Multiple sequence alignment - TraesCS4A01G139800

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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 TraesCS4A01G139800 chr4A 100.000 6411 0 0 1 6411 211666854 211673264 0.000000e+00 11839.0
1 TraesCS4A01G139800 chr4A 97.574 4576 100 7 588 5158 201151184 201146615 0.000000e+00 7825.0
2 TraesCS4A01G139800 chr4A 90.279 823 61 8 2559 3364 109630735 109629915 0.000000e+00 1059.0
3 TraesCS4A01G139800 chr4A 95.462 573 24 2 1 572 369628358 369627787 0.000000e+00 913.0
4 TraesCS4A01G139800 chr4A 98.024 506 9 1 5154 5659 201146536 201146032 0.000000e+00 878.0
5 TraesCS4A01G139800 chr4A 91.983 237 12 3 588 822 201170444 201170213 6.200000e-85 326.0
6 TraesCS4A01G139800 chr4A 82.759 174 12 3 5487 5657 109627139 109626981 8.670000e-29 139.0
7 TraesCS4A01G139800 chr4A 86.667 105 12 1 5554 5658 731096876 731096978 1.460000e-21 115.0
8 TraesCS4A01G139800 chr6B 97.260 3029 72 8 1974 4997 511282047 511279025 0.000000e+00 5123.0
9 TraesCS4A01G139800 chr6B 89.813 1286 105 16 4225 5488 412703061 412701780 0.000000e+00 1626.0
10 TraesCS4A01G139800 chr6B 89.673 978 83 11 2358 3327 412705431 412704464 0.000000e+00 1230.0
11 TraesCS4A01G139800 chr6B 96.512 430 15 0 1548 1977 511282762 511282333 0.000000e+00 712.0
12 TraesCS4A01G139800 chr6B 96.084 383 7 6 5284 5662 511277290 511276912 9.130000e-173 617.0
13 TraesCS4A01G139800 chr6B 96.552 232 2 2 4983 5209 511277550 511277320 4.690000e-101 379.0
14 TraesCS4A01G139800 chr3A 95.967 2777 101 8 2906 5678 530084546 530087315 0.000000e+00 4497.0
15 TraesCS4A01G139800 chr3A 92.963 1421 77 11 577 1977 530061089 530062506 0.000000e+00 2049.0
16 TraesCS4A01G139800 chr3A 96.161 573 21 1 1 572 664166636 664166064 0.000000e+00 935.0
17 TraesCS4A01G139800 chr3A 95.288 573 22 4 1 572 73528145 73528713 0.000000e+00 904.0
18 TraesCS4A01G139800 chr3A 96.859 191 6 0 2719 2909 530063576 530063766 2.880000e-83 320.0
19 TraesCS4A01G139800 chr5B 94.931 1440 65 6 4225 5659 688468766 688467330 0.000000e+00 2248.0
20 TraesCS4A01G139800 chr5B 94.861 1440 66 6 4225 5659 688438597 688437161 0.000000e+00 2242.0
21 TraesCS4A01G139800 chr5B 94.072 1299 60 7 2941 4225 688439937 688438642 0.000000e+00 1956.0
22 TraesCS4A01G139800 chr5B 94.893 842 39 4 3387 4225 688469651 688468811 0.000000e+00 1314.0
23 TraesCS4A01G139800 chr5B 95.122 574 24 4 2147 2717 688473852 688473280 0.000000e+00 902.0
24 TraesCS4A01G139800 chr5B 89.759 664 38 4 1343 1977 688474938 688474276 0.000000e+00 822.0
