Multiple sequence alignment - TraesCS7D01G177500

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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 TraesCS7D01G177500 chr7D 100.000 3994 0 0 926 4919 130116310 130112317 0.000000e+00 7376
1 TraesCS7D01G177500 chr7D 100.000 594 0 0 1 594 130117235 130116642 0.000000e+00 1098
2 TraesCS7D01G177500 chr7B 93.670 3191 116 34 1782 4916 91663061 91659901 0.000000e+00 4695
3 TraesCS7D01G177500 chr7B 93.054 835 28 10 926 1757 91663861 91663054 0.000000e+00 1194
4 TraesCS7D01G177500 chr7B 93.534 232 9 5 368 594 91664130 91663900 1.700000e-89 340
5 TraesCS7D01G177500 chr7B 91.391 151 13 0 7 157 733725785 733725935 1.790000e-49 207
6 TraesCS7D01G177500 chr7B 92.473 93 3 1 264 352 91664206 91664114 4.000000e-26 130
7 TraesCS7D01G177500 chr7A 92.619 2249 131 23 2138 4370 129261366 129259137 0.000000e+00 3201
8 TraesCS7D01G177500 chr7A 89.286 1232 56 33 926 2143 129262747 129261578 0.000000e+00 1474
9 TraesCS7D01G177500 chr7A 83.855 607 60 14 2 594 129263375 129262793 1.200000e-150 544
10 TraesCS7D01G177500 chr7A 86.777 242 9 9 4530 4760 129259049 129258820 1.060000e-61 248
11 TraesCS7D01G177500 chr7A 89.809 157 16 0 1 157 486095838 486095994 8.350000e-48 202
12 TraesCS7D01G177500 chr7A 88.636 88 4 1 4833 4914 129258717 129258630 8.710000e-18 102
13 TraesCS7D01G177500 chr6A 77.464 1380 274 28 2562 3920 551866152 551864789 0.000000e+00 791
14 TraesCS7D01G177500 chr6A 88.793 464 50 2 1162 1624 551867078 551866616 7.150000e-158 568
15 TraesCS7D01G177500 chr6D 77.358 1378 279 26 2562 3920 405484306 405482943 0.000000e+00 785
16 TraesCS7D01G177500 chr6D 88.793 464 50 2 1162 1624 405485221 405484759 7.150000e-158 568
17 TraesCS7D01G177500 chr6D 91.720 157 13 0 1 157 121157011 121157167 8.290000e-53 219
18 TraesCS7D01G177500 chr6B 77.391 1380 275 27 2562 3920 609381798 609380435 0.000000e+00 785
19 TraesCS7D01G177500 chr6B 88.578 464 51 2 1162 1624 609382695 609382233 3.320000e-156 562
20 TraesCS7D01G177500 chr6B 89.809 157 16 0 1 157 213226077 213226233 8.350000e-48 202
21 TraesCS7D01G177500 chr2B 89.809 157 16 0 1 157 764865705 764865861 8.350000e-48 202
22 TraesCS7D01G177500 chr3A 89.809 157 15 1 2 157 516631672 516631516 3.000000e-47 200
23 TraesCS7D01G177500 chr1A 89.677 155 16 0 1 155 510277666 510277820 1.080000e-46 198
24 TraesCS7D01G177500 chr5B 89.172 157 17 0 1 157 45396675 45396519 3.880000e-46 196


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 TraesCS7D01G177500 chr7D 130112317 130117235 4918 True 4237.00 7376 100.00000 1 4919 2 chr7D.!!$R1 4918
1 TraesCS7D01G177500 chr7B 91659901 91664206 4305 True 1589.75 4695 93.18275 264 4916 4 chr7B.!!$R1 4652
2 TraesCS7D01G177500 chr7A 129258630 129263375 4745 True 1113.80 3201 88.23460 2 4914 5 chr7A.!!$R1 4912
3 TraesCS7D01G177500 chr6A 551864789 551867078 2289 True 679.50 791 83.12850 1162 3920 2 chr6A.!!$R1 2758
4 TraesCS7D01G177500 chr6D 405482943 405485221 2278 True 676.50 785 83.07550 1162 3920 2 chr6D.!!$R1 2758
5 TraesCS7D01G177500 chr6B 609380435 609382695 2260 True 673.50 785 82.98450 1162 3920 2 chr6B.!!$R1 2758

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
458 475 0.037975 CCACTTGGTAACCGTAGCGT 60.038 55.000 0.0 0.0 0.00 5.07 F
1761 1798 1.005805 TGCAGCCTTCTCTCTCTCTCT 59.994 52.381 0.0 0.0 0.00 3.10 F
