Multiple sequence alignment - TraesCS1A01G015600

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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 TraesCS1A01G015600 chr1A 100.000 3681 0 0 1 3681 8294508 8298188 0.000000e+00 6798.0
1 TraesCS1A01G015600 chr1A 96.370 799 29 0 2883 3681 8304866 8305664 0.000000e+00 1315.0
2 TraesCS1A01G015600 chr1A 86.522 1061 91 24 814 1859 8311358 8312381 0.000000e+00 1120.0
3 TraesCS1A01G015600 chr1A 86.123 908 114 11 1932 2835 8312380 8313279 0.000000e+00 968.0
4 TraesCS1A01G015600 chr1A 86.728 761 54 15 984 1728 8320682 8321411 0.000000e+00 802.0
5 TraesCS1A01G015600 chr1A 84.028 720 101 12 2087 2803 8321808 8322516 0.000000e+00 680.0
6 TraesCS1A01G015600 chr1A 89.275 345 33 2 397 738 8310508 8310851 2.630000e-116 429.0
7 TraesCS1A01G015600 chr1A 87.671 73 7 1 1868 1940 388853295 388853225 2.360000e-12 84.2
8 TraesCS1A01G015600 chr1B 87.658 1426 135 13 342 1733 9262421 9263839 0.000000e+00 1620.0
9 TraesCS1A01G015600 chr1B 86.146 1422 155 17 342 1733 8916887 8915478 0.000000e+00 1496.0
10 TraesCS1A01G015600 chr1B 90.339 797 64 7 2883 3677 378616459 378615674 0.000000e+00 1033.0
11 TraesCS1A01G015600 chr1B 85.125 800 94 16 2087 2882 8914791 8914013 0.000000e+00 795.0
12 TraesCS1A01G015600 chr1B 84.769 801 95 16 2087 2882 9264213 9264991 0.000000e+00 778.0
13 TraesCS1A01G015600 chr1B 86.294 715 83 10 1016 1728 9269649 9270350 0.000000e+00 763.0
14 TraesCS1A01G015600 chr1B 85.675 733 89 14 2087 2815 9270548 9271268 0.000000e+00 758.0
15 TraesCS1A01G015600 chr1D 94.319 933 50 2 1951 2882 6793824 6794754 0.000000e+00 1426.0
16 TraesCS1A01G015600 chr1D 86.629 1062 93 27 814 1859 6817265 6818293 0.000000e+00 1129.0
17 TraesCS1A01G015600 chr1D 86.092 1021 100 16 40 1027 6788264 6789275 0.000000e+00 1061.0
18 TraesCS1A01G015600 chr1D 90.633 758 55 7 1021 1771 6789453 6790201 0.000000e+00 992.0
19 TraesCS1A01G015600 chr1D 85.262 916 117 13 1932 2835 6818292 6819201 0.000000e+00 928.0
20 TraesCS1A01G015600 chr1D 88.079 755 58 13 992 1728 6864235 6864975 0.000000e+00 867.0
21 TraesCS1A01G015600 chr1D 87.324 426 54 0 1299 1724 6732791 6732366 4.270000e-134 488.0
22 TraesCS1A01G015600 chr1D 89.773 352 30 3 394 740 6807947 6808297 2.610000e-121 446.0
23 TraesCS1A01G015600 chr1D 78.559 583 117 7 2096 2674 307218614 307219192 9.650000e-101 377.0
24 TraesCS1A01G015600 chr1D 80.989 263 50 0 1269 1531 307217809 307218071 3.720000e-50 209.0
25 TraesCS1A01G015600 chr1D 96.552 58 2 0 1807 1864 6793709 6793766 3.030000e-16 97.1
26 TraesCS1A01G015600 chr1D 90.909 66 6 0 1100 1165 6732881 6732816 5.060000e-14 89.8
27 TraesCS1A01G015600 chr6A 96.871 799 24 1 2883 3681 46780211 46781008 0.000000e+00 1336.0
28 TraesCS1A01G015600 chr6A 95.755 801 34 0 2881 3681 46774417 46775217 0.000000e+00 1291.0
29 TraesCS1A01G015600 chr7A 92.643 802 53 5 2883 3681 158231824 158232622 0.000000e+00 1149.0
30 TraesCS1A01G015600 chr7A 91.707 820 57 9 2868 3681 158225963 158226777 0.000000e+00 1127.0
31 TraesCS1A01G015600 chr3A 92.030 803 58 5 2883 3681 721419657 721420457 0.000000e+00 1123.0
32 TraesCS1A01G015600 chr7D 90.852 798 67 6 2883 3679 182481770 182480978 0.000000e+00 1064.0
33 TraesCS1A01G015600 chr2D 90.351 798 72 5 2883 3679 403984775 403985568 0.000000e+00 1042.0
34 TraesCS1A01G015600 chr2D 92.683 41 1 2 1860 1900 634411892 634411930 1.430000e-04 58.4
35 TraesCS1A01G015600 chr2D 94.595 37 1 1 1861 1897 539939919 539939884 5.140000e-04 56.5
36 TraesCS1A01G015600 chr4B 88.372 86 8 2 1082 1165 36664516 36664431 6.500000e-18 102.0
