Multiple sequence alignment - TraesCS3A01G069700

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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 TraesCS3A01G069700 chr3A 100.000 9724 0 0 1 9724 41999604 41989881 0.000000e+00 17917.0
1 TraesCS3A01G069700 chr3A 95.026 945 38 4 1279 2216 9074312 9075254 0.000000e+00 1476.0
2 TraesCS3A01G069700 chr3A 77.758 562 95 27 5659 6203 657276547 657275999 1.580000e-82 318.0
3 TraesCS3A01G069700 chr3A 81.388 317 39 9 9221 9530 701226659 701226962 3.510000e-59 241.0
4 TraesCS3A01G069700 chr6B 99.498 3188 16 0 2228 5415 530995409 530992222 0.000000e+00 5799.0
5 TraesCS3A01G069700 chr6B 98.614 938 9 2 1283 2216 530996633 530995696 0.000000e+00 1657.0
6 TraesCS3A01G069700 chr6B 80.899 534 89 12 5654 6179 45547007 45546479 9.090000e-110 409.0
7 TraesCS3A01G069700 chr3B 99.373 3188 20 0 2228 5415 743790623 743793810 0.000000e+00 5777.0
8 TraesCS3A01G069700 chr3B 93.875 2253 78 20 6555 8792 52771117 52773324 0.000000e+00 3341.0
9 TraesCS3A01G069700 chr3B 96.277 1370 44 4 7425 8790 51815572 51814206 0.000000e+00 2241.0
10 TraesCS3A01G069700 chr3B 98.727 943 8 3 1277 2216 743789395 743790336 0.000000e+00 1672.0
11 TraesCS3A01G069700 chr3B 98.932 936 7 2 1284 2216 123120731 123119796 0.000000e+00 1670.0
12 TraesCS3A01G069700 chr3B 94.660 1030 43 8 6376 7397 51816594 51815569 0.000000e+00 1587.0
13 TraesCS3A01G069700 chr3B 87.576 982 94 10 5416 6383 51817731 51816764 0.000000e+00 1112.0
14 TraesCS3A01G069700 chr3B 89.586 749 66 11 1 741 52769763 52770507 0.000000e+00 941.0
15 TraesCS3A01G069700 chr3B 91.000 700 42 12 54 746 51819113 51818428 0.000000e+00 924.0
16 TraesCS3A01G069700 chr3B 90.698 473 21 2 834 1283 52770528 52771000 8.350000e-170 608.0
17 TraesCS3A01G069700 chr3B 88.663 344 21 9 957 1282 51818068 51817725 4.230000e-108 403.0
18 TraesCS3A01G069700 chr3B 82.103 447 69 10 5659 6097 531792409 531791966 1.190000e-98 372.0
19 TraesCS3A01G069700 chr3B 81.410 312 36 11 9227 9530 49410960 49410663 1.630000e-57 235.0
20 TraesCS3A01G069700 chr3B 86.400 125 6 4 5415 5528 52770992 52771116 1.030000e-24 126.0
21 TraesCS3A01G069700 chr3B 96.970 33 0 1 6607 6639 52771117 52771148 5.000000e-03 54.7
22 TraesCS3A01G069700 chr2A 96.861 3186 97 2 2228 5413 737503056 737499874 0.000000e+00 5326.0
23 TraesCS3A01G069700 chr2A 96.487 3188 111 1 2228 5415 39174341 39171155 0.000000e+00 5265.0
24 TraesCS3A01G069700 chr2A 95.358 3188 148 0 2228 5415 575065632 575068819 0.000000e+00 5068.0
25 TraesCS3A01G069700 chr2A 95.000 940 38 3 1285 2216 737504281 737503343 0.000000e+00 1467.0
26 TraesCS3A01G069700 chr2A 81.862 419 52 7 9129 9530 57807381 57806970 2.020000e-86 331.0
27 TraesCS3A01G069700 chr5A 96.359 3186 116 0 2228 5413 603601433 603598248 0.000000e+00 5241.0
28 TraesCS3A01G069700 chr5A 94.899 941 39 4 1283 2216 380625747 380624809 0.000000e+00 1463.0
29 TraesCS3A01G069700 chr5A 91.875 160 13 0 9565 9724 32196575 32196416 3.530000e-54 224.0
30 TraesCS3A01G069700 chr5A 86.577 149 17 1 9565 9713 536973316 536973461 2.810000e-35 161.0
31 TraesCS3A01G069700 chr5A 80.612 98 12 5 6465 6555 53451884 53451787 1.750000e-07 69.4
32 TraesCS3A01G069700 chr1A 96.236 3188 119 1 2228 5415 48968799 48971985 0.000000e+00 5221.0
