Multiple sequence alignment - TraesCS2A01G297800

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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 TraesCS2A01G297800 chr2A 100.000 6283 0 0 1 6283 512224074 512230356 0.000000e+00 11603.0
1 TraesCS2A01G297800 chr2A 95.868 968 35 4 1 967 512202797 512203760 0.000000e+00 1561.0
2 TraesCS2A01G297800 chr2A 84.283 579 52 16 1 541 129867266 129867843 4.310000e-146 529.0
3 TraesCS2A01G297800 chr2A 93.536 263 15 2 1808 2069 606519063 606519324 2.120000e-104 390.0
4 TraesCS2A01G297800 chr2A 92.857 266 17 2 1808 2072 699241114 699240850 9.880000e-103 385.0
5 TraesCS2A01G297800 chr2D 97.971 3450 58 9 2158 5597 378054482 378057929 0.000000e+00 5973.0
6 TraesCS2A01G297800 chr2D 93.854 1025 52 5 791 1808 378052932 378053952 0.000000e+00 1533.0
7 TraesCS2A01G297800 chr2D 87.912 546 47 8 1 541 15192222 15192753 5.350000e-175 625.0
8 TraesCS2A01G297800 chr2D 87.103 504 49 6 3 501 463933482 463932990 1.980000e-154 556.0
9 TraesCS2A01G297800 chr2D 84.572 538 73 9 5755 6283 485467210 485466674 5.580000e-145 525.0
10 TraesCS2A01G297800 chr2D 92.830 265 17 2 1808 2071 315859248 315858985 3.550000e-102 383.0
11 TraesCS2A01G297800 chr2D 91.964 112 3 3 2056 2161 378054100 378054211 1.090000e-32 152.0
12 TraesCS2A01G297800 chr2B 97.362 3260 77 7 2346 5597 449166134 449169392 0.000000e+00 5535.0
13 TraesCS2A01G297800 chr2B 93.237 1035 57 8 778 1806 449164675 449165702 0.000000e+00 1511.0
14 TraesCS2A01G297800 chr2B 90.708 678 53 4 5615 6283 537843048 537842372 0.000000e+00 894.0
15 TraesCS2A01G297800 chr2B 96.183 262 8 2 2092 2351 449165795 449166056 1.620000e-115 427.0
16 TraesCS2A01G297800 chr7D 91.420 676 51 1 5615 6283 71820653 71821328 0.000000e+00 920.0
17 TraesCS2A01G297800 chr7D 85.227 528 58 15 5773 6283 20490087 20490611 5.580000e-145 525.0
18 TraesCS2A01G297800 chr7D 88.764 89 10 0 6195 6283 471226428 471226516 6.660000e-20 110.0
19 TraesCS2A01G297800 chr4A 90.680 676 56 5 5615 6283 698480947 698481622 0.000000e+00 893.0
20 TraesCS2A01G297800 chr4A 85.560 554 63 8 1 541 502257242 502256693 1.180000e-156 564.0
21 TraesCS2A01G297800 chr4A 92.481 266 18 2 1808 2072 207362951 207362687 4.600000e-101 379.0
22 TraesCS2A01G297800 chr4A 89.130 92 9 1 6192 6283 686000257 686000167 5.150000e-21 113.0
23 TraesCS2A01G297800 chr1A 90.547 677 55 3 5615 6283 4853661 4852986 0.000000e+00 887.0
24 TraesCS2A01G297800 chr1A 93.039 589 40 1 5615 6202 340008521 340009109 0.000000e+00 859.0
25 TraesCS2A01G297800 chr1A 93.609 266 13 4 1808 2071 539684260 539683997 1.640000e-105 394.0
26 TraesCS2A01G297800 chr1A 83.505 97 16 0 6187 6283 550787121 550787025 2.410000e-14 91.6
27 TraesCS2A01G297800 chr1D 88.534 689 59 6 5615 6283 3568464 3567776 0.000000e+00 817.0
28 TraesCS2A01G297800 chr1D 83.889 540 70 12 5760 6283 249621640 249621102 3.380000e-137 499.0
29 TraesCS2A01G297800 chr1D 84.884 86 13 0 6198 6283 458208912 458208827 3.120000e-13 87.9
30 TraesCS2A01G297800 chr1D 84.270 89 14 0 6195 6283 458267836 458267748 3.120000e-13 87.9
31 TraesCS2A01G297800 chr1D 85.057 87 10 3 6198 6283 463852492 463852408 1.120000e-12 86.1
32 TraesCS2A01G297800 chr7A 87.748 555 43 6 1 541 26810815 26811358 5.350000e-175 625.0
33 TraesCS2A01G297800 chr5A 87.044 548 58 5 1 547 189217377 189216842 1.940000e-169 606.0