2483 2758 0.807496 GGCTCCAGATGTGCTTGTTC 59.193 55.000 0.0 0.0 33.94 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1824 0.252479 AACTAGAGGACCTCGCGAGA 59.748 55.0 36.59 14.34 35.36 4.04 R
2689 2967 0.897621 GGCCTCAAAGTTGAATGGGG 59.102 55.0 0.00 0.00 36.64 4.96 R
4264 4598 0.539669 CTTGTCCCCAACTGTTCCCC 60.540 60.0 0.00 0.00 0.00 4.81 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
20 21 3.112709 GGGCACGTCAGCGAACTC 61.113 66.667 0.00 0.00 42.00 3.01
29 30 4.954147 CGTCAGCGAACTCCAGATCTGG 62.954 59.091 32.60 32.60 45.90 3.86
40 41 2.125106 GATCTGGCACCCGACCAC 60.125 66.667 0.00 0.00 32.49 4.16
82 83 0.178068 ACCATACCTGTCATCCACGC 59.822 55.000 0.00 0.00 0.00 5.34
84 85 1.406751 CCATACCTGTCATCCACGCAA 60.407 52.381 0.00 0.00 0.00 4.85
86 87 0.682292 TACCTGTCATCCACGCAACA 59.318 50.000 0.00 0.00 0.00 3.33
111 112 2.733593 AGCGCACGTTCCGTCTTC 60.734 61.111 11.47 0.00 38.32 2.87
117 118 1.135199 GCACGTTCCGTCTTCCAGATA 60.135 52.381 0.00 0.00 38.32 1.98
129 130 2.997485 TCCAGATATCGTCGATGCAG 57.003 50.000 17.98 6.66 0.00 4.41
132 133 2.227626 CCAGATATCGTCGATGCAGACT 59.772 50.000 17.98 6.78 38.90 3.24
170 171 5.416271 TCCTGGACTGTAACCAATTCTAC 57.584 43.478 0.00 0.00 36.95 2.59
175 176 7.166691 TGGACTGTAACCAATTCTACTACTC 57.833 40.000 0.00 0.00 34.25 2.59
204 205 4.000988 TCTTTTGCGGGTGAGAATTCTAC 58.999 43.478 8.25 7.17 0.00 2.59
226 227 1.532437 TCACTCGCTGAATGTGCTTTG 59.468 47.619 0.00 0.00 0.00 2.77
227 228 0.877071 ACTCGCTGAATGTGCTTTGG 59.123 50.000 0.00 0.00 0.00 3.28
234 235 3.696051 GCTGAATGTGCTTTGGGATCTTA 59.304 43.478 0.00 0.00 0.00 2.10
235 236 4.340381 GCTGAATGTGCTTTGGGATCTTAT 59.660 41.667 0.00 0.00 0.00 1.73
236 237 5.735354 GCTGAATGTGCTTTGGGATCTTATG 60.735 44.000 0.00 0.00 0.00 1.90
237 238 5.263599 TGAATGTGCTTTGGGATCTTATGT 58.736 37.500 0.00 0.00 0.00 2.29
334 343 6.558009 GTTAATTTTCGGGATAAACCAGTCC 58.442 40.000 0.00 0.00 41.20 3.85
335 344 4.586306 ATTTTCGGGATAAACCAGTCCT 57.414 40.909 0.00 0.00 41.20 3.85
336 345 5.703730 ATTTTCGGGATAAACCAGTCCTA 57.296 39.130 0.00 0.00 41.20 2.94
337 346 5.703730 TTTTCGGGATAAACCAGTCCTAT 57.296 39.130 0.00 0.00 41.20 2.57
338 347 6.811634 TTTTCGGGATAAACCAGTCCTATA 57.188 37.500 0.00 0.00 41.20 1.31
339 348 6.415206 TTTCGGGATAAACCAGTCCTATAG 57.585 41.667 0.00 0.00 41.20 1.31
340 349 5.070823 TCGGGATAAACCAGTCCTATAGT 57.929 43.478 0.00 0.00 41.20 2.12
341 350 6.204852 TCGGGATAAACCAGTCCTATAGTA 57.795 41.667 0.00 0.00 41.20 1.82
342 351 6.613699 TCGGGATAAACCAGTCCTATAGTAA 58.386 40.000 0.00 0.00 41.20 2.24
343 352 7.068702 TCGGGATAAACCAGTCCTATAGTAAA 58.931 38.462 0.00 0.00 41.20 2.01
344 353 7.014615 TCGGGATAAACCAGTCCTATAGTAAAC 59.985 40.741 0.00 0.00 41.20 2.01
345 354 7.015001 CGGGATAAACCAGTCCTATAGTAAACT 59.985 40.741 0.00 0.00 41.20 2.66
346 355 8.366401 GGGATAAACCAGTCCTATAGTAAACTC 58.634 40.741 0.00 0.00 41.20 3.01
347 356 9.145442 GGATAAACCAGTCCTATAGTAAACTCT 57.855 37.037 0.00 0.00 38.79 3.24
350 359 8.667592 AAACCAGTCCTATAGTAAACTCTTCT 57.332 34.615 0.00 0.00 0.00 2.85
351 360 7.648039 ACCAGTCCTATAGTAAACTCTTCTG 57.352 40.000 0.00 0.00 0.00 3.02
352 361 7.411808 ACCAGTCCTATAGTAAACTCTTCTGA 58.588 38.462 0.00 0.00 0.00 3.27
353 362 7.339976 ACCAGTCCTATAGTAAACTCTTCTGAC 59.660 40.741 0.00 0.00 0.00 3.51
354 363 7.201839 CCAGTCCTATAGTAAACTCTTCTGACC 60.202 44.444 0.00 0.00 0.00 4.02
