Multiple sequence alignment - TraesCS7A01G075000

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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 TraesCS7A01G075000 chr7A 100.000 2523 0 0 1 2523 40694394 40696916 0.000000e+00 4660.0
1 TraesCS7A01G075000 chr7A 88.105 496 23 9 1 490 435874434 435874899 7.880000e-155 556.0
2 TraesCS7A01G075000 chr7A 88.278 418 35 6 1 413 670171402 670171810 2.920000e-134 488.0
3 TraesCS7A01G075000 chr7A 84.343 198 28 3 506 701 40707376 40707572 9.210000e-45 191.0
4 TraesCS7A01G075000 chr7A 89.865 148 14 1 1855 2001 40951180 40951327 3.310000e-44 189.0
5 TraesCS7A01G075000 chr7D 87.282 1321 91 29 488 1769 41259063 41260345 0.000000e+00 1437.0
6 TraesCS7A01G075000 chr7D 89.929 844 42 15 488 1303 41366372 41365544 0.000000e+00 1048.0
7 TraesCS7A01G075000 chr7D 88.720 789 57 5 506 1270 41274852 41275632 0.000000e+00 935.0
8 TraesCS7A01G075000 chr7D 92.118 406 24 5 900 1303 41325334 41325733 1.310000e-157 566.0
9 TraesCS7A01G075000 chr7D 79.496 834 95 27 510 1305 41344140 41343345 8.000000e-145 523.0
10 TraesCS7A01G075000 chr7D 87.637 364 35 3 488 846 41306770 41307128 5.020000e-112 414.0
11 TraesCS7A01G075000 chr7D 81.285 358 31 15 510 851 41272914 41273251 8.950000e-65 257.0
12 TraesCS7A01G075000 chr7D 86.957 161 12 8 2366 2520 142882575 142882732 3.340000e-39 172.0
13 TraesCS7A01G075000 chr7D 87.402 127 12 3 488 613 41274725 41274848 2.620000e-30 143.0
14 TraesCS7A01G075000 chr4A 86.940 1294 101 27 514 1770 648133008 648134270 0.000000e+00 1391.0
15 TraesCS7A01G075000 chr4A 84.705 1288 110 42 557 1770 648260525 648261799 0.000000e+00 1206.0
16 TraesCS7A01G075000 chr4A 86.282 780 64 14 1007 1770 648654189 648654941 0.000000e+00 808.0
17 TraesCS7A01G075000 chr4A 86.000 500 53 11 1 492 680019066 680018576 1.030000e-143 520.0
18 TraesCS7A01G075000 chr4A 88.860 386 31 8 2031 2406 648263839 648264222 4.920000e-127 464.0
19 TraesCS7A01G075000 chr4A 86.517 356 45 3 953 1305 648337280 648337635 3.040000e-104 388.0
20 TraesCS7A01G075000 chr4A 92.574 202 14 1 1819 2019 648654939 648655140 3.180000e-74 289.0
21 TraesCS7A01G075000 chr4A 88.318 214 14 4 1819 2021 648261797 648262010 1.940000e-61 246.0
22 TraesCS7A01G075000 chr4A 88.608 158 18 0 1819 1976 648134268 648134425 2.560000e-45 193.0
23 TraesCS7A01G075000 chr4A 93.701 127 7 1 2398 2523 719163901 719164027 3.310000e-44 189.0
24 TraesCS7A01G075000 chr4A 86.420 162 12 4 1612 1770 648136728 648136882 4.320000e-38 169.0
25 TraesCS7A01G075000 chr4A 88.571 105 12 0 601 705 648335570 648335674 7.330000e-26 128.0
26 TraesCS7A01G075000 chr2A 91.833 502 20 5 1 492 447000595 447001085 0.000000e+00 680.0
27 TraesCS7A01G075000 chr2A 88.933 506 41 8 1 491 394263209 394262704 5.970000e-171 610.0
28 TraesCS7A01G075000 chr2A 88.294 504 40 12 1 488 112624459 112623959 1.010000e-163 586.0
29 TraesCS7A01G075000 chr2A 81.683 202 28 6 2185 2383 59560230 59560425 2.600000e-35 159.0
30 TraesCS7A01G075000 chr2A 78.972 214 35 6 2190 2399 138902642 138902435 1.220000e-28 137.0
31 TraesCS7A01G075000 chrUn 89.924 526 15 8 1 488 33332488 33331963 0.000000e+00 643.0
32 TraesCS7A01G075000 chrUn 89.924 526 15 8 1 488 462626870 462627395 0.000000e+00 643.0
33 TraesCS7A01G075000 chrUn 81.599 538 61 21 773 1283 48835683 48836209 6.500000e-111 411.0
34 TraesCS7A01G075000 chrUn 79.133 369 59 14 506 869 48825490 48825845 3.240000e-59 239.0
35 TraesCS7A01G075000 chr3A 89.544 526 17 8 1 488 725186670 725186145 1.270000e-177 632.0
36 TraesCS7A01G075000 chr3A 89.837 492 33 6 1 488 686390360 686390838 1.280000e-172 616.0