37 TraesCS1A01G015600 chr4B 88.372 86 8 2 1082 1165 36714462 36714377 6.500000e-18 102.0
38 TraesCS1A01G015600 chr4B 88.372 86 8 2 1082 1165 36763433 36763348 6.500000e-18 102.0
39 TraesCS1A01G015600 chr4B 91.111 45 0 4 1858 1899 33616481 33616524 1.430000e-04 58.4
40 TraesCS1A01G015600 chr7B 88.000 50 3 2 1851 1897 692179918 692179967 5.140000e-04 56.5
41 TraesCS1A01G015600 chr5B 100.000 28 0 0 1869 1896 508786116 508786089 7.000000e-03 52.8
42 TraesCS1A01G015600 chr5B 90.476 42 1 2 1858 1896 508788293 508788252 7.000000e-03 52.8
43 TraesCS1A01G015600 chr5B 90.476 42 1 2 1858 1896 508790146 508790105 7.000000e-03 52.8
44 TraesCS1A01G015600 chr5B 90.476 42 1 2 1858 1896 508792000 508791959 7.000000e-03 52.8


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 TraesCS1A01G015600 chr1A 8294508 8298188 3680 False 6798.000 6798 100.000000 1 3681 1 chr1A.!!$F1 3680
1 TraesCS1A01G015600 chr1A 8304866 8305664 798 False 1315.000 1315 96.370000 2883 3681 1 chr1A.!!$F2 798
2 TraesCS1A01G015600 chr1A 8310508 8313279 2771 False 839.000 1120 87.306667 397 2835 3 chr1A.!!$F3 2438
3 TraesCS1A01G015600 chr1A 8320682 8322516 1834 False 741.000 802 85.378000 984 2803 2 chr1A.!!$F4 1819
4 TraesCS1A01G015600 chr1B 9262421 9264991 2570 False 1199.000 1620 86.213500 342 2882 2 chr1B.!!$F1 2540
5 TraesCS1A01G015600 chr1B 8914013 8916887 2874 True 1145.500 1496 85.635500 342 2882 2 chr1B.!!$R2 2540
6 TraesCS1A01G015600 chr1B 378615674 378616459 785 True 1033.000 1033 90.339000 2883 3677 1 chr1B.!!$R1 794
7 TraesCS1A01G015600 chr1B 9269649 9271268 1619 False 760.500 763 85.984500 1016 2815 2 chr1B.!!$F2 1799
8 TraesCS1A01G015600 chr1D 6817265 6819201 1936 False 1028.500 1129 85.945500 814 2835 2 chr1D.!!$F4 2021
9 TraesCS1A01G015600 chr1D 6788264 6794754 6490 False 894.025 1426 91.899000 40 2882 4 chr1D.!!$F3 2842
10 TraesCS1A01G015600 chr1D 6864235 6864975 740 False 867.000 867 88.079000 992 1728 1 chr1D.!!$F2 736
11 TraesCS1A01G015600 chr1D 307217809 307219192 1383 False 293.000 377 79.774000 1269 2674 2 chr1D.!!$F5 1405
12 TraesCS1A01G015600 chr1D 6732366 6732881 515 True 288.900 488 89.116500 1100 1724 2 chr1D.!!$R1 624
13 TraesCS1A01G015600 chr6A 46780211 46781008 797 False 1336.000 1336 96.871000 2883 3681 1 chr6A.!!$F2 798
14 TraesCS1A01G015600 chr6A 46774417 46775217 800 False 1291.000 1291 95.755000 2881 3681 1 chr6A.!!$F1 800
15 TraesCS1A01G015600 chr7A 158231824 158232622 798 False 1149.000 1149 92.643000 2883 3681 1 chr7A.!!$F2 798
16 TraesCS1A01G015600 chr7A 158225963 158226777 814 False 1127.000 1127 91.707000 2868 3681 1 chr7A.!!$F1 813
17 TraesCS1A01G015600 chr3A 721419657 721420457 800 False 1123.000 1123 92.030000 2883 3681 1 chr3A.!!$F1 798
18 TraesCS1A01G015600 chr7D 182480978 182481770 792 True 1064.000 1064 90.852000 2883 3679 1 chr7D.!!$R1 796
19 TraesCS1A01G015600 chr2D 403984775 403985568 793 False 1042.000 1042 90.351000 2883 3679 1 chr2D.!!$F1 796

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
143 144 0.108615 AGCCTGTCGATCCAAGTTCG 60.109 55.0 0.0 0.0 37.94 3.95 F
144 145 0.108804 GCCTGTCGATCCAAGTTCGA 60.109 55.0 0.0 0.0 42.87 3.71 F
1759 2588 0.591170 TTAACACGCCAGCTTTCTGC 59.409 50.0 0.0 0.0 39.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 2442 1.332195 CGATGGCAGGTATCTCCTCA 58.668 55.000 0.00 0.00 46.24 3.86 R
2116 6980 1.888638 GTACCCGTTTGCACCGTGT 60.889 57.895 0.00 1.86 0.00 4.49 R
3305 8187 0.688487 TTCCTGTCCGGGTTAGGTTG 59.312 55.000 15.93 0.00 33.30 3.77 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
