Multiple sequence alignment - TraesCS2A01G292900

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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 TraesCS2A01G292900 chr2A 100.000 4959 0 0 1 4959 504280128 504275170 0.000000e+00 9158
1 TraesCS2A01G292900 chr2A 82.986 288 23 14 4186 4459 40762377 40762102 2.310000e-58 237
2 TraesCS2A01G292900 chr2D 95.245 2671 63 32 1814 4456 373222649 373225283 0.000000e+00 4170
3 TraesCS2A01G292900 chr2D 90.900 1033 21 18 731 1732 373221661 373222651 0.000000e+00 1319
4 TraesCS2A01G292900 chr2D 97.410 502 13 0 4458 4959 373225317 373225818 0.000000e+00 856
5 TraesCS2A01G292900 chr2D 92.308 91 7 0 1728 1818 24451745 24451835 4.030000e-26 130
6 TraesCS2A01G292900 chr2B 95.405 2459 55 16 1814 4241 442792736 442795167 0.000000e+00 3862
7 TraesCS2A01G292900 chr2B 91.819 1039 29 13 731 1732 442791719 442792738 0.000000e+00 1397
8 TraesCS2A01G292900 chr2B 98.207 502 9 0 4458 4959 442795445 442795946 0.000000e+00 878
9 TraesCS2A01G292900 chr2B 84.722 288 18 10 4186 4459 735827133 735827408 1.060000e-66 265
10 TraesCS2A01G292900 chr2B 83.681 288 21 10 4186 4459 780744335 780744060 1.070000e-61 248
11 TraesCS2A01G292900 chr2B 95.200 125 2 1 4336 4456 442795287 442795411 1.410000e-45 195
12 TraesCS2A01G292900 chr2B 93.103 87 5 1 1731 1816 21937024 21936938 5.210000e-25 126
13 TraesCS2A01G292900 chr7D 94.528 731 36 3 1 731 535846998 535847724 0.000000e+00 1125
14 TraesCS2A01G292900 chr1B 90.710 732 65 3 1 731 473557578 473556849 0.000000e+00 972
15 TraesCS2A01G292900 chr1B 83.681 288 20 13 4186 4459 665780462 665780736 3.830000e-61 246
16 TraesCS2A01G292900 chr1B 83.333 288 22 9 4186 4459 69432611 69432336 4.960000e-60 243
17 TraesCS2A01G292900 chr3D 89.835 728 72 2 1 728 44971894 44972619 0.000000e+00 933
18 TraesCS2A01G292900 chr3D 84.268 731 108 7 1 729 284850125 284849400 0.000000e+00 706
19 TraesCS2A01G292900 chr5A 96.429 560 18 2 170 729 669768505 669767948 0.000000e+00 922
20 TraesCS2A01G292900 chr5A 83.333 288 22 12 4186 4459 489496232 489496507 4.960000e-60 243
21 TraesCS2A01G292900 chr5B 88.738 737 79 4 1 735 540320329 540321063 0.000000e+00 898
22 TraesCS2A01G292900 chr5B 84.583 720 104 7 2 717 503776495 503777211 0.000000e+00 708
23 TraesCS2A01G292900 chr5B 89.691 97 7 3 1731 1826 51843382 51843288 2.420000e-23 121
24 TraesCS2A01G292900 chr6A 85.616 730 101 4 1 729 13040623 13041349 0.000000e+00 763
25 TraesCS2A01G292900 chr6A 82.624 282 18 9 4197 4459 196595 196864 2.320000e-53 220
26 TraesCS2A01G292900 chr6A 92.391 92 6 1 1728 1818 147460894 147460803 4.030000e-26 130
27 TraesCS2A01G292900 chr6B 85.499 731 99 6 1 729 63785606 63786331 0.000000e+00 756
28 TraesCS2A01G292900 chr6B 84.028 288 20 11 4186 4459 699126309 699126034 2.290000e-63 254
29 TraesCS2A01G292900 chr6B 83.333 288 22 14 4186 4459 35778627 35778902 4.960000e-60 243
30 TraesCS2A01G292900 chr6B 93.103 87 6 0 1731 1817 520230436 520230350 1.450000e-25 128
31 TraesCS2A01G292900 chr6B 91.954 87 7 0 1731 1817 520230351 520230437 6.740000e-24 122
32 TraesCS2A01G292900 chr4A 84.028 288 20 10 4186 4459 661952073 661951798 2.290000e-63 254
33 TraesCS2A01G292900 chr4A 81.944 288 26 11 4186 4459 245813503 245813778 2.320000e-53 220
34 TraesCS2A01G292900 chr3B 84.028 288 20 10 4186 4459 456362057 456361782 2.290000e-63 254
