Multiple sequence alignment - TraesCS4A01G163800

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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 TraesCS4A01G163800 chr4A 100.000 9010 0 0 1 9010 373801067 373810076 0.000000e+00 16639.0
1 TraesCS4A01G163800 chr4A 98.802 3674 15 6 1148 4818 606352627 606356274 0.000000e+00 6514.0
2 TraesCS4A01G163800 chr4A 90.223 1524 122 10 7462 8978 276800440 276798937 0.000000e+00 1964.0
3 TraesCS4A01G163800 chr4A 93.483 491 27 3 6961 7451 276800990 276800505 0.000000e+00 725.0
4 TraesCS4A01G163800 chr4A 91.667 84 7 0 5251 5334 559456588 559456671 5.720000e-22 117.0
5 TraesCS4A01G163800 chr3A 97.744 4167 87 4 4812 8978 730969908 730974067 0.000000e+00 7167.0
6 TraesCS4A01G163800 chr3A 93.634 2686 116 23 2138 4818 341603501 341606136 0.000000e+00 3962.0
7 TraesCS4A01G163800 chr3A 93.669 1153 40 14 1 1145 730968787 730969914 0.000000e+00 1694.0
8 TraesCS4A01G163800 chr6B 97.385 4169 85 4 4811 8978 565749385 565753530 0.000000e+00 7073.0
9 TraesCS4A01G163800 chr6B 94.393 1195 61 6 3627 4818 60485271 60484080 0.000000e+00 1831.0
10 TraesCS4A01G163800 chr6B 95.282 975 32 4 183 1145 565748420 565749392 0.000000e+00 1533.0
11 TraesCS4A01G163800 chr6B 91.823 1015 58 7 1143 2144 60487236 60486234 0.000000e+00 1391.0
12 TraesCS4A01G163800 chr6B 94.366 781 34 7 2169 2949 60486041 60485271 0.000000e+00 1190.0
13 TraesCS4A01G163800 chr6B 94.536 183 10 0 1 183 565747960 565748142 5.330000e-72 283.0
14 TraesCS4A01G163800 chr6B 94.667 75 4 0 5254 5328 278674697 278674623 5.720000e-22 117.0
15 TraesCS4A01G163800 chr6B 92.105 76 6 0 4746 4821 412458896 412458821 3.440000e-19 108.0
16 TraesCS4A01G163800 chr6B 87.097 93 10 2 5252 5344 697950477 697950387 4.450000e-18 104.0
17 TraesCS4A01G163800 chr6B 84.000 75 9 3 4746 4818 93272341 93272414 1.620000e-07 69.4
18 TraesCS4A01G163800 chr7A 98.887 3685 25 5 1144 4818 663754876 663751198 0.000000e+00 6564.0
19 TraesCS4A01G163800 chr7A 89.929 1549 104 17 7462 8978 713192472 713194000 0.000000e+00 1949.0
20 TraesCS4A01G163800 chr7A 91.564 1055 68 8 7931 8978 699549416 699548376 0.000000e+00 1435.0
21 TraesCS4A01G163800 chr7A 91.624 585 41 2 8394 8978 311862052 311862628 0.000000e+00 802.0
22 TraesCS4A01G163800 chr7A 94.297 491 24 2 6961 7451 699550095 699549609 0.000000e+00 749.0
23 TraesCS4A01G163800 chr7A 93.852 488 23 4 6961 7448 713191935 713192415 0.000000e+00 728.0
24 TraesCS4A01G163800 chr7A 93.103 145 9 1 7462 7606 699549554 699549411 2.550000e-50 211.0
25 TraesCS4A01G163800 chr7A 97.260 73 2 0 4746 4818 730186398 730186470 3.420000e-24 124.0
26 TraesCS4A01G163800 chr7A 97.260 73 2 0 4746 4818 730232292 730232364 3.420000e-24 124.0
27 TraesCS4A01G163800 chr7A 95.890 73 3 0 4746 4818 730197786 730197858 1.590000e-22 119.0
28 TraesCS4A01G163800 chr2B 98.750 3679 43 2 1142 4818 345454911 345451234 0.000000e+00 6536.0
29 TraesCS4A01G163800 chr2B 89.125 423 16 2 2567 2970 488015076 488014665 4.860000e-137 499.0
30 TraesCS4A01G163800 chr2B 87.500 96 11 1 5251 5345 338733832 338733737 9.560000e-20 110.0
31 TraesCS4A01G163800 chr7B 99.252 3474 23 2 1347 4818 178411335 178407863 0.000000e+00 6268.0
32 TraesCS4A01G163800 chr7B 99.600 250 1 0 1142 1391 178411585 178411336 2.970000e-124 457.0
33 TraesCS4A01G163800 chr1B 98.869 3007 27 5 1141 4144 258833832 258836834 0.000000e+00 5358.0
34 TraesCS4A01G163800 chr1B 96.081 689 11 1 4146 4818 258837466 258838154 0.000000e+00 1109.0
35 TraesCS4A01G163800 chr1B 89.590 586 30 4 2457 3022 629424395 629423821 0.000000e+00 715.0
36 TraesCS4A01G163800 chr1B 74.910 558 71 35 4315 4818 629421500 629420958 3.320000e-44 191.0