355 364 6.834969 AGTCCTATAGTAAACTCTTCTGACCC 59.165 42.308 0.00 0.00 0.00 4.46
356 365 6.040729 GTCCTATAGTAAACTCTTCTGACCCC 59.959 46.154 0.00 0.00 0.00 4.95
357 366 5.009811 CCTATAGTAAACTCTTCTGACCCCG 59.990 48.000 0.00 0.00 0.00 5.73
358 367 1.275573 AGTAAACTCTTCTGACCCCGC 59.724 52.381 0.00 0.00 0.00 6.13
359 368 1.001633 GTAAACTCTTCTGACCCCGCA 59.998 52.381 0.00 0.00 0.00 5.69
360 369 0.472471 AAACTCTTCTGACCCCGCAA 59.528 50.000 0.00 0.00 0.00 4.85
361 370 0.472471 AACTCTTCTGACCCCGCAAA 59.528 50.000 0.00 0.00 0.00 3.68
362 371 0.472471 ACTCTTCTGACCCCGCAAAA 59.528 50.000 0.00 0.00 0.00 2.44
363 372 1.133915 ACTCTTCTGACCCCGCAAAAA 60.134 47.619 0.00 0.00 0.00 1.94
420 437 6.575162 AAAAGCCACAAAGGTACATAGAAG 57.425 37.500 0.00 0.00 40.61 2.85
458 475 0.037975 CCACTTGGTAACCGTAGCGT 60.038 55.000 0.00 0.00 0.00 5.07
478 495 3.677976 CGTTACCCTCTGCCGAAATACTT 60.678 47.826 0.00 0.00 0.00 2.24
591 621 2.084610 TTTCCAGTCTCACATGAGCG 57.915 50.000 0.00 0.00 41.80 5.03
952 982 4.885270 CAACCACCGCCACCACCA 62.885 66.667 0.00 0.00 0.00 4.17
953 983 4.887190 AACCACCGCCACCACCAC 62.887 66.667 0.00 0.00 0.00 4.16
971 1001 1.460305 CCACCTCCGATCCCATCCT 60.460 63.158 0.00 0.00 0.00 3.24
973 1003 1.152226 ACCTCCGATCCCATCCTCC 60.152 63.158 0.00 0.00 0.00 4.30
974 1004 2.279069 CCTCCGATCCCATCCTCCG 61.279 68.421 0.00 0.00 0.00 4.63
1057 1091 1.517832 CACATGTCCGAGGACTCCC 59.482 63.158 21.35 0.00 44.80 4.30
1060 1094 4.753662 TGTCCGAGGACTCCCCCG 62.754 72.222 21.35 0.00 44.80 5.73
1549 1583 4.111053 GCTCCTTCCCGGGGTTCC 62.111 72.222 23.50 0.39 34.84 3.62
1641 1676 3.308188 GGTACTATGTCCCAGCCAAACTT 60.308 47.826 0.00 0.00 0.00 2.66
1649 1684 4.119862 GTCCCAGCCAAACTTTCTTTTTC 58.880 43.478 0.00 0.00 0.00 2.29
1655 1690 4.640647 AGCCAAACTTTCTTTTTCTCTCGT 59.359 37.500 0.00 0.00 0.00 4.18
1656 1691 5.820947 AGCCAAACTTTCTTTTTCTCTCGTA 59.179 36.000 0.00 0.00 0.00 3.43
1658 1693 6.238402 GCCAAACTTTCTTTTTCTCTCGTAGT 60.238 38.462 0.00 0.00 0.00 2.73
1660 1695 8.989980 CCAAACTTTCTTTTTCTCTCGTAGTAT 58.010 33.333 0.00 0.00 0.00 2.12
1708 1744 2.280524 TTCGGGTTGACACTGCGG 60.281 61.111 0.00 0.00 0.00 5.69
1728 1764 1.269448 GTTGGAATTGAAAGCTGCCGA 59.731 47.619 0.00 0.00 0.00 5.54
1759 1796 1.935799 TTGCAGCCTTCTCTCTCTCT 58.064 50.000 0.00 0.00 0.00 3.10
1761 1798 1.005805 TGCAGCCTTCTCTCTCTCTCT 59.994 52.381 0.00 0.00 0.00 3.10
1762 1799 1.678101 GCAGCCTTCTCTCTCTCTCTC 59.322 57.143 0.00 0.00 0.00 3.20
1763 1800 2.684927 GCAGCCTTCTCTCTCTCTCTCT 60.685 54.545 0.00 0.00 0.00 3.10
1764 1801 3.209410 CAGCCTTCTCTCTCTCTCTCTC 58.791 54.545 0.00 0.00 0.00 3.20
1765 1802 3.118112 CAGCCTTCTCTCTCTCTCTCTCT 60.118 52.174 0.00 0.00 0.00 3.10
1766 1803 3.135530 AGCCTTCTCTCTCTCTCTCTCTC 59.864 52.174 0.00 0.00 0.00 3.20
1767 1804 3.135530 GCCTTCTCTCTCTCTCTCTCTCT 59.864 52.174 0.00 0.00 0.00 3.10
1768 1805 4.742138 GCCTTCTCTCTCTCTCTCTCTCTC 60.742 54.167 0.00 0.00 0.00 3.20
1769 1806 4.653341 CCTTCTCTCTCTCTCTCTCTCTCT 59.347 50.000 0.00 0.00 0.00 3.10
1770 1807 5.221422 CCTTCTCTCTCTCTCTCTCTCTCTC 60.221 52.000 0.00 0.00 0.00 3.20