25 TraesCS4A01G139800 chr5B 87.318 686 50 11 1218 1867 688472333 688471649 0.000000e+00 750.0
26 TraesCS4A01G139800 chr6A 97.541 1220 28 1 1974 3191 86628516 86627297 0.000000e+00 2085.0
27 TraesCS4A01G139800 chr6A 92.761 1409 58 14 586 1977 86630183 86628802 0.000000e+00 1997.0
28 TraesCS4A01G139800 chr6A 96.928 879 24 3 4002 4877 86626398 86625520 0.000000e+00 1471.0
29 TraesCS4A01G139800 chr6A 96.875 768 23 1 4893 5660 86625038 86624272 0.000000e+00 1284.0
30 TraesCS4A01G139800 chr6A 95.119 758 34 3 5656 6411 86307001 86306245 0.000000e+00 1192.0
31 TraesCS4A01G139800 chr6A 88.889 135 14 1 5525 5659 359217839 359217972 1.430000e-36 165.0
32 TraesCS4A01G139800 chr2D 92.376 1456 88 12 4225 5659 74123276 74124729 0.000000e+00 2052.0
33 TraesCS4A01G139800 chr2D 91.459 1405 87 16 1981 3364 612523856 612525248 0.000000e+00 1899.0
34 TraesCS4A01G139800 chr2D 93.269 728 48 1 4225 4952 612526657 612527383 0.000000e+00 1072.0
35 TraesCS4A01G139800 chr2D 93.099 710 47 2 3365 4072 74122128 74122837 0.000000e+00 1038.0
36 TraesCS4A01G139800 chr2D 95.462 573 21 3 1 572 177998798 177998230 0.000000e+00 909.0
37 TraesCS4A01G139800 chr2D 90.644 481 26 7 2894 3364 74121098 74121569 7.060000e-174 621.0
38 TraesCS4A01G139800 chr2D 90.041 241 19 4 5249 5488 648647017 648647253 2.250000e-79 307.0
39 TraesCS4A01G139800 chr2D 90.840 131 12 0 1833 1963 612523463 612523593 6.610000e-40 176.0
40 TraesCS4A01G139800 chr2D 100.000 38 0 0 3327 3364 644992788 644992751 3.210000e-08 71.3
41 TraesCS4A01G139800 chr5D 89.498 1295 111 15 2049 3327 169787692 169788977 0.000000e+00 1615.0
42 TraesCS4A01G139800 chr5D 89.882 850 67 9 3365 4212 156622423 156623255 0.000000e+00 1075.0
43 TraesCS4A01G139800 chr5D 90.000 850 60 17 3366 4212 169789787 169790614 0.000000e+00 1075.0
44 TraesCS4A01G139800 chr5D 89.720 749 66 8 2588 3328 156620865 156621610 0.000000e+00 946.0
45 TraesCS4A01G139800 chr5D 86.861 274 24 6 1526 1795 435420568 435420303 4.860000e-76 296.0
46 TraesCS4A01G139800 chr1A 95.119 758 35 2 5656 6411 574544482 574543725 0.000000e+00 1194.0
47 TraesCS4A01G139800 chr1A 84.892 695 52 29 1141 1793 114548242 114548925 0.000000e+00 652.0
48 TraesCS4A01G139800 chr1A 87.368 95 7 4 586 678 112200967 112201058 3.160000e-18 104.0
49 TraesCS4A01G139800 chr1A 97.059 34 1 0 1091 1124 114548169 114548202 2.500000e-04 58.4
50 TraesCS4A01G139800 chr1A 92.105 38 3 0 568 605 557295118 557295155 3.000000e-03 54.7
51 TraesCS4A01G139800 chr7A 94.855 758 37 2 5656 6411 181825474 181826231 0.000000e+00 1182.0
52 TraesCS4A01G139800 chr7A 94.723 758 38 2 5656 6411 29085748 29086505 0.000000e+00 1177.0
