Multiple sequence alignment - TraesCS4A01G452900

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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 TraesCS4A01G452900 chr4A 100.000 2912 0 0 1 2912 717757950 717755039 0.000000e+00 5378.0
1 TraesCS4A01G452900 chr4A 92.453 1590 95 17 281 1853 717220644 717222225 0.000000e+00 2248.0
2 TraesCS4A01G452900 chr4A 96.641 1280 38 5 578 1853 717282633 717283911 0.000000e+00 2121.0
3 TraesCS4A01G452900 chr4A 94.766 1280 62 5 578 1853 717256124 717257402 0.000000e+00 1988.0
4 TraesCS4A01G452900 chr4A 93.958 1291 68 7 570 1856 717808180 717806896 0.000000e+00 1943.0
5 TraesCS4A01G452900 chr4A 96.627 593 10 2 1906 2497 717222227 717222810 0.000000e+00 976.0
6 TraesCS4A01G452900 chr4A 94.231 416 23 1 2497 2912 717806265 717805851 4.090000e-178 634.0
7 TraesCS4A01G452900 chr4A 91.038 424 22 4 2491 2912 717258058 717258467 2.530000e-155 558.0
8 TraesCS4A01G452900 chr4A 93.064 346 23 1 85 430 717255552 717255896 3.350000e-139 505.0
9 TraesCS4A01G452900 chr4A 96.029 277 8 1 1906 2182 717283913 717284186 5.720000e-122 448.0
10 TraesCS4A01G452900 chr4A 92.233 309 22 2 122 430 717282097 717282403 1.240000e-118 436.0
11 TraesCS4A01G452900 chr4A 93.174 293 12 3 1906 2198 717806897 717806613 9.650000e-115 424.0
12 TraesCS4A01G452900 chr4A 90.444 293 8 5 1906 2198 717257404 717257676 4.580000e-98 368.0
13 TraesCS4A01G452900 chr4A 97.857 140 3 0 2358 2497 717806516 717806377 2.900000e-60 243.0
14 TraesCS4A01G452900 chr4A 92.913 127 9 0 239 365 717818713 717818587 4.960000e-43 185.0
15 TraesCS4A01G452900 chr4A 93.388 121 8 0 435 555 717282452 717282572 2.310000e-41 180.0
16 TraesCS4A01G452900 chr4A 92.562 121 9 0 435 555 717255943 717256063 1.070000e-39 174.0
17 TraesCS4A01G452900 chr4A 96.226 106 4 0 2211 2316 717806628 717806523 1.070000e-39 174.0
18 TraesCS4A01G452900 chr4A 96.739 92 3 0 2406 2497 717284187 717284278 1.400000e-33 154.0
19 TraesCS4A01G452900 chr4A 93.750 96 6 0 157 252 717823845 717823750 8.410000e-31 145.0
20 TraesCS4A01G452900 chr4A 100.000 31 0 0 29 59 717757890 717757860 1.130000e-04 58.4
21 TraesCS4A01G452900 chr4A 100.000 31 0 0 61 91 717757922 717757892 1.130000e-04 58.4
22 TraesCS4A01G452900 chr4A 100.000 29 0 0 1851 1879 717222248 717222276 1.000000e-03 54.7
23 TraesCS4A01G452900 chr4A 100.000 29 0 0 1851 1879 717257425 717257453 1.000000e-03 54.7
24 TraesCS4A01G452900 chr4A 100.000 29 0 0 1851 1879 717283934 717283962 1.000000e-03 54.7
25 TraesCS4A01G452900 chr4A 100.000 29 0 0 1851 1879 717756024 717755996 1.000000e-03 54.7
26 TraesCS4A01G452900 chr7A 94.228 1282 64 7 570 1847 16436329 16435054 0.000000e+00 1949.0
27 TraesCS4A01G452900 chr7A 94.150 1282 65 7 570 1847 16324193 16322918 0.000000e+00 1943.0
28 TraesCS4A01G452900 chr7A 91.379 1044 76 10 435 1465 16432796 16431754 0.000000e+00 1417.0
29 TraesCS4A01G452900 chr7A 85.561 1212 121 27 239 1444 15790442 15791605 0.000000e+00 1219.0
30 TraesCS4A01G452900 chr7A 90.747 562 25 7 430 966 16395371 16394812 0.000000e+00 725.0
31 TraesCS4A01G452900 chr7A 88.966 580 54 7 1905 2481 15819553 15820125 0.000000e+00 708.0
32 TraesCS4A01G452900 chr7A 89.711 554 42 10 2211 2752 16317626 16317076 0.000000e+00 693.0
33 TraesCS4A01G452900 chr7A 95.192 416 16 2 2497 2912 16429403 16428992 0.000000e+00 654.0