1771 1808 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1772 1809 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1773 1810 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1774 1811 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1775 1812 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1776 1813 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1777 1814 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1778 1815 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1779 1816 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1780 1817 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1781 1818 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1782 1819 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1783 1820 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1784 1821 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1785 1822 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1786 1823 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1787 1824 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1788 1825 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1789 1826 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1794 1831 1.067060 CTCTCTCTCTCTCTCTCGCGA 59.933 57.143 9.26 9.26 0.00 5.87
1886 1925 6.146184 TGCTGCTAGATTTACTCGCATATTTC 59.854 38.462 0.00 0.00 44.23 2.17
2114 2161 4.492791 AACGAAACTTTTAATGGGTCCG 57.507 40.909 0.00 0.00 0.00 4.79
2122 2169 4.202599 ACTTTTAATGGGTCCGGGTTAACT 60.203 41.667 0.00 0.00 0.00 2.24
2301 2574 9.303116 AGAGAGTATACCATTTGATTCGTATCT 57.697 33.333 0.00 0.00 0.00 1.98
2309 2582 7.752695 ACCATTTGATTCGTATCTGAAAGTTC 58.247 34.615 3.59 0.00 33.76 3.01
2310 2583 7.607991 ACCATTTGATTCGTATCTGAAAGTTCT 59.392 33.333 3.59 0.00 33.76 3.01
2311 2584 8.454106 CCATTTGATTCGTATCTGAAAGTTCTT 58.546 33.333 3.59 0.00 33.76 2.52
2335 2608 5.121105 GTGGTATAATATTCGGGGCATACC 58.879 45.833 12.89 12.89 38.79 2.73
2343 2616 3.756933 TTCGGGGCATACCACTTATAC 57.243 47.619 0.00 0.00 42.91 1.47
2483 2758 0.807496 GGCTCCAGATGTGCTTGTTC 59.193 55.000 0.00 0.00 33.94 3.18
2493 2768 2.378038 TGTGCTTGTTCCTCTTGCTTT 58.622 42.857 0.00 0.00 0.00 3.51
2519 2794 7.038587 TGCTTCAGTTTATAAAGGAGTGGAGTA 60.039 37.037 0.00 0.00 0.00 2.59
2542 2817 2.359214 GAGTGTGGCATCTCATCGACTA 59.641 50.000 14.65 0.00 0.00 2.59
2689 2967 0.030638 ATGTTTGACTGCGTTGGTGC 59.969 50.000 0.00 0.00 0.00 5.01
2783 3061 0.601311 ACGTTTCAGTGGAGCAGCTC 60.601 55.000 14.69 14.69 0.00 4.09
2860 3138 1.483595 CCTGAGGCTCCACAAGGTGA 61.484 60.000 12.86 0.00 35.23 4.02
2861 3139 0.036577 CTGAGGCTCCACAAGGTGAG 60.037 60.000 12.86 0.00 35.23 3.51
2885 3163 2.081212 GTCGGTGTCTGAACTCGCG 61.081 63.158 0.00 0.00 0.00 5.87
2927 3205 3.495276 CGTCTATAGTCTGCCTCTCTGGA 60.495 52.174 0.00 0.00 38.35 3.86
3150 3431 8.621532 TTTTCATCTGTACTAAACTGCATCTT 57.378 30.769 0.00 0.00 0.00 2.40
3468 3799 0.680921 CCATGGATGACGGCTTTGGT 60.681 55.000 5.56 0.00 0.00 3.67
3651 3982 1.890489 TGCACTCGGTTACAGAAGCTA 59.110 47.619 9.85 0.00 0.00 3.32
3759 4090 1.152881 CAGGCTAACCATGAGGGGC 60.153 63.158 0.00 0.00 42.91 5.80
3795 4126 0.107654 AGCGGATGCCTAACTTGGTC 60.108 55.000 0.00 0.00 44.31 4.02
3825 4156 2.496899 TGGAGGAGCAAAATGAGGAC 57.503 50.000 0.00 0.00 0.00 3.85
3954 4285 0.404040 GGGAGTTTGGTGGTGATCCA 59.596 55.000 0.00 0.00 42.05 3.41
3963 4294 2.225091 TGGTGGTGATCCAAAGCAGAAT 60.225 45.455 0.00 0.00 46.15 2.40
4014 4345 2.972625 TGTTCTGTTATTCCTGAGCGG 58.027 47.619 0.00 0.00 0.00 5.52
4030 4361 2.464459 CGGGAGCTGGTCGATTTGC 61.464 63.158 0.00 0.00 0.00 3.68
4109 4440 7.279758 GGTTTTCATGATTTCACAGGAAACAAA 59.720 33.333 15.23 0.00 45.49 2.83