63 64 0.321346 TCTGATCCGAAGCACAAGCA 59.679 50.000 0.00 0.00 45.49 3.91
65 66 1.741706 CTGATCCGAAGCACAAGCATT 59.258 47.619 0.00 0.00 45.49 3.56
90 91 3.143675 TCGTGCAATGAGAGGCTTC 57.856 52.632 0.00 0.00 0.00 3.86
101 102 2.038007 AGGCTTCCTCGGAGCTCA 59.962 61.111 17.19 0.00 0.00 4.26
102 103 2.015227 GAGGCTTCCTCGGAGCTCAG 62.015 65.000 17.19 12.42 41.08 3.35
119 120 3.589988 CTCAGTGGTTAGTCATGTGGTC 58.410 50.000 0.00 0.00 0.00 4.02
125 126 1.726791 GTTAGTCATGTGGTCGTGCAG 59.273 52.381 0.00 0.00 0.00 4.41
134 135 2.125912 GTCGTGCAGCCTGTCGAT 60.126 61.111 14.58 0.00 34.93 3.59
137 138 2.265739 GTGCAGCCTGTCGATCCA 59.734 61.111 0.00 0.00 0.00 3.41
143 144 0.108615 AGCCTGTCGATCCAAGTTCG 60.109 55.000 0.00 0.00 37.94 3.95
144 145 0.108804 GCCTGTCGATCCAAGTTCGA 60.109 55.000 0.00 0.00 42.87 3.71
162 164 7.422878 AGTTCGACTCTCCAACTAAAATTTC 57.577 36.000 0.00 0.00 0.00 2.17
166 168 3.435671 ACTCTCCAACTAAAATTTCGGCG 59.564 43.478 0.00 0.00 0.00 6.46
174 176 9.926158 TCCAACTAAAATTTCGGCGTATATATA 57.074 29.630 6.85 0.00 0.00 0.86
200 202 4.869861 TCTTGTTTTGAAAGAAAGCCTTGC 59.130 37.500 0.00 0.00 34.79 4.01
217 219 4.348656 CCTTGCTCGACATTCATTTCATG 58.651 43.478 0.00 0.00 0.00 3.07
225 227 7.250445 TCGACATTCATTTCATGGTCTAATG 57.750 36.000 0.00 0.52 31.11 1.90
230 232 4.512484 TCATTTCATGGTCTAATGCGTGA 58.488 39.130 0.00 0.00 31.08 4.35
231 233 4.332543 TCATTTCATGGTCTAATGCGTGAC 59.667 41.667 0.00 0.00 31.08 3.67
233 235 3.610040 TCATGGTCTAATGCGTGACTT 57.390 42.857 0.00 0.00 34.01 3.01
235 237 3.056179 TCATGGTCTAATGCGTGACTTCA 60.056 43.478 0.00 0.00 34.01 3.02
237 239 3.064207 TGGTCTAATGCGTGACTTCAAC 58.936 45.455 0.00 0.00 34.01 3.18
246 248 5.493133 TGCGTGACTTCAACTTACAATTT 57.507 34.783 0.00 0.00 0.00 1.82
265 267 6.070881 ACAATTTTCAGGTGGCTTATTGCATA 60.071 34.615 0.00 0.00 45.15 3.14
267 269 2.930950 TCAGGTGGCTTATTGCATACC 58.069 47.619 0.00 0.00 45.13 2.73
273 275 3.630168 TGGCTTATTGCATACCACATGT 58.370 40.909 0.00 0.00 45.15 3.21
280 282 5.918426 ATTGCATACCACATGTCAATCAA 57.082 34.783 0.00 0.00 0.00 2.57
282 284 4.587891 TGCATACCACATGTCAATCAAGA 58.412 39.130 0.00 0.00 0.00 3.02
283 285 5.195185 TGCATACCACATGTCAATCAAGAT 58.805 37.500 0.00 0.00 0.00 2.40
292 294 7.149973 CACATGTCAATCAAGATTCCAAAAGT 58.850 34.615 0.00 0.00 0.00 2.66
296 298 6.262049 TGTCAATCAAGATTCCAAAAGTCGAA 59.738 34.615 0.00 0.00 0.00 3.71
308 310 2.684001 AAGTCGAACAAGTGACACCA 57.316 45.000 0.84 0.00 37.58 4.17
320 322 1.464608 GTGACACCACGATCAACATGG 59.535 52.381 0.00 0.00 37.90 3.66
373 375 1.067565 TGCTCAGGAATGACGACTGAC 60.068 52.381 0.00 0.00 36.41 3.51
421 423 1.644780 CTTCGTTTCTTCTCTCGTCGC 59.355 52.381 0.00 0.00 0.00 5.19
434 436 3.641986 GTCGCCGTTTTCACCGCA 61.642 61.111 0.00 0.00 0.00 5.69
435 437 3.641986 TCGCCGTTTTCACCGCAC 61.642 61.111 0.00 0.00 0.00 5.34
457 459 3.689649 CACCCCTAAATGAAGGACTTTCG 59.310 47.826 0.00 0.00 39.15 3.46
507 509 6.041182 GGGACTAGGAGAGACTTATTCCTTTC 59.959 46.154 8.79 6.80 41.46 2.62
517 519 5.359009 AGACTTATTCCTTTCACATGCCATG 59.641 40.000 2.40 2.40 0.00 3.66
556 558 6.983890 GGAAATCTAAAACCTTGCAGAAAACA 59.016 34.615 0.00 0.00 0.00 2.83
558 560 8.962884 AAATCTAAAACCTTGCAGAAAACAAT 57.037 26.923 0.00 0.00 0.00 2.71
589 591 4.320456 ACCGCACTGCCTGACCAG 62.320 66.667 0.00 0.00 38.78 4.00
646 648 3.511934 GGCGAGGATATAGTCTTGTGGAT 59.488 47.826 0.00 0.00 0.00 3.41
686 689 3.973206 TCTCGCCTACAAGAAAATGGA 57.027 42.857 0.00 0.00 0.00 3.41
786 1204 4.261801 CCAAAAGATAGGGAGCGAAGAAA 58.738 43.478 0.00 0.00 0.00 2.52