35 TraesCS2A01G292900 chr3B 83.681 288 21 9 4186 4459 807584316 807584591 1.070000e-61 248
36 TraesCS2A01G292900 chr7B 83.730 252 20 9 4186 4428 10831935 10831696 8.360000e-53 219
37 TraesCS2A01G292900 chr7B 92.308 91 7 0 1726 1816 41287011 41286921 4.030000e-26 130
38 TraesCS2A01G292900 chr7B 91.111 90 8 0 1728 1817 41286918 41287007 6.740000e-24 122
39 TraesCS2A01G292900 chr7A 92.941 85 4 2 1733 1816 153377812 153377895 6.740000e-24 122


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 TraesCS2A01G292900 chr2A 504275170 504280128 4958 True 9158 9158 100.000000 1 4959 1 chr2A.!!$R2 4958
1 TraesCS2A01G292900 chr2D 373221661 373225818 4157 False 2115 4170 94.518333 731 4959 3 chr2D.!!$F2 4228
2 TraesCS2A01G292900 chr2B 442791719 442795946 4227 False 1583 3862 95.157750 731 4959 4 chr2B.!!$F2 4228
3 TraesCS2A01G292900 chr7D 535846998 535847724 726 False 1125 1125 94.528000 1 731 1 chr7D.!!$F1 730
4 TraesCS2A01G292900 chr1B 473556849 473557578 729 True 972 972 90.710000 1 731 1 chr1B.!!$R2 730
5 TraesCS2A01G292900 chr3D 44971894 44972619 725 False 933 933 89.835000 1 728 1 chr3D.!!$F1 727
6 TraesCS2A01G292900 chr3D 284849400 284850125 725 True 706 706 84.268000 1 729 1 chr3D.!!$R1 728
7 TraesCS2A01G292900 chr5A 669767948 669768505 557 True 922 922 96.429000 170 729 1 chr5A.!!$R1 559
8 TraesCS2A01G292900 chr5B 540320329 540321063 734 False 898 898 88.738000 1 735 1 chr5B.!!$F2 734
9 TraesCS2A01G292900 chr5B 503776495 503777211 716 False 708 708 84.583000 2 717 1 chr5B.!!$F1 715
10 TraesCS2A01G292900 chr6A 13040623 13041349 726 False 763 763 85.616000 1 729 1 chr6A.!!$F2 728
11 TraesCS2A01G292900 chr6B 63785606 63786331 725 False 756 756 85.499000 1 729 1 chr6B.!!$F2 728

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
795 813 0.247735 CGTGTAGACGGAGAGAAGCG 60.248 60.000 4.16 0.0 42.18 4.68 F
1746 1792 0.042131 ATGTACTCCCTCGGTCCCAA 59.958 55.000 0.00 0.0 0.00 4.12 F
1747 1793 0.178926 TGTACTCCCTCGGTCCCAAA 60.179 55.000 0.00 0.0 0.00 3.28 F
1748 1794 0.978907 GTACTCCCTCGGTCCCAAAA 59.021 55.000 0.00 0.0 0.00 2.44 F
1749 1795 1.558294 GTACTCCCTCGGTCCCAAAAT 59.442 52.381 0.00 0.0 0.00 1.82 F
1750 1796 1.961133 ACTCCCTCGGTCCCAAAATA 58.039 50.000 0.00 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 1847 1.202545 GCTTCATACTCCCTCCGTTCC 60.203 57.143 0.00 0.00 0.00 3.62 R
2982 3049 0.918983 TCCATTCAACTAGCCAGGGG 59.081 55.000 0.00 0.00 0.00 4.79 R
3423 3490 1.238439 CTCGACAAGGTGGTTTGCAT 58.762 50.000 0.00 0.00 0.00 3.96 R
3735 3808 3.713858 TCCTCGTCTTCGTTGTTACAA 57.286 42.857 0.00 0.00 38.33 2.41 R
3794 3867 3.423154 CACGCTTCCTGTTCGGGC 61.423 66.667 0.00 0.00 0.00 6.13 R
3970 4047 2.799412 CAGAGTGACAGTGTCTCAAAGC 59.201 50.000 23.29 10.91 33.15 3.51 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
23 24 4.699192 TCCTATGTGGAGACCGGG 57.301 61.111 6.32 0.00 40.56 5.73
135 137 0.896940 CCAACAGCAGCCATCAGGTT 60.897 55.000 0.00 0.00 37.19 3.50
418 421 1.006832 AACTTCGTGGCATATCGCAC 58.993 50.000 0.00 0.00 45.17 5.34
493 496 0.802494 ATTCACGTTCGATTGTGGCC 59.198 50.000 15.11 0.00 36.74 5.36
535 539 6.903419 AGGAGAGCTAGTTTTTGATTTTTCG 58.097 36.000 0.00 0.00 0.00 3.46
552 556 4.735662 TTTCGGTATTTGAGGTTCAACG 57.264 40.909 0.00 0.00 35.89 4.10