37 TraesCS7A01G075000 chr3A 88.283 495 26 11 1 491 53292084 53291618 4.710000e-157 564.0
38 TraesCS7A01G075000 chr3A 93.651 126 6 2 2400 2523 52198988 52198863 1.190000e-43 187.0
39 TraesCS7A01G075000 chr3A 77.880 217 34 10 2186 2396 621489946 621490154 3.410000e-24 122.0
40 TraesCS7A01G075000 chr3A 86.111 108 13 2 2197 2302 299719690 299719583 5.700000e-22 115.0
41 TraesCS7A01G075000 chr3A 78.409 176 28 7 2221 2393 649799038 649798870 3.430000e-19 106.0
42 TraesCS7A01G075000 chr3A 95.238 42 1 1 1768 1809 633050199 633050159 5.830000e-07 65.8
43 TraesCS7A01G075000 chr1A 87.751 498 47 10 1 490 486412479 486411988 1.010000e-158 569.0
44 TraesCS7A01G075000 chr1A 79.812 213 29 9 2185 2391 118817207 118817003 2.620000e-30 143.0
45 TraesCS7A01G075000 chr1A 88.182 110 10 3 2195 2302 295336377 295336269 7.330000e-26 128.0
46 TraesCS7A01G075000 chr6A 87.475 503 46 10 1 488 48260044 48259544 4.710000e-157 564.0
47 TraesCS7A01G075000 chr6A 84.453 521 45 20 1 491 106457861 106457347 4.880000e-132 481.0
48 TraesCS7A01G075000 chr5A 87.371 483 35 18 1 473 382331208 382330742 4.780000e-147 531.0
49 TraesCS7A01G075000 chr5A 85.965 513 47 14 1 497 502280685 502280182 2.220000e-145 525.0
50 TraesCS7A01G075000 chr2B 84.296 433 34 16 1 407 680797598 680798022 2.350000e-105 392.0
51 TraesCS7A01G075000 chr2B 90.511 137 11 2 2388 2523 551568011 551567876 1.990000e-41 180.0
52 TraesCS7A01G075000 chr2B 81.295 139 11 7 2029 2155 45729638 45729773 5.740000e-17 99.0
53 TraesCS7A01G075000 chr2B 95.238 42 1 1 1769 1810 28631620 28631580 5.830000e-07 65.8
54 TraesCS7A01G075000 chr1B 92.537 134 8 2 2392 2523 626227019 626226886 9.210000e-45 191.0
55 TraesCS7A01G075000 chr1B 95.000 120 5 1 2405 2523 147663535 147663416 1.190000e-43 187.0
56 TraesCS7A01G075000 chr5D 93.600 125 6 2 2400 2523 542695711 542695588 4.290000e-43 185.0
57 TraesCS7A01G075000 chr5D 83.186 113 14 3 2195 2302 551180484 551180372 5.740000e-17 99.0
58 TraesCS7A01G075000 chr5D 95.238 42 1 1 1769 1810 339385201 339385241 5.830000e-07 65.8
59 TraesCS7A01G075000 chr1D 92.913 127 8 1 2398 2523 368090964 368091090 1.540000e-42 183.0
60 TraesCS7A01G075000 chr1D 91.489 47 2 2 1764 1810 356862306 356862350 2.100000e-06 63.9
61 TraesCS7A01G075000 chr5B 91.667 132 9 2 2391 2521 610006906 610007036 5.540000e-42 182.0
62 TraesCS7A01G075000 chr5B 95.349 43 1 1 1768 1810 246182710 246182669 1.620000e-07 67.6
63 TraesCS7A01G075000 chr3D 86.364 110 13 2 2195 2302 163403049 163403158 4.410000e-23 119.0
64 TraesCS7A01G075000 chr4B 79.141 163 28 5 2192 2351 621989272 621989431 9.540000e-20 108.0
65 TraesCS7A01G075000 chr6B 95.238 42 1 1 1769 1810 130944119 130944159 5.830000e-07 65.8
66 TraesCS7A01G075000 chr6D 88.889 54 3 3 1771 1823 8138305 8138254 2.100000e-06 63.9
67 TraesCS7A01G075000 chr2D 93.182 44 2 1 1766 1809 360737944 360737902 2.100000e-06 63.9
68 TraesCS7A01G075000 chr4D 89.796 49 4 1 1762 1810 39411181 39411228 7.540000e-06 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G075000 chr7A 40694394 40696916 2522 False 4660.000000 4660 100.000000 1 2523 1 chr7A.!!$F1 2522
1 TraesCS7A01G075000 chr7D 41259063 41260345 1282 False 1437.000000 1437 87.282000 488 1769 1 chr7D.!!$F1 1281
2 TraesCS7A01G075000 chr7D 41365544 41366372 828 True 1048.000000 1048 89.929000 488 1303 1 chr7D.!!$R2 815
3 TraesCS7A01G075000 chr7D 41343345 41344140 795 True 523.000000 523 79.496000 510 1305 1 chr7D.!!$R1 795
4 TraesCS7A01G075000 chr7D 41272914 41275632 2718 False 445.000000 935 85.802333 488 1270 3 chr7D.!!$F5 782
