 5906 1.253100 TTCGGTGCCCATTTTCTTCC 58.747 50.000 0.00 0.00 0.00 3.46
5471 5909 1.094785 CGATTCGGTGCCCATTTTCT 58.905 50.000 0.00 0.00 0.00 2.52
5472 5910 0.100503 CCGATTCGGTGCCCATTTTC 59.899 55.000 17.08 0.00 42.73 2.29
5474 5912 3.918544 CCGATTCGGTGCCCATTT 58.081 55.556 17.08 0.00 42.73 2.32
5507 5945 2.136728 GTGCTCGATCTAGCTCGTCTA 58.863 52.381 18.92 1.20 43.19 2.59
5508 5946 0.941542 GTGCTCGATCTAGCTCGTCT 59.058 55.000 18.92 0.00 43.19 4.18
5509 5947 0.658368 TGTGCTCGATCTAGCTCGTC 59.342 55.000 18.92 9.29 43.19 4.20
5511 5949 1.599171 CCTTGTGCTCGATCTAGCTCG 60.599 57.143 18.92 9.68 43.19 5.03
5512 5950 1.678627 TCCTTGTGCTCGATCTAGCTC 59.321 52.381 18.92 15.79 43.19 4.09
5513 5951 1.680735 CTCCTTGTGCTCGATCTAGCT 59.319 52.381 18.92 0.00 43.19 3.32
5515 5953 2.223688 CCACTCCTTGTGCTCGATCTAG 60.224 54.545 0.00 0.00 44.92 2.43
5516 5954 1.751351 CCACTCCTTGTGCTCGATCTA 59.249 52.381 0.00 0.00 44.92 1.98
5517 5955 0.534412 CCACTCCTTGTGCTCGATCT 59.466 55.000 0.00 0.00 44.92 2.75
5518 5956 0.460987 CCCACTCCTTGTGCTCGATC 60.461 60.000 0.00 0.00 44.92 3.69
5519 5957 1.599047 CCCACTCCTTGTGCTCGAT 59.401 57.895 0.00 0.00 44.92 3.59
5520 5958 3.059982 CCCACTCCTTGTGCTCGA 58.940 61.111 0.00 0.00 44.92 4.04
5521 5959 2.743928 GCCCACTCCTTGTGCTCG 60.744 66.667 0.00 0.00 44.92 5.03
5522 5960 2.360475 GGCCCACTCCTTGTGCTC 60.360 66.667 0.00 0.00 44.92 4.26
5528 5966 3.966543 CAACGGGGCCCACTCCTT 61.967 66.667 26.86 3.25 0.00 3.36
5531 5969 4.740822 ATGCAACGGGGCCCACTC 62.741 66.667 26.86 5.04 0.00 3.51
5535 5973 4.424711 TCTCATGCAACGGGGCCC 62.425 66.667 15.76 15.76 0.00 5.80
5536 5974 2.825836 CTCTCATGCAACGGGGCC 60.826 66.667 0.00 0.00 0.00 5.80
5537 5975 2.825836 CCTCTCATGCAACGGGGC 60.826 66.667 0.00 0.00 0.00 5.80
5538 5976 1.450312 GTCCTCTCATGCAACGGGG 60.450 63.158 0.00 0.00 0.00 5.73
5540 5978 0.460987 GAGGTCCTCTCATGCAACGG 60.461 60.000 12.02 0.00 42.02 4.44
5554 5992 3.116900 AGAAGGGGATTAGAGGAGAGGTC 60.117 52.174 0.00 0.00 0.00 3.85
5555 5993 2.869041 AGAAGGGGATTAGAGGAGAGGT 59.131 50.000 0.00 0.00 0.00 3.85
5557 5995 3.901222 GGAAGAAGGGGATTAGAGGAGAG 59.099 52.174 0.00 0.00 0.00 3.20
5558 5996 3.538129 AGGAAGAAGGGGATTAGAGGAGA 59.462 47.826 0.00 0.00 0.00 3.71
5559 5997 3.901222 GAGGAAGAAGGGGATTAGAGGAG 59.099 52.174 0.00 0.00 0.00 3.69
5560 5998 3.375430 GGAGGAAGAAGGGGATTAGAGGA 60.375 52.174 0.00 0.00 0.00 3.71
5561 5999 2.976185 GGAGGAAGAAGGGGATTAGAGG 59.024 54.545 0.00 0.00 0.00 3.69
5660 6248 2.346803 ACAAACCGATCGTCTGAATGG 58.653 47.619 15.09 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.