610 614 1.678360 CAAAACGTGCATGCACTCTC 58.322 50.000 39.46 20.47 44.16 3.20
664 668 0.538287 GCTTCTTGGTGACCAGCCTT 60.538 55.000 3.77 0.00 33.81 4.35
702 707 6.975772 CGGGAGAACACTTTTGTTGAATAAAA 59.024 34.615 0.10 0.10 46.43 1.52
707 712 7.706607 AGAACACTTTTGTTGAATAAAAGCTCC 59.293 33.333 21.82 11.76 46.43 4.70
720 725 1.852157 AAGCTCCCTGATTTGCCCGA 61.852 55.000 0.00 0.00 0.00 5.14
724 729 1.474077 CTCCCTGATTTGCCCGAAAAG 59.526 52.381 0.00 0.00 0.00 2.27
782 800 3.411418 ATCGAGGCGTGGCGTGTAG 62.411 63.158 0.00 0.00 0.00 2.74
795 813 0.247735 CGTGTAGACGGAGAGAAGCG 60.248 60.000 4.16 0.00 42.18 4.68
984 1017 1.786928 GCTTTTGCGGTTCGATTCGAG 60.787 52.381 8.98 0.00 34.35 4.04
1090 1123 4.400251 CCTCCCTCAGGGTCGGGT 62.400 72.222 10.50 0.00 44.74 5.28
1095 1128 3.771160 CTCAGGGTCGGGTTCGGG 61.771 72.222 0.00 0.00 36.95 5.14
1129 1162 4.798682 GGAGGAAGGGCGGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
1177 1210 2.115695 TGCATCCCAGCAGCAACA 59.884 55.556 0.00 0.00 40.11 3.33
1202 1235 4.388499 GCACGACCATGACCCCGT 62.388 66.667 0.00 0.00 35.46 5.28
1535 1574 1.065418 GGTCACCCACCCTTCATACTG 60.065 57.143 0.00 0.00 39.69 2.74
1538 1577 1.354368 CACCCACCCTTCATACTGGTT 59.646 52.381 0.00 0.00 0.00 3.67
1594 1633 5.246203 ACAGATGCTCCTCTTACTTGTGTTA 59.754 40.000 0.00 0.00 0.00 2.41
1626 1668 6.477360 TGTGTATGCAATTGAATCATTCATGC 59.523 34.615 16.15 16.15 42.88 4.06
1732 1778 5.406780 GCTCAATGTACTGCCTATCATGTAC 59.593 44.000 0.00 0.00 36.69 2.90
1733 1779 6.731292 TCAATGTACTGCCTATCATGTACT 57.269 37.500 0.00 0.00 36.98 2.73
1734 1780 6.749139 TCAATGTACTGCCTATCATGTACTC 58.251 40.000 0.00 0.00 36.98 2.59
1735 1781 5.730296 ATGTACTGCCTATCATGTACTCC 57.270 43.478 0.00 0.00 36.98 3.85
1736 1782 3.895656 TGTACTGCCTATCATGTACTCCC 59.104 47.826 0.00 0.00 36.98 4.30
1737 1783 3.336509 ACTGCCTATCATGTACTCCCT 57.663 47.619 0.00 0.00 0.00 4.20
1738 1784 3.235200 ACTGCCTATCATGTACTCCCTC 58.765 50.000 0.00 0.00 0.00 4.30
1739 1785 2.230025 CTGCCTATCATGTACTCCCTCG 59.770 54.545 0.00 0.00 0.00 4.63
1740 1786 1.546476 GCCTATCATGTACTCCCTCGG 59.454 57.143 0.00 0.00 0.00 4.63
1741 1787 2.877866 CCTATCATGTACTCCCTCGGT 58.122 52.381 0.00 0.00 0.00 4.69
1742 1788 2.820787 CCTATCATGTACTCCCTCGGTC 59.179 54.545 0.00 0.00 0.00 4.79
1743 1789 1.705873 ATCATGTACTCCCTCGGTCC 58.294 55.000 0.00 0.00 0.00 4.46
1744 1790 0.396695 TCATGTACTCCCTCGGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
1745 1791 0.686441 CATGTACTCCCTCGGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
1746 1792 0.042131 ATGTACTCCCTCGGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
1747 1793 0.178926 TGTACTCCCTCGGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
1748 1794 0.978907 GTACTCCCTCGGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1749 1795 1.558294 GTACTCCCTCGGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1750 1796 1.961133 ACTCCCTCGGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1751 1797 2.271777 ACTCCCTCGGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1752 1798 2.238898 ACTCCCTCGGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1753 1799 2.238898 CTCCCTCGGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1754 1800 2.026636 TCCCTCGGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1755 1801 2.290705 CCCTCGGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