37 TraesCS4A01G163800 chr1B 92.105 76 6 0 5253 5328 195591285 195591210 3.440000e-19 108.0
38 TraesCS4A01G163800 chr1B 90.789 76 7 0 5253 5328 556993856 556993781 1.600000e-17 102.0
39 TraesCS4A01G163800 chr7D 95.650 2046 47 15 2779 4819 548558452 548560460 0.000000e+00 3247.0
40 TraesCS4A01G163800 chr7D 94.310 1529 75 3 5348 6874 213066782 213068300 0.000000e+00 2331.0
41 TraesCS4A01G163800 chr7D 94.055 1026 43 6 1136 2144 548556798 548557822 0.000000e+00 1541.0
42 TraesCS4A01G163800 chr7D 93.899 967 48 10 1144 2104 55217936 55216975 0.000000e+00 1448.0
43 TraesCS4A01G163800 chr7D 89.943 875 58 7 278 1145 213065544 213066395 0.000000e+00 1101.0
44 TraesCS4A01G163800 chr7D 98.000 450 9 0 2138 2587 548558001 548558450 0.000000e+00 782.0
45 TraesCS4A01G163800 chr7D 91.193 545 36 2 1143 1686 619558640 619558107 0.000000e+00 730.0
46 TraesCS4A01G163800 chr7D 92.473 372 26 2 4811 5182 213066388 213066757 1.720000e-146 531.0
47 TraesCS4A01G163800 chr7D 98.438 64 1 0 6900 6963 213068299 213068362 7.390000e-21 113.0
48 TraesCS4A01G163800 chr7D 90.667 75 7 0 5254 5328 81361820 81361894 5.760000e-17 100.0
49 TraesCS4A01G163800 chr7D 79.070 86 16 2 4734 4818 561620203 561620287 3.510000e-04 58.4
50 TraesCS4A01G163800 chr6A 93.464 1530 95 4 5176 6705 161780035 161781559 0.000000e+00 2266.0
51 TraesCS4A01G163800 chr6A 93.081 1532 96 5 5179 6705 233958509 233956983 0.000000e+00 2233.0
52 TraesCS4A01G163800 chr6A 92.796 1527 105 4 5179 6705 299985201 299983680 0.000000e+00 2206.0
53 TraesCS4A01G163800 chr6A 88.735 648 48 12 278 924 161778646 161779269 0.000000e+00 769.0
54 TraesCS4A01G163800 chr6A 88.571 630 46 13 296 924 233959884 233959280 0.000000e+00 741.0
55 TraesCS4A01G163800 chr6A 87.057 649 57 10 278 925 299986588 299985966 0.000000e+00 708.0
56 TraesCS4A01G163800 chr6A 91.421 373 30 2 4811 5182 161779571 161779942 2.240000e-140 510.0
57 TraesCS4A01G163800 chr6A 90.909 374 31 2 4811 5182 233958977 233958605 4.860000e-137 499.0
58 TraesCS4A01G163800 chr6A 90.959 365 30 3 4818 5182 299985658 299985297 1.050000e-133 488.0
59 TraesCS4A01G163800 chr6A 95.489 266 10 1 6698 6963 299982917 299982654 3.010000e-114 424.0
60 TraesCS4A01G163800 chr6A 94.737 266 12 1 6698 6963 233956218 233955955 6.510000e-111 412.0
61 TraesCS4A01G163800 chr6A 94.361 266 13 1 6698 6963 161782326 161782589 3.030000e-109 407.0
62 TraesCS4A01G163800 chr6A 93.182 220 10 3 929 1143 233959191 233958972 1.460000e-82 318.0
63 TraesCS4A01G163800 chr6A 92.661 218 11 3 929 1141 299985879 299985662 8.790000e-80 309.0
64 TraesCS4A01G163800 chr6A 91.892 222 14 2 926 1143 161779355 161779576 3.160000e-79 307.0
65 TraesCS4A01G163800 chr5A 96.549 1275 35 6 3087 4358 598932705 598933973 0.000000e+00 2102.0
66 TraesCS4A01G163800 chr3D 92.980 1396 82 8 7586 8978 564547951 564546569 0.000000e+00 2021.0
67 TraesCS4A01G163800 chr3D 91.176 442 20 3 6961 7401 564548581 564548158 4.690000e-162 582.0
68 TraesCS4A01G163800 chr3D 92.000 75 6 0 5254 5328 108916346 108916272 1.240000e-18 106.0
69 TraesCS4A01G163800 chr3D 89.744 78 8 0 5251 5328 523157473 523157396 5.760000e-17 100.0
70 TraesCS4A01G163800 chr2A 92.061 1184 72 8 7802 8978 23543403 23544571 0.000000e+00 1646.0
71 TraesCS4A01G163800 chr2A 94.467 488 23 2 6961 7448 23542530 23543013 0.000000e+00 749.0
72 TraesCS4A01G163800 chr4D 93.737 990 29 6 1144 2104 308494673 308493688 0.000000e+00 1454.0
73 TraesCS4A01G163800 chr4D 93.333 75 5 0 5254 5328 482160745 482160671 2.660000e-20 111.0
74 TraesCS4A01G163800 chr4D 100.000 28 0 0 4792 4819 308494647 308494674 1.600000e-02 52.8