34 TraesCS4A01G452900 chr7A 96.241 399 14 1 2514 2912 16393696 16393299 0.000000e+00 652.0
35 TraesCS4A01G452900 chr7A 93.853 423 19 5 2497 2912 15820226 15820648 5.300000e-177 630.0
36 TraesCS4A01G452900 chr7A 92.654 422 25 4 2497 2912 15791655 15792076 1.150000e-168 603.0
37 TraesCS4A01G452900 chr7A 86.902 481 35 11 90 549 16324737 16324264 5.560000e-142 514.0
38 TraesCS4A01G452900 chr7A 86.902 481 35 11 90 549 16436873 16436400 5.560000e-142 514.0
39 TraesCS4A01G452900 chr7A 95.185 270 13 0 88 357 16395816 16395547 7.460000e-116 427.0
40 TraesCS4A01G452900 chr7A 92.808 292 19 2 1907 2198 16430050 16429761 3.470000e-114 422.0
41 TraesCS4A01G452900 chr7A 93.056 288 15 2 2211 2497 16394098 16393815 1.610000e-112 416.0
42 TraesCS4A01G452900 chr7A 92.517 294 14 2 1905 2198 16317896 16317611 5.810000e-112 414.0
43 TraesCS4A01G452900 chr7A 91.156 294 18 2 1905 2198 16394368 16394083 2.720000e-105 392.0
44 TraesCS4A01G452900 chr7A 95.385 195 8 1 2211 2404 16429776 16429582 2.820000e-80 309.0
45 TraesCS4A01G452900 chr7A 93.651 126 8 0 239 364 15818511 15818636 3.830000e-44 189.0
46 TraesCS4A01G452900 chr7A 92.857 84 5 1 167 249 16395459 16395542 1.420000e-23 121.0
47 TraesCS4A01G452900 chr7D 92.537 1273 82 7 594 1856 16997783 16996514 0.000000e+00 1812.0
48 TraesCS4A01G452900 chr7D 90.153 1310 73 18 570 1856 16756318 16757594 0.000000e+00 1653.0
49 TraesCS4A01G452900 chr7D 89.012 1174 73 13 245 1393 17126295 17125153 0.000000e+00 1402.0
50 TraesCS4A01G452900 chr7D 95.498 422 18 1 2491 2912 16758259 16758679 0.000000e+00 673.0
51 TraesCS4A01G452900 chr7D 93.285 417 26 2 2497 2912 17124356 17123941 5.330000e-172 614.0
52 TraesCS4A01G452900 chr7D 94.444 288 12 3 2211 2497 16757863 16758147 9.580000e-120 440.0
53 TraesCS4A01G452900 chr7D 93.220 295 11 3 1905 2198 16757592 16757878 2.680000e-115 425.0
54 TraesCS4A01G452900 chr7D 92.177 294 15 3 1905 2198 16996516 16996231 2.700000e-110 409.0
55 TraesCS4A01G452900 chr7D 93.156 263 16 2 2236 2497 17124735 17124474 4.550000e-103 385.0
56 TraesCS4A01G452900 chr7D 91.603 262 15 1 1905 2166 17124991 17124737 3.570000e-94 355.0
57 TraesCS4A01G452900 chr7D 88.940 217 21 3 35 250 17128344 17128130 6.190000e-67 265.0
58 TraesCS4A01G452900 chr7D 93.865 163 7 2 2335 2497 16996156 16995997 2.900000e-60 243.0
59 TraesCS4A01G452900 chr7B 91.304 1288 96 8 579 1855 655815355 655814073 0.000000e+00 1744.0
60 TraesCS4A01G452900 chr7B 87.648 591 42 15 1908 2497 655814071 655813511 0.000000e+00 658.0
61 TraesCS4A01G452900 chr7B 93.541 418 23 3 2497 2912 655813393 655812978 1.150000e-173 619.0
62 TraesCS4A01G452900 chr2A 86.196 326 20 6 258 559 745558904 745559228 2.160000e-86 329.0


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 TraesCS4A01G452900 chr4A 717755039 717757950 2911 True 1387.375000 5378 100.000000 1 2912 4 chr4A.!!$R3 2911
1 TraesCS4A01G452900 chr4A 717220644 717222810 2166 False 1092.900000 2248 96.360000 281 2497 3 chr4A.!!$F1 2216
2 TraesCS4A01G452900 chr4A 717805851 717808180 2329 True 683.600000 1943 95.089200 570 2912 5 chr4A.!!$R4 2342
3 TraesCS4A01G452900 chr4A 717255552 717258467 2915 False 607.950000 1988 93.645667 85 2912 6 chr4A.!!$F2 2827
4 TraesCS4A01G452900 chr4A 717282097 717284278 2181 False 565.616667 2121 95.838333 122 2497 6 chr4A.!!$F3 2375