53 TraesCS4A01G139800 chr7A 94.730 759 37 2 5656 6411 709607060 709606302 0.000000e+00 1177.0
54 TraesCS4A01G139800 chr2A 94.855 758 37 2 5656 6411 483618745 483619502 0.000000e+00 1182.0
55 TraesCS4A01G139800 chr2A 94.862 759 34 4 5656 6411 595376971 595376215 0.000000e+00 1181.0
56 TraesCS4A01G139800 chr2A 92.453 53 3 1 586 638 34558590 34558539 2.480000e-09 75.0
57 TraesCS4A01G139800 chr5A 94.723 758 38 2 5656 6411 442692070 442692827 0.000000e+00 1177.0
58 TraesCS4A01G139800 chr5A 94.737 760 35 3 5656 6411 539939905 539940663 0.000000e+00 1177.0
59 TraesCS4A01G139800 chr5A 95.637 573 24 1 1 572 15066342 15066914 0.000000e+00 918.0
60 TraesCS4A01G139800 chr5A 95.462 573 24 2 1 572 663031350 663031921 0.000000e+00 913.0
61 TraesCS4A01G139800 chr5A 82.796 93 12 4 586 676 573732942 573733032 5.330000e-11 80.5
62 TraesCS4A01G139800 chr1D 90.118 850 64 10 3365 4212 50893938 50894769 0.000000e+00 1086.0
63 TraesCS4A01G139800 chr1D 83.880 701 55 27 1141 1793 110337465 110338155 3.280000e-172 616.0
64 TraesCS4A01G139800 chr1D 97.059 34 1 0 1091 1124 110337389 110337422 2.500000e-04 58.4
65 TraesCS4A01G139800 chr3D 87.395 833 62 21 1974 2797 20724717 20723919 0.000000e+00 917.0
66 TraesCS4A01G139800 chr3D 95.637 573 20 3 1 572 169893158 169892590 0.000000e+00 915.0
67 TraesCS4A01G139800 chr3D 86.813 273 26 4 1526 1795 573314674 573314409 4.860000e-76 296.0
68 TraesCS4A01G139800 chr3D 88.550 131 15 0 1834 1964 24087663 24087533 6.650000e-35 159.0
69 TraesCS4A01G139800 chr7D 95.462 573 21 3 1 572 602986022 602985454 0.000000e+00 909.0
70 TraesCS4A01G139800 chr7D 87.179 273 25 4 1526 1795 177235494 177235229 1.040000e-77 302.0
71 TraesCS4A01G139800 chr7D 88.550 131 15 0 1834 1964 561335704 561335574 6.650000e-35 159.0
72 TraesCS4A01G139800 chrUn 95.462 573 17 6 1 572 31950471 31949907 0.000000e+00 905.0
73 TraesCS4A01G139800 chrUn 87.940 796 59 11 1218 1977 331637494 331638288 0.000000e+00 904.0
74 TraesCS4A01G139800 chrUn 95.122 574 24 4 2147 2717 331638712 331639284 0.000000e+00 902.0
75 TraesCS4A01G139800 chrUn 95.122 574 24 4 2147 2717 332052146 332051574 0.000000e+00 902.0
76 TraesCS4A01G139800 chr1B 83.221 745 55 27 1096 1782 167715502 167716234 2.540000e-173 619.0
77 TraesCS4A01G139800 chr7B 87.179 273 25 6 1526 1795 46150558 46150293 1.040000e-77 302.0
78 TraesCS4A01G139800 chr7B 77.966 118 17 8 571 686 83029529 83029419 1.490000e-06 65.8
79 TraesCS4A01G139800 chr4B 81.287 171 14 3 5490 5657 23359003 23358848 8.730000e-24 122.0