788 1206 4.828072 AAAGATAGGGAGCGAAGAAAGT 57.172 40.909 0.00 0.00 0.00 2.66
835 1287 2.480037 CACAGAACTTGATGCGTGCTTA 59.520 45.455 0.00 0.00 0.00 3.09
932 1409 3.713902 CTCAATTAGCAGCCGGGAT 57.286 52.632 2.18 0.00 0.00 3.85
945 1423 2.169978 AGCCGGGATCACCTTAGTTTAC 59.830 50.000 2.18 0.00 36.97 2.01
1027 1505 2.364324 TGTCAACTCCACTACTCACCAC 59.636 50.000 0.00 0.00 0.00 4.16
1067 1732 2.831526 GCAGTCTTCTTCTTCCTCCTCT 59.168 50.000 0.00 0.00 0.00 3.69
1188 1873 3.256631 ACGTACTATCCACTGAAACCGTT 59.743 43.478 0.00 0.00 0.00 4.44
1238 1935 1.395635 TGGATCATGCATGGCTGAAC 58.604 50.000 25.97 6.79 0.00 3.18
1354 2063 1.310933 CCGTGTACTACTCCCAGCGT 61.311 60.000 0.00 0.00 0.00 5.07
1474 2183 3.499737 GCGTGGAAGCCCATCGTG 61.500 66.667 0.00 0.00 45.68 4.35
1657 2442 3.382832 CCGAGGAGGCTGACGGTT 61.383 66.667 13.13 0.00 40.42 4.44
1732 2561 0.748005 ACGCGGGTACGTACCTACAT 60.748 55.000 36.70 19.71 46.19 2.29
1759 2588 0.591170 TTAACACGCCAGCTTTCTGC 59.409 50.000 0.00 0.00 39.00 4.26
1811 6625 5.047188 CCTGGACAACCAACAAACATAAAC 58.953 41.667 0.00 0.00 46.32 2.01
1864 6681 4.837093 TCATCCAACGAAAATACTCCCT 57.163 40.909 0.00 0.00 0.00 4.20
1866 6683 4.469945 TCATCCAACGAAAATACTCCCTCT 59.530 41.667 0.00 0.00 0.00 3.69
1868 6685 4.094476 TCCAACGAAAATACTCCCTCTCT 58.906 43.478 0.00 0.00 0.00 3.10
1869 6686 5.266788 TCCAACGAAAATACTCCCTCTCTA 58.733 41.667 0.00 0.00 0.00 2.43
1902 6719 8.782533 AAAGCGTTTTTGACACTAGATAAAAG 57.217 30.769 0.00 0.00 0.00 2.27
1903 6720 7.724305 AGCGTTTTTGACACTAGATAAAAGA 57.276 32.000 0.00 0.00 0.00 2.52
1904 6721 7.573627 AGCGTTTTTGACACTAGATAAAAGAC 58.426 34.615 0.00 0.00 0.00 3.01
1905 6722 6.515340 GCGTTTTTGACACTAGATAAAAGACG 59.485 38.462 14.68 14.68 34.15 4.18
1907 6724 7.568861 CGTTTTTGACACTAGATAAAAGACGCT 60.569 37.037 0.00 0.00 0.00 5.07
1908 6725 6.946229 TTTGACACTAGATAAAAGACGCTC 57.054 37.500 0.00 0.00 0.00 5.03
1909 6726 5.899120 TGACACTAGATAAAAGACGCTCT 57.101 39.130 0.00 0.00 0.00 4.09
1911 6728 7.387119 TGACACTAGATAAAAGACGCTCTTA 57.613 36.000 0.00 0.00 35.27 2.10
1912 6729 7.997482 TGACACTAGATAAAAGACGCTCTTAT 58.003 34.615 0.00 0.00 35.27 1.73
1913 6730 7.915923 TGACACTAGATAAAAGACGCTCTTATG 59.084 37.037 0.00 0.00 35.27 1.90
1914 6731 7.773149 ACACTAGATAAAAGACGCTCTTATGT 58.227 34.615 0.00 0.00 35.27 2.29
1915 6732 8.251721 ACACTAGATAAAAGACGCTCTTATGTT 58.748 33.333 0.00 0.00 35.27 2.71
1916 6733 8.535592 CACTAGATAAAAGACGCTCTTATGTTG 58.464 37.037 0.00 0.00 35.27 3.33
1917 6734 8.251721 ACTAGATAAAAGACGCTCTTATGTTGT 58.748 33.333 0.00 0.00 35.27 3.32
1918 6735 9.731819 CTAGATAAAAGACGCTCTTATGTTGTA 57.268 33.333 1.53 0.00 35.27 2.41
1919 6736 8.997621 AGATAAAAGACGCTCTTATGTTGTAA 57.002 30.769 1.53 0.00 35.27 2.41
1920 6737 9.431887 AGATAAAAGACGCTCTTATGTTGTAAA 57.568 29.630 1.53 0.00 35.27 2.01
1922 6739 9.821662 ATAAAAGACGCTCTTATGTTGTAAAAC 57.178 29.630 1.53 0.00 35.27 2.43
1923 6740 5.511088 AGACGCTCTTATGTTGTAAAACG 57.489 39.130 0.00 0.00 0.00 3.60
1924 6741 4.387862 AGACGCTCTTATGTTGTAAAACGG 59.612 41.667 0.00 0.00 0.00 4.44
1925 6742 4.309099 ACGCTCTTATGTTGTAAAACGGA 58.691 39.130 0.00 0.00 0.00 4.69
1926 6743 4.387862 ACGCTCTTATGTTGTAAAACGGAG 59.612 41.667 0.00 0.00 0.00 4.63
1927 6744 4.201685 CGCTCTTATGTTGTAAAACGGAGG 60.202 45.833 8.75 0.00 0.00 4.30
1928 6745 4.694037 GCTCTTATGTTGTAAAACGGAGGT 59.306 41.667 8.75 0.00 0.00 3.85
1929 6746 5.870978 GCTCTTATGTTGTAAAACGGAGGTA 59.129 40.000 8.75 0.00 0.00 3.08
1930 6747 6.035758 GCTCTTATGTTGTAAAACGGAGGTAG 59.964 42.308 8.75 0.00 0.00 3.18