4120 4451 6.734137 TCACAGGAAACAAATTATGTGTCAC 58.266 36.000 10.92 0.00 46.54 3.67
4123 4454 6.079763 CAGGAAACAAATTATGTGTCACTCG 58.920 40.000 4.27 0.00 46.54 4.18
4140 4471 2.563179 ACTCGTTGTACTGAAGGAGCAT 59.437 45.455 12.89 0.00 40.13 3.79
4277 4611 0.701731 TATGTGGGGGAACAGTTGGG 59.298 55.000 0.00 0.00 32.52 4.12
4310 4644 4.514577 ATTCGGGCTCGCACCTCG 62.515 66.667 0.00 0.00 40.15 4.63
4317 4651 2.279120 CTCGCACCTCGGCTGATC 60.279 66.667 0.00 0.00 39.05 2.92
4349 4683 0.911769 TTGATGAGTAGGGGCTGGTG 59.088 55.000 0.00 0.00 0.00 4.17
4353 4687 2.286425 AGTAGGGGCTGGTGGCAT 60.286 61.111 0.00 0.00 44.01 4.40
4392 4727 6.494835 AGCATGTTTTAGATGGTTCTTTCCTT 59.505 34.615 0.00 0.00 33.17 3.36
4403 4738 5.505780 TGGTTCTTTCCTTTCAAGACTTCA 58.494 37.500 0.00 0.00 29.70 3.02
4438 4773 0.178992 TGGGGAGGAGCTTGTGTTTG 60.179 55.000 0.00 0.00 0.00 2.93
4456 4799 0.770499 TGGTTCATCTGCCCAGACAA 59.230 50.000 0.00 0.00 40.75 3.18
4485 4829 1.064505 CTATGCCAGTGTGAATTGCCG 59.935 52.381 0.00 0.00 0.00 5.69
4502 4846 1.066303 GCCGTCTCCTGTCATCTACTG 59.934 57.143 0.00 0.00 0.00 2.74
4569 4916 4.044191 AGCCTCCCCTTTTGTTTGTACTAT 59.956 41.667 0.00 0.00 0.00 2.12
4573 4920 7.151976 CCTCCCCTTTTGTTTGTACTATTTTG 58.848 38.462 0.00 0.00 0.00 2.44
4574 4921 7.201965 CCTCCCCTTTTGTTTGTACTATTTTGT 60.202 37.037 0.00 0.00 0.00 2.83
4575 4922 8.763984 TCCCCTTTTGTTTGTACTATTTTGTA 57.236 30.769 0.00 0.00 0.00 2.41
4576 4923 8.852135 TCCCCTTTTGTTTGTACTATTTTGTAG 58.148 33.333 0.00 0.00 0.00 2.74
4577 4924 7.597369 CCCCTTTTGTTTGTACTATTTTGTAGC 59.403 37.037 0.00 0.00 0.00 3.58
4579 4926 8.357402 CCTTTTGTTTGTACTATTTTGTAGCCT 58.643 33.333 0.00 0.00 0.00 4.58
4600 4949 2.680841 TCCTCCAGACGTTGTTGTTTTG 59.319 45.455 0.00 0.00 0.00 2.44
4601 4950 2.422127 CCTCCAGACGTTGTTGTTTTGT 59.578 45.455 0.00 0.00 0.00 2.83
4602 4951 3.623960 CCTCCAGACGTTGTTGTTTTGTA 59.376 43.478 0.00 0.00 0.00 2.41
4603 4952 4.260620 CCTCCAGACGTTGTTGTTTTGTAG 60.261 45.833 0.00 0.00 0.00 2.74
4604 4953 4.505808 TCCAGACGTTGTTGTTTTGTAGA 58.494 39.130 0.00 0.00 0.00 2.59
4605 4954 4.330620 TCCAGACGTTGTTGTTTTGTAGAC 59.669 41.667 0.00 0.00 0.00 2.59
4606 4955 4.495184 CCAGACGTTGTTGTTTTGTAGACC 60.495 45.833 0.00 0.00 0.00 3.85
4607 4956 3.624410 AGACGTTGTTGTTTTGTAGACCC 59.376 43.478 0.00 0.00 0.00 4.46
4608 4957 3.613030 ACGTTGTTGTTTTGTAGACCCT 58.387 40.909 0.00 0.00 0.00 4.34
4612 4961 5.277634 CGTTGTTGTTTTGTAGACCCTTAGG 60.278 44.000 0.00 0.00 40.04 2.69
4753 5118 1.593196 TGTTGCTTGCCTACTGTCAC 58.407 50.000 0.00 0.00 0.00 3.67
4781 5161 5.120830 CACTAACATGCTTCTTGTGAGTACC 59.879 44.000 0.00 0.00 36.78 3.34
4801 5181 1.820519 CCCTACAACAACAGCATGCAT 59.179 47.619 21.98 4.26 42.53 3.96
4827 5221 3.243035 TGTTCTTTCGTTGCAATGAGTGG 60.243 43.478 20.09 14.13 0.00 4.00
4916 5332 6.295011 CCCTTGTTAATTAAGTTCACATGCCA 60.295 38.462 0.00 0.00 0.00 4.92
4917 5333 7.322664 CCTTGTTAATTAAGTTCACATGCCAT 58.677 34.615 0.00 0.00 0.00 4.40
4918 5334 7.489113 CCTTGTTAATTAAGTTCACATGCCATC 59.511 37.037 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.355837 TGGAGTTCGCTGACGTGC 60.356 61.111 0.00 0.00 41.18 5.34
29 30 1.445582 CTTAGTCGTGGTCGGGTGC 60.446 63.158 0.00 0.00 37.69 5.01
35 36 1.513586 CGGCGTCTTAGTCGTGGTC 60.514 63.158 0.00 0.00 34.13 4.02
40 41 0.248134 CCTCTTCGGCGTCTTAGTCG 60.248 60.000 6.85 0.00 41.09 4.18