80 TraesCS4A01G139800 chr2B 87.342 79 8 2 577 654 553765774 553765851 8.850000e-14 89.8


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 TraesCS4A01G139800 chr4A 211666854 211673264 6410 False 11839.00 11839 100.000000 1 6411 1 chr4A.!!$F1 6410
1 TraesCS4A01G139800 chr4A 201146032 201151184 5152 True 4351.50 7825 97.799000 588 5659 2 chr4A.!!$R4 5071
2 TraesCS4A01G139800 chr4A 369627787 369628358 571 True 913.00 913 95.462000 1 572 1 chr4A.!!$R2 571
3 TraesCS4A01G139800 chr4A 109626981 109630735 3754 True 599.00 1059 86.519000 2559 5657 2 chr4A.!!$R3 3098
4 TraesCS4A01G139800 chr6B 511276912 511282762 5850 True 1707.75 5123 96.602000 1548 5662 4 chr6B.!!$R2 4114
5 TraesCS4A01G139800 chr6B 412701780 412705431 3651 True 1428.00 1626 89.743000 2358 5488 2 chr6B.!!$R1 3130
6 TraesCS4A01G139800 chr3A 530084546 530087315 2769 False 4497.00 4497 95.967000 2906 5678 1 chr3A.!!$F2 2772
7 TraesCS4A01G139800 chr3A 530061089 530063766 2677 False 1184.50 2049 94.911000 577 2909 2 chr3A.!!$F3 2332
8 TraesCS4A01G139800 chr3A 664166064 664166636 572 True 935.00 935 96.161000 1 572 1 chr3A.!!$R1 571
9 TraesCS4A01G139800 chr3A 73528145 73528713 568 False 904.00 904 95.288000 1 572 1 chr3A.!!$F1 571
10 TraesCS4A01G139800 chr5B 688437161 688439937 2776 True 2099.00 2242 94.466500 2941 5659 2 chr5B.!!$R1 2718
11 TraesCS4A01G139800 chr5B 688467330 688474938 7608 True 1207.20 2248 92.404600 1218 5659 5 chr5B.!!$R2 4441
12 TraesCS4A01G139800 chr6A 86624272 86630183 5911 True 1709.25 2085 96.026250 586 5660 4 chr6A.!!$R2 5074
13 TraesCS4A01G139800 chr6A 86306245 86307001 756 True 1192.00 1192 95.119000 5656 6411 1 chr6A.!!$R1 755
14 TraesCS4A01G139800 chr2D 74121098 74124729 3631 False 1237.00 2052 92.039667 2894 5659 3 chr2D.!!$F2 2765
15 TraesCS4A01G139800 chr2D 612523463 612527383 3920 False 1049.00 1899 91.856000 1833 4952 3 chr2D.!!$F3 3119
16 TraesCS4A01G139800 chr2D 177998230 177998798 568 True 909.00 909 95.462000 1 572 1 chr2D.!!$R1 571
17 TraesCS4A01G139800 chr5D 169787692 169790614 2922 False 1345.00 1615 89.749000 2049 4212 2 chr5D.!!$F2 2163
18 TraesCS4A01G139800 chr5D 156620865 156623255 2390 False 1010.50 1075 89.801000 2588 4212 2 chr5D.!!$F1 1624
19 TraesCS4A01G139800 chr1A 574543725 574544482 757 True 1194.00 1194 95.119000 5656 6411 1 chr1A.!!$R1 755
20 TraesCS4A01G139800 chr1A 114548169 114548925 756 False 355.20 652 90.975500 1091 1793 2 chr1A.!!$F3 702
21 TraesCS4A01G139800 chr7A 181825474 181826231 757 False 1182.00 1182 94.855000 5656 6411 1 chr7A.!!$F2 755