75 TraesCS4A01G163800 chr2D 97.794 816 12 4 3087 3899 560292266 560291454 0.000000e+00 1402.0
76 TraesCS4A01G163800 chr2D 88.542 96 10 1 5251 5345 249879539 249879444 2.060000e-21 115.0
77 TraesCS4A01G163800 chr2D 90.411 73 7 0 4746 4818 106288893 106288965 7.450000e-16 97.1
78 TraesCS4A01G163800 chrUn 92.115 837 49 8 8142 8978 263139132 263138313 0.000000e+00 1164.0
79 TraesCS4A01G163800 chrUn 92.024 840 50 8 8139 8978 311658578 311659400 0.000000e+00 1164.0
80 TraesCS4A01G163800 chrUn 92.024 840 50 7 8139 8978 327805339 327806161 0.000000e+00 1164.0
81 TraesCS4A01G163800 chrUn 92.024 840 50 7 8139 8978 327835198 327836020 0.000000e+00 1164.0
82 TraesCS4A01G163800 chrUn 91.905 840 51 7 8139 8978 1288002 1288824 0.000000e+00 1158.0
83 TraesCS4A01G163800 chrUn 92.489 679 51 0 7462 8140 1286066 1286744 0.000000e+00 972.0
84 TraesCS4A01G163800 chrUn 92.845 601 43 0 7462 8062 313522248 313522848 0.000000e+00 872.0
85 TraesCS4A01G163800 chrUn 92.845 601 43 0 7462 8062 324875071 324875671 0.000000e+00 872.0
86 TraesCS4A01G163800 chrUn 92.972 498 25 4 8481 8978 1290725 1291212 0.000000e+00 717.0
87 TraesCS4A01G163800 chrUn 93.187 411 28 0 7462 7872 296264208 296264618 1.000000e-168 604.0
88 TraesCS4A01G163800 chrUn 90.519 443 22 3 6961 7401 313521639 313522063 1.310000e-157 568.0
89 TraesCS4A01G163800 chrUn 90.519 443 22 3 6961 7401 324874462 324874886 1.310000e-157 568.0
90 TraesCS4A01G163800 chrUn 90.667 75 7 0 5254 5328 341187359 341187285 5.760000e-17 100.0
91 TraesCS4A01G163800 chrUn 97.368 38 0 1 5248 5284 1925158 1925195 7.550000e-06 63.9
92 TraesCS4A01G163800 chrUn 79.070 86 16 2 4734 4818 43174516 43174432 3.510000e-04 58.4
93 TraesCS4A01G163800 chrUn 79.070 86 16 2 4734 4818 178597582 178597498 3.510000e-04 58.4
94 TraesCS4A01G163800 chrUn 94.595 37 1 1 5249 5285 47689584 47689619 1.000000e-03 56.5
95 TraesCS4A01G163800 chr1A 92.551 537 30 5 2462 2995 58344705 58344176 0.000000e+00 761.0
96 TraesCS4A01G163800 chr1A 98.148 108 2 0 2338 2445 107403204 107403311 1.190000e-43 189.0
97 TraesCS4A01G163800 chr6D 80.443 767 96 26 4034 4784 272798251 272798979 3.700000e-148 536.0
98 TraesCS4A01G163800 chr6D 93.333 75 5 0 5254 5328 155602045 155601971 2.660000e-20 111.0
99 TraesCS4A01G163800 chr6D 93.151 73 5 0 4746 4818 167261632 167261560 3.440000e-19 108.0
100 TraesCS4A01G163800 chr6D 89.333 75 8 0 5254 5328 13067041 13067115 2.680000e-15 95.3
101 TraesCS4A01G163800 chr6D 89.552 67 7 0 5262 5328 220939476 220939542 1.610000e-12 86.1
102 TraesCS4A01G163800 chr6D 100.000 31 0 0 4789 4819 323973548 323973578 3.510000e-04 58.4
103 TraesCS4A01G163800 chr6D 86.792 53 4 3 5247 5297 461926305 461926356 1.000000e-03 56.5
104 TraesCS4A01G163800 chr5D 98.013 151 3 0 2138 2288 168712322 168712472 6.940000e-66 263.0
105 TraesCS4A01G163800 chr5D 91.139 79 6 1 5254 5331 541806181 541806259 1.240000e-18 106.0
106 TraesCS4A01G163800 chr5D 85.915 71 10 0 4748 4818 168715026 168715096 9.700000e-10 76.8
107 TraesCS4A01G163800 chr1D 84.387 269 33 7 4427 4690 185108491 185108755 1.160000e-63 255.0
108 TraesCS4A01G163800 chr1D 94.595 74 4 0 4746 4819 470821594 470821521 2.060000e-21 115.0
109 TraesCS4A01G163800 chr1D 92.105 76 6 0 5253 5328 141706061 141705986 3.440000e-19 108.0
110 TraesCS4A01G163800 chr1D 90.411 73 7 0 5254 5326 116546610 116546682 7.450000e-16 97.1
111 TraesCS4A01G163800 chr1D 90.411 73 7 0 5258 5330 336365902 336365974 7.450000e-16 97.1
112 TraesCS4A01G163800 chr4B 91.667 84 7 0 5251 5334 58961640 58961557 5.720000e-22 117.0
113 TraesCS4A01G163800 chr3B 92.208 77 6 0 4746 4822 445588821 445588745 9.560000e-20 110.0