1931 6748 6.996509 TCTTATGTTGTAAAACGGAGGTAGT 58.003 36.000 0.00 0.00 0.00 2.73
1932 6749 8.121305 TCTTATGTTGTAAAACGGAGGTAGTA 57.879 34.615 0.00 0.00 0.00 1.82
1933 6750 8.584157 TCTTATGTTGTAAAACGGAGGTAGTAA 58.416 33.333 0.00 0.00 0.00 2.24
1934 6751 9.374838 CTTATGTTGTAAAACGGAGGTAGTAAT 57.625 33.333 0.00 0.00 0.00 1.89
1935 6752 9.723601 TTATGTTGTAAAACGGAGGTAGTAATT 57.276 29.630 0.00 0.00 0.00 1.40
1936 6753 8.625786 ATGTTGTAAAACGGAGGTAGTAATTT 57.374 30.769 0.00 0.00 0.00 1.82
1937 6754 8.086851 TGTTGTAAAACGGAGGTAGTAATTTC 57.913 34.615 0.00 0.00 0.00 2.17
1938 6755 7.714377 TGTTGTAAAACGGAGGTAGTAATTTCA 59.286 33.333 0.00 0.00 0.00 2.69
1939 6756 7.894376 TGTAAAACGGAGGTAGTAATTTCAG 57.106 36.000 0.00 0.00 0.00 3.02
1947 6764 7.119262 ACGGAGGTAGTAATTTCAGAACAAATG 59.881 37.037 0.00 0.00 0.00 2.32
1949 6766 8.451748 GGAGGTAGTAATTTCAGAACAAATGAC 58.548 37.037 0.00 0.00 29.82 3.06
2026 6889 1.405872 TGTATCTTGGATACCGCCGT 58.594 50.000 13.08 0.00 0.00 5.68
2037 6900 4.082408 TGGATACCGCCGTCATATCTAAAG 60.082 45.833 0.00 0.00 0.00 1.85
2116 6980 0.179156 GTTTCGACGGCGTGGAGATA 60.179 55.000 21.19 3.57 38.98 1.98
2193 7057 1.303309 GCAGATGAGTATGGTGGCAC 58.697 55.000 9.70 9.70 0.00 5.01
2602 7466 1.959226 GTTTGAGGTCGGCGCAGAA 60.959 57.895 12.98 0.00 0.00 3.02
2622 7486 6.564873 GCAGAACTGAACAAGTATGACAGAAC 60.565 42.308 5.97 0.00 38.56 3.01
2727 7591 3.880490 TCCGACAACAAAATAAGTGTGCT 59.120 39.130 0.00 0.00 0.00 4.40
2735 7599 2.566833 AATAAGTGTGCTGCAGGACA 57.433 45.000 33.97 33.97 44.12 4.02
2804 7679 5.521735 ACTTCGTATGATGATTGCTGAAGTC 59.478 40.000 4.92 0.00 40.34 3.01
2819 7694 4.201666 GCTGAAGTCGCTCAAGTTTCTATG 60.202 45.833 0.00 0.00 0.00 2.23
2950 7827 3.470567 CCGCAGCTCACGTCGAAC 61.471 66.667 0.00 0.00 0.00 3.95
3014 7891 0.848053 TTTTGAGGACCCGAAACCCT 59.152 50.000 0.00 0.00 0.00 4.34
3111 7988 4.070552 GAGGTTCGTCGCCCTGCT 62.071 66.667 7.88 0.00 0.00 4.24
3222 8104 0.665835 GTGTGTTGTTCAATCGGCCA 59.334 50.000 2.24 0.00 0.00 5.36
3305 8187 2.963548 TCCAAAACGTCAAAAACCCC 57.036 45.000 0.00 0.00 0.00 4.95
3562 8444 3.942351 TCGGTCCGAACTGACTCTA 57.058 52.632 12.68 0.00 35.82 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.464008 AGCAGTGTCTTCCATGAGAAAAA 58.536 39.130 0.00 0.00 32.88 1.94
19 20 4.067896 GAGCAGTGTCTTCCATGAGAAAA 58.932 43.478 0.00 0.00 32.88 2.29
20 21 3.326006 AGAGCAGTGTCTTCCATGAGAAA 59.674 43.478 0.00 0.00 32.88 2.52
21 22 2.902486 AGAGCAGTGTCTTCCATGAGAA 59.098 45.455 0.00 0.00 0.00 2.87
22 23 2.495270 GAGAGCAGTGTCTTCCATGAGA 59.505 50.000 0.00 0.00 0.00 3.27
23 24 2.496871 AGAGAGCAGTGTCTTCCATGAG 59.503 50.000 0.00 0.00 0.00 2.90
24 25 2.495270 GAGAGAGCAGTGTCTTCCATGA 59.505 50.000 0.00 0.00 0.00 3.07
25 26 2.496871 AGAGAGAGCAGTGTCTTCCATG 59.503 50.000 0.00 0.00 0.00 3.66
26 27 2.496871 CAGAGAGAGCAGTGTCTTCCAT 59.503 50.000 0.00 0.00 0.00 3.41
27 28 1.891811 CAGAGAGAGCAGTGTCTTCCA 59.108 52.381 0.00 0.00 0.00 3.53
28 29 2.166829 TCAGAGAGAGCAGTGTCTTCC 58.833 52.381 0.00 0.00 0.00 3.46
29 30 3.181487 GGATCAGAGAGAGCAGTGTCTTC 60.181 52.174 0.00 0.00 33.23 2.87
30 31 2.760092 GGATCAGAGAGAGCAGTGTCTT 59.240 50.000 0.00 0.00 33.23 3.01
31 32 2.378038 GGATCAGAGAGAGCAGTGTCT 58.622 52.381 0.00 0.00 33.23 3.41
32 33 1.065401 CGGATCAGAGAGAGCAGTGTC 59.935 57.143 0.00 0.00 33.23 3.67
33 34 1.102154 CGGATCAGAGAGAGCAGTGT 58.898 55.000 0.00 0.00 33.23 3.55
34 35 1.387539 TCGGATCAGAGAGAGCAGTG 58.612 55.000 0.00 0.00 33.23 3.66
35 36 2.023673 CTTCGGATCAGAGAGAGCAGT 58.976 52.381 0.00 0.00 33.23 4.40