33 TraesCS3A01G069700 chr1A 95.314 939 35 3 1286 2216 569143967 569143030 0.000000e+00 1482.0
34 TraesCS3A01G069700 chr1A 77.757 535 106 11 5653 6180 494852474 494853002 5.670000e-82 316.0
35 TraesCS3A01G069700 chr1A 76.703 558 86 29 5655 6203 391749780 391749258 4.480000e-68 270.0
36 TraesCS3A01G069700 chr1A 76.703 558 86 29 5655 6203 391838896 391838374 4.480000e-68 270.0
37 TraesCS3A01G069700 chr1A 74.737 570 101 20 5659 6224 252279890 252279360 2.130000e-51 215.0
38 TraesCS3A01G069700 chr1A 74.641 418 56 37 5655 6057 546237731 546238113 1.320000e-28 139.0
39 TraesCS3A01G069700 chr1A 78.788 99 13 6 6464 6555 474316260 474316163 1.050000e-04 60.2
40 TraesCS3A01G069700 chr6A 96.206 3189 120 1 2228 5415 29328171 29324983 0.000000e+00 5217.0
41 TraesCS3A01G069700 chr6A 80.682 352 53 13 5654 5997 524062006 524061662 9.690000e-65 259.0
42 TraesCS3A01G069700 chr6A 92.500 160 12 0 9565 9724 77774273 77774114 7.600000e-56 230.0
43 TraesCS3A01G069700 chr6A 77.287 317 67 4 5904 6220 117464992 117464681 2.160000e-41 182.0
44 TraesCS3A01G069700 chr6A 94.253 87 5 0 8789 8875 103761984 103761898 6.130000e-27 134.0
45 TraesCS3A01G069700 chr6A 90.526 95 8 1 8779 8873 65859656 65859749 3.690000e-24 124.0
46 TraesCS3A01G069700 chr7A 95.703 3188 136 1 2228 5415 689675490 689672304 0.000000e+00 5127.0
47 TraesCS3A01G069700 chr7A 94.904 942 40 5 1281 2216 621351366 621350427 0.000000e+00 1467.0
48 TraesCS3A01G069700 chr7A 94.532 951 43 4 1274 2216 488496066 488497015 0.000000e+00 1459.0
49 TraesCS3A01G069700 chr7A 86.154 65 6 3 737 799 581370326 581370389 6.300000e-07 67.6
50 TraesCS3A01G069700 chr3D 91.854 3155 210 22 5655 8790 30238921 30235795 0.000000e+00 4359.0
51 TraesCS3A01G069700 chr3D 92.554 873 45 10 8871 9724 30235797 30234926 0.000000e+00 1234.0
52 TraesCS3A01G069700 chr3D 92.961 753 45 6 1 747 30240502 30239752 0.000000e+00 1090.0
53 TraesCS3A01G069700 chr3D 91.601 381 14 1 921 1283 30239657 30239277 2.420000e-140 510.0
54 TraesCS3A01G069700 chr3D 89.316 234 14 4 5415 5640 30239285 30239055 5.750000e-72 283.0
55 TraesCS3A01G069700 chr3D 81.897 348 51 10 5654 5992 437737272 437737616 5.750000e-72 283.0
56 TraesCS3A01G069700 chr3D 83.113 302 41 10 5659 5953 319843908 319844206 5.790000e-67 267.0
57 TraesCS3A01G069700 chr3D 92.553 94 7 0 8789 8882 545547879 545547786 1.700000e-27 135.0
58 TraesCS3A01G069700 chr3D 97.297 37 0 1 6603 6639 30238038 30238003 2.930000e-05 62.1
59 TraesCS3A01G069700 chr7B 98.300 941 9 4 1281 2216 20047792 20048730 0.000000e+00 1642.0
60 TraesCS3A01G069700 chr7B 93.333 90 6 0 8792 8881 716043255 716043166 6.130000e-27 134.0
61 TraesCS3A01G069700 chr4A 88.898 1270 107 14 7507 8773 385781534 385780296 0.000000e+00 1533.0
62 TraesCS3A01G069700 chr4A 80.529 529 92 7 5659 6180 72971930 72972454 7.080000e-106 396.0
63 TraesCS3A01G069700 chr4A 94.737 38 0 2 6465 6501 632853100 632853064 3.790000e-04 58.4
64 TraesCS3A01G069700 chr4B 90.168 773 69 4 7495 8265 207124209 207123442 0.000000e+00 1000.0
65 TraesCS3A01G069700 chr4B 92.130 216 14 3 8247 8461 207118981 207118768 1.590000e-77 302.0
66 TraesCS3A01G069700 chr4B 86.429 280 27 3 6737 7007 207125365 207125088 7.380000e-76 296.0
