Multiple sequence alignment - TraesCS4A01G174900

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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 TraesCS4A01G174900 chr4A 100.000 7106 0 0 1 7106 445286439 445279334 0.000000e+00 13123.0
1 TraesCS4A01G174900 chr4A 95.875 3079 98 17 4034 7106 110275401 110272346 0.000000e+00 4955.0
2 TraesCS4A01G174900 chr4A 90.967 2668 149 38 4501 7106 167812423 167815060 0.000000e+00 3507.0
3 TraesCS4A01G174900 chr4A 94.280 1084 51 4 2875 3949 380730240 380731321 0.000000e+00 1648.0
4 TraesCS4A01G174900 chr4A 93.827 648 38 2 1219 1866 637612359 637611714 0.000000e+00 974.0
5 TraesCS4A01G174900 chr4A 93.837 649 35 4 1219 1864 637297722 637297076 0.000000e+00 972.0
6 TraesCS4A01G174900 chr4A 93.683 649 38 3 1219 1866 637403539 637402893 0.000000e+00 968.0
7 TraesCS4A01G174900 chr4A 93.529 649 39 3 1219 1866 637488963 637488317 0.000000e+00 963.0
8 TraesCS4A01G174900 chr4A 93.395 651 38 4 1219 1866 637354869 637354221 0.000000e+00 959.0
9 TraesCS4A01G174900 chr4A 96.226 371 12 2 1857 2226 637297048 637296679 2.190000e-169 606.0
10 TraesCS4A01G174900 chr4A 96.226 371 12 2 1857 2226 637354195 637353826 2.190000e-169 606.0
11 TraesCS4A01G174900 chr4A 95.687 371 14 2 1857 2226 637611688 637611319 4.750000e-166 595.0
12 TraesCS4A01G174900 chr4A 81.132 159 20 7 4227 4384 445282176 445282027 1.250000e-22 119.0
13 TraesCS4A01G174900 chr1A 96.634 2852 79 7 4264 7106 63976133 63973290 0.000000e+00 4719.0
14 TraesCS4A01G174900 chr1A 93.290 924 61 1 644 1567 19701094 19702016 0.000000e+00 1362.0
15 TraesCS4A01G174900 chr1A 93.374 649 42 1 1219 1866 108380364 108381012 0.000000e+00 959.0
16 TraesCS4A01G174900 chr1A 84.257 686 69 19 5105 5761 115269459 115268784 3.620000e-177 632.0
17 TraesCS4A01G174900 chr1A 86.994 346 24 15 4033 4371 63976324 63975993 3.130000e-98 370.0
18 TraesCS4A01G174900 chr1A 93.939 99 5 1 3940 4038 568058385 568058482 1.600000e-31 148.0
19 TraesCS4A01G174900 chr5A 98.006 2708 51 3 4400 7106 407306866 407309571 0.000000e+00 4698.0
20 TraesCS4A01G174900 chr5A 90.662 589 45 2 2343 2931 568800965 568801543 0.000000e+00 774.0
21 TraesCS4A01G174900 chr5A 91.484 364 25 5 6746 7106 646982689 646983049 4.950000e-136 496.0
22 TraesCS4A01G174900 chr5A 86.702 376 46 4 5387 5761 124665387 124665015 1.430000e-111 414.0
23 TraesCS4A01G174900 chr5A 86.595 373 46 4 5387 5758 123725064 123725433 6.640000e-110 409.0
24 TraesCS4A01G174900 chr5A 95.192 104 5 0 3940 4043 687339200 687339303 1.590000e-36 165.0
25 TraesCS4A01G174900 chr5A 81.579 114 9 4 3945 4055 229492788 229492684 4.570000e-12 84.2
26 TraesCS4A01G174900 chr5A 94.118 51 2 1 4005 4055 543933541 543933590 7.640000e-10 76.8
27 TraesCS4A01G174900 chr2D 93.805 1711 77 11 2343 4033 41463431 41465132 0.000000e+00 2545.0
28 TraesCS4A01G174900 chr2D 94.562 901 30 9 4814 5695 5499819 5498919 0.000000e+00 1375.0
29 TraesCS4A01G174900 chr2D 93.409 531 31 4 6580 7106 5462897 5463427 0.000000e+00 784.0
30 TraesCS4A01G174900 chr2D 95.038 262 12 1 1 261 163283799 163284060 1.840000e-110 411.0
31 TraesCS4A01G174900 chr2D 85.479 365 46 7 3510 3869 648684834 648684472 2.420000e-99 374.0
32 TraesCS4A01G174900 chr2D 75.725 276 40 11 2884 3147 407331860 407331600 5.830000e-21 113.0
33 TraesCS4A01G174900 chr3B 92.582 1402 83 4 578 1958 74019800 74021201 0.000000e+00 1993.0
34 TraesCS4A01G174900 chr3B 89.529 1146 66 17 1219 2343 241263386 241262274 0.000000e+00 1402.0
35 TraesCS4A01G174900 chr3B 92.071 845 63 3 533 1374 311765076 311764233 0.000000e+00 1186.0