34 TraesCS2A01G297800 chr5A 86.642 539 49 7 1 526 450171673 450172201 5.460000e-160 575.0
35 TraesCS2A01G297800 chr5A 84.354 588 70 14 5708 6280 611605897 611606477 1.980000e-154 556.0
36 TraesCS2A01G297800 chr5A 92.222 270 19 2 1803 2071 512225988 512225720 1.280000e-101 381.0
37 TraesCS2A01G297800 chr3A 86.531 542 55 11 1 526 609257247 609257786 1.170000e-161 580.0
38 TraesCS2A01G297800 chr3A 86.456 539 53 10 1 526 334865557 334866088 1.960000e-159 573.0
39 TraesCS2A01G297800 chr3A 85.631 515 59 12 35 540 662936628 662937136 1.550000e-145 527.0
40 TraesCS2A01G297800 chr3A 84.810 553 47 12 3 541 687672220 687671691 7.220000e-144 521.0
41 TraesCS2A01G297800 chr5B 85.551 526 58 12 5773 6283 429186853 429187375 9.270000e-148 534.0
42 TraesCS2A01G297800 chr5B 91.304 276 19 5 1804 2076 428579807 428579534 7.690000e-99 372.0
43 TraesCS2A01G297800 chr7B 84.820 527 60 13 5773 6283 478838991 478838469 4.340000e-141 512.0
44 TraesCS2A01G297800 chr6B 86.100 482 54 4 73 553 22386815 22386346 2.020000e-139 507.0
45 TraesCS2A01G297800 chr6B 90.244 82 8 0 6198 6279 457674738 457674657 2.400000e-19 108.0
46 TraesCS2A01G297800 chr6A 83.206 524 70 13 5773 6283 589638401 589638919 1.230000e-126 464.0
47 TraesCS2A01G297800 chr6A 82.443 524 75 10 5773 6283 589509757 589510276 5.780000e-120 442.0
48 TraesCS2A01G297800 chr6D 81.469 599 79 19 5704 6280 469353924 469354512 4.440000e-126 462.0
49 TraesCS2A01G297800 chr6D 87.778 90 9 2 6195 6283 44091964 44091876 3.100000e-18 104.0
50 TraesCS2A01G297800 chr6D 87.097 93 8 4 6192 6283 430877695 430877784 1.110000e-17 102.0
51 TraesCS2A01G297800 chr6D 85.057 87 10 3 6198 6283 54074690 54074774 1.120000e-12 86.1
52 TraesCS2A01G297800 chr4B 92.989 271 17 2 1808 2077 22857357 22857626 1.640000e-105 394.0
53 TraesCS2A01G297800 chr4B 88.043 92 10 1 6192 6283 450466230 450466320 2.400000e-19 108.0
54 TraesCS2A01G297800 chr3D 92.857 266 17 2 1804 2068 40324517 40324781 9.880000e-103 385.0
55 TraesCS2A01G297800 chr3D 87.500 88 9 2 6197 6283 552882765 552882679 4.010000e-17 100.0
56 TraesCS2A01G297800 chr5D 87.160 257 19 4 3 246 430718388 430718133 4.800000e-71 279.0
57 TraesCS2A01G297800 chr5D 88.362 232 27 0 6052 6283 545690941 545691172 4.800000e-71 279.0
58 TraesCS2A01G297800 chr3B 88.172 93 8 3 6192 6283 532193147 532193057 2.400000e-19 108.0
59 TraesCS2A01G297800 chr1B 86.598 97 13 0 6187 6283 628952084 628951988 2.400000e-19 108.0
60 TraesCS2A01G297800 chr1B 85.567 97 14 0 6187 6283 628876227 628876131 1.110000e-17 102.0


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 TraesCS2A01G297800 chr2A 512224074 512230356 6282 False 11603.000000 11603 100.000000 1 6283 1 chr2A.!!$F3 6282
1 TraesCS2A01G297800 chr2A 512202797 512203760 963 False 1561.000000 1561 95.868000 1 967 1 chr2A.!!$F2 966
2 TraesCS2A01G297800 chr2A 129867266 129867843 577 False 529.000000 529 84.283000 1 541 1 chr2A.!!$F1 540
3 TraesCS2A01G297800 chr2D 378052932 378057929 4997 False 2552.666667 5973 94.596333 791 5597 3 chr2D.!!$F2 4806
4 TraesCS2A01G297800 chr2D 15192222 15192753 531 False 625.000000 625 87.912000 1 541 1 chr2D.!!$F1 540
5 TraesCS2A01G297800 chr2D 485466674 485467210 536 True 525.000000 525 84.572000 5755 6283 1 chr2D.!!$R3 528
6 TraesCS2A01G297800 chr2B 449164675 449169392 4717 False 2491.000000 5535 95.594000 778 5597 3 chr2B.!!$F1 4819