36 37 1.269206 GCTTCGGATCAGAGAGAGCAG 60.269 57.143 11.64 0.53 33.23 4.24
37 38 0.743688 GCTTCGGATCAGAGAGAGCA 59.256 55.000 11.64 0.00 33.23 4.26
38 39 0.743688 TGCTTCGGATCAGAGAGAGC 59.256 55.000 10.10 10.10 0.00 4.09
63 64 1.736126 CTCATTGCACGAGAGCACAAT 59.264 47.619 6.49 0.00 45.61 2.71
65 66 0.318120 TCTCATTGCACGAGAGCACA 59.682 50.000 10.33 0.00 45.61 4.57
70 71 0.610174 AAGCCTCTCATTGCACGAGA 59.390 50.000 13.10 13.10 37.18 4.04
90 91 0.457851 CTAACCACTGAGCTCCGAGG 59.542 60.000 17.83 17.83 0.00 4.63
96 97 2.027745 CCACATGACTAACCACTGAGCT 60.028 50.000 0.00 0.00 0.00 4.09
101 102 1.968493 ACGACCACATGACTAACCACT 59.032 47.619 0.00 0.00 0.00 4.00
102 103 2.066262 CACGACCACATGACTAACCAC 58.934 52.381 0.00 0.00 0.00 4.16
119 120 2.887568 GGATCGACAGGCTGCACG 60.888 66.667 22.41 22.41 0.00 5.34
125 126 0.108804 TCGAACTTGGATCGACAGGC 60.109 55.000 0.00 0.00 43.76 4.85
134 135 2.317040 AGTTGGAGAGTCGAACTTGGA 58.683 47.619 0.00 0.00 41.62 3.53
137 138 7.307219 CGAAATTTTAGTTGGAGAGTCGAACTT 60.307 37.037 9.24 0.00 41.62 2.66
143 144 4.435651 CGCCGAAATTTTAGTTGGAGAGTC 60.436 45.833 0.00 0.00 0.00 3.36
144 145 3.435671 CGCCGAAATTTTAGTTGGAGAGT 59.564 43.478 0.00 0.00 0.00 3.24
148 149 8.836268 ATATATACGCCGAAATTTTAGTTGGA 57.164 30.769 0.00 0.00 0.00 3.53
174 176 7.414429 GCAAGGCTTTCTTTCAAAACAAGAATT 60.414 33.333 0.00 0.00 39.46 2.17
176 178 5.351189 GCAAGGCTTTCTTTCAAAACAAGAA 59.649 36.000 0.00 0.00 38.27 2.52
177 179 4.869861 GCAAGGCTTTCTTTCAAAACAAGA 59.130 37.500 0.00 0.00 32.41 3.02
181 183 3.487207 CGAGCAAGGCTTTCTTTCAAAAC 59.513 43.478 0.00 0.00 39.88 2.43
217 219 3.326747 AGTTGAAGTCACGCATTAGACC 58.673 45.455 0.00 0.00 35.38 3.85
225 227 5.968848 TGAAAATTGTAAGTTGAAGTCACGC 59.031 36.000 0.00 0.00 0.00 5.34
230 232 6.682861 GCCACCTGAAAATTGTAAGTTGAAGT 60.683 38.462 0.00 0.00 0.00 3.01
231 233 5.691754 GCCACCTGAAAATTGTAAGTTGAAG 59.308 40.000 0.00 0.00 0.00 3.02
233 235 4.892934 AGCCACCTGAAAATTGTAAGTTGA 59.107 37.500 0.00 0.00 0.00 3.18
235 237 5.869649 AAGCCACCTGAAAATTGTAAGTT 57.130 34.783 0.00 0.00 0.00 2.66
237 239 6.311200 GCAATAAGCCACCTGAAAATTGTAAG 59.689 38.462 0.00 0.00 37.23 2.34
246 248 3.287222 GGTATGCAATAAGCCACCTGAA 58.713 45.455 0.00 0.00 44.83 3.02
265 267 4.665451 TGGAATCTTGATTGACATGTGGT 58.335 39.130 1.15 0.00 0.00 4.16
267 269 7.149973 ACTTTTGGAATCTTGATTGACATGTG 58.850 34.615 1.15 0.00 0.00 3.21
270 272 6.430925 TCGACTTTTGGAATCTTGATTGACAT 59.569 34.615 0.09 0.00 0.00 3.06
273 275 6.262049 TGTTCGACTTTTGGAATCTTGATTGA 59.738 34.615 0.09 0.00 0.00 2.57
280 282 5.007724 GTCACTTGTTCGACTTTTGGAATCT 59.992 40.000 0.00 0.00 0.00 2.40
282 284 4.638421 TGTCACTTGTTCGACTTTTGGAAT 59.362 37.500 0.00 0.00 33.18 3.01
283 285 4.004314 TGTCACTTGTTCGACTTTTGGAA 58.996 39.130 0.00 0.00 33.18 3.53
292 294 0.456628 TCGTGGTGTCACTTGTTCGA 59.543 50.000 2.35 4.13 41.53 3.71
296 298 2.210116 GTTGATCGTGGTGTCACTTGT 58.790 47.619 2.35 0.00 41.53 3.16
308 310 3.872696 TCTATTGTGCCATGTTGATCGT 58.127 40.909 0.00 0.00 0.00 3.73
310 312 6.381481 TCATTCTATTGTGCCATGTTGATC 57.619 37.500 0.00 0.00 0.00 2.92
315 317 6.778834 TTCATTCATTCTATTGTGCCATGT 57.221 33.333 0.00 0.00 0.00 3.21
320 322 7.891782 CACAACATTCATTCATTCTATTGTGC 58.108 34.615 0.00 0.00 38.32 4.57
324 326 6.755141 GCTGCACAACATTCATTCATTCTATT 59.245 34.615 0.00 0.00 0.00 1.73
326 328 5.393352 GGCTGCACAACATTCATTCATTCTA 60.393 40.000 0.50 0.00 0.00 2.10
328 330 3.615496 GGCTGCACAACATTCATTCATTC 59.385 43.478 0.50 0.00 0.00 2.67
329 331 3.592059 GGCTGCACAACATTCATTCATT 58.408 40.909 0.50 0.00 0.00 2.57