5 TraesCS7A01G075000 chr4A 648260525 648264222 3697 False 638.666667 1206 87.294333 557 2406 3 chr4A.!!$F3 1849
6 TraesCS7A01G075000 chr4A 648133008 648136882 3874 False 584.333333 1391 87.322667 514 1976 3 chr4A.!!$F2 1462
7 TraesCS7A01G075000 chr4A 648654189 648655140 951 False 548.500000 808 89.428000 1007 2019 2 chr4A.!!$F5 1012
8 TraesCS7A01G075000 chr4A 648335570 648337635 2065 False 258.000000 388 87.544000 601 1305 2 chr4A.!!$F4 704
9 TraesCS7A01G075000 chr2A 394262704 394263209 505 True 610.000000 610 88.933000 1 491 1 chr2A.!!$R3 490
10 TraesCS7A01G075000 chr2A 112623959 112624459 500 True 586.000000 586 88.294000 1 488 1 chr2A.!!$R1 487
11 TraesCS7A01G075000 chrUn 33331963 33332488 525 True 643.000000 643 89.924000 1 488 1 chrUn.!!$R1 487
12 TraesCS7A01G075000 chrUn 462626870 462627395 525 False 643.000000 643 89.924000 1 488 1 chrUn.!!$F3 487
13 TraesCS7A01G075000 chrUn 48835683 48836209 526 False 411.000000 411 81.599000 773 1283 1 chrUn.!!$F2 510
14 TraesCS7A01G075000 chr3A 725186145 725186670 525 True 632.000000 632 89.544000 1 488 1 chr3A.!!$R6 487
15 TraesCS7A01G075000 chr6A 48259544 48260044 500 True 564.000000 564 87.475000 1 488 1 chr6A.!!$R1 487
16 TraesCS7A01G075000 chr6A 106457347 106457861 514 True 481.000000 481 84.453000 1 491 1 chr6A.!!$R2 490
17 TraesCS7A01G075000 chr5A 502280182 502280685 503 True 525.000000 525 85.965000 1 497 1 chr5A.!!$R2 496

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
508 1833 0.608308 AGGCGATCCATCATGGCATG 60.608 55.0 21.42 21.42 37.96 4.06 F
964 3898 0.921214 GTACGTACGCACCGTCGATC 60.921 60.0 16.72 0.00 41.54 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 4300 0.178990 ATTAATTCAGGAGGCCGGGC 60.179 55.000 22.67 22.67 0.0 6.13 R
2223 8309 1.204467 AGCAAATTTACATGGGGTGCG 59.796 47.619 0.00 0.00 35.7 5.34 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
80 81 1.626654 CGAACGCGCAGTCCAATCTT 61.627 55.000 5.73 0.00 0.00 2.40
162 163 1.033746 GGATACCTCGGACGACACCA 61.034 60.000 0.00 0.00 0.00 4.17
174 196 0.750546 CGACACCACCGAGGAGGATA 60.751 60.000 12.54 0.00 45.00 2.59
188 210 5.420421 CGAGGAGGATAATGGTGATGATAGT 59.580 44.000 0.00 0.00 0.00 2.12
505 1830 1.002430 TCTTAGGCGATCCATCATGGC 59.998 52.381 0.00 0.00 37.47 4.40
506 1831 0.764271 TTAGGCGATCCATCATGGCA 59.236 50.000 0.00 0.00 37.96 4.92
507 1832 0.986527 TAGGCGATCCATCATGGCAT 59.013 50.000 0.00 0.00 37.96 4.40
508 1833 0.608308 AGGCGATCCATCATGGCATG 60.608 55.000 21.42 21.42 37.96 4.06
547 1876 1.192146 TCCGTTTGAGTCCTGGGGAG 61.192 60.000 0.00 0.00 29.39 4.30
622 2082 2.025727 CCCCGATCGTAGCACGTC 59.974 66.667 15.09 5.40 43.14 4.34
732 2211 2.048877 CGTGGCCTCGTACCGTTT 60.049 61.111 18.86 0.00 0.00 3.60
959 3893 2.476051 CGAGTACGTACGCACCGT 59.524 61.111 25.70 6.44 44.35 4.83
960 3894 1.578618 CGAGTACGTACGCACCGTC 60.579 63.158 25.70 13.70 41.54 4.79
961 3895 1.578618 GAGTACGTACGCACCGTCG 60.579 63.158 22.40 1.31 41.54 5.12
962 3896 1.955529 GAGTACGTACGCACCGTCGA 61.956 60.000 22.40 0.00 41.54 4.20
964 3898 0.921214 GTACGTACGCACCGTCGATC 60.921 60.000 16.72 0.00 41.54 3.69
1342 4286 1.067776 CGTACGCCTCTCTTCCAGTTT 60.068 52.381 0.52 0.00 0.00 2.66
1356 4300 6.062095 TCTTCCAGTTTCTCCTTTAAACCTG 58.938 40.000 0.00 0.00 37.51 4.00
1364 4308 1.304134 CTTTAAACCTGCCCGGCCT 60.304 57.895 7.03 0.00 35.61 5.19
1380 4332 2.291741 CGGCCTCCTGAATTAATCAAGC 59.708 50.000 0.00 0.00 37.67 4.01
1402 4354 1.088340 CCGTTGATGCAGCTCTGGAG 61.088 60.000 2.53 0.00 33.50 3.86