36 TraesCS4A01G174900 chr3B 96.164 365 13 1 171 534 241261651 241262015 4.750000e-166 595.0
37 TraesCS4A01G174900 chr3B 94.643 280 14 1 255 534 400609769 400610047 3.940000e-117 433.0
38 TraesCS4A01G174900 chr3B 94.656 262 11 3 1 261 537868518 537868259 3.090000e-108 403.0
39 TraesCS4A01G174900 chr3B 78.348 351 53 8 4539 4866 357116562 357116212 9.340000e-49 206.0
40 TraesCS4A01G174900 chr3B 94.118 51 2 1 4005 4055 434650795 434650844 7.640000e-10 76.8
41 TraesCS4A01G174900 chr7A 93.478 1242 67 8 5867 7106 53341642 53342871 0.000000e+00 1832.0
42 TraesCS4A01G174900 chr7A 94.493 345 14 5 5538 5881 53340693 53341033 1.760000e-145 527.0
43 TraesCS4A01G174900 chr7A 80.876 685 84 29 3206 3855 369478139 369478811 4.950000e-136 496.0
44 TraesCS4A01G174900 chr7A 78.390 671 100 28 3218 3852 700604017 700604678 1.860000e-105 394.0
45 TraesCS4A01G174900 chr6B 89.164 1292 98 24 5820 7090 267749426 267750696 0.000000e+00 1572.0
46 TraesCS4A01G174900 chr6B 94.600 537 29 0 1261 1797 257300357 257299821 0.000000e+00 832.0
47 TraesCS4A01G174900 chr6B 95.263 380 17 1 1 379 558530975 558531354 1.020000e-167 601.0
48 TraesCS4A01G174900 chr6B 95.000 380 18 1 1 379 321863376 321862997 4.750000e-166 595.0
49 TraesCS4A01G174900 chr6B 88.158 456 37 11 5761 6208 599695748 599695302 1.760000e-145 527.0
50 TraesCS4A01G174900 chr6B 84.599 461 56 7 2882 3331 667770601 667771057 1.820000e-120 444.0
51 TraesCS4A01G174900 chr4B 90.306 1145 59 16 1219 2343 199719510 199720622 0.000000e+00 1452.0
52 TraesCS4A01G174900 chr4B 90.547 804 52 5 1558 2343 341927700 341926903 0.000000e+00 1042.0
53 TraesCS4A01G174900 chr4B 89.381 678 52 15 6437 7106 300019835 300020500 0.000000e+00 835.0
54 TraesCS4A01G174900 chr4B 93.419 547 22 8 1 534 341241098 341241643 0.000000e+00 798.0
55 TraesCS4A01G174900 chr4B 94.417 412 23 0 1932 2343 341242312 341241901 1.010000e-177 634.0
56 TraesCS4A01G174900 chr4B 97.260 365 9 1 171 534 199721245 199720881 1.010000e-172 617.0
57 TraesCS4A01G174900 chr4B 97.872 282 5 1 254 534 341926363 341926644 2.980000e-133 486.0
58 TraesCS4A01G174900 chr4B 94.656 262 13 1 1 261 240637033 240637294 8.580000e-109 405.0
59 TraesCS4A01G174900 chr4B 94.444 198 11 0 996 1193 341243147 341242950 8.960000e-79 305.0
60 TraesCS4A01G174900 chr3D 93.030 990 61 5 533 1517 562971674 562970688 0.000000e+00 1439.0
61 TraesCS4A01G174900 chr3D 84.843 508 31 11 4517 5002 12953898 12953415 3.000000e-128 470.0
62 TraesCS4A01G174900 chr3D 86.819 349 40 6 3510 3854 380263568 380263914 1.120000e-102 385.0
63 TraesCS4A01G174900 chr3D 86.286 350 41 7 3510 3854 141370451 141370798 2.420000e-99 374.0
64 TraesCS4A01G174900 chr3D 85.479 365 46 7 3510 3869 610797402 610797040 2.420000e-99 374.0
65 TraesCS4A01G174900 chr3D 86.667 180 23 1 3218 3397 269962591 269962769 1.560000e-46 198.0
66 TraesCS4A01G174900 chr7D 93.515 771 31 9 2943 3705 474070719 474069960 0.000000e+00 1129.0
67 TraesCS4A01G174900 chr7D 93.692 650 39 1 1219 1866 537258764 537258115 0.000000e+00 972.0
68 TraesCS4A01G174900 chr7D 91.171 589 42 2 2343 2931 366737067 366737645 0.000000e+00 791.0
69 TraesCS4A01G174900 chr7D 95.991 449 18 0 2495 2943 474072956 474072508 0.000000e+00 730.0
70 TraesCS4A01G174900 chr7D 93.023 301 18 2 3740 4040 474069961 474069664 3.040000e-118 436.0
71 TraesCS4A01G174900 chr7D 85.753 365 45 7 3510 3869 472890669 472890307 5.200000e-101 379.0
72 TraesCS4A01G174900 chr7D 86.119 353 42 7 3507 3854 619217925 619218275 2.420000e-99 374.0