7 TraesCS2A01G297800 chr2B 537842372 537843048 676 True 894.000000 894 90.708000 5615 6283 1 chr2B.!!$R1 668
8 TraesCS2A01G297800 chr7D 71820653 71821328 675 False 920.000000 920 91.420000 5615 6283 1 chr7D.!!$F2 668
9 TraesCS2A01G297800 chr7D 20490087 20490611 524 False 525.000000 525 85.227000 5773 6283 1 chr7D.!!$F1 510
10 TraesCS2A01G297800 chr4A 698480947 698481622 675 False 893.000000 893 90.680000 5615 6283 1 chr4A.!!$F1 668
11 TraesCS2A01G297800 chr4A 502256693 502257242 549 True 564.000000 564 85.560000 1 541 1 chr4A.!!$R2 540
12 TraesCS2A01G297800 chr1A 4852986 4853661 675 True 887.000000 887 90.547000 5615 6283 1 chr1A.!!$R1 668
13 TraesCS2A01G297800 chr1A 340008521 340009109 588 False 859.000000 859 93.039000 5615 6202 1 chr1A.!!$F1 587
14 TraesCS2A01G297800 chr1D 3567776 3568464 688 True 817.000000 817 88.534000 5615 6283 1 chr1D.!!$R1 668
15 TraesCS2A01G297800 chr1D 249621102 249621640 538 True 499.000000 499 83.889000 5760 6283 1 chr1D.!!$R2 523
16 TraesCS2A01G297800 chr7A 26810815 26811358 543 False 625.000000 625 87.748000 1 541 1 chr7A.!!$F1 540
17 TraesCS2A01G297800 chr5A 189216842 189217377 535 True 606.000000 606 87.044000 1 547 1 chr5A.!!$R1 546
18 TraesCS2A01G297800 chr5A 450171673 450172201 528 False 575.000000 575 86.642000 1 526 1 chr5A.!!$F1 525
19 TraesCS2A01G297800 chr5A 611605897 611606477 580 False 556.000000 556 84.354000 5708 6280 1 chr5A.!!$F2 572
20 TraesCS2A01G297800 chr3A 609257247 609257786 539 False 580.000000 580 86.531000 1 526 1 chr3A.!!$F2 525
21 TraesCS2A01G297800 chr3A 334865557 334866088 531 False 573.000000 573 86.456000 1 526 1 chr3A.!!$F1 525
22 TraesCS2A01G297800 chr3A 662936628 662937136 508 False 527.000000 527 85.631000 35 540 1 chr3A.!!$F3 505
23 TraesCS2A01G297800 chr3A 687671691 687672220 529 True 521.000000 521 84.810000 3 541 1 chr3A.!!$R1 538
24 TraesCS2A01G297800 chr5B 429186853 429187375 522 False 534.000000 534 85.551000 5773 6283 1 chr5B.!!$F1 510
25 TraesCS2A01G297800 chr7B 478838469 478838991 522 True 512.000000 512 84.820000 5773 6283 1 chr7B.!!$R1 510
26 TraesCS2A01G297800 chr6A 589638401 589638919 518 False 464.000000 464 83.206000 5773 6283 1 chr6A.!!$F2 510
27 TraesCS2A01G297800 chr6A 589509757 589510276 519 False 442.000000 442 82.443000 5773 6283 1 chr6A.!!$F1 510
28 TraesCS2A01G297800 chr6D 469353924 469354512 588 False 462.000000 462 81.469000 5704 6280 1 chr6D.!!$F3 576

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
986 1075 0.325272 AAAACCTCTCGCTCCCTTCC 59.675 55.000 0.0 0.0 0.00 3.46 F
1555 1648 0.178944 TGTGACGAGGGGAAGAAGGA 60.179 55.000 0.0 0.0 0.00 3.36 F
1556 1649 0.533032 GTGACGAGGGGAAGAAGGAG 59.467 60.000 0.0 0.0 0.00 3.69 F
2292 2747 1.064685 CCCCGTCTATTTTCCCAGCTT 60.065 52.381 0.0 0.0 0.00 3.74 F
2989 3528 1.891150 CTCTGCTTGCCATTTGGTCTT 59.109 47.619 0.0 0.0 37.57 3.01 F
4190 4733 2.063156 TCATTTGCAACGTTCATGGC 57.937 45.000 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2740 0.749091 TCGGATCATTGCAAGCTGGG 60.749 55.000 4.94 0.0 0.00 4.45 R
2771 3310 3.557595 AGCTACGTTTATGCTGCTTCATC 59.442 43.478 0.00 0.0 35.54 2.92 R
3310 3850 4.399004 AGCTCATCAGTTATGTCCTCAC 57.601 45.455 0.00 0.0 36.89 3.51 R
4235 4778 2.029623 GAGTTATGTCCACGCTCCCTA 58.970 52.381 0.00 0.0 0.00 3.53 R
4401 4944 1.674962 CAATTTCCTAGCAGCAGCCTC 59.325 52.381 0.00 0.0 43.56 4.70 R