330 332 2.093869 GGGCTGCACAACATTCATTCAT 60.094 45.455 0.50 0.00 0.00 2.57
331 333 1.273048 GGGCTGCACAACATTCATTCA 59.727 47.619 0.50 0.00 0.00 2.57
358 360 2.927014 GCTTTCGTCAGTCGTCATTCCT 60.927 50.000 0.00 0.00 40.80 3.36
361 363 2.440539 AGCTTTCGTCAGTCGTCATT 57.559 45.000 0.00 0.00 40.80 2.57
373 375 2.749076 TCCATGGTCAATGAAGCTTTCG 59.251 45.455 12.58 0.00 38.72 3.46
421 423 2.330041 GGTGTGCGGTGAAAACGG 59.670 61.111 0.00 0.00 0.00 4.44
434 436 4.663334 GAAAGTCCTTCATTTAGGGGTGT 58.337 43.478 0.00 0.00 35.90 4.16
435 437 3.689649 CGAAAGTCCTTCATTTAGGGGTG 59.310 47.826 0.00 0.00 35.90 4.61
507 509 2.943449 TGCATTGTACATGGCATGTG 57.057 45.000 36.61 23.15 44.60 3.21
556 558 2.351276 GTGGACCGCACCTCCATT 59.649 61.111 0.00 0.00 40.04 3.16
589 591 2.100916 TCACTATCTACTTTCCCAGCGC 59.899 50.000 0.00 0.00 0.00 5.92
646 648 5.009610 CGAGAAAGGAAAATGAAAGGAACCA 59.990 40.000 0.00 0.00 0.00 3.67
686 689 1.975471 TCCTAAGGAAAATCCCCGGT 58.025 50.000 0.00 0.00 37.19 5.28
740 1158 5.369685 ACGATGATGTGTATTGTTGCAAA 57.630 34.783 0.00 0.00 0.00 3.68
782 1200 8.783660 TTATATGTACTCCTCCATCACTTTCT 57.216 34.615 0.00 0.00 0.00 2.52
786 1204 7.514127 ACCAATTATATGTACTCCTCCATCACT 59.486 37.037 0.00 0.00 0.00 3.41
788 1206 7.872061 ACCAATTATATGTACTCCTCCATCA 57.128 36.000 0.00 0.00 0.00 3.07
1027 1505 1.337260 GCTGAGTGGTGTGGTAGTGAG 60.337 57.143 0.00 0.00 0.00 3.51
1067 1732 6.938507 AGCTTTTCTTGATCAATTAATGGCA 58.061 32.000 8.96 0.00 0.00 4.92
1657 2442 1.332195 CGATGGCAGGTATCTCCTCA 58.668 55.000 0.00 0.00 46.24 3.86
1742 2571 3.034030 GCAGAAAGCTGGCGTGTT 58.966 55.556 0.00 0.00 42.53 3.32
1759 2588 2.807967 TGTTTGACCGAGCATTTCTGAG 59.192 45.455 0.00 0.00 0.00 3.35
1822 6638 6.028146 TGAACTAACGGTACTATTTCTGCA 57.972 37.500 0.00 0.00 0.00 4.41
1882 6699 7.573627 AGCGTCTTTTATCTAGTGTCAAAAAC 58.426 34.615 0.00 0.00 0.00 2.43
1886 6703 6.268825 AGAGCGTCTTTTATCTAGTGTCAA 57.731 37.500 0.00 0.00 0.00 3.18
1888 6705 7.916450 ACATAAGAGCGTCTTTTATCTAGTGTC 59.084 37.037 5.74 0.00 37.89 3.67
1890 6707 8.535592 CAACATAAGAGCGTCTTTTATCTAGTG 58.464 37.037 5.74 0.00 37.89 2.74
1892 6709 8.635877 ACAACATAAGAGCGTCTTTTATCTAG 57.364 34.615 5.74 0.00 37.89 2.43
1894 6711 8.997621 TTACAACATAAGAGCGTCTTTTATCT 57.002 30.769 5.74 0.00 37.89 1.98
1896 6713 9.821662 GTTTTACAACATAAGAGCGTCTTTTAT 57.178 29.630 5.74 2.34 34.10 1.40
1897 6714 8.005466 CGTTTTACAACATAAGAGCGTCTTTTA 58.995 33.333 5.74 0.28 34.10 1.52
1901 6718 4.387862 CCGTTTTACAACATAAGAGCGTCT 59.612 41.667 0.00 0.00 32.54 4.18
1902 6719 4.386652 TCCGTTTTACAACATAAGAGCGTC 59.613 41.667 0.00 0.00 32.54 5.19
1903 6720 4.309099 TCCGTTTTACAACATAAGAGCGT 58.691 39.130 0.00 0.00 32.54 5.07
1904 6721 4.201685 CCTCCGTTTTACAACATAAGAGCG 60.202 45.833 0.00 0.00 32.54 5.03
1905 6722 4.694037 ACCTCCGTTTTACAACATAAGAGC 59.306 41.667 0.00 0.00 32.54 4.09
1907 6724 6.996509 ACTACCTCCGTTTTACAACATAAGA 58.003 36.000 0.00 0.00 32.54 2.10
1908 6725 8.761575 TTACTACCTCCGTTTTACAACATAAG 57.238 34.615 0.00 0.00 32.54 1.73
1909 6726 9.723601 AATTACTACCTCCGTTTTACAACATAA 57.276 29.630 0.00 0.00 32.54 1.90
1911 6728 8.625786 AAATTACTACCTCCGTTTTACAACAT 57.374 30.769 0.00 0.00 32.54 2.71
1912 6729 7.714377 TGAAATTACTACCTCCGTTTTACAACA 59.286 33.333 0.00 0.00 32.54 3.33
1913 6730 8.086851 TGAAATTACTACCTCCGTTTTACAAC 57.913 34.615 0.00 0.00 0.00 3.32
1914 6731 8.149647 TCTGAAATTACTACCTCCGTTTTACAA 58.850 33.333 0.00 0.00 0.00 2.41
1915 6732 7.669427 TCTGAAATTACTACCTCCGTTTTACA 58.331 34.615 0.00 0.00 0.00 2.41
1916 6733 8.438513 GTTCTGAAATTACTACCTCCGTTTTAC 58.561 37.037 0.00 0.00 0.00 2.01