73 TraesCS4A01G174900 chr5B 90.662 846 74 5 533 1374 210332053 210332897 0.000000e+00 1120.0
74 TraesCS4A01G174900 chr5B 93.590 546 16 9 1 534 610736140 610736678 0.000000e+00 797.0
75 TraesCS4A01G174900 chr5B 86.507 667 68 13 5105 5761 86077957 86077303 0.000000e+00 713.0
76 TraesCS4A01G174900 chr5B 93.689 412 26 0 1932 2343 610737350 610736939 1.010000e-172 617.0
77 TraesCS4A01G174900 chr5B 94.643 280 14 1 255 534 443700076 443699798 3.940000e-117 433.0
78 TraesCS4A01G174900 chr5B 93.564 202 13 0 996 1197 610746775 610746574 1.160000e-77 302.0
79 TraesCS4A01G174900 chr5B 90.299 134 8 4 6328 6458 220845246 220845115 3.410000e-38 171.0
80 TraesCS4A01G174900 chr7B 94.150 547 18 8 1 534 155542553 155543098 0.000000e+00 821.0
81 TraesCS4A01G174900 chr7B 87.946 589 71 0 609 1197 239790943 239791531 0.000000e+00 695.0
82 TraesCS4A01G174900 chr7B 95.388 412 19 0 1932 2343 155543768 155543357 0.000000e+00 656.0
83 TraesCS4A01G174900 chr7B 79.228 674 94 25 3218 3854 486719997 486720661 1.830000e-115 427.0
84 TraesCS4A01G174900 chr7B 94.656 262 13 1 1 261 749648989 749648728 8.580000e-109 405.0
85 TraesCS4A01G174900 chr7B 93.916 263 14 2 1 261 122018720 122018982 5.170000e-106 396.0
86 TraesCS4A01G174900 chr7B 93.583 187 12 0 1011 1197 155544580 155544394 5.430000e-71 279.0
87 TraesCS4A01G174900 chr7B 75.988 329 50 15 2888 3190 3138617 3138942 7.430000e-30 143.0
88 TraesCS4A01G174900 chr4D 91.002 589 42 3 2343 2931 58644313 58644890 0.000000e+00 784.0
89 TraesCS4A01G174900 chr4D 86.286 350 41 7 3510 3854 24103935 24104282 2.420000e-99 374.0
90 TraesCS4A01G174900 chr4D 74.908 271 40 10 2884 3141 328890964 328891219 1.630000e-16 99.0
91 TraesCS4A01G174900 chr2A 90.339 590 46 3 2343 2931 443988273 443987694 0.000000e+00 763.0
92 TraesCS4A01G174900 chr2A 93.224 487 30 3 5974 6458 461740731 461740246 0.000000e+00 713.0
93 TraesCS4A01G174900 chr2A 92.647 340 23 2 5010 5349 331206793 331206456 8.280000e-134 488.0
94 TraesCS4A01G174900 chr2A 91.570 344 26 3 5548 5890 461741071 461740730 8.340000e-129 472.0
95 TraesCS4A01G174900 chr2A 95.146 103 4 1 3940 4042 82183805 82183704 2.050000e-35 161.0
96 TraesCS4A01G174900 chr2A 76.852 216 29 12 3002 3196 82191008 82190793 1.260000e-17 102.0
97 TraesCS4A01G174900 chr2B 96.053 380 14 1 1 379 596615793 596615414 1.010000e-172 617.0
98 TraesCS4A01G174900 chr2B 95.000 380 18 1 1 379 376457378 376457757 4.750000e-166 595.0
99 TraesCS4A01G174900 chr2B 93.950 281 16 1 254 534 227811206 227810927 2.370000e-114 424.0
100 TraesCS4A01G174900 chr2B 84.127 126 19 1 533 657 376460472 376460347 3.480000e-23 121.0
101 TraesCS4A01G174900 chr6A 89.313 393 29 8 5820 6203 546601391 546601003 1.390000e-131 481.0
102 TraesCS4A01G174900 chr6A 82.096 458 62 9 2888 3331 590954306 590954757 2.420000e-99 374.0
103 TraesCS4A01G174900 chr6A 93.966 116 3 2 6217 6328 546600939 546600824 9.480000e-39 172.0
104 TraesCS4A01G174900 chr6A 90.517 116 10 1 6328 6442 493535608 493535723 1.230000e-32 152.0
105 TraesCS4A01G174900 chr1B 91.618 346 27 2 5009 5354 256539986 256539643 1.790000e-130 477.0
106 TraesCS4A01G174900 chr1B 91.167 317 17 5 6523 6838 163080648 163080342 3.070000e-113 420.0
107 TraesCS4A01G174900 chr1B 84.127 189 17 10 6059 6235 732296 732109 3.410000e-38 171.0
108 TraesCS4A01G174900 chr6D 84.848 462 49 10 2882 3329 441742510 441742964 5.060000e-121 446.0
109 TraesCS4A01G174900 chr6D 84.314 459 47 17 5784 6221 400653083 400652629 6.590000e-115 425.0
110 TraesCS4A01G174900 chr6D 88.235 119 14 0 6217 6335 400652592 400652474 7.430000e-30 143.0