6119 6715 0.031716 AGGGTAGAGATGGCAGCTGA 60.032 55.000 20.43 0.0 0.00 4.26 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
89 103 7.513969 CGAAAAATTGAACAAACCGAGGTAAAC 60.514 37.037 0.00 0.00 0.00 2.01
208 228 9.974980 TTGTAACATAGTCATTTTTCCCTTTTC 57.025 29.630 0.00 0.00 0.00 2.29
216 236 6.827762 AGTCATTTTTCCCTTTTCAAAATGCA 59.172 30.769 10.41 0.00 43.24 3.96
602 683 3.119990 AGCAACCATCGGAAAAATACACG 60.120 43.478 0.00 0.00 0.00 4.49
650 731 7.631811 GCCTCTTCTACATGCTACTAGAGTTTT 60.632 40.741 0.00 0.00 0.00 2.43
942 1031 4.813526 CCGTCGTCCTCGCTCACG 62.814 72.222 0.00 0.00 42.01 4.35
945 1034 2.667199 TCGTCCTCGCTCACGTGA 60.667 61.111 18.88 18.88 41.18 4.35
977 1066 0.602905 AGCCGAACCAAAACCTCTCG 60.603 55.000 0.00 0.00 0.00 4.04
986 1075 0.325272 AAAACCTCTCGCTCCCTTCC 59.675 55.000 0.00 0.00 0.00 3.46
989 1078 3.157949 CTCTCGCTCCCTTCCCCC 61.158 72.222 0.00 0.00 0.00 5.40
1047 1137 4.424711 CCCACCCCACCACCATCG 62.425 72.222 0.00 0.00 0.00 3.84
1114 1204 0.392461 GCCAACCCAACGCTAGATCA 60.392 55.000 0.00 0.00 0.00 2.92
1446 1536 2.214181 GACAGTGCTCGACGGATGGT 62.214 60.000 0.00 0.00 0.00 3.55
1492 1582 2.564947 GCATCGACCTCTCTGGGATTAT 59.435 50.000 0.00 0.00 41.11 1.28
1551 1644 2.283529 GGCTGTGACGAGGGGAAGA 61.284 63.158 0.00 0.00 0.00 2.87
1554 1647 0.247736 CTGTGACGAGGGGAAGAAGG 59.752 60.000 0.00 0.00 0.00 3.46
1555 1648 0.178944 TGTGACGAGGGGAAGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
1556 1649 0.533032 GTGACGAGGGGAAGAAGGAG 59.467 60.000 0.00 0.00 0.00 3.69
1584 1677 3.369052 GGTGGTGAAGATGATACGGAACA 60.369 47.826 0.00 0.00 0.00 3.18
1690 1783 3.963428 ACTGAGCTTGGTAAGTTCGAT 57.037 42.857 0.00 0.00 41.10 3.59
1775 1870 7.201435 GCTTTGGAAATCGAATTTGTTATGACC 60.201 37.037 0.00 0.00 31.47 4.02
1778 1873 5.163693 GGAAATCGAATTTGTTATGACCGGT 60.164 40.000 6.92 6.92 31.47 5.28
1810 1905 6.047231 GGATCCGTAGCAACAAAATACTACT 58.953 40.000 0.00 0.00 34.23 2.57
1811 1906 6.200475 GGATCCGTAGCAACAAAATACTACTC 59.800 42.308 0.00 0.00 34.23 2.59
1814 1909 5.416947 CGTAGCAACAAAATACTACTCCCT 58.583 41.667 0.00 0.00 34.23 4.20
1815 1910 5.519206 CGTAGCAACAAAATACTACTCCCTC 59.481 44.000 0.00 0.00 34.23 4.30
1817 1912 5.491982 AGCAACAAAATACTACTCCCTCTG 58.508 41.667 0.00 0.00 0.00 3.35
1818 1913 5.248477 AGCAACAAAATACTACTCCCTCTGA 59.752 40.000 0.00 0.00 0.00 3.27
1820 1915 6.599638 GCAACAAAATACTACTCCCTCTGATT 59.400 38.462 0.00 0.00 0.00 2.57
1821 1916 7.121315 GCAACAAAATACTACTCCCTCTGATTT 59.879 37.037 0.00 0.00 0.00 2.17
1822 1917 9.014297 CAACAAAATACTACTCCCTCTGATTTT 57.986 33.333 0.00 0.00 0.00 1.82
1833 1928 8.494016 ACTCCCTCTGATTTTTATTTAGTTCG 57.506 34.615 0.00 0.00 0.00 3.95
1835 1930 6.036735 TCCCTCTGATTTTTATTTAGTTCGCG 59.963 38.462 0.00 0.00 0.00 5.87
1836 1931 6.183360 CCCTCTGATTTTTATTTAGTTCGCGT 60.183 38.462 5.77 0.00 0.00 6.01
1837 1932 7.010738 CCCTCTGATTTTTATTTAGTTCGCGTA 59.989 37.037 5.77 0.00 0.00 4.42
1838 1933 8.548721 CCTCTGATTTTTATTTAGTTCGCGTAT 58.451 33.333 5.77 0.00 0.00 3.06
1839 1934 9.916397 CTCTGATTTTTATTTAGTTCGCGTATT 57.084 29.630 5.77 0.00 0.00 1.89
1842 1937 9.640974 TGATTTTTATTTAGTTCGCGTATTAGC 57.359 29.630 5.77 0.00 0.00 3.09
1846 1941 9.480538 TTTTATTTAGTTCGCGTATTAGCTTTG 57.519 29.630 5.77 0.00 34.40 2.77
1847 1942 5.459110 TTTAGTTCGCGTATTAGCTTTGG 57.541 39.130 5.77 0.00 34.40 3.28