1528 4480 5.813383 ACATGTCTTGATGTCTGAAGGAAT 58.187 37.500 0.00 0.00 30.34 3.01
1560 4519 3.613910 GCCATGTAAAACGAGTTGGCATT 60.614 43.478 6.86 0.00 46.87 3.56
1576 4539 1.335324 GCATTTCGGCATATGTGGAGC 60.335 52.381 4.29 0.00 0.00 4.70
1588 4555 2.363788 TGTGGAGCATAACTGACGTC 57.636 50.000 9.11 9.11 0.00 4.34
1593 4560 2.292569 GGAGCATAACTGACGTCCGATA 59.707 50.000 14.12 6.24 0.00 2.92
1594 4561 3.057456 GGAGCATAACTGACGTCCGATAT 60.057 47.826 14.12 8.50 0.00 1.63
1634 4602 2.707257 TGCCAGATCCTCTGCATCAATA 59.293 45.455 0.00 0.00 42.98 1.90
1759 4733 4.932799 ACGTTGTATGTATACAGCTGCAAA 59.067 37.500 15.27 0.00 43.44 3.68
1767 4741 8.864849 GTATGTATACAGCTGCAAATTGCAACG 61.865 40.741 21.68 14.39 43.64 4.10
1774 4748 1.977188 GCAAATTGCAACGTACTCCC 58.023 50.000 13.73 0.00 44.26 4.30
1775 4749 1.539827 GCAAATTGCAACGTACTCCCT 59.460 47.619 13.73 0.00 44.26 4.20
1776 4750 2.030274 GCAAATTGCAACGTACTCCCTT 60.030 45.455 13.73 0.00 44.26 3.95
1777 4751 3.821841 CAAATTGCAACGTACTCCCTTC 58.178 45.455 0.00 0.00 0.00 3.46
1778 4752 1.722011 ATTGCAACGTACTCCCTTCG 58.278 50.000 0.00 0.00 0.00 3.79
1779 4753 0.390124 TTGCAACGTACTCCCTTCGT 59.610 50.000 0.00 0.00 39.49 3.85
1780 4754 1.246649 TGCAACGTACTCCCTTCGTA 58.753 50.000 0.00 0.00 36.80 3.43
1781 4755 1.612950 TGCAACGTACTCCCTTCGTAA 59.387 47.619 0.00 0.00 36.80 3.18
1782 4756 2.035704 TGCAACGTACTCCCTTCGTAAA 59.964 45.455 0.00 0.00 36.80 2.01
1783 4757 3.059166 GCAACGTACTCCCTTCGTAAAA 58.941 45.455 0.00 0.00 36.80 1.52
1784 4758 3.122445 GCAACGTACTCCCTTCGTAAAAG 59.878 47.826 0.00 0.00 36.80 2.27
1785 4759 4.549458 CAACGTACTCCCTTCGTAAAAGA 58.451 43.478 0.00 0.00 36.80 2.52
1786 4760 4.853924 ACGTACTCCCTTCGTAAAAGAA 57.146 40.909 0.00 0.00 36.05 2.52
1787 4761 5.200368 ACGTACTCCCTTCGTAAAAGAAA 57.800 39.130 0.00 0.00 36.05 2.52
1788 4762 5.787380 ACGTACTCCCTTCGTAAAAGAAAT 58.213 37.500 0.00 0.00 36.05 2.17
1789 4763 6.924111 ACGTACTCCCTTCGTAAAAGAAATA 58.076 36.000 0.00 0.00 36.05 1.40
1790 4764 7.550712 ACGTACTCCCTTCGTAAAAGAAATAT 58.449 34.615 0.00 0.00 36.05 1.28
1791 4765 8.686334 ACGTACTCCCTTCGTAAAAGAAATATA 58.314 33.333 0.00 0.00 36.05 0.86
1792 4766 9.520204 CGTACTCCCTTCGTAAAAGAAATATAA 57.480 33.333 0.00 0.00 0.00 0.98
1795 4769 9.597170 ACTCCCTTCGTAAAAGAAATATAAGAC 57.403 33.333 0.00 0.00 0.00 3.01
1796 4770 8.953368 TCCCTTCGTAAAAGAAATATAAGACC 57.047 34.615 0.00 0.00 0.00 3.85
1797 4771 7.707893 TCCCTTCGTAAAAGAAATATAAGACCG 59.292 37.037 0.00 0.00 0.00 4.79
1798 4772 7.493645 CCCTTCGTAAAAGAAATATAAGACCGT 59.506 37.037 0.00 0.00 0.00 4.83
1799 4773 8.876790 CCTTCGTAAAAGAAATATAAGACCGTT 58.123 33.333 0.00 0.00 0.00 4.44
1813 4787 7.834881 ATAAGACCGTTTAGATCACTATGGA 57.165 36.000 0.00 0.00 0.00 3.41
1814 4788 5.776173 AGACCGTTTAGATCACTATGGAG 57.224 43.478 0.00 0.00 0.00 3.86
1815 4789 4.585162 AGACCGTTTAGATCACTATGGAGG 59.415 45.833 0.00 0.00 0.00 4.30
1816 4790 3.641906 ACCGTTTAGATCACTATGGAGGG 59.358 47.826 0.00 0.00 0.00 4.30
1817 4791 3.895656 CCGTTTAGATCACTATGGAGGGA 59.104 47.826 0.00 0.00 40.22 4.20
1832 4808 8.621073 ACTATGGAGGGAGTATATGTATGTACA 58.379 37.037 0.00 0.00 40.98 2.90
1883 4859 0.098728 GCACACGCAACTGAAGTGTT 59.901 50.000 8.15 0.00 45.60 3.32
1893 4869 5.277297 CGCAACTGAAGTGTTTAATCTGTGA 60.277 40.000 0.00 0.00 0.00 3.58
1931 4907 4.455533 TGTGTTTCTTCCGAATTCTGATGG 59.544 41.667 3.52 0.00 0.00 3.51
2004 6266 1.682740 TGTCGTGGTACAGTGACAGA 58.317 50.000 0.00 0.00 45.79 3.41
2019 6281 4.118410 GTGACAGAGGCTATCTTCATGTG 58.882 47.826 0.00 0.00 35.47 3.21
2020 6282 4.026052 TGACAGAGGCTATCTTCATGTGA 58.974 43.478 0.00 0.00 35.47 3.58