111 TraesCS4A01G174900 chr6D 94.118 51 2 1 4005 4055 291692013 291692062 7.640000e-10 76.8


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 TraesCS4A01G174900 chr4A 445279334 445286439 7105 True 13123.0 13123 100.000000 1 7106 1 chr4A.!!$R2 7105
1 TraesCS4A01G174900 chr4A 110272346 110275401 3055 True 4955.0 4955 95.875000 4034 7106 1 chr4A.!!$R1 3072
2 TraesCS4A01G174900 chr4A 167812423 167815060 2637 False 3507.0 3507 90.967000 4501 7106 1 chr4A.!!$F1 2605
3 TraesCS4A01G174900 chr4A 380730240 380731321 1081 False 1648.0 1648 94.280000 2875 3949 1 chr4A.!!$F2 1074
4 TraesCS4A01G174900 chr4A 637402893 637403539 646 True 968.0 968 93.683000 1219 1866 1 chr4A.!!$R4 647
5 TraesCS4A01G174900 chr4A 637488317 637488963 646 True 963.0 963 93.529000 1219 1866 1 chr4A.!!$R5 647
6 TraesCS4A01G174900 chr4A 637296679 637297722 1043 True 789.0 972 95.031500 1219 2226 2 chr4A.!!$R6 1007
7 TraesCS4A01G174900 chr4A 637611319 637612359 1040 True 784.5 974 94.757000 1219 2226 2 chr4A.!!$R8 1007
8 TraesCS4A01G174900 chr4A 637353826 637354869 1043 True 782.5 959 94.810500 1219 2226 2 chr4A.!!$R7 1007
9 TraesCS4A01G174900 chr1A 63973290 63976324 3034 True 2544.5 4719 91.814000 4033 7106 2 chr1A.!!$R2 3073
10 TraesCS4A01G174900 chr1A 19701094 19702016 922 False 1362.0 1362 93.290000 644 1567 1 chr1A.!!$F1 923
11 TraesCS4A01G174900 chr1A 108380364 108381012 648 False 959.0 959 93.374000 1219 1866 1 chr1A.!!$F2 647
12 TraesCS4A01G174900 chr1A 115268784 115269459 675 True 632.0 632 84.257000 5105 5761 1 chr1A.!!$R1 656
13 TraesCS4A01G174900 chr5A 407306866 407309571 2705 False 4698.0 4698 98.006000 4400 7106 1 chr5A.!!$F2 2706
14 TraesCS4A01G174900 chr5A 568800965 568801543 578 False 774.0 774 90.662000 2343 2931 1 chr5A.!!$F4 588
15 TraesCS4A01G174900 chr2D 41463431 41465132 1701 False 2545.0 2545 93.805000 2343 4033 1 chr2D.!!$F2 1690
16 TraesCS4A01G174900 chr2D 5498919 5499819 900 True 1375.0 1375 94.562000 4814 5695 1 chr2D.!!$R1 881
17 TraesCS4A01G174900 chr2D 5462897 5463427 530 False 784.0 784 93.409000 6580 7106 1 chr2D.!!$F1 526
18 TraesCS4A01G174900 chr3B 74019800 74021201 1401 False 1993.0 1993 92.582000 578 1958 1 chr3B.!!$F1 1380
19 TraesCS4A01G174900 chr3B 241262274 241263386 1112 True 1402.0 1402 89.529000 1219 2343 1 chr3B.!!$R1 1124
20 TraesCS4A01G174900 chr3B 311764233 311765076 843 True 1186.0 1186 92.071000 533 1374 1 chr3B.!!$R2 841
21 TraesCS4A01G174900 chr7A 53340693 53342871 2178 False 1179.5 1832 93.985500 5538 7106 2 chr7A.!!$F3 1568
22 TraesCS4A01G174900 chr7A 369478139 369478811 672 False 496.0 496 80.876000 3206 3855 1 chr7A.!!$F1 649
23 TraesCS4A01G174900 chr7A 700604017 700604678 661 False 394.0 394 78.390000 3218 3852 1 chr7A.!!$F2 634
24 TraesCS4A01G174900 chr6B 267749426 267750696 1270 False 1572.0 1572 89.164000 5820 7090 1 chr6B.!!$F1 1270
25 TraesCS4A01G174900 chr6B 257299821 257300357 536 True 832.0 832 94.600000 1261 1797 1 chr6B.!!$R1 536
26 TraesCS4A01G174900 chr4B 199719510 199720622 1112 False 1452.0 1452 90.306000 1219 2343 1 chr4B.!!$F1 1124
27 TraesCS4A01G174900 chr4B 341926903 341927700 797 True 1042.0 1042 90.547000 1558 2343 1 chr4B.!!$R2 785
28 TraesCS4A01G174900 chr4B 300019835 300020500 665 False 835.0 835 89.381000 6437 7106 1 chr4B.!!$F3 669
29 TraesCS4A01G174900 chr4B 341241098 341241643 545 False 798.0 798 93.419000 1 534 1 chr4B.!!$F4 533
30 TraesCS4A01G174900 chr4B 341241901 341243147 1246 True 469.5 634 94.430500 996 2343 2 chr4B.!!$R3 1347