5 TraesCS4A01G452900 chr7A 16322918 16324737 1819 True 1228.500000 1943 90.526000 90 1847 2 chr7A.!!$R2 1757
6 TraesCS4A01G452900 chr7A 15790442 15792076 1634 False 911.000000 1219 89.107500 239 2912 2 chr7A.!!$F2 2673
7 TraesCS4A01G452900 chr7A 16428992 16436873 7881 True 877.500000 1949 92.649000 90 2912 6 chr7A.!!$R4 2822
8 TraesCS4A01G452900 chr7A 16317076 16317896 820 True 553.500000 693 91.114000 1905 2752 2 chr7A.!!$R1 847
9 TraesCS4A01G452900 chr7A 16393299 16395816 2517 True 522.400000 725 93.277000 88 2912 5 chr7A.!!$R3 2824
10 TraesCS4A01G452900 chr7A 15818511 15820648 2137 False 509.000000 708 92.156667 239 2912 3 chr7A.!!$F3 2673
11 TraesCS4A01G452900 chr7D 16995997 16997783 1786 True 821.333333 1812 92.859667 594 2497 3 chr7D.!!$R1 1903
12 TraesCS4A01G452900 chr7D 16756318 16758679 2361 False 797.750000 1653 93.328750 570 2912 4 chr7D.!!$F1 2342
13 TraesCS4A01G452900 chr7D 17123941 17128344 4403 True 604.200000 1402 91.199200 35 2912 5 chr7D.!!$R2 2877
14 TraesCS4A01G452900 chr7B 655812978 655815355 2377 True 1007.000000 1744 90.831000 579 2912 3 chr7B.!!$R1 2333

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
109 110 0.250295 CCCGTTTCTCTTCACCTGCA 60.250 55.000 0.0 0.0 0.0 4.41 F
883 6629 1.302832 CCCTGTCCAGCCACTTGTC 60.303 63.158 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 6920 0.824109 CCAGCACCGACAAGGAGATA 59.176 55.0 0.0 0.0 45.0 1.98 R
2793 10029 0.471591 TGGCTGCACTTGGGGATTTT 60.472 50.0 0.5 0.0 0.0 1.82 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
18 19 3.948735 AATACCCCCATATTCGGCG 57.051 52.632 0.00 0.00 0.00 6.46
19 20 0.322187 AATACCCCCATATTCGGCGC 60.322 55.000 0.00 0.00 0.00 6.53
20 21 2.515996 ATACCCCCATATTCGGCGCG 62.516 60.000 0.00 0.00 0.00 6.86
23 24 3.049674 CCCATATTCGGCGCGCAT 61.050 61.111 34.42 20.41 0.00 4.73
24 25 2.476051 CCATATTCGGCGCGCATC 59.524 61.111 34.42 15.90 0.00 3.91
25 26 2.476051 CATATTCGGCGCGCATCC 59.524 61.111 34.42 15.07 0.00 3.51
26 27 2.029288 CATATTCGGCGCGCATCCT 61.029 57.895 34.42 16.67 0.00 3.24
27 28 1.301716 ATATTCGGCGCGCATCCTT 60.302 52.632 34.42 15.33 0.00 3.36
28 29 1.291877 ATATTCGGCGCGCATCCTTC 61.292 55.000 34.42 13.41 0.00 3.46
29 30 2.363711 TATTCGGCGCGCATCCTTCT 62.364 55.000 34.42 12.37 0.00 2.85
30 31 3.824028 TATTCGGCGCGCATCCTTCTT 62.824 52.381 34.42 10.87 0.00 2.52
31 32 2.566057 TTCGGCGCGCATCCTTCTTA 62.566 55.000 34.42 3.85 0.00 2.10
32 33 2.871427 CGGCGCGCATCCTTCTTAC 61.871 63.158 34.42 10.15 0.00 2.34
33 34 1.521681 GGCGCGCATCCTTCTTACT 60.522 57.895 34.42 0.00 0.00 2.24
38 39 1.209275 CGCATCCTTCTTACTCGGCG 61.209 60.000 0.00 0.00 37.17 6.46
62 63 0.457851 CTTCCTCATCCTCGTCGCTT 59.542 55.000 0.00 0.00 0.00 4.68
65 66 1.025812 CCTCATCCTCGTCGCTTACT 58.974 55.000 0.00 0.00 0.00 2.24
66 67 1.002251 CCTCATCCTCGTCGCTTACTC 60.002 57.143 0.00 0.00 0.00 2.59
67 68 0.656259 TCATCCTCGTCGCTTACTCG 59.344 55.000 0.00 0.00 0.00 4.18
68 69 0.317103 CATCCTCGTCGCTTACTCGG 60.317 60.000 0.00 0.00 0.00 4.63
69 70 2.061182 ATCCTCGTCGCTTACTCGGC 62.061 60.000 0.00 0.00 0.00 5.54
76 77 4.821589 GCTTACTCGGCGGCTGCT 62.822 66.667 18.85 0.00 42.25 4.24
77 78 2.125512 CTTACTCGGCGGCTGCTT 60.126 61.111 18.85 2.05 42.25 3.91
83 84 4.845580 CGGCGGCTGCTTCCTCAT 62.846 66.667 18.85 0.00 42.25 2.90