22 TraesCS4A01G139800 chr7A 29085748 29086505 757 False 1177.00 1177 94.723000 5656 6411 1 chr7A.!!$F1 755
23 TraesCS4A01G139800 chr7A 709606302 709607060 758 True 1177.00 1177 94.730000 5656 6411 1 chr7A.!!$R1 755
24 TraesCS4A01G139800 chr2A 483618745 483619502 757 False 1182.00 1182 94.855000 5656 6411 1 chr2A.!!$F1 755
25 TraesCS4A01G139800 chr2A 595376215 595376971 756 True 1181.00 1181 94.862000 5656 6411 1 chr2A.!!$R2 755
26 TraesCS4A01G139800 chr5A 442692070 442692827 757 False 1177.00 1177 94.723000 5656 6411 1 chr5A.!!$F2 755
27 TraesCS4A01G139800 chr5A 539939905 539940663 758 False 1177.00 1177 94.737000 5656 6411 1 chr5A.!!$F3 755
28 TraesCS4A01G139800 chr5A 15066342 15066914 572 False 918.00 918 95.637000 1 572 1 chr5A.!!$F1 571
29 TraesCS4A01G139800 chr5A 663031350 663031921 571 False 913.00 913 95.462000 1 572 1 chr5A.!!$F5 571
30 TraesCS4A01G139800 chr1D 50893938 50894769 831 False 1086.00 1086 90.118000 3365 4212 1 chr1D.!!$F1 847
31 TraesCS4A01G139800 chr1D 110337389 110338155 766 False 337.20 616 90.469500 1091 1793 2 chr1D.!!$F2 702
32 TraesCS4A01G139800 chr3D 20723919 20724717 798 True 917.00 917 87.395000 1974 2797 1 chr3D.!!$R1 823
33 TraesCS4A01G139800 chr3D 169892590 169893158 568 True 915.00 915 95.637000 1 572 1 chr3D.!!$R3 571
34 TraesCS4A01G139800 chr7D 602985454 602986022 568 True 909.00 909 95.462000 1 572 1 chr7D.!!$R3 571
35 TraesCS4A01G139800 chrUn 31949907 31950471 564 True 905.00 905 95.462000 1 572 1 chrUn.!!$R1 571
36 TraesCS4A01G139800 chrUn 331637494 331639284 1790 False 903.00 904 91.531000 1218 2717 2 chrUn.!!$F1 1499
37 TraesCS4A01G139800 chrUn 332051574 332052146 572 True 902.00 902 95.122000 2147 2717 1 chrUn.!!$R2 570
38 TraesCS4A01G139800 chr1B 167715502 167716234 732 False 619.00 619 83.221000 1096 1782 1 chr1B.!!$F1 686

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
268 270 0.892358 AGCTTATCCCATGCCATGCG 60.892 55.000 0.00 0.0 0.00 4.73 F
1691 1789 0.724549 TGTGTGTCAACGTGCTTGTC 59.275 50.000 0.00 0.0 0.00 3.18 F
1808 1907 1.066143 TCTAGCAGGCTACAAGGTTGC 60.066 52.381 0.00 0.0 33.89 4.17 F
3281 3741 0.527385 TTTGTGCGCAAAGTTGAGGC 60.527 50.000 21.05 0.0 39.43 4.70 F
3956 7849 4.998671 TTTGAATGGACAATGTGTGTGT 57.001 36.364 0.00 0.0 41.96 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1929 2028 0.443869 CTGAACGGTTTGAGGCATCG 59.556 55.000 0.00 0.00 0.00 3.84 R
3281 3741 2.430332 ACACGATTATTGGCCCCAATTG 59.570 45.455 16.96 11.37 43.32 2.32 R
3630 7402 3.055385 TCCCGGAAGAAGAACATACCTTG 60.055 47.826 0.73 0.00 0.00 3.61 R