1849 1944 2.928116 AGTTCGCGTATTAGCTTTGGTC 59.072 45.455 5.77 0.00 34.40 4.02
1850 1945 2.658373 TCGCGTATTAGCTTTGGTCA 57.342 45.000 5.77 0.00 34.40 4.02
1851 1946 2.962125 TCGCGTATTAGCTTTGGTCAA 58.038 42.857 5.77 0.00 34.40 3.18
1852 1947 3.327626 TCGCGTATTAGCTTTGGTCAAA 58.672 40.909 5.77 0.00 34.40 2.69
1868 1963 8.865590 TTTGGTCAAAGTCAAGCTTTATAAAC 57.134 30.769 0.00 0.00 44.95 2.01
1869 1964 7.817418 TGGTCAAAGTCAAGCTTTATAAACT 57.183 32.000 0.00 0.00 44.95 2.66
1870 1965 8.232913 TGGTCAAAGTCAAGCTTTATAAACTT 57.767 30.769 0.00 0.00 44.95 2.66
1878 1973 9.736023 AGTCAAGCTTTATAAACTTTGACAAAG 57.264 29.630 29.41 23.41 44.10 2.77
2014 2109 9.545105 TTCTATAAACTTGGTGAAACTTTACGA 57.455 29.630 0.00 0.00 36.74 3.43
2015 2110 9.545105 TCTATAAACTTGGTGAAACTTTACGAA 57.455 29.630 0.00 0.00 36.74 3.85
2016 2111 9.807386 CTATAAACTTGGTGAAACTTTACGAAG 57.193 33.333 7.33 7.33 38.22 3.79
2043 2138 6.985188 GACTTCAGTCAAACCTAATATGCA 57.015 37.500 1.86 0.00 44.18 3.96
2044 2139 6.992063 ACTTCAGTCAAACCTAATATGCAG 57.008 37.500 0.00 0.00 0.00 4.41
2045 2140 6.711277 ACTTCAGTCAAACCTAATATGCAGA 58.289 36.000 0.00 0.00 0.00 4.26
2046 2141 6.820656 ACTTCAGTCAAACCTAATATGCAGAG 59.179 38.462 0.00 0.00 0.00 3.35
2047 2142 6.299805 TCAGTCAAACCTAATATGCAGAGT 57.700 37.500 0.00 0.00 0.00 3.24
2048 2143 7.418337 TCAGTCAAACCTAATATGCAGAGTA 57.582 36.000 0.00 0.00 0.00 2.59
2049 2144 7.847096 TCAGTCAAACCTAATATGCAGAGTAA 58.153 34.615 0.00 0.00 0.00 2.24
2050 2145 8.318412 TCAGTCAAACCTAATATGCAGAGTAAA 58.682 33.333 0.00 0.00 0.00 2.01
2051 2146 9.113838 CAGTCAAACCTAATATGCAGAGTAAAT 57.886 33.333 0.00 0.00 0.00 1.40
2285 2740 7.159372 TCAGCTTAATATCCCCGTCTATTTTC 58.841 38.462 0.00 0.00 0.00 2.29
2292 2747 1.064685 CCCCGTCTATTTTCCCAGCTT 60.065 52.381 0.00 0.00 0.00 3.74
2338 2793 6.699642 GTGCAGCAATTCTACCTTTAAAAACA 59.300 34.615 0.00 0.00 0.00 2.83
2549 3088 7.626452 GCACTTCTTCTGTACAGTTGAAACTTT 60.626 37.037 21.99 9.22 37.08 2.66
2694 3233 3.231160 GCAACACATACTGGTTTAACGC 58.769 45.455 0.00 0.00 0.00 4.84
2771 3310 7.664082 AGATAGGATTTGATGCTTACGAATG 57.336 36.000 0.00 0.00 31.56 2.67
2828 3367 7.923344 AGTATGACTTCTTTTAGATGACATCGG 59.077 37.037 9.77 0.58 36.64 4.18
2989 3528 1.891150 CTCTGCTTGCCATTTGGTCTT 59.109 47.619 0.00 0.00 37.57 3.01
3238 3778 5.180117 CAGATCTGTGTGAAAAACTAGTGGG 59.820 44.000 14.95 0.00 0.00 4.61
3341 3881 7.215789 ACATAACTGATGAGCTTGATCTAAGG 58.784 38.462 7.87 0.79 39.06 2.69
3525 4065 5.278169 GCATATCTGGCAAGAAGTACAATGG 60.278 44.000 0.00 0.00 35.59 3.16
3738 4281 3.116079 TCCCAAGGTTTACGTCTTCAC 57.884 47.619 0.00 0.00 0.00 3.18
3944 4487 5.771666 AGACAAGTTCAATCATGTCATTGGT 59.228 36.000 7.42 0.00 43.53 3.67
4095 4638 4.647424 ATTTTTGTGTTGACATCGTGGT 57.353 36.364 0.00 0.00 30.13 4.16
4190 4733 2.063156 TCATTTGCAACGTTCATGGC 57.937 45.000 0.00 0.00 0.00 4.40
4235 4778 3.537580 TGGCGAAAAAGTAATAGCGGAT 58.462 40.909 0.00 0.00 0.00 4.18
4401 4944 0.803768 CGAGGATTCACAGGCTGTCG 60.804 60.000 19.13 12.66 0.00 4.35
4500 5043 3.563390 GTGAGATTAGAATCAAGCAGGCC 59.437 47.826 0.00 0.00 37.89 5.19
4518 5061 2.357952 GGCCGCTAAATAAACTCCCTTG 59.642 50.000 0.00 0.00 0.00 3.61
4558 5102 8.528044 TTCTAATTACTGAAGTGGTGGTTTTT 57.472 30.769 0.00 0.00 0.00 1.94
5210 5754 8.258007 TCCATTTCCTGTAGTAACTAATGACTG 58.742 37.037 0.00 0.00 0.00 3.51
5290 5834 3.243234 TGTCTTGTTTGTACCATTTGCCG 60.243 43.478 0.00 0.00 0.00 5.69