2022 6284 3.771479 ACAGAGGCTATCTTCATGTGACA 59.229 43.478 0.00 0.00 35.47 3.58
2023 6285 4.141981 ACAGAGGCTATCTTCATGTGACAG 60.142 45.833 0.00 0.00 35.47 3.51
2028 6290 0.994247 ATCTTCATGTGACAGGGGCA 59.006 50.000 0.00 0.00 0.00 5.36
2029 6291 0.994247 TCTTCATGTGACAGGGGCAT 59.006 50.000 0.00 0.00 0.00 4.40
2051 8133 7.710475 GGCATAAAAAGTATGTATGGTGCAAAT 59.290 33.333 0.00 0.00 0.00 2.32
2100 8182 5.571784 ATTGATGTCATGTTGTGGATGTC 57.428 39.130 0.00 0.00 0.00 3.06
2104 8186 5.124297 TGATGTCATGTTGTGGATGTCAATC 59.876 40.000 0.00 0.00 0.00 2.67
2105 8187 4.396522 TGTCATGTTGTGGATGTCAATCA 58.603 39.130 0.00 0.00 34.17 2.57
2106 8188 5.011586 TGTCATGTTGTGGATGTCAATCAT 58.988 37.500 0.00 0.00 39.77 2.45
2146 8232 9.787532 TTGATCTAAGTTTGACTTGAAACAAAG 57.212 29.630 3.70 0.00 39.11 2.77
2165 8251 9.550811 AAACAAAGCTAATATGTAGCGTAAAAC 57.449 29.630 0.00 0.00 44.73 2.43
2168 8254 7.837202 AAGCTAATATGTAGCGTAAAACACA 57.163 32.000 0.00 0.00 44.73 3.72
2188 8274 3.202595 ACAGAGGGAGTAGTTCGATAGGT 59.797 47.826 0.00 0.00 0.00 3.08
2193 8279 5.764432 AGGGAGTAGTTCGATAGGTTAGTT 58.236 41.667 0.00 0.00 0.00 2.24
2220 8306 7.974730 AGTGGGAGTAACTTAGCTAGTAAAT 57.025 36.000 0.00 0.00 35.54 1.40
2223 8309 9.526713 GTGGGAGTAACTTAGCTAGTAAATAAC 57.473 37.037 0.00 0.00 35.54 1.89
2224 8310 8.408601 TGGGAGTAACTTAGCTAGTAAATAACG 58.591 37.037 0.00 0.00 35.54 3.18
2225 8311 7.380870 GGGAGTAACTTAGCTAGTAAATAACGC 59.619 40.741 0.00 0.00 35.54 4.84
2226 8312 7.917505 GGAGTAACTTAGCTAGTAAATAACGCA 59.082 37.037 0.00 0.00 35.54 5.24
2230 8318 3.189618 AGCTAGTAAATAACGCACCCC 57.810 47.619 0.00 0.00 0.00 4.95
2250 8338 5.104982 ACCCCATGTAAATTTGCTTATGTGG 60.105 40.000 7.80 7.08 0.00 4.17
2262 8350 5.811399 TGCTTATGTGGCATGTAGTTAAC 57.189 39.130 0.00 0.00 34.56 2.01
2287 8375 6.080969 AGGAGAGAGAGGTTGTTAGTATCA 57.919 41.667 0.00 0.00 0.00 2.15
2410 8501 8.135382 TCATTATGGAGCTAAATAGTACTCCC 57.865 38.462 0.00 0.00 46.76 4.30
2411 8502 7.956315 TCATTATGGAGCTAAATAGTACTCCCT 59.044 37.037 0.00 0.00 46.76 4.20
2412 8503 7.778185 TTATGGAGCTAAATAGTACTCCCTC 57.222 40.000 0.00 0.00 46.76 4.30
2413 8504 4.481072 TGGAGCTAAATAGTACTCCCTCC 58.519 47.826 0.00 7.44 46.76 4.30
2415 8506 4.143543 GAGCTAAATAGTACTCCCTCCGT 58.856 47.826 0.00 0.00 0.00 4.69
2416 8507 4.143543 AGCTAAATAGTACTCCCTCCGTC 58.856 47.826 0.00 0.00 0.00 4.79
2417 8508 3.255395 GCTAAATAGTACTCCCTCCGTCC 59.745 52.174 0.00 0.00 0.00 4.79
2418 8509 3.393426 AAATAGTACTCCCTCCGTCCA 57.607 47.619 0.00 0.00 0.00 4.02
2420 8511 2.905415 TAGTACTCCCTCCGTCCAAA 57.095 50.000 0.00 0.00 0.00 3.28
2421 8512 2.019807 AGTACTCCCTCCGTCCAAAA 57.980 50.000 0.00 0.00 0.00 2.44
2422 8513 2.332117 AGTACTCCCTCCGTCCAAAAA 58.668 47.619 0.00 0.00 0.00 1.94
2423 8514 2.910977 AGTACTCCCTCCGTCCAAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2424 8515 4.098894 AGTACTCCCTCCGTCCAAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2425 8516 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
2426 8517 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
2427 8518 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
2430 8521 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
2431 8522 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
2433 8524 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
2434 8525 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
2436 8527 6.263392 TCCGTCCAAAAATACTTGTCATCAAA 59.737 34.615 0.00 0.00 32.87 2.69
2437 8528 6.920758 CCGTCCAAAAATACTTGTCATCAAAA 59.079 34.615 0.00 0.00 32.87 2.44