82 83 3.276091 TGCGCTGGGTTCGTGTTG 61.276 61.111 9.73 0.00 0.00 3.33
86 87 4.903010 AACGTGCGCTGGGTTCGT 62.903 61.111 9.73 7.19 36.31 3.85
108 109 3.057946 TCTGCATCGACGATATCTGGAAG 60.058 47.826 10.57 1.90 0.00 3.46
111 112 2.227626 AGTCTGCATCGACGATATCTGG 59.772 50.000 10.57 0.00 38.90 3.86
117 118 3.316588 AGATTGTAGTCTGCATCGACGAT 59.683 43.478 4.05 4.05 38.90 3.73
129 130 2.131183 GAGCGGATGCAGATTGTAGTC 58.869 52.381 0.00 0.00 46.23 2.59
132 133 1.123077 AGGAGCGGATGCAGATTGTA 58.877 50.000 0.00 0.00 46.23 2.41
170 171 6.148811 TCACCCGCAAAAGAAATAAAGAGTAG 59.851 38.462 0.00 0.00 0.00 2.57
175 176 5.371115 TCTCACCCGCAAAAGAAATAAAG 57.629 39.130 0.00 0.00 0.00 1.85
250 252 8.387354 CCAAAATCTCACACTAAAACAAAAACC 58.613 33.333 0.00 0.00 0.00 3.27
334 343 5.507650 GCGGGGTCAGAAGAGTTTACTATAG 60.508 48.000 0.00 0.00 0.00 1.31
335 344 4.340381 GCGGGGTCAGAAGAGTTTACTATA 59.660 45.833 0.00 0.00 0.00 1.31
336 345 3.132467 GCGGGGTCAGAAGAGTTTACTAT 59.868 47.826 0.00 0.00 0.00 2.12
337 346 2.494870 GCGGGGTCAGAAGAGTTTACTA 59.505 50.000 0.00 0.00 0.00 1.82
338 347 1.275573 GCGGGGTCAGAAGAGTTTACT 59.724 52.381 0.00 0.00 0.00 2.24
339 348 1.001633 TGCGGGGTCAGAAGAGTTTAC 59.998 52.381 0.00 0.00 0.00 2.01
340 349 1.344065 TGCGGGGTCAGAAGAGTTTA 58.656 50.000 0.00 0.00 0.00 2.01
341 350 0.472471 TTGCGGGGTCAGAAGAGTTT 59.528 50.000 0.00 0.00 0.00 2.66
342 351 0.472471 TTTGCGGGGTCAGAAGAGTT 59.528 50.000 0.00 0.00 0.00 3.01
343 352 0.472471 TTTTGCGGGGTCAGAAGAGT 59.528 50.000 0.00 0.00 0.00 3.24
344 353 1.604604 TTTTTGCGGGGTCAGAAGAG 58.395 50.000 0.00 0.00 0.00 2.85
345 354 3.811031 TTTTTGCGGGGTCAGAAGA 57.189 47.368 0.00 0.00 0.00 2.87
366 375 9.517868 AGTACTGTACAGAAGAGTTTACTGTAT 57.482 33.333 29.30 3.40 44.84 2.29
458 475 4.563140 AAAGTATTTCGGCAGAGGGTAA 57.437 40.909 0.00 0.00 27.08 2.85
501 526 5.071788 GGAGGGAGGAACCATTTTTCTTTTT 59.928 40.000 0.00 0.00 41.20 1.94
506 531 2.092323 CGGAGGGAGGAACCATTTTTC 58.908 52.381 0.00 0.00 41.20 2.29
952 982 1.766461 GGATGGGATCGGAGGTGGT 60.766 63.158 0.00 0.00 0.00 4.16
953 983 1.460305 AGGATGGGATCGGAGGTGG 60.460 63.158 0.00 0.00 0.00 4.61
954 984 1.476007 GGAGGATGGGATCGGAGGTG 61.476 65.000 0.00 0.00 0.00 4.00
955 985 1.152226 GGAGGATGGGATCGGAGGT 60.152 63.158 0.00 0.00 0.00 3.85
971 1001 4.144727 GGGAGGAGGAGGAGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
1649 1684 6.489127 ACAGCAAGCTATATACTACGAGAG 57.511 41.667 0.00 0.00 0.00 3.20
1655 1690 4.378149 GCGTCGACAGCAAGCTATATACTA 60.378 45.833 21.73 0.00 34.19 1.82
1656 1691 3.609644 GCGTCGACAGCAAGCTATATACT 60.610 47.826 21.73 0.00 34.19 2.12
1658 1693 2.292292 TGCGTCGACAGCAAGCTATATA 59.708 45.455 25.30 6.06 42.18 0.86
1660 1695 0.454196 TGCGTCGACAGCAAGCTATA 59.546 50.000 25.30 7.23 42.18 1.31
1708 1744 1.269448 TCGGCAGCTTTCAATTCCAAC 59.731 47.619 0.00 0.00 0.00 3.77
1728 1764 2.601905 AGGCTGCAAAGATTCAACCTT 58.398 42.857 0.50 0.00 0.00 3.50
1759 1796 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1761 1798 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1762 1799 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1763 1800 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1764 1801 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1765 1802 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1766 1803 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1767 1804 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1768 1805 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