5303 5847 4.141287 CCATTTGCCGGTAATTATCTCCA 58.859 43.478 5.59 0.00 0.00 3.86
5387 5931 4.833478 AATATCTGGTGTGCTTCACTCT 57.167 40.909 11.12 0.15 45.50 3.24
5483 6028 2.016318 CACTGAAGTTCCACTGCAACA 58.984 47.619 0.00 0.00 32.29 3.33
5532 6077 8.258708 AGTTCCACAAGAATGTATAGTTAGACC 58.741 37.037 0.00 0.00 37.82 3.85
5597 6144 5.926542 TGTGCTGATAGTTCTTTGTGTAGAC 59.073 40.000 0.00 0.00 0.00 2.59
5598 6145 5.061064 GTGCTGATAGTTCTTTGTGTAGACG 59.939 44.000 0.00 0.00 0.00 4.18
5599 6146 4.031878 GCTGATAGTTCTTTGTGTAGACGC 59.968 45.833 0.00 0.00 0.00 5.19
5600 6147 4.163552 TGATAGTTCTTTGTGTAGACGCG 58.836 43.478 3.53 3.53 0.00 6.01
5601 6148 1.779569 AGTTCTTTGTGTAGACGCGG 58.220 50.000 12.47 0.00 0.00 6.46
5602 6149 0.163146 GTTCTTTGTGTAGACGCGGC 59.837 55.000 12.47 7.86 0.00 6.53
5603 6150 0.947180 TTCTTTGTGTAGACGCGGCC 60.947 55.000 9.25 0.00 0.00 6.13
5604 6151 2.726691 CTTTGTGTAGACGCGGCCG 61.727 63.158 24.05 24.05 41.14 6.13
5653 6201 2.359088 GGTTACTCCGTCCACTGGT 58.641 57.895 0.00 0.00 0.00 4.00
5700 6255 2.930019 TGGCTGGGAGGTGGAGTG 60.930 66.667 0.00 0.00 0.00 3.51
5878 6445 1.351017 CCACTAACCTTCTTGGAGGCA 59.649 52.381 0.00 0.00 40.65 4.75
5992 6560 0.181587 TGTCGCACCCCTTCTTGAAA 59.818 50.000 0.00 0.00 0.00 2.69
6027 6596 3.964031 AGTTGGCCAGGTTATTTTGTTCA 59.036 39.130 5.11 0.00 0.00 3.18
6118 6714 3.484524 CAACACTGCTCCATGTTGC 57.515 52.632 4.34 0.00 46.53 4.17
6119 6715 0.956633 CAACACTGCTCCATGTTGCT 59.043 50.000 4.34 0.00 46.53 3.91
6120 6716 1.068748 CAACACTGCTCCATGTTGCTC 60.069 52.381 4.34 0.00 46.53 4.26
6144 6743 0.466372 GCCATCTCTACCCTTTGCCC 60.466 60.000 0.00 0.00 0.00 5.36
6145 6744 0.918983 CCATCTCTACCCTTTGCCCA 59.081 55.000 0.00 0.00 0.00 5.36
6241 6858 1.285641 CCATGGTTGCCGTTGTGTC 59.714 57.895 2.57 0.00 0.00 3.67
6242 6859 1.451337 CCATGGTTGCCGTTGTGTCA 61.451 55.000 2.57 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 5.838531 ATTGTTTACCTCGGTTTGTTCAA 57.161 34.783 0.00 0.00 0.00 2.69
216 236 2.596346 TGATGGTTGTGGACATGCTTT 58.404 42.857 0.00 0.00 0.00 3.51
421 502 8.850454 AATTAAAATATGATTCGGTTTCGGTG 57.150 30.769 0.00 0.00 36.95 4.94
592 673 4.050553 TCGTCGTTTCCTCGTGTATTTTT 58.949 39.130 0.00 0.00 0.00 1.94
602 683 0.669625 CTGGGGTTCGTCGTTTCCTC 60.670 60.000 0.00 0.00 0.00 3.71
650 731 2.426024 GCTGTTCTGGATACTACCGTGA 59.574 50.000 0.00 0.00 37.61 4.35
897 986 3.215606 GATCAGACCGCGCGAATGC 62.216 63.158 34.63 16.88 37.91 3.56
898 987 1.543941 GAGATCAGACCGCGCGAATG 61.544 60.000 34.63 25.03 0.00 2.67
909 998 3.941081 GGGACGCCAGAGATCAGA 58.059 61.111 0.00 0.00 0.00 3.27
942 1031 2.202544 CTCGGTCGCTCAGCTCAC 60.203 66.667 0.00 0.00 0.00 3.51
948 1037 4.415332 GTTCGGCTCGGTCGCTCA 62.415 66.667 0.00 0.00 0.00 4.26
1114 1204 0.178903 TGAGTAGGCTGGGGAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
1373 1463 4.467084 TGGATCCGCTTCCGCACC 62.467 66.667 7.39 0.00 38.74 5.01
1391 1481 2.439156 AGCTCCGCAATCTTGGGC 60.439 61.111 1.72 0.00 39.52 5.36
1425 1515 3.685214 ATCCGTCGAGCACTGTCGC 62.685 63.158 0.00 0.00 39.90 5.19
1473 1563 3.169099 CCATAATCCCAGAGAGGTCGAT 58.831 50.000 0.00 0.00 34.66 3.59
1531 1621 2.788191 CTTCCCCTCGTCACAGCCAC 62.788 65.000 0.00 0.00 0.00 5.01
1536 1626 0.178944 TCCTTCTTCCCCTCGTCACA 60.179 55.000 0.00 0.00 0.00 3.58
1551 1644 0.401395 TTCACCACCTCCCACTCCTT 60.401 55.000 0.00 0.00 0.00 3.36