2438 8529 7.598493 CCGTCCAAAAATACTTGTCATCAAAAT 59.402 33.333 0.00 0.00 32.87 1.82
2440 8531 8.711457 GTCCAAAAATACTTGTCATCAAAATGG 58.289 33.333 0.00 0.00 33.42 3.16
2441 8532 8.646004 TCCAAAAATACTTGTCATCAAAATGGA 58.354 29.630 0.00 0.00 33.42 3.41
2442 8533 9.439500 CCAAAAATACTTGTCATCAAAATGGAT 57.561 29.630 0.00 0.00 33.42 3.41
2449 8540 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
2450 8541 7.454380 ACTTGTCATCAAAATGGATAAAAGGGA 59.546 33.333 0.00 0.00 33.42 4.20
2452 8543 7.784037 TGTCATCAAAATGGATAAAAGGGATG 58.216 34.615 0.00 0.00 33.42 3.51
2453 8544 7.399765 TGTCATCAAAATGGATAAAAGGGATGT 59.600 33.333 0.00 0.00 33.29 3.06
2454 8545 8.912988 GTCATCAAAATGGATAAAAGGGATGTA 58.087 33.333 0.00 0.00 33.29 2.29
2456 8547 9.918630 CATCAAAATGGATAAAAGGGATGTATC 57.081 33.333 0.00 0.00 0.00 2.24
2457 8548 9.887862 ATCAAAATGGATAAAAGGGATGTATCT 57.112 29.630 0.00 0.00 0.00 1.98
2518 8609 9.919416 TCCATTTTGATGATAAGTATTTCTGGA 57.081 29.630 0.00 0.00 0.00 3.86
2519 8610 9.956720 CCATTTTGATGATAAGTATTTCTGGAC 57.043 33.333 0.00 0.00 0.00 4.02
2520 8611 9.655769 CATTTTGATGATAAGTATTTCTGGACG 57.344 33.333 0.00 0.00 0.00 4.79
2521 8612 7.786178 TTTGATGATAAGTATTTCTGGACGG 57.214 36.000 0.00 0.00 0.00 4.79
2522 8613 6.724893 TGATGATAAGTATTTCTGGACGGA 57.275 37.500 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.963962 CCACCTGCTGCAACAAGATT 59.036 50.000 3.02 0.00 0.00 2.40
80 81 4.519612 TGCCCACCTGCTGCAACA 62.520 61.111 3.02 0.00 30.85 3.33
162 163 2.471815 TCACCATTATCCTCCTCGGT 57.528 50.000 0.00 0.00 0.00 4.69
174 196 7.667575 ACTCTAAGTCACTATCATCACCATT 57.332 36.000 0.00 0.00 0.00 3.16
508 1833 3.202548 TCCACTATGGAGACGGTCC 57.797 57.895 4.14 0.00 42.67 4.46
540 1869 3.760035 CGTCCACGTCCTCCCCAG 61.760 72.222 0.00 0.00 34.11 4.45
622 2082 2.726691 GCGGTGATCGGTCGTTGTG 61.727 63.158 0.00 0.00 39.69 3.33
732 2211 1.211969 GAGCGAAGAGGCACGTACA 59.788 57.895 0.00 0.00 34.64 2.90
964 3898 5.641209 ACGGAGAGAGAAATCAATCAAGTTG 59.359 40.000 0.00 0.00 39.25 3.16
1275 4217 1.353358 TCGAGGGTGTACTTGGAGAGA 59.647 52.381 0.00 0.00 0.00 3.10
1326 4270 1.404851 GGAGAAACTGGAAGAGAGGCG 60.405 57.143 0.00 0.00 37.43 5.52
1342 4286 0.326927 CCGGGCAGGTTTAAAGGAGA 59.673 55.000 0.00 0.00 34.51 3.71
1356 4300 0.178990 ATTAATTCAGGAGGCCGGGC 60.179 55.000 22.67 22.67 0.00 6.13
1364 4308 4.843728 ACGGAAGCTTGATTAATTCAGGA 58.156 39.130 2.10 0.00 33.37 3.86
1380 4332 0.725686 CAGAGCTGCATCAACGGAAG 59.274 55.000 1.02 0.00 0.00 3.46
1408 4360 1.654220 CAAGTCCACCACCTTTGCG 59.346 57.895 0.00 0.00 0.00 4.85
1411 4363 1.152546 GCCCAAGTCCACCACCTTT 60.153 57.895 0.00 0.00 0.00 3.11
1464 4416 4.811969 AGATGATGATCTGATCTCAGCC 57.188 45.455 21.01 15.54 43.46 4.85
1560 4519 3.138304 GTTATGCTCCACATATGCCGAA 58.862 45.455 1.58 0.00 40.93 4.30
1576 4539 7.337718 CAAAGAAATATCGGACGTCAGTTATG 58.662 38.462 18.91 3.57 0.00 1.90
1588 4555 5.095691 CCGATCAACCAAAGAAATATCGG 57.904 43.478 6.47 6.47 45.64 4.18
1593 4560 3.191371 GCAGACCGATCAACCAAAGAAAT 59.809 43.478 0.00 0.00 0.00 2.17
1594 4561 2.552315 GCAGACCGATCAACCAAAGAAA 59.448 45.455 0.00 0.00 0.00 2.52
1634 4602 7.814264 ATACCTAAGCTAACACTACGTACAT 57.186 36.000 0.00 0.00 0.00 2.29
1718 4689 1.003223 CGTCGCCACGTACATATCTCA 60.003 52.381 0.00 0.00 41.42 3.27
1739 4710 6.264832 GCAATTTGCAGCTGTATACATACAA 58.735 36.000 16.64 5.31 44.26 2.41
1759 4733 1.001633 ACGAAGGGAGTACGTTGCAAT 59.998 47.619 0.59 0.00 36.91 3.56
1769 4743 9.597170 GTCTTATATTTCTTTTACGAAGGGAGT 57.403 33.333 0.00 0.00 0.00 3.85
1770 4744 9.043079 GGTCTTATATTTCTTTTACGAAGGGAG 57.957 37.037 0.00 0.00 0.00 4.30