1769 1806 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
1770 1807 3.551863 GCGAGAGAGAGAGAGAGAGAGAG 60.552 56.522 0.00 0.00 0.00 3.20
1771 1808 2.362397 GCGAGAGAGAGAGAGAGAGAGA 59.638 54.545 0.00 0.00 0.00 3.10
1772 1809 2.748605 GCGAGAGAGAGAGAGAGAGAG 58.251 57.143 0.00 0.00 0.00 3.20
1773 1810 1.067060 CGCGAGAGAGAGAGAGAGAGA 59.933 57.143 0.00 0.00 0.00 3.10
1774 1811 1.067060 TCGCGAGAGAGAGAGAGAGAG 59.933 57.143 3.71 0.00 34.08 3.20
1775 1812 1.107945 TCGCGAGAGAGAGAGAGAGA 58.892 55.000 3.71 0.00 34.08 3.10
1776 1813 3.659850 TCGCGAGAGAGAGAGAGAG 57.340 57.895 3.71 0.00 34.08 3.20
1787 1824 0.252479 AACTAGAGGACCTCGCGAGA 59.748 55.000 36.59 14.34 35.36 4.04
1788 1825 0.658897 GAACTAGAGGACCTCGCGAG 59.341 60.000 29.06 29.06 35.36 5.03
1789 1826 0.252479 AGAACTAGAGGACCTCGCGA 59.748 55.000 15.97 9.26 35.36 5.87
1794 1831 3.837399 AGGTTGAGAACTAGAGGACCT 57.163 47.619 0.00 0.00 0.00 3.85
2114 2161 4.081586 CAGAGAGTGGGAGTTAGTTAACCC 60.082 50.000 0.88 0.00 42.37 4.11
2122 2169 4.894114 GCCTATTACAGAGAGTGGGAGTTA 59.106 45.833 0.00 0.00 0.00 2.24
2278 2551 9.692749 TTCAGATACGAATCAAATGGTATACTC 57.307 33.333 2.25 0.00 34.28 2.59
2301 2574 9.104965 CCGAATATTATACCACAAGAACTTTCA 57.895 33.333 0.00 0.00 0.00 2.69
2309 2582 4.647611 TGCCCCGAATATTATACCACAAG 58.352 43.478 0.00 0.00 0.00 3.16
2310 2583 4.708576 TGCCCCGAATATTATACCACAA 57.291 40.909 0.00 0.00 0.00 3.33
2311 2584 4.919774 ATGCCCCGAATATTATACCACA 57.080 40.909 0.00 0.00 0.00 4.17
2343 2616 9.403110 CTTTGACCATGAATTTGAGTAAGAAAG 57.597 33.333 0.00 0.00 0.00 2.62
2465 2740 0.807496 GGAACAAGCACATCTGGAGC 59.193 55.000 0.00 0.00 0.00 4.70
2483 2758 3.722728 AAACTGAAGCAAAGCAAGAGG 57.277 42.857 0.00 0.00 0.00 3.69
2493 2768 6.121776 TCCACTCCTTTATAAACTGAAGCA 57.878 37.500 0.00 0.00 0.00 3.91
2519 2794 0.179127 CGATGAGATGCCACACTCGT 60.179 55.000 0.00 0.00 36.11 4.18
2542 2817 8.488651 GTGCCTACACAAGTATTAAGTACATT 57.511 34.615 0.00 0.00 46.61 2.71
2689 2967 0.897621 GGCCTCAAAGTTGAATGGGG 59.102 55.000 0.00 0.00 36.64 4.96
2860 3138 1.480212 TTCAGACACCGACATGCCCT 61.480 55.000 0.00 0.00 0.00 5.19
2861 3139 1.003839 TTCAGACACCGACATGCCC 60.004 57.895 0.00 0.00 0.00 5.36
2885 3163 2.694760 CGAGGCTGCAAAAGAGGGC 61.695 63.158 0.50 0.00 0.00 5.19
3014 3292 1.134848 GGTGTCAGATCCTCAGCAGTC 60.135 57.143 0.00 0.00 0.00 3.51
3150 3431 5.072600 ACCCACAGTATCAAGAACCTAAACA 59.927 40.000 0.00 0.00 0.00 2.83
3198 3529 2.223456 ACGAAGATCAGAGCATGTCTCG 60.223 50.000 10.27 6.30 46.44 4.04
3468 3799 2.741759 TGCAGTTCTTCACTATCGCA 57.258 45.000 0.00 0.00 32.76 5.10
3651 3982 3.304829 GAAAGGGCTATCTCTGACCTCT 58.695 50.000 0.00 0.00 43.30 3.69
3759 4090 1.036707 GCTGAGCTACCTCCCTACAG 58.963 60.000 0.00 0.00 37.29 2.74
3795 4126 2.972625 TGCTCCTCCATTACTTCAACG 58.027 47.619 0.00 0.00 0.00 4.10
3825 4156 1.202651 ACGGTCTCTGTTTCCACCTTG 60.203 52.381 0.00 0.00 0.00 3.61
3954 4285 7.428826 CAGTAGGACAAGAAAAATTCTGCTTT 58.571 34.615 0.00 0.00 40.59 3.51
4014 4345 2.464459 CCGCAAATCGACCAGCTCC 61.464 63.158 0.00 0.00 41.67 4.70
4030 4361 5.334105 CCAGTTAACTTGATCAAGAACACCG 60.334 44.000 36.15 21.90 40.79 4.94
4109 4440 6.020971 TCAGTACAACGAGTGACACATAAT 57.979 37.500 8.59 0.00 0.00 1.28