109 110 0.250295 CCCGTTTCTCTTCACCTGCA 60.250 55.000 0.00 0.00 0.00 4.41
185 186 6.878923 TGGATTCTTTCTGCTTATTCTCGAAA 59.121 34.615 0.00 0.00 0.00 3.46
201 202 6.142818 TCTCGAAAAAGAAAAGCAATCCAA 57.857 33.333 0.00 0.00 0.00 3.53
262 2103 5.415077 AGATAATAATAGAGGGTGTCGGTCG 59.585 44.000 0.00 0.00 0.00 4.79
359 2284 9.013229 AGATACAGTATTTGTTTGAGAAATGCA 57.987 29.630 0.00 0.00 41.29 3.96
511 2505 3.877508 AGTACCTTTGTTCAGTTCAGTGC 59.122 43.478 0.00 0.00 0.00 4.40
546 2540 2.147958 GTGTGGCGTTGATGTCCTAAA 58.852 47.619 0.00 0.00 0.00 1.85
549 2550 3.071479 GTGGCGTTGATGTCCTAAAGAA 58.929 45.455 0.00 0.00 0.00 2.52
638 6376 3.127099 TGTGTCGAACAGGGAGAGT 57.873 52.632 0.00 0.00 33.78 3.24
730 6468 1.617536 AAGGATGGGCAGAGCTCCA 60.618 57.895 10.93 1.40 34.50 3.86
786 6524 4.493747 CGTTCCGCGACCTCCTCC 62.494 72.222 8.23 0.00 44.77 4.30
871 6615 2.270527 GCTTCTCCAGCCCCTGTC 59.729 66.667 0.00 0.00 43.65 3.51
873 6617 1.920325 CTTCTCCAGCCCCTGTCCA 60.920 63.158 0.00 0.00 0.00 4.02
875 6619 4.106925 CTCCAGCCCCTGTCCAGC 62.107 72.222 0.00 0.00 0.00 4.85
880 6624 3.971702 GCCCCTGTCCAGCCACTT 61.972 66.667 0.00 0.00 0.00 3.16
883 6629 1.302832 CCCTGTCCAGCCACTTGTC 60.303 63.158 0.00 0.00 0.00 3.18
914 6660 2.094182 TCTCGCATAACTGTTGGACCTC 60.094 50.000 2.69 0.00 0.00 3.85
1170 6919 1.609841 CCTGTTGCATCTGCTGACTCA 60.610 52.381 3.53 0.00 42.66 3.41
1171 6920 2.357075 CTGTTGCATCTGCTGACTCAT 58.643 47.619 3.53 0.00 42.66 2.90
1239 6993 3.365364 GGAGCGATTCTTGGACAAAACAG 60.365 47.826 0.00 0.00 0.00 3.16
1256 7010 5.367945 AAACAGAGTCCTAAAGTTGGTCA 57.632 39.130 0.00 0.00 0.00 4.02
1289 7043 2.676748 ACAAAATGTGGCCTTCAAGGA 58.323 42.857 7.98 0.00 37.67 3.36
1393 7151 4.963373 TGTGTTCGAGGAAGATAAAACCA 58.037 39.130 0.00 0.00 0.00 3.67
1717 8788 4.303257 GGGCTGCAGTCCAACTAC 57.697 61.111 32.45 2.98 40.23 2.73
1855 8935 3.345808 CCGTGAGTGCGGTTGGTG 61.346 66.667 0.00 0.00 46.11 4.17
1856 8936 3.345808 CGTGAGTGCGGTTGGTGG 61.346 66.667 0.00 0.00 0.00 4.61
1857 8937 2.978010 GTGAGTGCGGTTGGTGGG 60.978 66.667 0.00 0.00 0.00 4.61
1858 8938 3.164977 TGAGTGCGGTTGGTGGGA 61.165 61.111 0.00 0.00 0.00 4.37
1859 8939 2.358737 GAGTGCGGTTGGTGGGAG 60.359 66.667 0.00 0.00 0.00 4.30
1860 8940 3.901797 GAGTGCGGTTGGTGGGAGG 62.902 68.421 0.00 0.00 0.00 4.30
1861 8941 3.948719 GTGCGGTTGGTGGGAGGA 61.949 66.667 0.00 0.00 0.00 3.71
1862 8942 2.933287 TGCGGTTGGTGGGAGGAT 60.933 61.111 0.00 0.00 0.00 3.24
1863 8943 2.355115 GCGGTTGGTGGGAGGATT 59.645 61.111 0.00 0.00 0.00 3.01
1864 8944 1.749258 GCGGTTGGTGGGAGGATTC 60.749 63.158 0.00 0.00 0.00 2.52
1865 8945 1.991230 CGGTTGGTGGGAGGATTCT 59.009 57.895 0.00 0.00 0.00 2.40
1866 8946 1.200519 CGGTTGGTGGGAGGATTCTA 58.799 55.000 0.00 0.00 0.00 2.10
1867 8947 1.134491 CGGTTGGTGGGAGGATTCTAC 60.134 57.143 0.00 0.00 0.00 2.59
1868 8948 2.197465 GGTTGGTGGGAGGATTCTACT 58.803 52.381 0.00 0.00 0.00 2.57
1869 8949 3.381335 GGTTGGTGGGAGGATTCTACTA 58.619 50.000 0.00 0.00 0.00 1.82
1870 8950 3.974642 GGTTGGTGGGAGGATTCTACTAT 59.025 47.826 0.00 0.00 0.00 2.12
1871 8951 4.202367 GGTTGGTGGGAGGATTCTACTATG 60.202 50.000 0.00 0.00 0.00 2.23
1872 8952 4.280789 TGGTGGGAGGATTCTACTATGT 57.719 45.455 0.00 0.00 0.00 2.29
1873 8953 4.631234 TGGTGGGAGGATTCTACTATGTT 58.369 43.478 0.00 0.00 0.00 2.71