114 TraesCS4A01G163800 chr5B 85.393 89 13 0 6592 6680 19027108 19027020 9.630000e-15 93.5


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 TraesCS4A01G163800 chr4A 373801067 373810076 9009 False 16639.000000 16639 100.000000 1 9010 1 chr4A.!!$F1 9009
1 TraesCS4A01G163800 chr4A 606352627 606356274 3647 False 6514.000000 6514 98.802000 1148 4818 1 chr4A.!!$F3 3670
2 TraesCS4A01G163800 chr4A 276798937 276800990 2053 True 1344.500000 1964 91.853000 6961 8978 2 chr4A.!!$R1 2017
3 TraesCS4A01G163800 chr3A 730968787 730974067 5280 False 4430.500000 7167 95.706500 1 8978 2 chr3A.!!$F2 8977
4 TraesCS4A01G163800 chr3A 341603501 341606136 2635 False 3962.000000 3962 93.634000 2138 4818 1 chr3A.!!$F1 2680
5 TraesCS4A01G163800 chr6B 565747960 565753530 5570 False 2963.000000 7073 95.734333 1 8978 3 chr6B.!!$F2 8977
6 TraesCS4A01G163800 chr6B 60484080 60487236 3156 True 1470.666667 1831 93.527333 1143 4818 3 chr6B.!!$R4 3675
7 TraesCS4A01G163800 chr7A 663751198 663754876 3678 True 6564.000000 6564 98.887000 1144 4818 1 chr7A.!!$R1 3674
8 TraesCS4A01G163800 chr7A 713191935 713194000 2065 False 1338.500000 1949 91.890500 6961 8978 2 chr7A.!!$F5 2017
9 TraesCS4A01G163800 chr7A 311862052 311862628 576 False 802.000000 802 91.624000 8394 8978 1 chr7A.!!$F1 584
10 TraesCS4A01G163800 chr7A 699548376 699550095 1719 True 798.333333 1435 92.988000 6961 8978 3 chr7A.!!$R2 2017
11 TraesCS4A01G163800 chr2B 345451234 345454911 3677 True 6536.000000 6536 98.750000 1142 4818 1 chr2B.!!$R2 3676
12 TraesCS4A01G163800 chr7B 178407863 178411585 3722 True 3362.500000 6268 99.426000 1142 4818 2 chr7B.!!$R1 3676
13 TraesCS4A01G163800 chr1B 258833832 258838154 4322 False 3233.500000 5358 97.475000 1141 4818 2 chr1B.!!$F1 3677
14 TraesCS4A01G163800 chr1B 629420958 629424395 3437 True 453.000000 715 82.250000 2457 4818 2 chr1B.!!$R3 2361
15 TraesCS4A01G163800 chr7D 548556798 548560460 3662 False 1856.666667 3247 95.901667 1136 4819 3 chr7D.!!$F4 3683
16 TraesCS4A01G163800 chr7D 55216975 55217936 961 True 1448.000000 1448 93.899000 1144 2104 1 chr7D.!!$R1 960
17 TraesCS4A01G163800 chr7D 213065544 213068362 2818 False 1019.000000 2331 93.791000 278 6963 4 chr7D.!!$F3 6685
18 TraesCS4A01G163800 chr7D 619558107 619558640 533 True 730.000000 730 91.193000 1143 1686 1 chr7D.!!$R2 543
19 TraesCS4A01G163800 chr6A 161778646 161782589 3943 False 851.800000 2266 91.974600 278 6963 5 chr6A.!!$F1 6685
20 TraesCS4A01G163800 chr6A 233955955 233959884 3929 True 840.600000 2233 92.096000 296 6963 5 chr6A.!!$R1 6667
21 TraesCS4A01G163800 chr6A 299982654 299986588 3934 True 827.000000 2206 91.792400 278 6963 5 chr6A.!!$R2 6685
22 TraesCS4A01G163800 chr5A 598932705 598933973 1268 False 2102.000000 2102 96.549000 3087 4358 1 chr5A.!!$F1 1271
23 TraesCS4A01G163800 chr3D 564546569 564548581 2012 True 1301.500000 2021 92.078000 6961 8978 2 chr3D.!!$R3 2017
24 TraesCS4A01G163800 chr2A 23542530 23544571 2041 False 1197.500000 1646 93.264000 6961 8978 2 chr2A.!!$F1 2017
25 TraesCS4A01G163800 chr4D 308493688 308494673 985 True 1454.000000 1454 93.737000 1144 2104 1 chr4D.!!$R1 960
26 TraesCS4A01G163800 chr2D 560291454 560292266 812 True 1402.000000 1402 97.794000 3087 3899 1 chr2D.!!$R2 812
27 TraesCS4A01G163800 chrUn 263138313 263139132 819 True 1164.000000 1164 92.115000 8142 8978 1 chrUn.!!$R3 836
28 TraesCS4A01G163800 chrUn 311658578 311659400 822 False 1164.000000 1164 92.024000 8139 8978 1 chrUn.!!$F4 839
29 TraesCS4A01G163800 chrUn 327805339 327806161 822 False 1164.000000 1164 92.024000 8139 8978 1 chrUn.!!$F5 839
30 TraesCS4A01G163800 chrUn 327835198 327836020 822 False 1164.000000 1164 92.024000 8139 8978 1 chrUn.!!$F6 839