1554 1647 1.065854 CATCTTCACCACCTCCCACTC 60.066 57.143 0.00 0.00 0.00 3.51
1555 1648 0.987294 CATCTTCACCACCTCCCACT 59.013 55.000 0.00 0.00 0.00 4.00
1556 1649 0.984230 TCATCTTCACCACCTCCCAC 59.016 55.000 0.00 0.00 0.00 4.61
1690 1783 6.631971 TCATTCACTGTTCAAATGCTACAA 57.368 33.333 0.00 0.00 31.84 2.41
1747 1842 5.905480 AACAAATTCGATTTCCAAAGCAC 57.095 34.783 0.00 0.00 0.00 4.40
1775 1870 0.748450 TACGGATCCCAAAGCTACCG 59.252 55.000 6.06 0.00 44.77 4.02
1778 1873 1.491668 TGCTACGGATCCCAAAGCTA 58.508 50.000 21.72 10.50 33.66 3.32
1810 1905 6.036735 CGCGAACTAAATAAAAATCAGAGGGA 59.963 38.462 0.00 0.00 0.00 4.20
1811 1906 6.183360 ACGCGAACTAAATAAAAATCAGAGGG 60.183 38.462 15.93 0.00 0.00 4.30
1817 1912 9.859692 AGCTAATACGCGAACTAAATAAAAATC 57.140 29.630 15.93 0.00 34.40 2.17
1820 1915 9.480538 CAAAGCTAATACGCGAACTAAATAAAA 57.519 29.630 15.93 0.00 34.40 1.52
1821 1916 8.117988 CCAAAGCTAATACGCGAACTAAATAAA 58.882 33.333 15.93 0.00 34.40 1.40
1822 1917 7.278424 ACCAAAGCTAATACGCGAACTAAATAA 59.722 33.333 15.93 0.00 34.40 1.40
1828 1923 2.928116 GACCAAAGCTAATACGCGAACT 59.072 45.455 15.93 0.00 34.40 3.01
1829 1924 2.669434 TGACCAAAGCTAATACGCGAAC 59.331 45.455 15.93 0.00 34.40 3.95
1830 1925 2.962125 TGACCAAAGCTAATACGCGAA 58.038 42.857 15.93 0.00 34.40 4.70
1832 1927 3.670203 CTTTGACCAAAGCTAATACGCG 58.330 45.455 3.53 3.53 40.94 6.01
1852 1947 9.736023 CTTTGTCAAAGTTTATAAAGCTTGACT 57.264 29.630 30.01 13.37 39.29 3.41
1988 2083 9.545105 TCGTAAAGTTTCACCAAGTTTATAGAA 57.455 29.630 0.00 0.00 40.73 2.10
1989 2084 9.545105 TTCGTAAAGTTTCACCAAGTTTATAGA 57.455 29.630 0.00 0.00 40.73 1.98
1990 2085 9.807386 CTTCGTAAAGTTTCACCAAGTTTATAG 57.193 33.333 0.00 0.00 40.73 1.31
1991 2086 9.328845 ACTTCGTAAAGTTTCACCAAGTTTATA 57.671 29.630 0.00 0.00 43.28 0.98
1992 2087 8.217131 ACTTCGTAAAGTTTCACCAAGTTTAT 57.783 30.769 0.00 0.00 43.28 1.40
1993 2088 7.614124 ACTTCGTAAAGTTTCACCAAGTTTA 57.386 32.000 0.00 0.00 43.28 2.01
1994 2089 6.505044 ACTTCGTAAAGTTTCACCAAGTTT 57.495 33.333 0.00 0.00 43.28 2.66
2020 2115 6.818644 TCTGCATATTAGGTTTGACTGAAGTC 59.181 38.462 3.41 3.41 44.97 3.01
2021 2116 6.711277 TCTGCATATTAGGTTTGACTGAAGT 58.289 36.000 0.00 0.00 0.00 3.01
2022 2117 6.820656 ACTCTGCATATTAGGTTTGACTGAAG 59.179 38.462 0.00 0.00 0.00 3.02
2023 2118 6.711277 ACTCTGCATATTAGGTTTGACTGAA 58.289 36.000 0.00 0.00 0.00 3.02
2024 2119 6.299805 ACTCTGCATATTAGGTTTGACTGA 57.700 37.500 0.00 0.00 0.00 3.41
2025 2120 8.492673 TTTACTCTGCATATTAGGTTTGACTG 57.507 34.615 0.00 0.00 0.00 3.51
2037 2132 8.621286 CCCTTCGTTTTTATTTACTCTGCATAT 58.379 33.333 0.00 0.00 0.00 1.78
2038 2133 7.825270 TCCCTTCGTTTTTATTTACTCTGCATA 59.175 33.333 0.00 0.00 0.00 3.14
2039 2134 6.657541 TCCCTTCGTTTTTATTTACTCTGCAT 59.342 34.615 0.00 0.00 0.00 3.96
2040 2135 5.998981 TCCCTTCGTTTTTATTTACTCTGCA 59.001 36.000 0.00 0.00 0.00 4.41
2041 2136 6.148976 ACTCCCTTCGTTTTTATTTACTCTGC 59.851 38.462 0.00 0.00 0.00 4.26
2042 2137 7.668525 ACTCCCTTCGTTTTTATTTACTCTG 57.331 36.000 0.00 0.00 0.00 3.35
2043 2138 9.955102 AATACTCCCTTCGTTTTTATTTACTCT 57.045 29.630 0.00 0.00 0.00 3.24
2053 2148 9.847224 ACATGATTATAATACTCCCTTCGTTTT 57.153 29.630 0.00 0.00 0.00 2.43
2054 2149 9.847224 AACATGATTATAATACTCCCTTCGTTT 57.153 29.630 0.00 0.00 0.00 3.60
2285 2740 0.749091 TCGGATCATTGCAAGCTGGG 60.749 55.000 4.94 0.00 0.00 4.45