67 TraesCS3A01G069700 chr4B 91.803 61 5 0 7440 7500 207124307 207124247 1.740000e-12 86.1
68 TraesCS3A01G069700 chr4D 90.000 650 54 8 7868 8513 164905028 164904386 0.000000e+00 830.0
69 TraesCS3A01G069700 chr4D 79.502 522 90 11 5659 6171 391100340 391100853 1.200000e-93 355.0
70 TraesCS3A01G069700 chr4D 87.624 202 25 0 8513 8714 164888429 164888228 1.630000e-57 235.0
71 TraesCS3A01G069700 chr4D 75.601 541 87 30 5659 6187 505970122 505969615 9.830000e-55 226.0
72 TraesCS3A01G069700 chr4D 95.294 85 4 0 8789 8873 455894151 455894235 1.700000e-27 135.0
73 TraesCS3A01G069700 chr4D 93.023 86 6 0 8788 8873 224838522 224838607 1.030000e-24 126.0
74 TraesCS3A01G069700 chr4D 90.426 94 9 0 8782 8875 119051132 119051225 3.690000e-24 124.0
75 TraesCS3A01G069700 chr4D 91.209 91 8 0 8789 8879 225215609 225215519 3.690000e-24 124.0
76 TraesCS3A01G069700 chr4D 90.217 92 9 0 8782 8873 103894619 103894710 4.770000e-23 121.0
77 TraesCS3A01G069700 chr4D 90.217 92 8 1 8786 8877 8783935 8784025 1.720000e-22 119.0
78 TraesCS3A01G069700 chr7D 83.459 399 56 8 5656 6046 170560389 170560785 7.180000e-96 363.0
79 TraesCS3A01G069700 chr7D 95.294 85 4 0 8789 8873 171549004 171549088 1.700000e-27 135.0
80 TraesCS3A01G069700 chr7D 81.443 97 12 5 6465 6555 582304601 582304505 3.770000e-09 75.0
81 TraesCS3A01G069700 chr7D 94.737 38 1 1 6465 6501 513255144 513255107 3.790000e-04 58.4
82 TraesCS3A01G069700 chr5B 78.750 560 94 20 5675 6219 498085303 498084754 1.550000e-92 351.0
83 TraesCS3A01G069700 chr5B 96.000 50 1 1 749 797 660371217 660371266 8.100000e-11 80.5
84 TraesCS3A01G069700 chr5B 94.231 52 1 2 744 793 542675595 542675544 2.910000e-10 78.7
85 TraesCS3A01G069700 chr5B 90.000 60 4 2 749 806 662858550 662858491 1.050000e-09 76.8
86 TraesCS3A01G069700 chr5B 88.710 62 3 3 736 795 6417685 6417744 1.350000e-08 73.1
87 TraesCS3A01G069700 chrUn 77.905 525 89 16 5654 6173 95004191 95003689 1.590000e-77 302.0
88 TraesCS3A01G069700 chrUn 78.960 404 70 12 5654 6046 24298344 24297945 2.690000e-65 261.0
89 TraesCS3A01G069700 chrUn 81.081 259 48 1 5929 6187 2158418 2158675 1.280000e-48 206.0
90 TraesCS3A01G069700 chrUn 94.444 90 4 1 8789 8877 378270652 378270563 4.740000e-28 137.0
91 TraesCS3A01G069700 chrUn 92.708 96 6 1 8783 8877 447954256 447954351 4.740000e-28 137.0
92 TraesCS3A01G069700 chrUn 91.667 96 7 1 8783 8877 320620063 320620158 2.200000e-26 132.0
93 TraesCS3A01G069700 chrUn 92.941 85 6 0 8789 8873 197752479 197752395 3.690000e-24 124.0
94 TraesCS3A01G069700 chrUn 92.941 85 6 0 8789 8873 222975854 222975770 3.690000e-24 124.0
95 TraesCS3A01G069700 chrUn 92.941 85 6 0 8789 8873 303647988 303647904 3.690000e-24 124.0
96 TraesCS3A01G069700 chrUn 90.323 93 9 0 8788 8880 67634374 67634466 1.330000e-23 122.0
97 TraesCS3A01G069700 chrUn 91.954 87 7 0 8789 8875 100223823 100223737 1.330000e-23 122.0
98 TraesCS3A01G069700 chrUn 91.765 85 6 1 8789 8873 184676555 184676472 6.170000e-22 117.0
99 TraesCS3A01G069700 chrUn 89.247 93 9 1 8789 8880 108327677 108327585 2.220000e-21 115.0
100 TraesCS3A01G069700 chrUn 86.275 102 13 1 8788 8889 197752394 197752494 1.030000e-19 110.0
101 TraesCS3A01G069700 chr1D 79.318 440 78 12 5656 6086 450742402 450742837 7.380000e-76 296.0