31 TraesCS4A01G163800 chrUn 1286066 1291212 5146 False 949.000000 1158 92.455333 7462 8978 3 chrUn.!!$F7 1516
32 TraesCS4A01G163800 chrUn 313521639 313522848 1209 False 720.000000 872 91.682000 6961 8062 2 chrUn.!!$F8 1101
33 TraesCS4A01G163800 chrUn 324874462 324875671 1209 False 720.000000 872 91.682000 6961 8062 2 chrUn.!!$F9 1101
34 TraesCS4A01G163800 chr1A 58344176 58344705 529 True 761.000000 761 92.551000 2462 2995 1 chr1A.!!$R1 533
35 TraesCS4A01G163800 chr6D 272798251 272798979 728 False 536.000000 536 80.443000 4034 4784 1 chr6D.!!$F3 750

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
238 519 0.036952 CTGCCTGTACTGTCTGTGGG 60.037 60.000 0.00 0.00 0.00 4.61 F
818 1119 0.537143 CTGCCATGGCCGCCTTTATA 60.537 55.000 33.44 10.87 41.09 0.98 F
1257 1651 1.002544 CTTTGCTTCTTCCTCCTCCGT 59.997 52.381 0.00 0.00 0.00 4.69 F
1894 2349 2.039480 GGGAGAGGGAAGGTTAAAACGT 59.961 50.000 0.00 0.00 0.00 3.99 F
4201 7024 3.323775 TGGAGTACAAGAAGGGGAAAGT 58.676 45.455 0.00 0.00 0.00 2.66 F
4784 7708 4.306600 GGAGGTGATTTTCGCAAAATGTT 58.693 39.130 10.33 0.00 40.97 2.71 F
5700 8727 0.251787 ACCATTCCAAACAGGCCCTC 60.252 55.000 0.00 0.00 37.29 4.30 F
7135 10945 1.275505 GCCGGTCGACTTTAGCTTAC 58.724 55.000 16.46 0.00 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 2048 2.046892 GGCAGCAGAAGGAAGCGA 60.047 61.111 0.00 0.00 35.48 4.93 R
1913 2368 3.117888 ACAGAACCTGAACCTGAACATGT 60.118 43.478 0.00 0.00 35.18 3.21 R
4201 7024 1.925455 CCCCTCTTCTTGCCTCCCA 60.925 63.158 0.00 0.00 0.00 4.37 R
4784 7708 1.539496 CGGGAAAAGTTGTCTCCGACA 60.539 52.381 14.47 0.00 41.09 4.35 R
5128 8055 0.811616 GGCGGAAAGAGCATCGATGT 60.812 55.000 25.47 13.02 42.67 3.06 R
6631 9664 3.921677 TCGAGTTGCTTTAACAGTAGGG 58.078 45.455 0.00 0.00 41.88 3.53 R
7958 11924 2.527624 AGTGACAGCAGAGGGCCA 60.528 61.111 6.18 0.00 46.50 5.36 R
8990 16612 0.673022 GCAGACTGCCACAGAAGGAG 60.673 60.000 17.01 0.00 37.42 3.69 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
24 25 5.529430 CACTACACCACAACACTTAATTGGA 59.471 40.000 0.00 0.00 0.00 3.53
72 73 4.876107 CCAGATTAACGGCAAACTATCTGT 59.124 41.667 0.00 0.00 38.06 3.41
109 110 4.224370 ACTGCCGGAAGAAATACTTAAGGA 59.776 41.667 19.18 0.00 39.13 3.36
123 124 1.344065 TAAGGACGGAAGAACTGCCA 58.656 50.000 0.00 0.00 0.00 4.92
143 144 2.096713 CAGTAGAAGTTGAGCAACGCAC 60.097 50.000 7.62 5.09 45.50 5.34
238 519 0.036952 CTGCCTGTACTGTCTGTGGG 60.037 60.000 0.00 0.00 0.00 4.61
245 526 0.830444 TACTGTCTGTGGGGCGAACT 60.830 55.000 0.00 0.00 0.00 3.01
276 557 3.958147 CTCATTGGCGCGGGACACT 62.958 63.158 7.89 0.00 0.00 3.55
505 795 1.382629 CCCTCCACCGTTCCCAAAT 59.617 57.895 0.00 0.00 0.00 2.32
695 987 2.108157 GAGCCACGTGTGACCACA 59.892 61.111 15.65 0.00 41.93 4.17
705 997 0.610174 TGTGACCACAGATCTGGCTC 59.390 55.000 26.08 16.40 36.21 4.70
706 998 0.901124 GTGACCACAGATCTGGCTCT 59.099 55.000 26.08 2.50 34.20 4.09
707 999 1.134848 GTGACCACAGATCTGGCTCTC 60.135 57.143 26.08 14.47 34.20 3.20
818 1119 0.537143 CTGCCATGGCCGCCTTTATA 60.537 55.000 33.44 10.87 41.09 0.98
1046 1433 5.418840 CCCTTATTCTTGTGCACCTAATTGT 59.581 40.000 15.69 0.00 0.00 2.71
1257 1651 1.002544 CTTTGCTTCTTCCTCCTCCGT 59.997 52.381 0.00 0.00 0.00 4.69
1766 2221 4.680237 CCCCGCGTCTGCTGTTGA 62.680 66.667 4.92 0.00 39.65 3.18
1892 2347 4.383931 AAGGGAGAGGGAAGGTTAAAAC 57.616 45.455 0.00 0.00 0.00 2.43
1893 2348 2.305052 AGGGAGAGGGAAGGTTAAAACG 59.695 50.000 0.00 0.00 0.00 3.60
1894 2349 2.039480 GGGAGAGGGAAGGTTAAAACGT 59.961 50.000 0.00 0.00 0.00 3.99
1895 2350 3.497405 GGGAGAGGGAAGGTTAAAACGTT 60.497 47.826 0.00 0.00 39.45 3.99