4120 4451 2.724977 TGCTCCTTCAGTACAACGAG 57.275 50.000 0.00 0.00 0.00 4.18
4123 4454 3.003480 GTGGATGCTCCTTCAGTACAAC 58.997 50.000 0.00 0.00 37.46 3.32
4140 4471 1.338973 GAGATACGCATAACCGGTGGA 59.661 52.381 8.52 0.00 0.00 4.02
4264 4598 0.539669 CTTGTCCCCAACTGTTCCCC 60.540 60.000 0.00 0.00 0.00 4.81
4277 4611 3.873952 CCCGAATTCTGATTCTCTTGTCC 59.126 47.826 3.52 0.00 39.61 4.02
4310 4644 1.005156 GCTCGGATCAGGATCAGCC 60.005 63.158 11.12 0.00 39.54 4.85
4313 4647 2.041701 TCAATGCTCGGATCAGGATCA 58.958 47.619 11.12 0.00 39.54 2.92
4314 4648 2.827800 TCAATGCTCGGATCAGGATC 57.172 50.000 0.55 0.55 37.11 3.36
4315 4649 2.636403 TCATCAATGCTCGGATCAGGAT 59.364 45.455 0.00 0.00 0.00 3.24
4317 4651 2.224233 ACTCATCAATGCTCGGATCAGG 60.224 50.000 0.00 0.00 0.00 3.86
4349 4683 2.284190 GCTAACTGGACTCTGAATGCC 58.716 52.381 0.00 0.00 0.00 4.40
4353 4687 4.623932 AACATGCTAACTGGACTCTGAA 57.376 40.909 0.00 0.00 0.00 3.02
4392 4727 3.909732 ACCCATGGTTTGAAGTCTTGAA 58.090 40.909 11.73 0.00 27.29 2.69
4427 4762 2.035066 GCAGATGAACCAAACACAAGCT 59.965 45.455 0.00 0.00 0.00 3.74
4428 4763 2.397549 GCAGATGAACCAAACACAAGC 58.602 47.619 0.00 0.00 0.00 4.01
4429 4764 2.288395 GGGCAGATGAACCAAACACAAG 60.288 50.000 0.00 0.00 0.00 3.16
4438 4773 1.815003 CTTTGTCTGGGCAGATGAACC 59.185 52.381 0.00 0.00 39.97 3.62
4456 4799 3.266772 TCACACTGGCATAGGAATTCCTT 59.733 43.478 31.45 16.41 46.09 3.36
4485 4829 4.036262 CACTAGCAGTAGATGACAGGAGAC 59.964 50.000 0.00 0.00 0.00 3.36
4502 4846 4.377839 TGACATCTTCTACAGCACTAGC 57.622 45.455 0.00 0.00 42.56 3.42
4569 4916 1.275291 CGTCTGGAGGAGGCTACAAAA 59.725 52.381 0.00 0.00 0.00 2.44
4573 4920 0.173708 CAACGTCTGGAGGAGGCTAC 59.826 60.000 0.00 0.00 33.56 3.58
4574 4921 0.251653 ACAACGTCTGGAGGAGGCTA 60.252 55.000 0.00 0.00 33.56 3.93
4575 4922 1.122019 AACAACGTCTGGAGGAGGCT 61.122 55.000 0.00 0.00 33.56 4.58
4576 4923 0.951040 CAACAACGTCTGGAGGAGGC 60.951 60.000 0.00 0.00 33.56 4.70
4577 4924 0.393077 ACAACAACGTCTGGAGGAGG 59.607 55.000 0.00 0.00 36.08 4.30
4579 4926 2.680841 CAAAACAACAACGTCTGGAGGA 59.319 45.455 0.00 0.00 0.00 3.71
4600 4949 1.508256 ATGGTGGCCTAAGGGTCTAC 58.492 55.000 3.32 0.00 38.23 2.59
4601 4950 2.280308 AATGGTGGCCTAAGGGTCTA 57.720 50.000 3.32 0.00 38.23 2.59
4602 4951 2.280308 TAATGGTGGCCTAAGGGTCT 57.720 50.000 3.32 0.00 38.23 3.85
4603 4952 3.595190 AATAATGGTGGCCTAAGGGTC 57.405 47.619 3.32 0.00 37.81 4.46
4604 4953 5.679817 AATAATAATGGTGGCCTAAGGGT 57.320 39.130 3.32 0.00 34.45 4.34
4605 4954 7.643123 AGATAATAATAATGGTGGCCTAAGGG 58.357 38.462 3.32 0.00 0.00 3.95
4606 4955 8.552296 AGAGATAATAATAATGGTGGCCTAAGG 58.448 37.037 3.32 0.00 0.00 2.69
4607 4956 9.965902 AAGAGATAATAATAATGGTGGCCTAAG 57.034 33.333 3.32 0.00 0.00 2.18
4608 4957 9.739276 CAAGAGATAATAATAATGGTGGCCTAA 57.261 33.333 3.32 0.00 0.00 2.69
4645 5001 4.099419 TCTCAGCATAATAAAGGCGAGACA 59.901 41.667 0.00 0.00 34.66 3.41
4745 5110 3.864540 GCATGTTAGTGGCTGTGACAGTA 60.865 47.826 14.82 0.88 33.43 2.74
4753 5118 2.816087 ACAAGAAGCATGTTAGTGGCTG 59.184 45.455 0.00 0.00 38.04 4.85
4781 5161 1.246649 TGCATGCTGTTGTTGTAGGG 58.753 50.000 20.33 0.00 0.00 3.53
4801 5181 2.929531 TTGCAACGAAAGAACAGCAA 57.070 40.000 0.00 0.00 39.38 3.91
4810 5204 0.313672 GGCCACTCATTGCAACGAAA 59.686 50.000 0.00 0.00 0.00 3.46
4813 5207 1.210931 CTGGCCACTCATTGCAACG 59.789 57.895 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.