31 TraesCS4A01G174900 chr3D 562970688 562971674 986 True 1439.0 1439 93.030000 533 1517 1 chr3D.!!$R2 984
32 TraesCS4A01G174900 chr7D 537258115 537258764 649 True 972.0 972 93.692000 1219 1866 1 chr7D.!!$R2 647
33 TraesCS4A01G174900 chr7D 366737067 366737645 578 False 791.0 791 91.171000 2343 2931 1 chr7D.!!$F1 588
34 TraesCS4A01G174900 chr7D 474069664 474072956 3292 True 765.0 1129 94.176333 2495 4040 3 chr7D.!!$R3 1545
35 TraesCS4A01G174900 chr5B 210332053 210332897 844 False 1120.0 1120 90.662000 533 1374 1 chr5B.!!$F1 841
36 TraesCS4A01G174900 chr5B 610736140 610736678 538 False 797.0 797 93.590000 1 534 1 chr5B.!!$F2 533
37 TraesCS4A01G174900 chr5B 86077303 86077957 654 True 713.0 713 86.507000 5105 5761 1 chr5B.!!$R1 656
38 TraesCS4A01G174900 chr7B 155542553 155543098 545 False 821.0 821 94.150000 1 534 1 chr7B.!!$F3 533
39 TraesCS4A01G174900 chr7B 239790943 239791531 588 False 695.0 695 87.946000 609 1197 1 chr7B.!!$F4 588
40 TraesCS4A01G174900 chr7B 155543357 155544580 1223 True 467.5 656 94.485500 1011 2343 2 chr7B.!!$R2 1332
41 TraesCS4A01G174900 chr7B 486719997 486720661 664 False 427.0 427 79.228000 3218 3854 1 chr7B.!!$F5 636
42 TraesCS4A01G174900 chr4D 58644313 58644890 577 False 784.0 784 91.002000 2343 2931 1 chr4D.!!$F2 588
43 TraesCS4A01G174900 chr2A 443987694 443988273 579 True 763.0 763 90.339000 2343 2931 1 chr2A.!!$R4 588
44 TraesCS4A01G174900 chr2A 461740246 461741071 825 True 592.5 713 92.397000 5548 6458 2 chr2A.!!$R5 910
45 TraesCS4A01G174900 chr6A 546600824 546601391 567 True 326.5 481 91.639500 5820 6328 2 chr6A.!!$R1 508
46 TraesCS4A01G174900 chr6D 400652474 400653083 609 True 284.0 425 86.274500 5784 6335 2 chr6D.!!$R1 551

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
866 886 2.272471 CGAGGGAAAAGGGGAGCC 59.728 66.667 0.00 0.00 0.00 4.70 F
1156 1176 0.469705 TTCCTGCTGGCCACACAATT 60.470 50.000 0.00 0.00 0.00 2.32 F
1176 1196 0.868406 CTTGAACTGACGGCCTTGAC 59.132 55.000 0.00 0.00 0.00 3.18 F
2463 3010 0.035056 CTTCTACAGGCAACAGGGGG 60.035 60.000 0.00 0.00 41.41 5.40 F
3051 5400 0.179081 CGGCACCTCTAAGGGCTTAC 60.179 60.000 0.00 0.00 40.58 2.34 F
3797 6196 0.450184 GGTCTCTGAGCTCGTCTCAC 59.550 60.000 9.64 1.78 46.34 3.51 F
4406 6839 2.186903 CCTACAACGCCGCCATCT 59.813 61.111 0.00 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2919 0.105760 AGAGCCATCGATGTCCTCCT 60.106 55.000 26.69 17.23 0.00 3.69 R
2428 2975 1.552337 AGAAGATGAGGCGAGCTTTGA 59.448 47.619 0.00 0.00 0.00 2.69 R
2905 3460 2.281761 CAGGCCAGCCACGAAGTT 60.282 61.111 12.03 0.00 41.61 2.66 R
3268 5619 0.234625 TGCTTGCGTCAATCGAACAC 59.765 50.000 0.00 0.00 42.86 3.32 R
4107 6511 0.901124 GATCGCCCCTATGCTGATCT 59.099 55.000 0.00 0.00 37.81 2.75 R
5182 7637 5.357314 ACATGGCATTGAGATTTCAGAAGAG 59.643 40.000 0.00 0.00 34.15 2.85 R
6663 9882 0.663153 GAGTGGACAAACACACCAGC 59.337 55.000 0.00 0.00 43.72 4.85 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
143 144 6.349611 CCCTCCAAACTACAAGAACATGATTG 60.350 42.308 0.00 4.12 0.00 2.67
213 226 9.859427 TTTATAAGCAAACTGATGGAAATCTTG 57.141 29.630 0.00 0.00 0.00 3.02
216 229 4.828939 AGCAAACTGATGGAAATCTTGACA 59.171 37.500 0.00 0.00 0.00 3.58
337 350 8.477419 TGGAAGGTGAACTCATAATTTTTCTT 57.523 30.769 0.00 0.00 0.00 2.52
463 477 4.634004 GTCGATACATGTCCAACCATTTCA 59.366 41.667 0.00 0.00 0.00 2.69
633 653 3.579302 CCCCTTCCCCAGCACACA 61.579 66.667 0.00 0.00 0.00 3.72
866 886 2.272471 CGAGGGAAAAGGGGAGCC 59.728 66.667 0.00 0.00 0.00 4.70