1904 2359 5.494632 AAGGTTAAAACGTTCAGGTTCTG 57.505 39.130 0.00 0.00 32.05 3.02
1905 2360 4.520179 AGGTTAAAACGTTCAGGTTCTGT 58.480 39.130 0.00 0.00 32.61 3.41
1906 2361 4.945543 AGGTTAAAACGTTCAGGTTCTGTT 59.054 37.500 0.00 0.00 32.61 3.16
1907 2362 6.114767 AGGTTAAAACGTTCAGGTTCTGTTA 58.885 36.000 0.00 0.00 32.61 2.41
1908 2363 6.598850 AGGTTAAAACGTTCAGGTTCTGTTAA 59.401 34.615 0.00 0.00 32.61 2.01
1909 2364 6.688385 GGTTAAAACGTTCAGGTTCTGTTAAC 59.312 38.462 0.00 9.28 33.76 2.01
1910 2365 7.414429 GGTTAAAACGTTCAGGTTCTGTTAACT 60.414 37.037 18.45 0.00 34.34 2.24
1911 2366 5.479716 AAACGTTCAGGTTCTGTTAACTG 57.520 39.130 0.00 6.66 32.61 3.16
1912 2367 4.395959 ACGTTCAGGTTCTGTTAACTGA 57.604 40.909 10.80 10.80 38.12 3.41
1913 2368 4.761975 ACGTTCAGGTTCTGTTAACTGAA 58.238 39.130 20.25 20.25 44.87 3.02
2017 2497 7.227512 ACAGAGCAATCTATACCTGTAATTTGC 59.772 37.037 0.00 0.00 33.65 3.68
2316 2994 4.314121 TCCAATTGCAAACATGCCTAAAC 58.686 39.130 1.71 0.00 0.00 2.01
4201 7024 3.323775 TGGAGTACAAGAAGGGGAAAGT 58.676 45.455 0.00 0.00 0.00 2.66
4784 7708 4.306600 GGAGGTGATTTTCGCAAAATGTT 58.693 39.130 10.33 0.00 40.97 2.71
4835 7759 6.726764 AGGGAGTAGGTATCATCTTATTGGTC 59.273 42.308 0.00 0.00 0.00 4.02
4900 7827 9.904198 TGAATTGTATCTTAATCATCAGACCAA 57.096 29.630 0.00 0.00 0.00 3.67
5058 7985 8.680903 AGTCTGATAAAAATAGAACAATGCAGG 58.319 33.333 0.00 0.00 0.00 4.85
5128 8055 2.847234 ACGCTGGAAGGTCACCCA 60.847 61.111 0.00 0.00 0.00 4.51
5167 8094 0.773644 ACTTCCACAAGCCACCAGAT 59.226 50.000 0.00 0.00 32.09 2.90
5187 8212 6.169094 CAGATTGTATAGTTCATGCCCCTAG 58.831 44.000 0.00 0.00 0.00 3.02
5562 8589 3.543680 ACAGGATATCACCCACTTTCG 57.456 47.619 4.83 0.00 0.00 3.46
5700 8727 0.251787 ACCATTCCAAACAGGCCCTC 60.252 55.000 0.00 0.00 37.29 4.30
6402 9430 8.712228 ATAAAAGGAAGAAGGTGATCTGTTTT 57.288 30.769 0.00 0.00 0.00 2.43
6631 9664 9.278734 GCTAATTTGTAGAGCAATGTAGAAAAC 57.721 33.333 0.00 0.00 36.89 2.43
6645 9678 7.683437 ATGTAGAAAACCCTACTGTTAAAGC 57.317 36.000 0.00 0.00 39.67 3.51
7135 10945 1.275505 GCCGGTCGACTTTAGCTTAC 58.724 55.000 16.46 0.00 0.00 2.34
7204 11014 3.181450 CGCTCTTCCTATTTCCATTCCCT 60.181 47.826 0.00 0.00 0.00 4.20
7564 11501 3.986442 AAATGTTGCAACAAAATGGGC 57.014 38.095 34.06 3.56 43.03 5.36
7825 11791 7.798710 TCCCCATAACCATTTTGATTTGTAA 57.201 32.000 0.00 0.00 0.00 2.41
8032 11998 1.804151 GCTTTGCGTGGACACTGATTA 59.196 47.619 0.56 0.00 0.00 1.75
8185 13410 5.070001 ACAGAATGAACCAATCCTTTTCGA 58.930 37.500 0.00 0.00 39.69 3.71
8202 13427 4.771590 TTCGATTTGCTTTCTTCTGCAT 57.228 36.364 0.00 0.00 39.07 3.96
8241 13466 3.442076 AGAAGGAACCATCGTCTAAGGT 58.558 45.455 0.00 0.00 37.20 3.50
8263 13488 4.397417 GTGCATCAAATCAAGCTAGAGGTT 59.603 41.667 0.00 0.00 35.98 3.50
8308 13533 0.468226 AGTCTTGCGAAAGGTGACCA 59.532 50.000 3.63 0.00 0.00 4.02
8338 13563 5.938322 ACATTTTATCCTGTTACAAGCACG 58.062 37.500 0.00 0.00 0.00 5.34
8911 16532 6.957631 AGTTGGTGGAGTGATAATGTAATGA 58.042 36.000 0.00 0.00 0.00 2.57
8978 16600 2.766263 TGGTGGTTGTTTTGGCACATAA 59.234 40.909 0.00 0.00 39.30 1.90
8979 16601 3.197766 TGGTGGTTGTTTTGGCACATAAA 59.802 39.130 0.00 0.00 39.30 1.40
8980 16602 3.558006 GGTGGTTGTTTTGGCACATAAAC 59.442 43.478 6.37 6.37 39.30 2.01
8981 16603 4.184629 GTGGTTGTTTTGGCACATAAACA 58.815 39.130 10.97 10.97 42.61 2.83
8982 16604 4.813697 GTGGTTGTTTTGGCACATAAACAT 59.186 37.500 14.68 0.00 43.20 2.71
8983 16605 4.813161 TGGTTGTTTTGGCACATAAACATG 59.187 37.500 14.68 0.00 43.20 3.21
8984 16606 4.813697 GGTTGTTTTGGCACATAAACATGT 59.186 37.500 14.68 0.00 43.20 3.21
8985 16607 5.986135 GGTTGTTTTGGCACATAAACATGTA 59.014 36.000 14.68 0.73 43.20 2.29