1756 1802 3.007635 CCTCGGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
1757 1803 3.307480 CCTCGGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
1758 1804 3.933332 CTCGGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
1759 1805 3.325425 TCGGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
1760 1806 4.069304 CGGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
1761 1807 4.083484 CGGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
1762 1808 5.070685 GGTCCCAAAATAAGTGTCTCAACT 58.929 41.667 0.00 0.00 0.00 3.16
1763 1809 5.535030 GGTCCCAAAATAAGTGTCTCAACTT 59.465 40.000 0.00 0.00 42.89 2.66
1764 1810 6.040504 GGTCCCAAAATAAGTGTCTCAACTTT 59.959 38.462 0.00 0.00 40.77 2.66
1765 1811 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
1766 1812 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
1767 1813 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
1768 1814 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
1769 1815 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
1775 1821 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
1776 1822 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
1777 1823 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
1778 1824 9.310716 GTGTCTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
1793 1839 9.473640 ACTAACTTTAGTACAAGCTTAAGACAC 57.526 33.333 6.67 0.42 41.92 3.67
1794 1840 9.694137 CTAACTTTAGTACAAGCTTAAGACACT 57.306 33.333 6.67 7.00 31.75 3.55
1795 1841 8.959705 AACTTTAGTACAAGCTTAAGACACTT 57.040 30.769 6.67 0.00 31.75 3.16
1802 1848 8.784043 AGTACAAGCTTAAGACACTTATTTTGG 58.216 33.333 6.67 0.00 0.00 3.28
1803 1849 7.817418 ACAAGCTTAAGACACTTATTTTGGA 57.183 32.000 6.67 0.00 0.00 3.53
1804 1850 8.232913 ACAAGCTTAAGACACTTATTTTGGAA 57.767 30.769 6.67 0.00 0.00 3.53
1805 1851 8.135529 ACAAGCTTAAGACACTTATTTTGGAAC 58.864 33.333 6.67 0.00 0.00 3.62
1806 1852 6.899114 AGCTTAAGACACTTATTTTGGAACG 58.101 36.000 6.67 0.00 0.00 3.95
1807 1853 6.072673 AGCTTAAGACACTTATTTTGGAACGG 60.073 38.462 6.67 0.00 0.00 4.44
1808 1854 6.072893 GCTTAAGACACTTATTTTGGAACGGA 60.073 38.462 6.67 0.00 0.00 4.69
1809 1855 5.941948 AAGACACTTATTTTGGAACGGAG 57.058 39.130 0.00 0.00 0.00 4.63
1810 1856 4.324267 AGACACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
1811 1857 3.418047 ACACTTATTTTGGAACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
1812 1858 3.073356 ACACTTATTTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 0.00 4.20
1813 1859 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
1814 1860 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
1815 1861 4.533311 ACTTATTTTGGAACGGAGGGAGTA 59.467 41.667 0.00 0.00 0.00 2.59
2035 2081 2.749621 GGCACCAGTTGATTCAGGTAAG 59.250 50.000 0.00 0.00 32.01 2.34
2084 2130 8.590204 TCAGGTAATGTTGACTCTGTTAATACA 58.410 33.333 0.00 0.00 0.00 2.29
2155 2206 6.109359 GTGGATCATATTACTGAGGGCATAC 58.891 44.000 0.00 0.00 0.00 2.39
2173 2224 4.576463 GCATACGGAAAATGTTCAGGAGAT 59.424 41.667 0.68 0.00 35.25 2.75
2185 2236 8.591114 AATGTTCAGGAGATCTTTCATTTCAT 57.409 30.769 0.00 0.00 0.00 2.57
2524 2591 8.470805 GGAATGAGAGAGTTCTTACATGTCTTA 58.529 37.037 0.00 0.00 32.53 2.10
2674 2741 3.770040 TGCCACGTGATCCTCCCG 61.770 66.667 19.30 0.00 0.00 5.14
3234 3301 5.726793 AGAGTGGAAATACATTACAGGGAGT 59.273 40.000 0.00 0.00 30.54 3.85