2292 2747 3.135994 CAGATGTCATCGGATCATTGCA 58.864 45.455 7.13 0.00 0.00 4.08
2372 2910 7.704899 CACATGACGGAATAACAGATTAGTACA 59.295 37.037 0.00 0.00 0.00 2.90
2549 3088 4.927978 ATTCAAAACGGAATTGTCACCA 57.072 36.364 0.00 0.00 33.85 4.17
2694 3233 4.885413 TGATCTTGGTGCTGAAAAATTGG 58.115 39.130 0.00 0.00 0.00 3.16
2771 3310 3.557595 AGCTACGTTTATGCTGCTTCATC 59.442 43.478 0.00 0.00 35.54 2.92
2828 3367 6.015180 TGGCAATATCAATAGGAATTGGCTTC 60.015 38.462 17.60 0.00 42.74 3.86
2846 3385 9.585099 GTCAATGAATTTGAAGTAATGGCAATA 57.415 29.630 0.00 0.00 45.71 1.90
2944 3483 6.094603 GGATTGCATAAGTGACAGAATCAAGT 59.905 38.462 0.00 0.00 39.72 3.16
2989 3528 8.630054 AAAACACACCTAAGCAATGACTAATA 57.370 30.769 0.00 0.00 0.00 0.98
3176 3716 8.614994 AACAAGAATTTTAAAAGTCGACACAG 57.385 30.769 19.50 11.02 37.99 3.66
3238 3778 4.735662 TTCCGTTTACTGTACAATGTGC 57.264 40.909 0.00 0.00 0.00 4.57
3310 3850 4.399004 AGCTCATCAGTTATGTCCTCAC 57.601 45.455 0.00 0.00 36.89 3.51
3341 3881 5.771165 AGTACTTTCTAGCACCCTAGCTATC 59.229 44.000 0.00 0.00 45.32 2.08
3525 4065 5.123936 AGGAACCACTAGTGTCACTTTTTC 58.876 41.667 21.18 10.80 0.00 2.29
3667 4207 8.157476 TGCCAGGATAGAAGGATATCTTAAAAC 58.843 37.037 2.05 0.00 35.50 2.43
3738 4281 5.783111 CTTTGGGGAAAACAAAGTATGGAG 58.217 41.667 9.16 0.00 45.94 3.86
3770 4313 8.675705 TTGAGAACTGTTGAAGATAATGAACA 57.324 30.769 0.00 0.00 0.00 3.18
4095 4638 7.065324 GCACCATTATTAGTTGTACTGTAGCAA 59.935 37.037 0.00 0.00 0.00 3.91
4190 4733 7.915397 CCAATATTGAGGAACTTTGGATTTACG 59.085 37.037 17.23 0.00 41.55 3.18
4235 4778 2.029623 GAGTTATGTCCACGCTCCCTA 58.970 52.381 0.00 0.00 0.00 3.53
4329 4872 5.291614 CCTCCAAGTCATTTTTGTGTTTGTG 59.708 40.000 0.00 0.00 0.00 3.33
4401 4944 1.674962 CAATTTCCTAGCAGCAGCCTC 59.325 52.381 0.00 0.00 43.56 4.70
4500 5043 5.861787 CCAAAACAAGGGAGTTTATTTAGCG 59.138 40.000 0.00 0.00 40.60 4.26
4508 5051 6.016555 ACATATAGCCAAAACAAGGGAGTTT 58.983 36.000 0.00 0.00 43.13 2.66
4558 5102 5.538813 TGTACCTGAAAGTTAGCAAGAGAGA 59.461 40.000 0.00 0.00 0.00 3.10
5210 5754 4.471548 TGGGCTCTACTAATCTACTGTCC 58.528 47.826 0.00 0.00 0.00 4.02
5387 5931 8.442384 CGTATATTGATGCTGCAAATACATGTA 58.558 33.333 6.36 8.27 30.71 2.29
5483 6028 5.363562 TCAGTGATATCCAGAAGCAACAT 57.636 39.130 0.00 0.00 0.00 2.71
5608 6155 4.748679 CAAAGCTCGCCGTGCAGC 62.749 66.667 14.01 0.57 34.62 5.25
5609 6156 3.020026 CTCAAAGCTCGCCGTGCAG 62.020 63.158 14.01 3.18 0.00 4.41
5610 6157 3.043713 CTCAAAGCTCGCCGTGCA 61.044 61.111 14.01 0.00 0.00 4.57
5611 6158 3.793144 CCTCAAAGCTCGCCGTGC 61.793 66.667 2.41 2.41 0.00 5.34
5612 6159 3.793144 GCCTCAAAGCTCGCCGTG 61.793 66.667 0.00 0.00 0.00 4.94
5878 6445 4.165779 GGCGAAATCAACATTTCAACGAT 58.834 39.130 7.92 0.00 45.87 3.73
5992 6560 4.521146 CTGGCCAACTTCTTGATGATACT 58.479 43.478 7.01 0.00 0.00 2.12
6027 6596 0.976073 CACCGACATCCCCACCTACT 60.976 60.000 0.00 0.00 0.00 2.57
6118 6714 0.392336 GGGTAGAGATGGCAGCTGAG 59.608 60.000 20.43 0.00 0.00 3.35
6119 6715 0.031716 AGGGTAGAGATGGCAGCTGA 60.032 55.000 20.43 0.00 0.00 4.26
6120 6716 0.835941 AAGGGTAGAGATGGCAGCTG 59.164 55.000 11.34 10.11 0.00 4.24
6144 6743 3.243501 CCAACAGAACACCACCAAAGATG 60.244 47.826 0.00 0.00 0.00 2.90
6145 6744 2.958355 CCAACAGAACACCACCAAAGAT 59.042 45.455 0.00 0.00 0.00 2.40
6179 6791 1.071471 AGGGACGACACAAAGGCAG 59.929 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.