8986 16608 6.648725 GGTTGTTTTGGCACATAAACATGTAT 59.351 34.615 14.68 0.00 43.20 2.29
8987 16609 7.359933 GGTTGTTTTGGCACATAAACATGTATG 60.360 37.037 14.68 2.52 43.20 2.39
8988 16610 6.753180 TGTTTTGGCACATAAACATGTATGT 58.247 32.000 10.97 8.20 43.89 2.29
8989 16611 7.886338 TGTTTTGGCACATAAACATGTATGTA 58.114 30.769 12.75 0.84 41.70 2.29
8990 16612 7.810282 TGTTTTGGCACATAAACATGTATGTAC 59.190 33.333 12.75 8.29 41.70 2.90
8991 16613 7.695480 TTTGGCACATAAACATGTATGTACT 57.305 32.000 12.75 0.00 41.70 2.73
8992 16614 6.918892 TGGCACATAAACATGTATGTACTC 57.081 37.500 12.75 7.29 41.70 2.59
8993 16615 5.820423 TGGCACATAAACATGTATGTACTCC 59.180 40.000 12.75 13.56 41.70 3.85
8994 16616 6.055588 GGCACATAAACATGTATGTACTCCT 58.944 40.000 12.75 0.00 41.70 3.69
8995 16617 6.542370 GGCACATAAACATGTATGTACTCCTT 59.458 38.462 12.75 0.00 41.70 3.36
8996 16618 7.254795 GGCACATAAACATGTATGTACTCCTTC 60.255 40.741 12.75 0.00 41.70 3.46
8997 16619 7.495934 GCACATAAACATGTATGTACTCCTTCT 59.504 37.037 12.75 0.00 41.70 2.85
8998 16620 8.820933 CACATAAACATGTATGTACTCCTTCTG 58.179 37.037 12.75 0.74 41.70 3.02
8999 16621 8.540388 ACATAAACATGTATGTACTCCTTCTGT 58.460 33.333 11.70 0.57 41.79 3.41
9000 16622 8.820933 CATAAACATGTATGTACTCCTTCTGTG 58.179 37.037 0.00 0.00 40.80 3.66
9001 16623 5.344743 ACATGTATGTACTCCTTCTGTGG 57.655 43.478 0.00 0.00 39.68 4.17
9002 16624 3.887621 TGTATGTACTCCTTCTGTGGC 57.112 47.619 0.00 0.00 0.00 5.01
9003 16625 3.169908 TGTATGTACTCCTTCTGTGGCA 58.830 45.455 0.00 0.00 0.00 4.92
9004 16626 3.195610 TGTATGTACTCCTTCTGTGGCAG 59.804 47.826 0.00 0.00 0.00 4.85
9005 16627 1.717032 TGTACTCCTTCTGTGGCAGT 58.283 50.000 0.00 0.00 32.61 4.40
9006 16628 1.618837 TGTACTCCTTCTGTGGCAGTC 59.381 52.381 0.00 0.00 32.61 3.51
9007 16629 1.896465 GTACTCCTTCTGTGGCAGTCT 59.104 52.381 0.00 0.00 32.61 3.24
9008 16630 0.683973 ACTCCTTCTGTGGCAGTCTG 59.316 55.000 0.00 0.00 32.61 3.51
9009 16631 0.673022 CTCCTTCTGTGGCAGTCTGC 60.673 60.000 16.93 16.93 44.08 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.964688 TCCGGCAGTAATAAGATTCCTGA 59.035 43.478 0.00 0.00 0.00 3.86
109 110 1.629043 TCTACTGGCAGTTCTTCCGT 58.371 50.000 27.24 0.58 0.00 4.69
123 124 2.135933 GTGCGTTGCTCAACTTCTACT 58.864 47.619 10.56 0.00 39.08 2.57
143 144 0.387878 TTGCCGGCAGTTTAAATGCG 60.388 50.000 30.75 6.75 44.80 4.73
238 519 2.427095 AGCCAATTATTTCCAGTTCGCC 59.573 45.455 0.00 0.00 0.00 5.54
245 526 3.181477 CGCCAATGAGCCAATTATTTCCA 60.181 43.478 0.00 0.00 0.00 3.53
311 593 3.311110 GGTGAGGTGAGGTGCGGA 61.311 66.667 0.00 0.00 0.00 5.54
480 769 4.608774 ACGGTGGAGGGTGGTCGA 62.609 66.667 0.00 0.00 0.00 4.20
695 987 0.398381 GGTGGAGGAGAGCCAGATCT 60.398 60.000 0.00 0.00 35.77 2.75
705 997 4.463879 CTGCCGCTGGTGGAGGAG 62.464 72.222 4.18 0.00 37.02 3.69
846 1148 1.317613 CTCCAGATCTCCGTCCAGAG 58.682 60.000 0.00 0.00 35.04 3.35
1046 1433 7.154191 AGATAATTTATTGAGAGAGCCCCAA 57.846 36.000 0.00 0.00 0.00 4.12
1593 2048 2.046892 GGCAGCAGAAGGAAGCGA 60.047 61.111 0.00 0.00 35.48 4.93
1892 2347 5.079397 GTTCAGTTAACAGAACCTGAACG 57.921 43.478 25.43 0.00 40.40 3.95
1910 2365 3.576078 ACCTGAACCTGAACATGTTCA 57.424 42.857 33.20 33.20 46.23 3.18
1911 2366 4.023707 CAGAACCTGAACCTGAACATGTTC 60.024 45.833 28.10 28.10 39.81 3.18
1912 2367 3.885297 CAGAACCTGAACCTGAACATGTT 59.115 43.478 11.78 11.78 32.44 2.71
1913 2368 3.117888 ACAGAACCTGAACCTGAACATGT 60.118 43.478 0.00 0.00 35.18 3.21
1914 2369 3.480470 ACAGAACCTGAACCTGAACATG 58.520 45.455 0.45 0.00 35.18 3.21
1915 2370 3.864789 ACAGAACCTGAACCTGAACAT 57.135 42.857 0.45 0.00 35.18 2.71
1916 2371 3.644966 AACAGAACCTGAACCTGAACA 57.355 42.857 0.45 0.00 35.18 3.18
2017 2497 4.184629 GGAGTAACAGAGGCATAACAGTG 58.815 47.826 0.00 0.00 0.00 3.66