3735 3808 9.286170 GAAAACCCTGAAAAGTCTAGAATACTT 57.714 33.333 0.00 0.00 38.82 2.24
3794 3867 2.572290 TCTCATGGCTGATTCATGCAG 58.428 47.619 0.00 0.00 41.11 4.41
3970 4047 2.093447 ACTTGTCTAGAGGAAATGCCCG 60.093 50.000 0.00 0.00 37.37 6.13
3980 4057 0.881118 GAAATGCCCGCTTTGAGACA 59.119 50.000 0.00 0.00 0.00 3.41
3987 4064 0.861837 CCGCTTTGAGACACTGTCAC 59.138 55.000 11.80 5.84 34.60 3.67
4035 4113 1.658409 GGTTTTCGCAGCACAGCAC 60.658 57.895 0.00 0.00 0.00 4.40
4036 4114 1.063972 GTTTTCGCAGCACAGCACA 59.936 52.632 0.00 0.00 0.00 4.57
4037 4115 0.931662 GTTTTCGCAGCACAGCACAG 60.932 55.000 0.00 0.00 0.00 3.66
4038 4116 2.666715 TTTTCGCAGCACAGCACAGC 62.667 55.000 0.00 0.00 0.00 4.40
4039 4117 4.914388 TCGCAGCACAGCACAGCA 62.914 61.111 0.00 0.00 0.00 4.41
4041 4119 2.649034 GCAGCACAGCACAGCATT 59.351 55.556 0.00 0.00 0.00 3.56
4042 4120 1.443872 GCAGCACAGCACAGCATTC 60.444 57.895 0.00 0.00 0.00 2.67
4044 4122 0.386858 CAGCACAGCACAGCATTCAC 60.387 55.000 0.00 0.00 0.00 3.18
4045 4123 0.536687 AGCACAGCACAGCATTCACT 60.537 50.000 0.00 0.00 0.00 3.41
4046 4124 0.313043 GCACAGCACAGCATTCACTT 59.687 50.000 0.00 0.00 0.00 3.16
4047 4125 1.269413 GCACAGCACAGCATTCACTTT 60.269 47.619 0.00 0.00 0.00 2.66
4048 4126 2.030893 GCACAGCACAGCATTCACTTTA 60.031 45.455 0.00 0.00 0.00 1.85
4049 4127 3.558505 CACAGCACAGCATTCACTTTAC 58.441 45.455 0.00 0.00 0.00 2.01
4086 4164 1.215647 CTACTCACCGGTCAGCACC 59.784 63.158 4.93 0.00 39.69 5.01
4110 4191 6.534793 CCATAAAATGGTTACATCCAAGCAAC 59.465 38.462 0.00 0.00 45.54 4.17
4126 4207 2.159043 AGCAACTACTGATGTCCCATCG 60.159 50.000 0.25 0.00 0.00 3.84
4162 4243 6.127479 ACGCAAACCCATAACATAATTGTGAT 60.127 34.615 9.40 0.00 35.83 3.06
4170 4251 4.963276 AACATAATTGTGATGTCCGTGG 57.037 40.909 9.40 0.00 36.50 4.94
4267 4349 7.793948 ACTTATTACTGGACCTTACTTGAGT 57.206 36.000 0.00 0.00 0.00 3.41
4268 4350 8.203681 ACTTATTACTGGACCTTACTTGAGTT 57.796 34.615 0.00 0.00 0.00 3.01
4269 4351 9.317827 ACTTATTACTGGACCTTACTTGAGTTA 57.682 33.333 0.00 0.00 0.00 2.24
4270 4352 9.583765 CTTATTACTGGACCTTACTTGAGTTAC 57.416 37.037 0.00 0.00 0.00 2.50
4271 4353 7.793948 ATTACTGGACCTTACTTGAGTTACT 57.206 36.000 0.00 0.00 0.00 2.24
4272 4354 8.890410 ATTACTGGACCTTACTTGAGTTACTA 57.110 34.615 0.00 0.00 0.00 1.82
4273 4355 6.587206 ACTGGACCTTACTTGAGTTACTAC 57.413 41.667 0.00 0.00 0.00 2.73
4274 4356 6.313324 ACTGGACCTTACTTGAGTTACTACT 58.687 40.000 0.00 0.00 37.31 2.57
4275 4357 6.208994 ACTGGACCTTACTTGAGTTACTACTG 59.791 42.308 0.00 0.00 33.84 2.74
4276 4358 5.047519 TGGACCTTACTTGAGTTACTACTGC 60.048 44.000 0.00 0.00 33.84 4.40
4277 4359 5.185442 GGACCTTACTTGAGTTACTACTGCT 59.815 44.000 0.00 0.00 33.84 4.24
4278 4360 6.376581 GGACCTTACTTGAGTTACTACTGCTA 59.623 42.308 0.00 0.00 33.84 3.49
4279 4361 7.155655 ACCTTACTTGAGTTACTACTGCTAC 57.844 40.000 0.00 0.00 33.84 3.58
4280 4362 6.718454 ACCTTACTTGAGTTACTACTGCTACA 59.282 38.462 0.00 0.00 33.84 2.74
4281 4363 7.396623 ACCTTACTTGAGTTACTACTGCTACAT 59.603 37.037 0.00 0.00 33.84 2.29
4282 4364 8.900781 CCTTACTTGAGTTACTACTGCTACATA 58.099 37.037 0.00 0.00 33.84 2.29
4283 4365 9.719279 CTTACTTGAGTTACTACTGCTACATAC 57.281 37.037 0.00 0.00 33.84 2.39
4284 4366 7.941431 ACTTGAGTTACTACTGCTACATACT 57.059 36.000 0.00 0.00 33.84 2.12