4862 9064 0.539051 AGATTCTCAGGAAGCCCACG 59.461 55.000 0.00 0.00 38.49 4.94 R
5734 12493 0.104120 TACCATCTCCCGCACATTCG 59.896 55.000 0.00 0.00 0.00 3.34 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
116 117 1.025041 CTCACCTGGACGATGATCGA 58.975 55.000 22.88 0.00 43.74 3.59
143 144 2.586258 GCATTAAGCTCGAGGAGACA 57.414 50.000 15.58 0.00 41.15 3.41
268 270 0.892358 AGCTTATCCCATGCCATGCG 60.892 55.000 0.00 0.00 0.00 4.73
273 275 1.986632 ATCCCATGCCATGCGAGACA 61.987 55.000 0.00 0.00 0.00 3.41
464 467 4.508551 TTGATGAGGGTATGCTTGTCAT 57.491 40.909 0.00 0.00 39.17 3.06
671 674 6.488683 CCTATAGTTTTTGACAGTTCAACCCA 59.511 38.462 0.00 0.00 41.64 4.51
1411 1462 3.050703 CTGCAAGGTACGCGAATCT 57.949 52.632 15.93 3.22 0.00 2.40
1604 1686 8.674607 GTTTCTTCGTAATGATTTGGATTACCT 58.325 33.333 0.00 0.00 34.19 3.08
1618 1700 5.245531 TGGATTACCTCAGTCATGTTCAAC 58.754 41.667 0.00 0.00 37.04 3.18
1691 1789 0.724549 TGTGTGTCAACGTGCTTGTC 59.275 50.000 0.00 0.00 0.00 3.18
1693 1791 1.275657 GTGTCAACGTGCTTGTCCG 59.724 57.895 0.00 0.00 0.00 4.79
1808 1907 1.066143 TCTAGCAGGCTACAAGGTTGC 60.066 52.381 0.00 0.00 33.89 4.17
1851 1950 4.093291 CGGCTGCTCCTTCTGGCT 62.093 66.667 0.00 0.00 0.00 4.75
1929 2028 2.074113 GAGATTCCCTCCCCATGCCC 62.074 65.000 0.00 0.00 35.87 5.36
1966 2065 3.067106 TCAGCAAGCACTAGCAAGTAAC 58.933 45.455 0.00 0.00 45.49 2.50
1968 2067 4.021456 TCAGCAAGCACTAGCAAGTAACTA 60.021 41.667 0.00 0.00 45.49 2.24
2095 2486 4.331968 ACTGAATAATTTTGGGAGCGACA 58.668 39.130 0.00 0.00 0.00 4.35
2240 2634 3.149899 CAGGAGGACTGCATGTGAC 57.850 57.895 0.00 0.00 40.97 3.67
2295 2700 2.028930 AGCTCCAGCAGTTAGTACACAC 60.029 50.000 0.48 0.00 45.16 3.82
2598 3003 3.372206 AGATTTGTCGAAGCAGCATACAC 59.628 43.478 0.00 0.00 0.00 2.90
2802 3260 2.429971 TGCTTGGAACATGTGAGCAAAA 59.570 40.909 18.39 2.64 40.09 2.44
2832 3290 4.458397 ACATGCACCTTCTTGGATGATAG 58.542 43.478 11.05 0.00 45.55 2.08
2978 3436 5.061853 CAGGAGATGTACCTACGTAGCTAA 58.938 45.833 17.41 1.46 35.84 3.09
3281 3741 0.527385 TTTGTGCGCAAAGTTGAGGC 60.527 50.000 21.05 0.00 39.43 4.70
3430 7193 5.801176 CATAAATGCTGATTCGTTCATGC 57.199 39.130 0.00 0.00 32.72 4.06
3500 7263 5.369993 TGAAGGAGTAGTAGAGCAGAGGATA 59.630 44.000 0.00 0.00 0.00 2.59
3630 7402 5.940470 TCTTTACTCCTGATTTCAGCCTTTC 59.060 40.000 1.90 0.00 42.47 2.62
3956 7849 4.998671 TTTGAATGGACAATGTGTGTGT 57.001 36.364 0.00 0.00 41.96 3.72
4089 8042 8.288689 ACACACATGGAAAACTTAAACTTAGT 57.711 30.769 0.00 0.00 0.00 2.24
4862 9064 6.740122 GCAAGAGACAGGGATAATACTTCCTC 60.740 46.154 0.00 0.00 33.53 3.71