1874 8954 4.408921 TGGTGGGAGGATTCTACTATGTTG 59.591 45.833 0.00 0.00 0.00 3.33
1875 8955 4.381411 GTGGGAGGATTCTACTATGTTGC 58.619 47.826 0.00 0.00 0.00 4.17
1876 8956 4.037222 TGGGAGGATTCTACTATGTTGCA 58.963 43.478 0.00 0.00 0.00 4.08
1877 8957 4.101585 TGGGAGGATTCTACTATGTTGCAG 59.898 45.833 0.00 0.00 0.00 4.41
1878 8958 4.101741 GGGAGGATTCTACTATGTTGCAGT 59.898 45.833 0.00 0.00 0.00 4.40
1879 8959 5.053145 GGAGGATTCTACTATGTTGCAGTG 58.947 45.833 0.00 0.00 0.00 3.66
1880 8960 5.163405 GGAGGATTCTACTATGTTGCAGTGA 60.163 44.000 0.00 0.00 0.00 3.41
1881 8961 6.463614 GGAGGATTCTACTATGTTGCAGTGAT 60.464 42.308 0.00 0.00 0.00 3.06
1882 8962 6.893583 AGGATTCTACTATGTTGCAGTGATT 58.106 36.000 0.00 0.00 0.00 2.57
1883 8963 6.989169 AGGATTCTACTATGTTGCAGTGATTC 59.011 38.462 0.00 0.00 0.00 2.52
1884 8964 6.989169 GGATTCTACTATGTTGCAGTGATTCT 59.011 38.462 0.00 0.00 0.00 2.40
1885 8965 8.144478 GGATTCTACTATGTTGCAGTGATTCTA 58.856 37.037 0.00 0.00 0.00 2.10
1886 8966 8.879342 ATTCTACTATGTTGCAGTGATTCTAC 57.121 34.615 0.00 0.00 0.00 2.59
1887 8967 7.646548 TCTACTATGTTGCAGTGATTCTACT 57.353 36.000 0.00 0.00 0.00 2.57
1888 8968 8.747538 TCTACTATGTTGCAGTGATTCTACTA 57.252 34.615 0.00 0.00 0.00 1.82
1889 8969 9.355916 TCTACTATGTTGCAGTGATTCTACTAT 57.644 33.333 0.00 0.00 0.00 2.12
1890 8970 9.404348 CTACTATGTTGCAGTGATTCTACTATG 57.596 37.037 0.00 0.00 0.00 2.23
1891 8971 7.786030 ACTATGTTGCAGTGATTCTACTATGT 58.214 34.615 0.00 0.00 0.00 2.29
1892 8972 8.260818 ACTATGTTGCAGTGATTCTACTATGTT 58.739 33.333 0.00 0.00 0.00 2.71
1893 8973 7.928307 ATGTTGCAGTGATTCTACTATGTTT 57.072 32.000 0.00 0.00 0.00 2.83
1894 8974 7.364522 TGTTGCAGTGATTCTACTATGTTTC 57.635 36.000 0.00 0.00 0.00 2.78
1895 8975 6.371548 TGTTGCAGTGATTCTACTATGTTTCC 59.628 38.462 0.00 0.00 0.00 3.13
1896 8976 6.299805 TGCAGTGATTCTACTATGTTTCCT 57.700 37.500 0.00 0.00 0.00 3.36
1897 8977 6.711277 TGCAGTGATTCTACTATGTTTCCTT 58.289 36.000 0.00 0.00 0.00 3.36
1898 8978 6.595326 TGCAGTGATTCTACTATGTTTCCTTG 59.405 38.462 0.00 0.00 0.00 3.61
1899 8979 6.595716 GCAGTGATTCTACTATGTTTCCTTGT 59.404 38.462 0.00 0.00 0.00 3.16
1900 8980 7.119846 GCAGTGATTCTACTATGTTTCCTTGTT 59.880 37.037 0.00 0.00 0.00 2.83
1901 8981 9.653287 CAGTGATTCTACTATGTTTCCTTGTTA 57.347 33.333 0.00 0.00 0.00 2.41
1902 8982 9.654663 AGTGATTCTACTATGTTTCCTTGTTAC 57.345 33.333 0.00 0.00 0.00 2.50
1903 8983 8.880750 GTGATTCTACTATGTTTCCTTGTTACC 58.119 37.037 0.00 0.00 0.00 2.85
2147 9240 1.406539 CCTGGGCACTTGATAACATGC 59.593 52.381 0.00 0.00 37.35 4.06
2166 9259 0.824759 CGCTAGGCCTGTAACTTCCT 59.175 55.000 17.99 0.00 0.00 3.36
2173 9266 4.082125 AGGCCTGTAACTTCCTTTTCATG 58.918 43.478 3.11 0.00 0.00 3.07
2254 9348 4.793216 GGTTGTTGATTATTCACGTGATGC 59.207 41.667 20.80 7.78 0.00 3.91
2407 9506 3.378512 AGTGAGGATGCAAGTCCATAGA 58.621 45.455 9.02 0.00 40.90 1.98
2492 9712 8.755696 TCATCACAAAGTTTATATTTTGCACC 57.244 30.769 0.00 0.00 37.71 5.01
2495 9715 8.359060 TCACAAAGTTTATATTTTGCACCAAC 57.641 30.769 0.00 0.00 37.71 3.77
2548 9770 1.780503 ATAAAAGCCCAGGCACATCC 58.219 50.000 12.03 0.00 44.88 3.51
2591 9817 5.929058 TGCTGAAGAGTGATATGAAGACT 57.071 39.130 0.00 0.00 0.00 3.24
2602 9828 8.072321 AGTGATATGAAGACTCAAGAAGCTAA 57.928 34.615 0.00 0.00 34.49 3.09
2725 9952 2.603075 ATGTACACTGGGTGGCAAAT 57.397 45.000 0.00 0.00 37.94 2.32