4285 4367 7.763356 ACTTGAGTTACTACTGCTACATACTG 58.237 38.462 0.00 0.00 33.84 2.74
4290 4372 8.975663 AGTTACTACTGCTACATACTGTATCA 57.024 34.615 0.00 0.00 30.30 2.15
4456 4612 1.343465 CACAACACCCGACCTTACTCT 59.657 52.381 0.00 0.00 0.00 3.24
4470 4658 7.013464 CCGACCTTACTCTACTGATAACTCATT 59.987 40.741 0.00 0.00 0.00 2.57
4501 4689 3.406200 CTGCAGGGGAGTGGGGAG 61.406 72.222 5.57 0.00 0.00 4.30
4540 4728 3.015327 ACTACTTCTAGCTACCACGGTG 58.985 50.000 0.00 0.00 0.00 4.94
4773 4961 1.000396 CAGGCCTTGGAAGAAGGGG 60.000 63.158 0.00 0.00 37.88 4.79
4926 5114 5.007234 TGAGACCACATTTGTAAGTGTTTCG 59.993 40.000 0.00 0.00 33.99 3.46
4941 5129 0.400213 TTTCGTCATTGCCAGGTCCT 59.600 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.706802 TGCTCGATCTTCATCTCTGAC 57.293 47.619 0.00 0.00 0.00 3.51
418 421 2.099263 ACAGTCGGTCTCCATTATCACG 59.901 50.000 0.00 0.00 0.00 4.35
493 496 6.323739 GCTCTCCTATTTCATCTAGGATAGGG 59.676 46.154 11.49 0.00 42.93 3.53
535 539 5.927954 TTACACGTTGAACCTCAAATACC 57.072 39.130 0.00 0.00 38.22 2.73
552 556 2.558359 AGATTTGCTGCCCTGTTTACAC 59.442 45.455 0.00 0.00 0.00 2.90
610 614 1.063006 CCAGCAATCGGTCGCATTG 59.937 57.895 9.47 9.47 34.80 2.82
702 707 1.852157 TTCGGGCAAATCAGGGAGCT 61.852 55.000 0.00 0.00 0.00 4.09
707 712 3.658757 TTTCTTTTCGGGCAAATCAGG 57.341 42.857 0.00 0.00 0.00 3.86
724 729 7.303634 TGCCTCTATGAACGTTATCTTTTTC 57.696 36.000 0.00 0.00 0.00 2.29
782 800 3.743091 CTCGGCGCTTCTCTCCGTC 62.743 68.421 7.64 0.00 43.35 4.79
818 836 2.195139 GACGGGGAGGATCGGAGA 59.805 66.667 0.00 0.00 45.75 3.71
819 837 3.288290 CGACGGGGAGGATCGGAG 61.288 72.222 0.00 0.00 34.37 4.63
1095 1128 1.595382 CCTCGCATGGGATCCGAAC 60.595 63.158 13.45 0.00 0.00 3.95
1177 1210 3.749064 ATGGTCGTGCGCTCTCGT 61.749 61.111 9.73 0.00 38.14 4.18
1535 1574 1.066645 ACCGACCGAAATACTCCAACC 60.067 52.381 0.00 0.00 0.00 3.77
1538 1577 1.066716 CCAACCGACCGAAATACTCCA 60.067 52.381 0.00 0.00 0.00 3.86
1732 1778 2.238898 ACTTATTTTGGGACCGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
1733 1779 2.026636 CACTTATTTTGGGACCGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
1734 1780 2.290705 ACACTTATTTTGGGACCGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
1735 1781 3.007635 GACACTTATTTTGGGACCGAGG 58.992 50.000 0.00 0.00 0.00 4.63
1736 1782 3.933332 GAGACACTTATTTTGGGACCGAG 59.067 47.826 0.00 0.00 0.00 4.63
1737 1783 3.325425 TGAGACACTTATTTTGGGACCGA 59.675 43.478 0.00 0.00 0.00 4.69
1738 1784 3.670625 TGAGACACTTATTTTGGGACCG 58.329 45.455 0.00 0.00 0.00 4.79
1739 1785 5.070685 AGTTGAGACACTTATTTTGGGACC 58.929 41.667 0.00 0.00 0.00 4.46
1740 1786 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
1741 1787 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
1742 1788 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
1743 1789 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
1749 1795 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
1750 1796 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
1751 1797 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
1752 1798 9.310716 ACTAAAGTTAGTACAAAGTTGAGACAC 57.689 33.333 1.81 0.00 41.92 3.67
1767 1813 9.473640 GTGTCTTAAGCTTGTACTAAAGTTAGT 57.526 33.333 9.86 8.67 45.39 2.24
1768 1814 9.694137 AGTGTCTTAAGCTTGTACTAAAGTTAG 57.306 33.333 9.86 0.00 36.82 2.34
1770 1816 8.959705 AAGTGTCTTAAGCTTGTACTAAAGTT 57.040 30.769 9.86 0.00 0.00 2.66