5135 11315 1.728971 CCGAAGAACAGATGTCACTGC 59.271 52.381 0.00 0.00 41.06 4.40
5247 11521 8.432805 CCCTCTGATGGTTAGACTGTTAATAAT 58.567 37.037 0.00 0.00 0.00 1.28
5269 11543 5.670792 TCTTTTAGATTTCCACTAGGCGA 57.329 39.130 0.00 0.00 33.74 5.54
5505 12258 7.024340 TGATCATTCTTTGAGAAAGCTATGC 57.976 36.000 0.00 0.00 37.82 3.14
5734 12493 8.801715 TTGACAGCTTATTTTCATTCTTCAAC 57.198 30.769 0.00 0.00 0.00 3.18
5772 12531 3.181452 GGTAGACAAAACCCACTACACCA 60.181 47.826 0.00 0.00 37.52 4.17
5880 12639 6.957631 ACTCCTCAACATTATGGTCAATACA 58.042 36.000 0.00 0.00 0.00 2.29
5883 12642 7.345691 TCCTCAACATTATGGTCAATACATGT 58.654 34.615 2.69 2.69 30.40 3.21
5917 12676 4.584325 TGTGTTCAACTACGGTAACTACCT 59.416 41.667 4.45 0.00 44.25 3.08
6004 12767 9.838339 AAAACTAGTACATCATTGCTAGCTATT 57.162 29.630 17.23 1.28 35.58 1.73
6124 12887 6.051717 CAGGTCATCCTACGAATCTCAATTT 58.948 40.000 0.00 0.00 43.07 1.82
6138 12901 8.072567 CGAATCTCAATTTTCCATACCAGATTC 58.927 37.037 7.86 7.86 40.46 2.52
6177 12940 4.344679 ACATGCAAGTCAAAGGATGGAAAA 59.655 37.500 0.00 0.00 37.82 2.29
6225 12990 3.569701 TCTTGGAAGCAAAAGAAAGCGAT 59.430 39.130 0.00 0.00 35.48 4.58
6229 12994 0.593128 AGCAAAAGAAAGCGATGCGT 59.407 45.000 0.00 0.00 41.72 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.388649 ACAGACCTCGATCGTTGTGC 60.389 55.000 15.94 7.76 0.00 4.57
72 73 1.154016 CGCACAGACCTCGATCGTT 60.154 57.895 15.94 0.25 0.00 3.85
143 144 4.121317 TGTGTACCGTTTCAACTTCGAAT 58.879 39.130 0.00 0.00 0.00 3.34
273 275 6.776887 AATCCATCCTCTCCAAGACATAAT 57.223 37.500 0.00 0.00 0.00 1.28
374 376 8.834004 TGGGTTACGCTCCTAGAATTATATAT 57.166 34.615 0.36 0.00 0.00 0.86
581 584 9.373603 ACTCAATGTGTGCTTTATTATTACGTA 57.626 29.630 0.00 0.00 0.00 3.57
582 585 8.263940 ACTCAATGTGTGCTTTATTATTACGT 57.736 30.769 0.00 0.00 0.00 3.57
583 586 8.604035 AGACTCAATGTGTGCTTTATTATTACG 58.396 33.333 0.00 0.00 0.00 3.18
584 587 9.922305 GAGACTCAATGTGTGCTTTATTATTAC 57.078 33.333 0.00 0.00 0.00 1.89
600 603 1.676014 GGTGAACCCGGAGACTCAATG 60.676 57.143 0.73 0.00 0.00 2.82
624 627 4.448363 GACTCTTTTACAAAAGCGTCGT 57.552 40.909 17.13 8.89 45.19 4.34
627 630 3.816994 AGGGACTCTTTTACAAAAGCGT 58.183 40.909 9.24 9.24 44.09 5.07
671 674 4.164981 TGGGTTACTAACATGAGGACTGT 58.835 43.478 0.00 0.00 0.00 3.55
868 873 2.820037 GGCAGTGGAAGGCTACGC 60.820 66.667 0.00 0.00 0.00 4.42
871 876 4.096003 GCCGGCAGTGGAAGGCTA 62.096 66.667 24.80 0.00 45.67 3.93
906 911 2.981909 AGTTCCTCGTCGTCGGCA 60.982 61.111 1.55 0.00 37.69 5.69
1604 1686 4.971939 TCATTGGAGTTGAACATGACTGA 58.028 39.130 0.00 0.00 0.00 3.41