1771 4745 7.707893 CGGTCTTATATTTCTTTTACGAAGGGA 59.292 37.037 0.00 0.00 0.00 4.20
1772 4746 7.493645 ACGGTCTTATATTTCTTTTACGAAGGG 59.506 37.037 0.00 0.00 0.00 3.95
1773 4747 8.416485 ACGGTCTTATATTTCTTTTACGAAGG 57.584 34.615 0.00 0.00 0.00 3.46
1787 4761 9.529823 TCCATAGTGATCTAAACGGTCTTATAT 57.470 33.333 0.00 0.00 0.00 0.86
1788 4762 8.929260 TCCATAGTGATCTAAACGGTCTTATA 57.071 34.615 0.00 0.00 0.00 0.98
1789 4763 7.039644 CCTCCATAGTGATCTAAACGGTCTTAT 60.040 40.741 0.00 0.00 0.00 1.73
1790 4764 6.264744 CCTCCATAGTGATCTAAACGGTCTTA 59.735 42.308 0.00 0.00 0.00 2.10
1791 4765 5.069251 CCTCCATAGTGATCTAAACGGTCTT 59.931 44.000 0.00 0.00 0.00 3.01
1792 4766 4.585162 CCTCCATAGTGATCTAAACGGTCT 59.415 45.833 0.00 0.00 0.00 3.85
1793 4767 4.262079 CCCTCCATAGTGATCTAAACGGTC 60.262 50.000 0.00 0.00 0.00 4.79
1794 4768 3.641906 CCCTCCATAGTGATCTAAACGGT 59.358 47.826 0.00 0.00 0.00 4.83
1795 4769 3.895656 TCCCTCCATAGTGATCTAAACGG 59.104 47.826 0.00 0.00 0.00 4.44
1796 4770 4.585162 ACTCCCTCCATAGTGATCTAAACG 59.415 45.833 0.00 0.00 0.00 3.60
1797 4771 7.784470 ATACTCCCTCCATAGTGATCTAAAC 57.216 40.000 0.00 0.00 0.00 2.01
1798 4772 9.480861 CATATACTCCCTCCATAGTGATCTAAA 57.519 37.037 0.00 0.00 0.00 1.85
1799 4773 8.624670 ACATATACTCCCTCCATAGTGATCTAA 58.375 37.037 0.00 0.00 0.00 2.10
1800 4774 8.176216 ACATATACTCCCTCCATAGTGATCTA 57.824 38.462 0.00 0.00 0.00 1.98
1801 4775 7.050493 ACATATACTCCCTCCATAGTGATCT 57.950 40.000 0.00 0.00 0.00 2.75
1802 4776 8.855110 CATACATATACTCCCTCCATAGTGATC 58.145 40.741 0.00 0.00 0.00 2.92
1803 4777 8.347591 ACATACATATACTCCCTCCATAGTGAT 58.652 37.037 0.00 0.00 0.00 3.06
1804 4778 7.709601 ACATACATATACTCCCTCCATAGTGA 58.290 38.462 0.00 0.00 0.00 3.41
1805 4779 7.962995 ACATACATATACTCCCTCCATAGTG 57.037 40.000 0.00 0.00 0.00 2.74
1806 4780 8.621073 TGTACATACATATACTCCCTCCATAGT 58.379 37.037 0.00 0.00 0.00 2.12
1807 4781 9.647918 ATGTACATACATATACTCCCTCCATAG 57.352 37.037 6.56 0.00 44.54 2.23
1809 4783 9.647918 CTATGTACATACATATACTCCCTCCAT 57.352 37.037 11.62 0.00 45.19 3.41
1810 4784 8.621073 ACTATGTACATACATATACTCCCTCCA 58.379 37.037 11.62 0.00 45.19 3.86
1811 4785 8.904834 CACTATGTACATACATATACTCCCTCC 58.095 40.741 11.62 0.00 45.19 4.30
1812 4786 8.407064 GCACTATGTACATACATATACTCCCTC 58.593 40.741 11.62 0.00 45.19 4.30
1813 4787 7.342284 GGCACTATGTACATACATATACTCCCT 59.658 40.741 11.62 0.00 45.19 4.20
1814 4788 7.123697 TGGCACTATGTACATACATATACTCCC 59.876 40.741 11.62 8.75 45.19 4.30
1815 4789 8.063200 TGGCACTATGTACATACATATACTCC 57.937 38.462 11.62 10.54 45.19 3.85
1816 4790 9.521503 CATGGCACTATGTACATACATATACTC 57.478 37.037 11.62 4.73 45.19 2.59
1817 4791 9.255029 TCATGGCACTATGTACATACATATACT 57.745 33.333 11.62 0.00 45.19 2.12
1832 4808 3.051581 AGATGGTCCTTCATGGCACTAT 58.948 45.455 7.47 0.00 35.26 2.12
1893 4869 9.260002 GGAAGAAACACAAAACATAATCAACAT 57.740 29.630 0.00 0.00 0.00 2.71
1931 4907 4.337555 AGTCCTTGTTATGCTGAATGATGC 59.662 41.667 0.00 0.00 0.00 3.91
1966 4942 6.260271 CACGACAGGTACAGAGATTACATCTA 59.740 42.308 0.00 0.00 40.38 1.98
1967 4943 5.066634 CACGACAGGTACAGAGATTACATCT 59.933 44.000 0.00 0.00 43.70 2.90
2004 6266 2.437281 CCCTGTCACATGAAGATAGCCT 59.563 50.000 0.00 0.00 0.00 4.58
2019 6281 6.016276 CCATACATACTTTTTATGCCCCTGTC 60.016 42.308 0.00 0.00 0.00 3.51
2020 6282 5.833131 CCATACATACTTTTTATGCCCCTGT 59.167 40.000 0.00 0.00 0.00 4.00
2022 6284 5.833131 CACCATACATACTTTTTATGCCCCT 59.167 40.000 0.00 0.00 0.00 4.79
2023 6285 5.508994 GCACCATACATACTTTTTATGCCCC 60.509 44.000 0.00 0.00 0.00 5.80