1776 1822 8.784043 CCAAAATAAGTGTCTTAAGCTTGTACT 58.216 33.333 9.86 3.34 0.00 2.73
1777 1823 8.780249 TCCAAAATAAGTGTCTTAAGCTTGTAC 58.220 33.333 9.86 5.00 0.00 2.90
1778 1824 8.911918 TCCAAAATAAGTGTCTTAAGCTTGTA 57.088 30.769 9.86 0.00 0.00 2.41
1779 1825 7.817418 TCCAAAATAAGTGTCTTAAGCTTGT 57.183 32.000 9.86 0.00 0.00 3.16
1780 1826 7.323656 CGTTCCAAAATAAGTGTCTTAAGCTTG 59.676 37.037 9.86 0.00 0.00 4.01
1781 1827 7.360361 CGTTCCAAAATAAGTGTCTTAAGCTT 58.640 34.615 3.48 3.48 0.00 3.74
1782 1828 6.072673 CCGTTCCAAAATAAGTGTCTTAAGCT 60.073 38.462 0.00 0.00 0.00 3.74
1783 1829 6.072893 TCCGTTCCAAAATAAGTGTCTTAAGC 60.073 38.462 0.00 0.00 0.00 3.09
1784 1830 7.360946 CCTCCGTTCCAAAATAAGTGTCTTAAG 60.361 40.741 0.00 0.00 0.00 1.85
1785 1831 6.428771 CCTCCGTTCCAAAATAAGTGTCTTAA 59.571 38.462 0.00 0.00 0.00 1.85
1786 1832 5.935789 CCTCCGTTCCAAAATAAGTGTCTTA 59.064 40.000 0.00 0.00 0.00 2.10
1787 1833 4.760204 CCTCCGTTCCAAAATAAGTGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
1788 1834 4.324267 CCTCCGTTCCAAAATAAGTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
1789 1835 3.439129 CCCTCCGTTCCAAAATAAGTGTC 59.561 47.826 0.00 0.00 0.00 3.67
1790 1836 3.073356 TCCCTCCGTTCCAAAATAAGTGT 59.927 43.478 0.00 0.00 0.00 3.55
1791 1837 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
1792 1838 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
1793 1839 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
1794 1840 5.190132 TCATACTCCCTCCGTTCCAAAATAA 59.810 40.000 0.00 0.00 0.00 1.40
1795 1841 4.717778 TCATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
1796 1842 3.521937 TCATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
1797 1843 2.907696 TCATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
1798 1844 2.542550 TCATACTCCCTCCGTTCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
1799 1845 2.241281 TCATACTCCCTCCGTTCCAA 57.759 50.000 0.00 0.00 0.00 3.53
1800 1846 2.108168 CTTCATACTCCCTCCGTTCCA 58.892 52.381 0.00 0.00 0.00 3.53
1801 1847 1.202545 GCTTCATACTCCCTCCGTTCC 60.203 57.143 0.00 0.00 0.00 3.62
1802 1848 1.757699 AGCTTCATACTCCCTCCGTTC 59.242 52.381 0.00 0.00 0.00 3.95
1803 1849 1.867363 AGCTTCATACTCCCTCCGTT 58.133 50.000 0.00 0.00 0.00 4.44
1804 1850 1.482593 CAAGCTTCATACTCCCTCCGT 59.517 52.381 0.00 0.00 0.00 4.69
1805 1851 1.482593 ACAAGCTTCATACTCCCTCCG 59.517 52.381 0.00 0.00 0.00 4.63
1806 1852 4.755266 TTACAAGCTTCATACTCCCTCC 57.245 45.455 0.00 0.00 0.00 4.30
1807 1853 8.910351 AATTATTACAAGCTTCATACTCCCTC 57.090 34.615 0.00 0.00 0.00 4.30
1808 1854 9.125026 CAAATTATTACAAGCTTCATACTCCCT 57.875 33.333 0.00 0.00 0.00 4.20
1809 1855 8.903820 ACAAATTATTACAAGCTTCATACTCCC 58.096 33.333 0.00 0.00 0.00 4.30
2101 2149 4.952335 CCTGAAAACCATCATTAAGGCTCT 59.048 41.667 0.00 0.00 0.00 4.09
2102 2150 4.706962 ACCTGAAAACCATCATTAAGGCTC 59.293 41.667 0.00 0.00 0.00 4.70
2155 2206 5.412594 TGAAAGATCTCCTGAACATTTTCCG 59.587 40.000 0.00 0.00 0.00 4.30
2185 2236 3.379688 CAGTCTGGACATCGATTCTCTCA 59.620 47.826 0.00 0.00 0.00 3.27
2420 2487 6.429624 CCATCGTCATATATGTTTGTGTTGG 58.570 40.000 12.42 9.28 0.00 3.77
2524 2591 5.930837 TGAGTGACACCCAAAAAGAATTT 57.069 34.783 0.84 0.00 42.41 1.82
2674 2741 5.300539 TCCTCACTCATCTACAGAATAGCAC 59.699 44.000 0.00 0.00 0.00 4.40