1917 6734 8.149647 TGTTCTGAAATTACTACCTCCGTTTTA 58.850 33.333 0.00 0.00 0.00 1.52
1918 6735 6.993902 TGTTCTGAAATTACTACCTCCGTTTT 59.006 34.615 0.00 0.00 0.00 2.43
1919 6736 6.527423 TGTTCTGAAATTACTACCTCCGTTT 58.473 36.000 0.00 0.00 0.00 3.60
1920 6737 6.105397 TGTTCTGAAATTACTACCTCCGTT 57.895 37.500 0.00 0.00 0.00 4.44
1921 6738 5.733620 TGTTCTGAAATTACTACCTCCGT 57.266 39.130 0.00 0.00 0.00 4.69
1922 6739 7.333423 TCATTTGTTCTGAAATTACTACCTCCG 59.667 37.037 0.00 0.00 0.00 4.63
1923 6740 8.451748 GTCATTTGTTCTGAAATTACTACCTCC 58.548 37.037 0.00 0.00 0.00 4.30
1924 6741 8.451748 GGTCATTTGTTCTGAAATTACTACCTC 58.548 37.037 0.00 0.00 0.00 3.85
1925 6742 7.942341 TGGTCATTTGTTCTGAAATTACTACCT 59.058 33.333 0.00 0.00 0.00 3.08
1926 6743 8.106247 TGGTCATTTGTTCTGAAATTACTACC 57.894 34.615 0.00 0.00 0.00 3.18
1932 6749 9.829507 TGTAAAATGGTCATTTGTTCTGAAATT 57.170 25.926 9.37 0.00 40.57 1.82
1933 6750 9.829507 TTGTAAAATGGTCATTTGTTCTGAAAT 57.170 25.926 9.37 0.00 40.57 2.17
1934 6751 9.311916 CTTGTAAAATGGTCATTTGTTCTGAAA 57.688 29.630 9.37 0.00 40.57 2.69
1935 6752 8.474025 ACTTGTAAAATGGTCATTTGTTCTGAA 58.526 29.630 9.37 0.00 40.57 3.02
1936 6753 8.006298 ACTTGTAAAATGGTCATTTGTTCTGA 57.994 30.769 9.37 0.00 40.57 3.27
1937 6754 7.920151 TGACTTGTAAAATGGTCATTTGTTCTG 59.080 33.333 9.37 4.38 40.57 3.02
1938 6755 8.006298 TGACTTGTAAAATGGTCATTTGTTCT 57.994 30.769 9.37 0.00 40.57 3.01
1939 6756 8.816640 ATGACTTGTAAAATGGTCATTTGTTC 57.183 30.769 9.37 4.87 43.95 3.18
1947 6764 3.689649 AGCGGATGACTTGTAAAATGGTC 59.310 43.478 0.00 0.00 0.00 4.02
1949 6766 5.123186 TGTTAGCGGATGACTTGTAAAATGG 59.877 40.000 0.00 0.00 0.00 3.16
2004 6866 3.199677 CGGCGGTATCCAAGATACAAAA 58.800 45.455 14.81 0.00 0.00 2.44
2026 6889 7.576861 TGATACACGACCACTTTAGATATGA 57.423 36.000 0.00 0.00 0.00 2.15
2037 6900 3.309682 CACCATTCATGATACACGACCAC 59.690 47.826 0.00 0.00 0.00 4.16
2116 6980 1.888638 GTACCCGTTTGCACCGTGT 60.889 57.895 0.00 1.86 0.00 4.49
2174 7038 1.303309 GTGCCACCATACTCATCTGC 58.697 55.000 0.00 0.00 0.00 4.26
2179 7043 0.327924 CAAGGGTGCCACCATACTCA 59.672 55.000 17.22 0.00 41.02 3.41
2193 7057 0.816421 ACGACACCGGTTTTCAAGGG 60.816 55.000 2.97 0.00 40.78 3.95
2443 7307 5.003804 GTCCCTTTGAATGCTTCTCTGTAA 58.996 41.667 0.00 0.00 0.00 2.41
2455 7319 2.369394 GCGATGAAGGTCCCTTTGAAT 58.631 47.619 0.00 0.00 36.26 2.57
2488 7352 2.283529 GCCTCCTTCCTCACGGTCA 61.284 63.158 0.00 0.00 0.00 4.02
2602 7466 4.982916 GTCGTTCTGTCATACTTGTTCAGT 59.017 41.667 0.00 0.00 39.87 3.41
2622 7486 1.473278 GGTCTGAGGTGTAGAAGGTCG 59.527 57.143 0.00 0.00 0.00 4.79
2711 7575 3.636300 TCCTGCAGCACACTTATTTTGTT 59.364 39.130 8.66 0.00 0.00 2.83
2727 7591 6.986231 CACATACATCTAATTAGTGTCCTGCA 59.014 38.462 18.09 6.88 0.00 4.41
2761 7635 7.199766 ACGAAGTTTATTGCTTCATGAAACAA 58.800 30.769 22.73 22.73 37.78 2.83
2819 7694 4.327680 ACTTGGCAGAGAGTAATGTTTCC 58.672 43.478 4.13 0.00 0.00 3.13
2836 7711 3.703001 AACAGTGTATGGGAGACTTGG 57.297 47.619 0.00 0.00 26.30 3.61
2950 7827 4.493747 GCTTCCGGTCGGGTCTCG 62.494 72.222 9.68 0.00 40.90 4.04
3045 7922 4.489771 GCAGCCCATAGCCACCGT 62.490 66.667 0.00 0.00 45.47 4.83
3111 7988 4.438797 CGTTCTTCGTTCGTTCTTCTTGTA 59.561 41.667 0.00 0.00 34.52 2.41
3305 8187 0.688487 TTCCTGTCCGGGTTAGGTTG 59.312 55.000 15.93 0.00 33.30 3.77
3554 8436 6.419413 GTCAGAAACAGAAGTTGTAGAGTCAG 59.581 42.308 0.00 0.00 39.73 3.51
3562 8444 4.589908 ACAAGGTCAGAAACAGAAGTTGT 58.410 39.130 0.00 0.00 43.45 3.32


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

AutoCloner maintained by Alex Coulton.