935 955 3.321648 ATGTCCCGAGCACCAGCA 61.322 61.111 0.00 0.00 45.49 4.41
994 1014 2.362369 ATCCACCACTCGAGCAGGG 61.362 63.158 23.68 19.37 0.00 4.45
1020 1040 2.690778 GGTGACAACATCCAGCGGC 61.691 63.158 0.00 0.00 0.00 6.53
1025 1045 4.473520 AACATCCAGCGGCCCTCG 62.474 66.667 0.00 0.00 42.76 4.63
1057 1077 2.989639 CCCTGCCTTCATCACCGA 59.010 61.111 0.00 0.00 0.00 4.69
1121 1141 1.604604 TGCCTGTACAAAGTTCAGCC 58.395 50.000 0.00 0.00 31.20 4.85
1156 1176 0.469705 TTCCTGCTGGCCACACAATT 60.470 50.000 0.00 0.00 0.00 2.32
1176 1196 0.868406 CTTGAACTGACGGCCTTGAC 59.132 55.000 0.00 0.00 0.00 3.18
1253 1273 2.764010 TGCTAGCCGGATTCTTGTTCTA 59.236 45.455 13.29 0.00 0.00 2.10
1292 1312 7.384660 TGGTTATTTGAACTTTAATTGCAGCTG 59.615 33.333 10.11 10.11 0.00 4.24
1416 1442 5.157940 ACAAGACTGGACTCGTACTACTA 57.842 43.478 0.00 0.00 0.00 1.82
1645 2156 2.568623 ACTGTGGATGGGTGAGAAAC 57.431 50.000 0.00 0.00 0.00 2.78
1672 2183 3.138304 TCTTGTACAGTTGTGCCATGAC 58.862 45.455 0.00 0.00 0.00 3.06
1733 2244 2.116533 CCTGCTTGCATCGCCATCA 61.117 57.895 6.10 0.00 0.00 3.07
1783 2294 2.639327 GCCATTCACAGCCACCACC 61.639 63.158 0.00 0.00 0.00 4.61
1787 2298 2.017668 ATTCACAGCCACCACCCCAA 62.018 55.000 0.00 0.00 0.00 4.12
1810 2321 3.360423 TTCAACGCCACCACCCCAA 62.360 57.895 0.00 0.00 0.00 4.12
1950 2497 5.940192 TTTTACAGCAAGTCCATGTAGTG 57.060 39.130 0.00 0.00 31.50 2.74
2102 2649 5.797051 TCTCTCATGATGTGATGTTGTTGA 58.203 37.500 0.00 0.00 35.97 3.18
2108 2655 6.882678 TCATGATGTGATGTTGTTGATCTCTT 59.117 34.615 0.00 0.00 0.00 2.85
2129 2676 4.584638 TGTAGCTAAAACATGGTCCCAT 57.415 40.909 0.00 0.00 37.08 4.00
2162 2709 7.716998 CCTATAGCTGACCACAATCTGTAATTT 59.283 37.037 0.00 0.00 0.00 1.82
2269 2816 7.672660 ACAATTATTACATGGATGATGGATGCT 59.327 33.333 0.00 0.00 36.23 3.79
2372 2919 2.742116 GCCCCAGCCGGATACAAGA 61.742 63.158 5.05 0.00 0.00 3.02
2381 2928 2.320781 CCGGATACAAGAGGAGGACAT 58.679 52.381 0.00 0.00 0.00 3.06
2428 2975 0.251787 GACTTGAATGCCCCAACCCT 60.252 55.000 0.00 0.00 0.00 4.34
2463 3010 0.035056 CTTCTACAGGCAACAGGGGG 60.035 60.000 0.00 0.00 41.41 5.40
2464 3011 2.044946 CTACAGGCAACAGGGGGC 60.045 66.667 0.00 0.00 41.41 5.80
2465 3012 3.976701 CTACAGGCAACAGGGGGCG 62.977 68.421 0.00 0.00 41.41 6.13
2469 3016 4.660938 GGCAACAGGGGGCGTCTT 62.661 66.667 0.00 0.00 0.00 3.01
2557 3110 0.460311 CTCCTAGCGTTGGATCCGTT 59.540 55.000 7.39 0.00 32.56 4.44
2639 3192 0.694771 AAGAAGGTGCAGAGCCATCA 59.305 50.000 0.00 0.00 0.00 3.07
2643 3196 1.279496 AGGTGCAGAGCCATCAACTA 58.721 50.000 0.00 0.00 0.00 2.24
2675 3229 3.007182 TGGTTAAAGAAGGTACAGGGTCG 59.993 47.826 0.00 0.00 0.00 4.79
2774 3329 2.437897 CCAAGCTGGGTGAAGCCT 59.562 61.111 0.00 0.00 44.68 4.58
2785 3340 0.877743 GTGAAGCCTTCAAGGTGAGC 59.122 55.000 9.08 0.00 42.15 4.26
2799 3354 2.012673 GGTGAGCTGATCGATTGCTTT 58.987 47.619 21.94 6.95 37.16 3.51
2905 3460 0.391130 GCTCACAGCCACCATCGTAA 60.391 55.000 0.00 0.00 34.48 3.18
3051 5400 0.179081 CGGCACCTCTAAGGGCTTAC 60.179 60.000 0.00 0.00 40.58 2.34
3168 5519 7.412891 CGAGATGACACAGTTATGCAAAATGTA 60.413 37.037 12.14 1.90 0.00 2.29
3204 5555 5.045942 TGAGACATTTACATTGGCAGGTCTA 60.046 40.000 0.00 0.00 34.76 2.59
3276 5627 7.387119 TGTACTACATTGTAGAGTGTTCGAT 57.613 36.000 26.58 6.88 0.00 3.59
3420 5785 4.021981 GGCCAATTGCTCTAACTCAACTTT 60.022 41.667 0.00 0.00 40.92 2.66
3499 5887 0.954938 TATGCTTCGCTGCTTGCACA 60.955 50.000 11.83 0.24 43.06 4.57
3505 5898 2.827051 CGCTGCTTGCACACACTGT 61.827 57.895 0.00 0.00 43.06 3.55
3531 5925 8.845413 AATTCAAGGCAGATCTAGATTACATC 57.155 34.615 6.70 0.00 0.00 3.06