4201 7024 1.925455 CCCCTCTTCTTGCCTCCCA 60.925 63.158 0.00 0.00 0.00 4.37
4784 7708 1.539496 CGGGAAAAGTTGTCTCCGACA 60.539 52.381 14.47 0.00 41.09 4.35
4835 7759 5.395768 CCCAGGAACAGAACCAGTATTCTAG 60.396 48.000 0.00 0.00 36.78 2.43
5058 7985 0.840722 TGGGACAGGGGAAGGAACTC 60.841 60.000 0.00 0.00 38.49 3.01
5128 8055 0.811616 GGCGGAAAGAGCATCGATGT 60.812 55.000 25.47 13.02 42.67 3.06
5167 8094 5.216622 AGACTAGGGGCATGAACTATACAA 58.783 41.667 0.00 0.00 0.00 2.41
5187 8212 3.426695 GCAACTTGACATGGCATGTAGAC 60.427 47.826 31.48 19.98 45.03 2.59
5299 8324 8.259411 TCCTAAATATAAGACGTTTTGGCAGTA 58.741 33.333 0.83 0.00 30.97 2.74
5562 8589 6.194796 TGTCAATTTATTGAGCTAAGGCAC 57.805 37.500 5.44 0.00 46.44 5.01
6012 9039 8.581253 AGCTACTACCAAAATTAGCAGAAAAT 57.419 30.769 2.56 0.00 39.59 1.82
6402 9430 7.120432 TGCAATTGTACAATAGATGCAGTAACA 59.880 33.333 29.52 14.78 37.23 2.41
6543 9576 7.340232 ACCTAATATGTGCATGACAAAGTGAAT 59.660 33.333 0.00 0.00 38.36 2.57
6631 9664 3.921677 TCGAGTTGCTTTAACAGTAGGG 58.078 45.455 0.00 0.00 41.88 3.53
6645 9678 5.838531 ATAGGACCTAAGAACTCGAGTTG 57.161 43.478 34.23 21.16 38.56 3.16
6973 10781 9.469097 AGAGATATCTTGTACTGTTTCTAGTGT 57.531 33.333 6.70 0.00 32.19 3.55
7135 10945 5.726980 TCAAGACATTCAAAAATGGAGGG 57.273 39.130 3.45 0.00 45.48 4.30
7459 11338 8.567948 ACAATTCAAGTCAGTAACATTAACAGG 58.432 33.333 0.00 0.00 0.00 4.00
7564 11501 7.814264 AAATATGCTTAGTTCTGGAATCAGG 57.186 36.000 0.00 0.00 41.23 3.86
7755 11694 9.087871 TCATTTTTCCTCTGTATTTCCATTTCA 57.912 29.630 0.00 0.00 0.00 2.69
7958 11924 2.527624 AGTGACAGCAGAGGGCCA 60.528 61.111 6.18 0.00 46.50 5.36
8032 11998 6.954352 AGTAACCCTCCAAGAGAAATAAGT 57.046 37.500 0.00 0.00 0.00 2.24
8185 13410 3.671008 TGCATGCAGAAGAAAGCAAAT 57.329 38.095 18.46 0.00 44.88 2.32
8202 13427 3.264922 TCTCCCTCTGGATGATATGCA 57.735 47.619 0.00 0.00 40.80 3.96
8241 13466 4.226427 ACCTCTAGCTTGATTTGATGCA 57.774 40.909 0.00 0.00 0.00 3.96
8263 13488 4.832248 ACTCGACTAAAATGGATGCAGAA 58.168 39.130 0.00 0.00 0.00 3.02
8308 13533 7.238486 TGTAACAGGATAAAATGTTTGCCAT 57.762 32.000 0.00 0.00 40.09 4.40
8487 13712 9.575868 TCCATTCCAGTTATAGTAACAAAACAA 57.424 29.630 3.05 0.00 0.00 2.83
8911 16532 1.756538 CCAGGTTCAACAAACAAGGCT 59.243 47.619 0.00 0.00 39.81 4.58
8955 16577 1.556911 TGTGCCAAAACAACCACCAAT 59.443 42.857 0.00 0.00 0.00 3.16
8978 16600 5.734720 CCACAGAAGGAGTACATACATGTT 58.265 41.667 2.30 0.00 41.97 2.71
8979 16601 4.383118 GCCACAGAAGGAGTACATACATGT 60.383 45.833 2.69 2.69 44.48 3.21
8980 16602 4.122776 GCCACAGAAGGAGTACATACATG 58.877 47.826 0.00 0.00 0.00 3.21
8981 16603 3.774766 TGCCACAGAAGGAGTACATACAT 59.225 43.478 0.00 0.00 0.00 2.29
8982 16604 3.169908 TGCCACAGAAGGAGTACATACA 58.830 45.455 0.00 0.00 0.00 2.29
8983 16605 3.195825 ACTGCCACAGAAGGAGTACATAC 59.804 47.826 0.78 0.00 35.18 2.39
8984 16606 3.441101 ACTGCCACAGAAGGAGTACATA 58.559 45.455 0.78 0.00 35.18 2.29
8985 16607 2.234908 GACTGCCACAGAAGGAGTACAT 59.765 50.000 0.78 0.00 35.18 2.29
8986 16608 1.618837 GACTGCCACAGAAGGAGTACA 59.381 52.381 0.78 0.00 35.18 2.90
8987 16609 1.896465 AGACTGCCACAGAAGGAGTAC 59.104 52.381 0.78 0.00 35.18 2.73
8988 16610 1.895798 CAGACTGCCACAGAAGGAGTA 59.104 52.381 0.78 0.00 35.18 2.59
8989 16611 0.683973 CAGACTGCCACAGAAGGAGT 59.316 55.000 0.78 0.00 35.18 3.85
8990 16612 0.673022 GCAGACTGCCACAGAAGGAG 60.673 60.000 17.01 0.00 37.42 3.69
8991 16613 1.372683 GCAGACTGCCACAGAAGGA 59.627 57.895 17.01 0.00 37.42 3.36
8992 16614 3.978272 GCAGACTGCCACAGAAGG 58.022 61.111 17.01 0.00 37.42 3.46


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

AutoCloner maintained by Alex Coulton.