2982 3049 0.918983 TCCATTCAACTAGCCAGGGG 59.081 55.000 0.00 0.00 0.00 4.79
2985 3052 2.441001 AGGGATCCATTCAACTAGCCAG 59.559 50.000 15.23 0.00 0.00 4.85
3234 3301 3.460103 GACTCACGTGTTTTTAGGGTCA 58.540 45.455 16.51 0.00 0.00 4.02
3302 3369 9.532697 CAGCAAAACAAAATAAATGTTATGAGC 57.467 29.630 0.00 0.00 39.98 4.26
3423 3490 1.238439 CTCGACAAGGTGGTTTGCAT 58.762 50.000 0.00 0.00 0.00 3.96
3735 3808 3.713858 TCCTCGTCTTCGTTGTTACAA 57.286 42.857 0.00 0.00 38.33 2.41
3794 3867 3.423154 CACGCTTCCTGTTCGGGC 61.423 66.667 0.00 0.00 0.00 6.13
3970 4047 2.799412 CAGAGTGACAGTGTCTCAAAGC 59.201 50.000 23.29 10.91 33.15 3.51
3980 4057 4.141482 ACCAACCATAAACAGAGTGACAGT 60.141 41.667 0.00 0.00 0.00 3.55
4035 4113 4.673580 GCATCTGTGGTAAAGTGAATGCTG 60.674 45.833 0.00 0.00 0.00 4.41
4036 4114 3.441572 GCATCTGTGGTAAAGTGAATGCT 59.558 43.478 0.00 0.00 0.00 3.79
4037 4115 3.191162 TGCATCTGTGGTAAAGTGAATGC 59.809 43.478 0.00 0.00 0.00 3.56
4038 4116 4.216042 TGTGCATCTGTGGTAAAGTGAATG 59.784 41.667 0.00 0.00 0.00 2.67
4039 4117 4.397420 TGTGCATCTGTGGTAAAGTGAAT 58.603 39.130 0.00 0.00 0.00 2.57
4041 4119 3.181455 ACTGTGCATCTGTGGTAAAGTGA 60.181 43.478 0.00 0.00 0.00 3.41
4042 4120 3.141398 ACTGTGCATCTGTGGTAAAGTG 58.859 45.455 0.00 0.00 0.00 3.16
4044 4122 5.674569 GCATAACTGTGCATCTGTGGTAAAG 60.675 44.000 0.00 0.00 44.43 1.85
4045 4123 4.155826 GCATAACTGTGCATCTGTGGTAAA 59.844 41.667 0.00 0.00 44.43 2.01
4046 4124 3.689161 GCATAACTGTGCATCTGTGGTAA 59.311 43.478 0.00 0.00 44.43 2.85
4047 4125 3.270027 GCATAACTGTGCATCTGTGGTA 58.730 45.455 0.00 0.00 44.43 3.25
4048 4126 2.086869 GCATAACTGTGCATCTGTGGT 58.913 47.619 0.00 0.00 44.43 4.16
4049 4127 2.838386 GCATAACTGTGCATCTGTGG 57.162 50.000 0.00 0.00 44.43 4.17
4086 4164 7.322664 AGTTGCTTGGATGTAACCATTTTATG 58.677 34.615 0.00 0.00 39.82 1.90
4126 4207 1.349234 GGTTTGCGTTGATGAATGCC 58.651 50.000 6.65 0.00 42.60 4.40
4170 4251 5.181748 AGGATTTAGAAGTCATGTGTCTGC 58.818 41.667 0.00 0.00 0.00 4.26
4241 4323 8.095169 ACTCAAGTAAGGTCCAGTAATAAGTTG 58.905 37.037 0.00 0.00 0.00 3.16
4279 4361 5.348724 AGTCGTTGTTGCTTGATACAGTATG 59.651 40.000 0.00 0.00 46.00 2.39
4280 4362 5.479306 AGTCGTTGTTGCTTGATACAGTAT 58.521 37.500 0.00 0.00 0.00 2.12
4281 4363 4.878439 AGTCGTTGTTGCTTGATACAGTA 58.122 39.130 0.00 0.00 0.00 2.74
4282 4364 3.728845 AGTCGTTGTTGCTTGATACAGT 58.271 40.909 0.00 0.00 0.00 3.55
4283 4365 4.923871 AGTAGTCGTTGTTGCTTGATACAG 59.076 41.667 0.00 0.00 0.00 2.74
4284 4366 4.684242 CAGTAGTCGTTGTTGCTTGATACA 59.316 41.667 0.00 0.00 0.00 2.29
4285 4367 4.434330 GCAGTAGTCGTTGTTGCTTGATAC 60.434 45.833 0.00 0.00 0.00 2.24
4290 4372 1.948104 TGCAGTAGTCGTTGTTGCTT 58.052 45.000 0.00 0.00 35.85 3.91
4320 4402 3.484524 GCATCTGGTTGCAGTTGTG 57.515 52.632 0.00 0.00 42.31 3.33
4327 4409 1.730064 CAAGCAATTGCATCTGGTTGC 59.270 47.619 30.89 15.93 42.21 4.17
4329 4411 2.088950 GCAAGCAATTGCATCTGGTT 57.911 45.000 30.89 13.37 46.60 3.67
4470 4658 3.118811 CCCCTGCAGTTTTTCTGTTGAAA 60.119 43.478 13.81 0.00 45.23 2.69
4501 4689 0.323957 GTAGTCCCACAGTTCCCCAC 59.676 60.000 0.00 0.00 0.00 4.61
4540 4728 5.408604 ACGTTGTGTTCTGAAGAATATCCAC 59.591 40.000 0.00 1.04 36.33 4.02
4926 5114 0.615331 TCAGAGGACCTGGCAATGAC 59.385 55.000 0.00 0.00 43.12 3.06


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

AutoCloner maintained by Alex Coulton.