3532 5926 6.352016 TCAAGGCAGATCTAGATTACATCC 57.648 41.667 6.70 4.77 0.00 3.51
3785 6184 9.626045 GGTTTTTAGAATAAATTGTGGTCTCTG 57.374 33.333 0.00 0.00 0.00 3.35
3797 6196 0.450184 GGTCTCTGAGCTCGTCTCAC 59.550 60.000 9.64 1.78 46.34 3.51
4002 6405 8.173542 ACGCCGAAATTTTATTATCCCTTATT 57.826 30.769 0.00 0.00 0.00 1.40
4003 6406 8.635328 ACGCCGAAATTTTATTATCCCTTATTT 58.365 29.630 0.00 0.00 0.00 1.40
4084 6488 2.300152 GCATCACTATTCTGATCCCGGA 59.700 50.000 0.73 0.00 0.00 5.14
4107 6511 9.056005 CGGAATCAGAATAACTATTTGGATCAA 57.944 33.333 0.00 0.00 0.00 2.57
4164 6568 3.075884 CCCCGATCGGTAAAACAAAAGA 58.924 45.455 31.22 0.00 0.00 2.52
4274 6678 4.888325 CTCCCTCCCTGCCCCGAT 62.888 72.222 0.00 0.00 0.00 4.18
4277 6681 4.181010 CCTCCCTGCCCCGATGTG 62.181 72.222 0.00 0.00 0.00 3.21
4278 6682 4.864334 CTCCCTGCCCCGATGTGC 62.864 72.222 0.00 0.00 0.00 4.57
4280 6684 4.511246 CCCTGCCCCGATGTGCAT 62.511 66.667 0.00 0.00 36.79 3.96
4281 6685 2.903855 CCTGCCCCGATGTGCATC 60.904 66.667 0.00 2.26 36.79 3.91
4406 6839 2.186903 CCTACAACGCCGCCATCT 59.813 61.111 0.00 0.00 0.00 2.90
6537 9730 4.481930 TTTGAACAAGAGTTATGTGGCG 57.518 40.909 0.00 0.00 38.30 5.69
6663 9882 4.520492 AGTTGTATCTCCAGGTGCAAAAAG 59.480 41.667 0.00 0.00 0.00 2.27
6934 10166 8.778358 ACTCAAAATAACAGAGCAGTCTAAAAG 58.222 33.333 0.00 0.00 32.71 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 8.607713 TGGAGGGAAAACATAATAAGTTCTACA 58.392 33.333 0.00 0.00 0.00 2.74
196 209 5.278660 GCACTGTCAAGATTTCCATCAGTTT 60.279 40.000 0.00 0.00 33.35 2.66
213 226 5.796350 ATAAAATACCGAAGTGCACTGTC 57.204 39.130 22.49 17.81 0.00 3.51
216 229 6.128007 CCTTGAATAAAATACCGAAGTGCACT 60.128 38.462 15.25 15.25 0.00 4.40
296 309 9.802039 TTCACCTTCCATAAAGTTTGTAAGTAT 57.198 29.630 0.00 0.00 32.69 2.12
463 477 4.964593 ACATTTGCTTGCTTTCCAGAAAT 58.035 34.783 0.00 0.00 0.00 2.17
524 539 1.305930 GGGATCGGGTTGTGCTTCAC 61.306 60.000 0.00 0.00 34.56 3.18
620 640 2.350895 CCGATGTGTGCTGGGGAA 59.649 61.111 0.00 0.00 0.00 3.97
765 785 1.421485 CAGTTGTGCGCGAAGATCC 59.579 57.895 12.10 0.00 0.00 3.36
767 787 2.680913 GCCAGTTGTGCGCGAAGAT 61.681 57.895 12.10 0.00 0.00 2.40
847 867 2.603652 GCTCCCCTTTTCCCTCGGT 61.604 63.158 0.00 0.00 0.00 4.69
866 886 2.110967 CCATCAACAGGGAGCAGCG 61.111 63.158 0.00 0.00 0.00 5.18
963 983 1.971167 GTGGATGGCGCTGGTTCAA 60.971 57.895 7.64 0.00 0.00 2.69
994 1014 1.067635 GGATGTTGTCACCATTGCCAC 60.068 52.381 0.00 0.00 0.00 5.01
1020 1040 3.073735 AGCAGAGGCAGACGAGGG 61.074 66.667 0.00 0.00 44.61 4.30
1025 1045 4.828925 GGGCGAGCAGAGGCAGAC 62.829 72.222 0.00 0.00 44.61 3.51
1057 1077 0.602562 CATGGATTTGCACGGTTGGT 59.397 50.000 0.00 0.00 0.00 3.67
1121 1141 3.924686 GCAGGAAATGTGCTTGAATCTTG 59.075 43.478 0.00 0.00 37.96 3.02
1156 1176 0.756294 TCAAGGCCGTCAGTTCAAGA 59.244 50.000 0.00 0.00 0.00 3.02
1176 1196 2.703409 GCCATCAGCACGCGTAAG 59.297 61.111 13.44 0.50 42.97 2.34
1253 1273 3.306472 AATAACCACGGCACCCATAAT 57.694 42.857 0.00 0.00 0.00 1.28
1292 1312 3.247442 TGTACGCACACACTGTAATAGC 58.753 45.455 0.00 0.00 0.00 2.97
1672 2183 2.125269 GTCGGGGTCGTCCAATGG 60.125 66.667 0.04 0.00 37.22 3.16
1702 2213 3.394836 GCAGGAGGTCGGGAAGCT 61.395 66.667 0.00 0.00 38.79 3.74
1832 2343 2.041922 CGAGGGGTGGGATCCAGA 60.042 66.667 15.23 0.00 32.34 3.86
1976 2523 7.497249 CCAGGATTTAAATGAACTCTCACTAGG 59.503 40.741 5.17 0.00 33.30 3.02
2102 2649 6.116126 GGACCATGTTTTAGCTACAAGAGAT 58.884 40.000 0.00 0.00 0.00 2.75
2108 2655 4.584638 ATGGGACCATGTTTTAGCTACA 57.415 40.909 2.41 0.00 35.03 2.74