2065 8147 9.857656 AACATGACATCAATACCATTAGAATCT 57.142 29.630 0.00 0.00 0.00 2.40
2070 8152 7.282901 TCCACAACATGACATCAATACCATTAG 59.717 37.037 0.00 0.00 0.00 1.73
2119 8201 9.787532 TTTGTTTCAAGTCAAACTTAGATCAAG 57.212 29.630 0.00 0.00 36.03 3.02
2146 8232 7.306632 CCTCTGTGTTTTACGCTACATATTAGC 60.307 40.741 6.77 6.77 37.21 3.09
2165 8251 3.566322 CCTATCGAACTACTCCCTCTGTG 59.434 52.174 0.00 0.00 0.00 3.66
2168 8254 4.523168 AACCTATCGAACTACTCCCTCT 57.477 45.455 0.00 0.00 0.00 3.69
2219 8305 4.679372 GCAAATTTACATGGGGTGCGTTAT 60.679 41.667 0.00 0.00 0.00 1.89
2220 8306 3.367498 GCAAATTTACATGGGGTGCGTTA 60.367 43.478 0.00 0.00 0.00 3.18
2221 8307 2.611722 GCAAATTTACATGGGGTGCGTT 60.612 45.455 0.00 0.00 0.00 4.84
2223 8309 1.204467 AGCAAATTTACATGGGGTGCG 59.796 47.619 0.00 0.00 35.70 5.34
2224 8310 3.333029 AAGCAAATTTACATGGGGTGC 57.667 42.857 0.00 0.00 0.00 5.01
2225 8311 5.811613 CACATAAGCAAATTTACATGGGGTG 59.188 40.000 0.00 0.00 0.00 4.61
2226 8312 5.104982 CCACATAAGCAAATTTACATGGGGT 60.105 40.000 11.10 0.00 0.00 4.95
2230 8318 6.535865 ACATGCCACATAAGCAAATTTACATG 59.464 34.615 0.00 0.00 44.83 3.21
2250 8338 4.335874 TCTCTCTCCTCGTTAACTACATGC 59.664 45.833 3.71 0.00 0.00 4.06
2262 8350 3.349022 ACTAACAACCTCTCTCTCCTCG 58.651 50.000 0.00 0.00 0.00 4.63
2303 8391 7.775053 TTTTTCTTGGGAAGCACTATGTTAT 57.225 32.000 0.00 0.00 32.61 1.89
2339 8428 9.442047 AGTGTGATATAGCTTCATTTAATAGCC 57.558 33.333 0.00 0.00 35.53 3.93
2385 8476 7.956315 AGGGAGTACTATTTAGCTCCATAATGA 59.044 37.037 10.98 0.00 46.84 2.57
2401 8492 2.905415 TTTGGACGGAGGGAGTACTA 57.095 50.000 0.00 0.00 0.00 1.82
2402 8493 2.019807 TTTTGGACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
2403 8494 2.845363 TTTTTGGACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2407 8498 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
2408 8499 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
2409 8500 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
2410 8501 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
2411 8502 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
2412 8503 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
2413 8504 7.922505 TTTTGATGACAAGTATTTTTGGACG 57.077 32.000 0.00 0.00 37.32 4.79
2415 8506 8.646004 TCCATTTTGATGACAAGTATTTTTGGA 58.354 29.630 0.00 0.00 37.32 3.53
2416 8507 8.830201 TCCATTTTGATGACAAGTATTTTTGG 57.170 30.769 0.00 0.00 37.32 3.28
2423 8514 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
2424 8515 7.454380 TCCCTTTTATCCATTTTGATGACAAGT 59.546 33.333 0.00 0.00 37.32 3.16
2425 8516 7.839907 TCCCTTTTATCCATTTTGATGACAAG 58.160 34.615 0.00 0.00 37.32 3.16
2426 8517 7.789202 TCCCTTTTATCCATTTTGATGACAA 57.211 32.000 0.00 0.00 0.00 3.18
2427 8518 7.399765 ACATCCCTTTTATCCATTTTGATGACA 59.600 33.333 0.00 0.00 33.22 3.58
2430 8521 9.918630 GATACATCCCTTTTATCCATTTTGATG 57.081 33.333 0.00 0.00 34.68 3.07
2431 8522 9.887862 AGATACATCCCTTTTATCCATTTTGAT 57.112 29.630 0.00 0.00 0.00 2.57
2493 8584 9.956720 GTCCAGAAATACTTATCATCAAAATGG 57.043 33.333 0.00 0.00 33.42 3.16
2494 8585 9.655769 CGTCCAGAAATACTTATCATCAAAATG 57.344 33.333 0.00 0.00 0.00 2.32
2495 8586 8.840321 CCGTCCAGAAATACTTATCATCAAAAT 58.160 33.333 0.00 0.00 0.00 1.82
2496 8587 8.044309 TCCGTCCAGAAATACTTATCATCAAAA 58.956 33.333 0.00 0.00 0.00 2.44
2497 8588 7.561251 TCCGTCCAGAAATACTTATCATCAAA 58.439 34.615 0.00 0.00 0.00 2.69
2498 8589 7.119709 TCCGTCCAGAAATACTTATCATCAA 57.880 36.000 0.00 0.00 0.00 2.57
2499 8590 6.724893 TCCGTCCAGAAATACTTATCATCA 57.275 37.500 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.