1618 1700 3.608707 GCTTGCGCAAGATATCATTGGAG 60.609 47.826 45.25 21.53 40.79 3.86
1691 1789 6.743575 AATGAATTAACCTCTTGAAGTCGG 57.256 37.500 0.00 0.00 0.00 4.79
1851 1950 0.465705 GGTCTTCATGCCTCGATCCA 59.534 55.000 0.00 0.00 0.00 3.41
1929 2028 0.443869 CTGAACGGTTTGAGGCATCG 59.556 55.000 0.00 0.00 0.00 3.84
2095 2486 2.578021 ACTGGCTTGTAATCATCACCCT 59.422 45.455 0.00 0.00 0.00 4.34
2240 2634 4.499183 AGATCTTCTTGTGCCTTAACTCG 58.501 43.478 0.00 0.00 0.00 4.18
2295 2700 3.742369 GTGAAAATGCACTGTTGATTGGG 59.258 43.478 0.00 0.00 35.91 4.12
2511 2916 4.471025 TGAACATAGAGGAGGAATCTGCAA 59.529 41.667 0.00 0.00 33.43 4.08
2802 3260 4.394920 CCAAGAAGGTGCATGTACGTAAAT 59.605 41.667 9.58 0.00 0.00 1.40
2832 3290 6.937392 AGGAGGTACAAACATAGAGAAGTTC 58.063 40.000 0.00 0.00 0.00 3.01
3281 3741 2.430332 ACACGATTATTGGCCCCAATTG 59.570 45.455 16.96 11.37 43.32 2.32
3430 7193 4.802039 TGCGCCTCTTACTTCTAATAAACG 59.198 41.667 4.18 0.00 0.00 3.60
3630 7402 3.055385 TCCCGGAAGAAGAACATACCTTG 60.055 47.826 0.73 0.00 0.00 3.61
3956 7849 9.790389 AATTTCACATAGTGTTCGTTTAAACAA 57.210 25.926 18.07 8.72 40.62 2.83
4486 8685 7.831690 TGGTTGCTTAATACTTTGATACATGGA 59.168 33.333 0.00 0.00 0.00 3.41
4746 8948 4.040217 AGCAAATCCCTGCATAAACAAACA 59.960 37.500 0.00 0.00 45.18 2.83
4862 9064 0.539051 AGATTCTCAGGAAGCCCACG 59.461 55.000 0.00 0.00 38.49 4.94
5135 11315 1.884235 ACAACAAAAGAGAGCCCGAG 58.116 50.000 0.00 0.00 0.00 4.63
5247 11521 5.416947 GTCGCCTAGTGGAAATCTAAAAGA 58.583 41.667 0.00 0.00 34.57 2.52
5734 12493 0.104120 TACCATCTCCCGCACATTCG 59.896 55.000 0.00 0.00 0.00 3.34
5772 12531 5.357032 CCTTGTAAGTTAATTCGGAGCCATT 59.643 40.000 0.00 0.00 0.00 3.16
5842 12601 8.723942 ATGTTGAGGAGTTTGATTGTAGATAC 57.276 34.615 0.00 0.00 0.00 2.24
5880 12639 4.006780 TGAACACATGCACTAGTGACAT 57.993 40.909 27.08 23.02 39.03 3.06
5883 12642 4.071961 AGTTGAACACATGCACTAGTGA 57.928 40.909 27.08 11.86 39.03 3.41
5917 12676 6.652205 AAAATCTTACCAGGGTATCTCCAA 57.348 37.500 0.00 0.00 38.11 3.53
6124 12887 9.189156 CATTTCTTTTAGGAATCTGGTATGGAA 57.811 33.333 0.00 0.00 0.00 3.53
6138 12901 5.902613 TGCATGTCTCCATTTCTTTTAGG 57.097 39.130 0.00 0.00 0.00 2.69
6177 12940 6.055588 CCTCCTTACGATTGTCCATACATTT 58.944 40.000 0.00 0.00 34.97 2.32
6225 12990 4.200838 TCATGTCTCCAATTCTTACGCA 57.799 40.909 0.00 0.00 0.00 5.24
6260 13025 4.271807 AGACCCTGACTCTCCATTATGA 57.728 45.455 0.00 0.00 0.00 2.15
6305 13070 7.317722 GGTAGGACCTAAATACCATCTTCAT 57.682 40.000 1.75 0.00 39.05 2.57


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

AutoCloner maintained by Alex Coulton.