2793 10029 5.790593 ACTAGAAGGAACATAGCGACAAAA 58.209 37.500 0.00 0.00 0.00 2.44
2856 10093 4.554134 CGGTACAACGACACGATCTCATAT 60.554 45.833 0.00 0.00 35.47 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.298667 GCGCCGAATATGGGGGTAT 59.701 57.895 0.00 0.00 41.97 2.73
2 3 2.745037 GCGCCGAATATGGGGGTA 59.255 61.111 0.00 0.00 41.97 3.69
3 4 4.619227 CGCGCCGAATATGGGGGT 62.619 66.667 0.00 0.00 41.97 4.95
6 7 3.027170 GATGCGCGCCGAATATGGG 62.027 63.158 30.77 0.00 0.00 4.00
7 8 2.476051 GATGCGCGCCGAATATGG 59.524 61.111 30.77 0.00 0.00 2.74
8 9 1.568612 AAGGATGCGCGCCGAATATG 61.569 55.000 30.77 0.00 0.00 1.78
9 10 1.291877 GAAGGATGCGCGCCGAATAT 61.292 55.000 30.77 15.42 0.00 1.28
10 11 1.954146 GAAGGATGCGCGCCGAATA 60.954 57.895 30.77 10.13 0.00 1.75
11 12 3.272334 GAAGGATGCGCGCCGAAT 61.272 61.111 30.77 16.30 0.00 3.34
12 13 2.566057 TAAGAAGGATGCGCGCCGAA 62.566 55.000 30.77 11.06 0.00 4.30
13 14 3.071232 TAAGAAGGATGCGCGCCGA 62.071 57.895 30.77 11.98 0.00 5.54
14 15 2.584970 TAAGAAGGATGCGCGCCG 60.585 61.111 30.77 0.00 0.00 6.46
15 16 1.491505 GAGTAAGAAGGATGCGCGCC 61.492 60.000 30.77 14.42 0.00 6.53
16 17 1.812214 CGAGTAAGAAGGATGCGCGC 61.812 60.000 27.26 27.26 0.00 6.86
17 18 1.209275 CCGAGTAAGAAGGATGCGCG 61.209 60.000 0.00 0.00 0.00 6.86
18 19 1.491505 GCCGAGTAAGAAGGATGCGC 61.492 60.000 0.00 0.00 0.00 6.09
19 20 1.209275 CGCCGAGTAAGAAGGATGCG 61.209 60.000 0.00 0.00 34.52 4.73
20 21 0.876342 CCGCCGAGTAAGAAGGATGC 60.876 60.000 0.00 0.00 0.00 3.91
21 22 0.876342 GCCGCCGAGTAAGAAGGATG 60.876 60.000 0.00 0.00 0.00 3.51
22 23 1.043673 AGCCGCCGAGTAAGAAGGAT 61.044 55.000 0.00 0.00 0.00 3.24
23 24 1.681327 AGCCGCCGAGTAAGAAGGA 60.681 57.895 0.00 0.00 0.00 3.36
24 25 1.519455 CAGCCGCCGAGTAAGAAGG 60.519 63.158 0.00 0.00 0.00 3.46
25 26 2.167861 GCAGCCGCCGAGTAAGAAG 61.168 63.158 0.00 0.00 0.00 2.85
26 27 2.125673 GCAGCCGCCGAGTAAGAA 60.126 61.111 0.00 0.00 0.00 2.52
27 28 2.558554 GAAGCAGCCGCCGAGTAAGA 62.559 60.000 0.00 0.00 39.83 2.10
28 29 2.125512 AAGCAGCCGCCGAGTAAG 60.126 61.111 0.00 0.00 39.83 2.34
29 30 2.125673 GAAGCAGCCGCCGAGTAA 60.126 61.111 0.00 0.00 39.83 2.24
30 31 4.143333 GGAAGCAGCCGCCGAGTA 62.143 66.667 0.00 0.00 39.83 2.59
38 39 1.227497 CGAGGATGAGGAAGCAGCC 60.227 63.158 0.00 0.00 44.50 4.85
50 51 2.023318 CCGAGTAAGCGACGAGGAT 58.977 57.895 0.00 0.00 33.06 3.24
62 63 4.143333 GGAAGCAGCCGCCGAGTA 62.143 66.667 0.00 0.00 39.83 2.59
66 67 4.845580 ATGAGGAAGCAGCCGCCG 62.846 66.667 0.00 0.00 39.83 6.46
67 68 2.899339 GATGAGGAAGCAGCCGCC 60.899 66.667 0.00 0.00 39.83 6.13
68 69 2.899339 GGATGAGGAAGCAGCCGC 60.899 66.667 0.00 0.00 34.28 6.53
70 71 1.227497 CGAGGATGAGGAAGCAGCC 60.227 63.158 0.00 0.00 44.50 4.85
71 72 0.529555 GACGAGGATGAGGAAGCAGC 60.530 60.000 0.00 0.00 0.00 5.25
73 74 1.330655 GGGACGAGGATGAGGAAGCA 61.331 60.000 0.00 0.00 0.00 3.91
74 75 1.443828 GGGACGAGGATGAGGAAGC 59.556 63.158 0.00 0.00 0.00 3.86
109 110 1.590932 GCGGATCTGATGCAACATCT 58.409 50.000 5.48 0.00 0.00 2.90
185 186 7.503549 AGTCTCAATTTGGATTGCTTTTCTTT 58.496 30.769 0.00 0.00 41.94 2.52
201 202 5.880901 TCTAAAGCAGGGAAAGTCTCAATT 58.119 37.500 0.00 0.00 0.00 2.32
359 2284 4.022068 CAGATTACACACCACAATTGCCTT 60.022 41.667 5.05 0.00 0.00 4.35
511 2505 2.279741 CCACACTACGTTCCCATCATG 58.720 52.381 0.00 0.00 0.00 3.07