2129 2676 6.553953 TTGTGGTCAGCTATAGGATGTTTA 57.446 37.500 1.04 0.00 32.48 2.01
2162 2709 4.787551 ACCAGGACAACATGTAGTTTCAA 58.212 39.130 0.00 0.00 38.74 2.69
2251 2798 4.564199 GCTACAGCATCCATCATCCATGTA 60.564 45.833 0.00 0.00 41.59 2.29
2269 2816 6.588756 CCGTTACTTTCATCTAGTTTGCTACA 59.411 38.462 0.00 0.00 0.00 2.74
2372 2919 0.105760 AGAGCCATCGATGTCCTCCT 60.106 55.000 26.69 17.23 0.00 3.69
2428 2975 1.552337 AGAAGATGAGGCGAGCTTTGA 59.448 47.619 0.00 0.00 0.00 2.69
2463 3010 4.821589 CGCCAGGAGGGAAGACGC 62.822 72.222 0.00 0.00 40.01 5.19
2464 3011 4.821589 GCGCCAGGAGGGAAGACG 62.822 72.222 0.00 0.00 40.01 4.18
2465 3012 4.475135 GGCGCCAGGAGGGAAGAC 62.475 72.222 24.80 0.00 40.01 3.01
2514 3067 2.682136 TTGGCCAGATCCCGACGA 60.682 61.111 5.11 0.00 0.00 4.20
2643 3196 8.973182 TGTACCTTCTTTAACCAAACAAAATCT 58.027 29.630 0.00 0.00 0.00 2.40
2774 3329 3.264947 CAATCGATCAGCTCACCTTGAA 58.735 45.455 0.00 0.00 0.00 2.69
2785 3340 4.083110 AGTGGACAAAAAGCAATCGATCAG 60.083 41.667 0.00 0.00 0.00 2.90
2799 3354 4.447138 AAATAGGGTGACAGTGGACAAA 57.553 40.909 0.00 0.00 0.00 2.83
2905 3460 2.281761 CAGGCCAGCCACGAAGTT 60.282 61.111 12.03 0.00 41.61 2.66
3268 5619 0.234625 TGCTTGCGTCAATCGAACAC 59.765 50.000 0.00 0.00 42.86 3.32
3276 5627 1.300971 GCCATCTCTGCTTGCGTCAA 61.301 55.000 0.00 0.00 0.00 3.18
3420 5785 4.018960 ACTCTACAGGAAAGTACCGACCTA 60.019 45.833 2.72 0.00 34.73 3.08
3499 5887 5.171339 AGATCTGCCTTGAATTACAGTGT 57.829 39.130 0.00 0.00 0.00 3.55
3505 5898 9.935241 GATGTAATCTAGATCTGCCTTGAATTA 57.065 33.333 5.51 0.00 41.17 1.40
3531 5925 4.398319 CAATATAGGTGGGTTGCTTAGGG 58.602 47.826 0.00 0.00 0.00 3.53
3532 5926 4.141251 ACCAATATAGGTGGGTTGCTTAGG 60.141 45.833 9.47 0.00 41.30 2.69
3662 6057 9.311916 TGGAATTTTCATTTTAGACACAACAAG 57.688 29.630 0.00 0.00 0.00 3.16
3785 6184 1.400846 TGGATTACGTGAGACGAGCTC 59.599 52.381 2.73 2.73 46.05 4.09
3898 6301 9.051679 AGGCCACTTTGTTAATTTAAATCAAAC 57.948 29.630 5.01 14.84 0.00 2.93
3940 6343 9.722056 CCATTGAGAACAAAATAACTATAGTGC 57.278 33.333 6.06 0.00 39.54 4.40
4044 6447 9.013229 AGTGATGCTCTCTCTTTATGTATAGAG 57.987 37.037 0.00 0.00 39.38 2.43
4045 6448 8.932434 AGTGATGCTCTCTCTTTATGTATAGA 57.068 34.615 0.00 0.00 0.00 1.98
4049 6452 9.360901 AGAATAGTGATGCTCTCTCTTTATGTA 57.639 33.333 0.00 0.00 0.00 2.29
4050 6453 8.143193 CAGAATAGTGATGCTCTCTCTTTATGT 58.857 37.037 0.00 0.00 0.00 2.29
4051 6454 8.358895 TCAGAATAGTGATGCTCTCTCTTTATG 58.641 37.037 0.00 0.00 0.00 1.90
4052 6455 8.476064 TCAGAATAGTGATGCTCTCTCTTTAT 57.524 34.615 0.00 0.00 0.00 1.40
4053 6456 7.888250 TCAGAATAGTGATGCTCTCTCTTTA 57.112 36.000 0.00 0.00 0.00 1.85
4054 6457 6.788598 TCAGAATAGTGATGCTCTCTCTTT 57.211 37.500 0.00 0.00 0.00 2.52
4064 6468 4.607293 TTCCGGGATCAGAATAGTGATG 57.393 45.455 0.00 0.00 37.29 3.07
4066 6470 4.223144 TGATTCCGGGATCAGAATAGTGA 58.777 43.478 22.20 0.00 32.91 3.41
4107 6511 0.901124 GATCGCCCCTATGCTGATCT 59.099 55.000 0.00 0.00 37.81 2.75
4257 6661 4.888325 ATCGGGGCAGGGAGGGAG 62.888 72.222 0.00 0.00 0.00 4.30
4260 6664 4.181010 CACATCGGGGCAGGGAGG 62.181 72.222 0.00 0.00 0.00 4.30
4261 6665 4.864334 GCACATCGGGGCAGGGAG 62.864 72.222 0.00 0.00 0.00 4.30
4263 6667 4.511246 ATGCACATCGGGGCAGGG 62.511 66.667 0.00 0.00 44.24 4.45
4264 6668 2.903855 GATGCACATCGGGGCAGG 60.904 66.667 0.00 0.00 44.24 4.85
5182 7637 5.357314 ACATGGCATTGAGATTTCAGAAGAG 59.643 40.000 0.00 0.00 34.15 2.85
6663 9882 0.663153 GAGTGGACAAACACACCAGC 59.337 55.000 0.00 0.00 43.72 4.85


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

AutoCloner maintained by Alex Coulton.