546 2540 0.598065 GAATTGCCTGGTGCGTTTCT 59.402 50.000 0.00 0.00 45.60 2.52
549 2550 3.365535 GGAATTGCCTGGTGCGTT 58.634 55.556 0.00 0.00 45.60 4.84
638 6376 2.867287 CCATTATTTGCACGATGGCA 57.133 45.000 0.00 0.00 43.19 4.92
730 6468 3.063084 GTCGGAGCAGGTCGTCCT 61.063 66.667 0.00 0.00 46.37 3.85
863 6607 3.971702 AAGTGGCTGGACAGGGGC 61.972 66.667 1.01 0.00 0.00 5.80
867 6611 0.946221 GTCGACAAGTGGCTGGACAG 60.946 60.000 11.55 0.00 0.00 3.51
868 6612 1.069090 GTCGACAAGTGGCTGGACA 59.931 57.895 11.55 0.00 0.00 4.02
869 6613 0.946221 CTGTCGACAAGTGGCTGGAC 60.946 60.000 20.49 0.00 0.00 4.02
870 6614 1.367471 CTGTCGACAAGTGGCTGGA 59.633 57.895 20.49 0.00 0.00 3.86
871 6615 1.669115 CCTGTCGACAAGTGGCTGG 60.669 63.158 20.49 11.41 0.00 4.85
873 6617 2.031163 GCCTGTCGACAAGTGGCT 59.969 61.111 30.03 0.00 40.36 4.75
875 6619 0.389166 GAGAGCCTGTCGACAAGTGG 60.389 60.000 20.49 17.97 0.00 4.00
876 6620 0.600557 AGAGAGCCTGTCGACAAGTG 59.399 55.000 20.49 11.93 0.00 3.16
914 6660 3.193903 TCTCCATGTGCATTTGTGGAATG 59.806 43.478 11.69 0.00 46.43 2.67
1170 6919 1.414181 CCAGCACCGACAAGGAGATAT 59.586 52.381 0.00 0.00 45.00 1.63
1171 6920 0.824109 CCAGCACCGACAAGGAGATA 59.176 55.000 0.00 0.00 45.00 1.98
1239 6993 6.204108 TCGAAAAATGACCAACTTTAGGACTC 59.796 38.462 0.00 0.00 0.00 3.36
1256 7010 6.293353 GGCCACATTTTGTTCAATCGAAAAAT 60.293 34.615 0.00 0.00 28.30 1.82
1289 7043 2.706190 GACCCTAGGGCATATGTCTTGT 59.294 50.000 28.88 2.87 39.32 3.16
1393 7151 7.630242 TTTCATTTGCCGAATAGAGATCTTT 57.370 32.000 0.00 0.00 0.00 2.52
1853 8933 4.141711 TGCAACATAGTAGAATCCTCCCAC 60.142 45.833 0.00 0.00 0.00 4.61
1854 8934 4.037222 TGCAACATAGTAGAATCCTCCCA 58.963 43.478 0.00 0.00 0.00 4.37
1855 8935 4.101741 ACTGCAACATAGTAGAATCCTCCC 59.898 45.833 0.00 0.00 0.00 4.30
1856 8936 5.053145 CACTGCAACATAGTAGAATCCTCC 58.947 45.833 0.00 0.00 0.00 4.30
1857 8937 5.907207 TCACTGCAACATAGTAGAATCCTC 58.093 41.667 0.00 0.00 0.00 3.71
1858 8938 5.939764 TCACTGCAACATAGTAGAATCCT 57.060 39.130 0.00 0.00 0.00 3.24
1859 8939 6.989169 AGAATCACTGCAACATAGTAGAATCC 59.011 38.462 0.00 0.00 0.00 3.01
1860 8940 8.973378 GTAGAATCACTGCAACATAGTAGAATC 58.027 37.037 0.00 0.00 0.00 2.52
1861 8941 8.700051 AGTAGAATCACTGCAACATAGTAGAAT 58.300 33.333 0.00 0.00 33.69 2.40
1862 8942 8.067751 AGTAGAATCACTGCAACATAGTAGAA 57.932 34.615 0.00 0.00 33.69 2.10
1863 8943 7.646548 AGTAGAATCACTGCAACATAGTAGA 57.353 36.000 0.00 0.00 33.69 2.59
1864 8944 9.404348 CATAGTAGAATCACTGCAACATAGTAG 57.596 37.037 0.00 0.00 33.69 2.57
1865 8945 8.914011 ACATAGTAGAATCACTGCAACATAGTA 58.086 33.333 0.00 0.00 33.69 1.82
1866 8946 7.786030 ACATAGTAGAATCACTGCAACATAGT 58.214 34.615 0.00 0.00 33.69 2.12
1867 8947 8.654230 AACATAGTAGAATCACTGCAACATAG 57.346 34.615 0.00 0.00 33.69 2.23
1868 8948 9.098355 GAAACATAGTAGAATCACTGCAACATA 57.902 33.333 0.00 0.00 33.69 2.29
1869 8949 7.066284 GGAAACATAGTAGAATCACTGCAACAT 59.934 37.037 0.00 0.00 33.69 2.71
1870 8950 6.371548 GGAAACATAGTAGAATCACTGCAACA 59.628 38.462 0.00 0.00 33.69 3.33
1871 8951 6.595716 AGGAAACATAGTAGAATCACTGCAAC 59.404 38.462 0.00 0.00 33.69 4.17
1872 8952 6.711277 AGGAAACATAGTAGAATCACTGCAA 58.289 36.000 0.00 0.00 33.69 4.08
1873 8953 6.299805 AGGAAACATAGTAGAATCACTGCA 57.700 37.500 0.00 0.00 33.69 4.41
1874 8954 6.595716 ACAAGGAAACATAGTAGAATCACTGC 59.404 38.462 0.00 0.00 0.00 4.40
1875 8955 8.553459 AACAAGGAAACATAGTAGAATCACTG 57.447 34.615 0.00 0.00 0.00 3.66
1876 8956 9.654663 GTAACAAGGAAACATAGTAGAATCACT 57.345 33.333 0.00 0.00 0.00 3.41
1877 8957 8.880750 GGTAACAAGGAAACATAGTAGAATCAC 58.119 37.037 0.00 0.00 0.00 3.06
1878 8958 7.762615 CGGTAACAAGGAAACATAGTAGAATCA 59.237 37.037 0.00 0.00 0.00 2.57
1879 8959 7.763071 ACGGTAACAAGGAAACATAGTAGAATC 59.237 37.037 0.00 0.00 0.00 2.52
1880 8960 7.548075 CACGGTAACAAGGAAACATAGTAGAAT 59.452 37.037 0.00 0.00 0.00 2.40
1881 8961 6.869913 CACGGTAACAAGGAAACATAGTAGAA 59.130 38.462 0.00 0.00 0.00 2.10
1882 8962 6.209192 TCACGGTAACAAGGAAACATAGTAGA 59.791 38.462 0.00 0.00 0.00 2.59
1883 8963 6.392354 TCACGGTAACAAGGAAACATAGTAG 58.608 40.000 0.00 0.00 0.00 2.57
1884 8964 6.343716 TCACGGTAACAAGGAAACATAGTA 57.656 37.500 0.00 0.00 0.00 1.82
1885 8965 5.217978 TCACGGTAACAAGGAAACATAGT 57.782 39.130 0.00 0.00 0.00 2.12
1886 8966 6.737254 AATCACGGTAACAAGGAAACATAG 57.263 37.500 0.00 0.00 0.00 2.23
1887 8967 6.314400 GCTAATCACGGTAACAAGGAAACATA 59.686 38.462 0.00 0.00 0.00 2.29
1888 8968 5.123344 GCTAATCACGGTAACAAGGAAACAT 59.877 40.000 0.00 0.00 0.00 2.71
1889 8969 4.453136 GCTAATCACGGTAACAAGGAAACA 59.547 41.667 0.00 0.00 0.00 2.83
1890 8970 4.694037 AGCTAATCACGGTAACAAGGAAAC 59.306 41.667 0.00 0.00 0.00 2.78
1891 8971 4.901868 AGCTAATCACGGTAACAAGGAAA 58.098 39.130 0.00 0.00 0.00 3.13
1892 8972 4.546829 AGCTAATCACGGTAACAAGGAA 57.453 40.909 0.00 0.00 0.00 3.36
1893 8973 4.222145 AGAAGCTAATCACGGTAACAAGGA 59.778 41.667 0.00 0.00 0.00 3.36
1894 8974 4.330074 CAGAAGCTAATCACGGTAACAAGG 59.670 45.833 0.00 0.00 0.00 3.61
1895 8975 5.168569 TCAGAAGCTAATCACGGTAACAAG 58.831 41.667 0.00 0.00 0.00 3.16
1896 8976 5.142061 TCAGAAGCTAATCACGGTAACAA 57.858 39.130 0.00 0.00 0.00 2.83
1897 8977 4.794278 TCAGAAGCTAATCACGGTAACA 57.206 40.909 0.00 0.00 0.00 2.41
1898 8978 6.270815 TGTATCAGAAGCTAATCACGGTAAC 58.729 40.000 0.00 0.00 0.00 2.50
1899 8979 6.459670 TGTATCAGAAGCTAATCACGGTAA 57.540 37.500 0.00 0.00 0.00 2.85
1900 8980 5.507482 GCTGTATCAGAAGCTAATCACGGTA 60.507 44.000 0.66 0.00 36.47 4.02
1901 8981 4.737946 GCTGTATCAGAAGCTAATCACGGT 60.738 45.833 0.66 0.00 36.47 4.83
1902 8982 3.738282 GCTGTATCAGAAGCTAATCACGG 59.262 47.826 0.66 0.00 36.47 4.94
1903 8983 4.963237 GCTGTATCAGAAGCTAATCACG 57.037 45.455 0.66 0.00 36.47 4.35
2147 9240 0.824759 AGGAAGTTACAGGCCTAGCG 59.175 55.000 3.98 0.00 0.00 4.26
2173 9266 8.573035 AGACAAGTTACTCTTAGCTATCTATGC 58.427 37.037 0.00 0.00 34.66 3.14
2254 9348 4.802999 TGAGATAGTCATATGCTCAAGCG 58.197 43.478 7.32 0.00 45.83 4.68
2407 9506 7.796054 ACTTGCAGTCTATATTAACCTGATGT 58.204 34.615 0.00 0.00 0.00 3.06
2434 9534 4.946772 TGCTGCTTATATGTTTGTTGGCTA 59.053 37.500 0.00 0.00 0.00 3.93
2492 9712 5.703978 TTGTTTGGTCCATACATCTGTTG 57.296 39.130 14.95 0.00 0.00 3.33
2495 9715 4.218200 TGCTTTGTTTGGTCCATACATCTG 59.782 41.667 14.95 9.68 0.00 2.90
2548 9770 2.200792 TTTTTGTGTGCACCATGTCG 57.799 45.000 15.69 0.00 0.00 4.35
2602 9828 6.610075 AGGGTTTGCATCTTGAAACAATAT 57.390 33.333 0.00 0.00 34.36 1.28
2793 10029 0.471591 TGGCTGCACTTGGGGATTTT 60.472 50.000 0.50 0.00 0.00 1.82
2796 10032 1.607467 GTTGGCTGCACTTGGGGAT 60.607 57.895 0.50 0.00 0.00 3.85
2856 10093 2.618816 CCTACATCCTTTGCAGCTTGGA 60.619 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.