102 TraesCS3A01G069700 chr1D 75.627 558 95 20 5658 6203 136963717 136963189 1.260000e-58 239.0
103 TraesCS3A01G069700 chr1D 89.759 166 16 1 9559 9724 271795275 271795439 2.750000e-50 211.0
104 TraesCS3A01G069700 chr1D 79.930 284 47 6 5674 5947 14276641 14276358 5.960000e-47 200.0
105 TraesCS3A01G069700 chr1D 82.028 217 36 3 5797 6011 59561436 59561221 2.160000e-41 182.0
106 TraesCS3A01G069700 chr1D 94.318 88 5 0 8788 8875 409047052 409047139 1.700000e-27 135.0
107 TraesCS3A01G069700 chr1D 79.188 197 30 9 5659 5847 418516532 418516339 1.030000e-24 126.0
108 TraesCS3A01G069700 chr1D 90.426 94 9 0 8788 8881 47644742 47644835 3.690000e-24 124.0
109 TraesCS3A01G069700 chr1D 77.729 229 30 17 5674 5889 451794826 451795046 4.770000e-23 121.0
110 TraesCS3A01G069700 chr1D 77.665 197 33 9 5659 5847 418619209 418619016 1.030000e-19 110.0
111 TraesCS3A01G069700 chr1D 77.297 185 26 14 5655 5831 95836712 95836888 2.890000e-15 95.3
112 TraesCS3A01G069700 chr1D 91.071 56 4 1 739 793 259726688 259726743 3.770000e-09 75.0
113 TraesCS3A01G069700 chr2B 80.769 390 62 12 5659 6038 418963254 418963640 9.550000e-75 292.0
114 TraesCS3A01G069700 chr2B 97.826 46 0 1 748 793 30578997 30578953 2.910000e-10 78.7
115 TraesCS3A01G069700 chr2B 82.667 75 8 5 726 800 33544408 33544477 2.930000e-05 62.1
116 TraesCS3A01G069700 chr2D 78.469 418 73 14 5659 6063 7129639 7129226 3.480000e-64 257.0
117 TraesCS3A01G069700 chr2D 91.667 96 7 1 8783 8877 44516970 44517065 2.200000e-26 132.0
118 TraesCS3A01G069700 chr5D 80.058 346 62 7 5838 6179 413288321 413287979 5.830000e-62 250.0
119 TraesCS3A01G069700 chr5D 74.953 531 93 26 5655 6174 414230351 414230852 3.560000e-49 207.0
120 TraesCS3A01G069700 chr5D 95.349 86 4 0 8788 8873 539450692 539450777 4.740000e-28 137.0
121 TraesCS3A01G069700 chr5D 95.349 86 4 0 8789 8874 561630084 561629999 4.740000e-28 137.0
122 TraesCS3A01G069700 chr5D 90.909 99 9 0 8789 8887 350223613 350223711 6.130000e-27 134.0
123 TraesCS3A01G069700 chr5D 93.103 87 6 0 8789 8875 447627018 447626932 2.850000e-25 128.0
124 TraesCS3A01G069700 chr5D 90.000 100 8 2 8775 8874 519201429 519201526 2.850000e-25 128.0
125 TraesCS3A01G069700 chr6D 89.873 158 16 0 9565 9722 448628472 448628629 4.600000e-48 204.0
126 TraesCS3A01G069700 chr6D 76.800 375 61 22 5655 6010 470939060 470939427 4.640000e-43 187.0
127 TraesCS3A01G069700 chr6D 80.476 210 41 0 5928 6137 371532335 371532544 2.810000e-35 161.0
128 TraesCS3A01G069700 chr6D 79.268 246 35 11 5656 5888 13965268 13965510 3.640000e-34 158.0
129 TraesCS3A01G069700 chr6D 91.398 93 8 0 8788 8880 356639878 356639970 2.850000e-25 128.0
130 TraesCS3A01G069700 chr6D 91.398 93 8 0 8781 8873 387886082 387885990 2.850000e-25 128.0
131 TraesCS3A01G069700 chr1B 89.899 99 9 1 8777 8874 482722128 482722030 1.030000e-24 126.0
132 TraesCS3A01G069700 chr1B 89.899 99 9 1 8777 8874 482753288 482753190 1.030000e-24 126.0
133 TraesCS3A01G069700 chr1B 95.833 48 1 1 748 794 297337085 297337132 1.050000e-09 76.8
134 TraesCS3A01G069700 chr1B 94.118 51 2 1 744 793 666574819 666574869 1.050000e-09 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 TraesCS3A01G069700 chr3A 41989881 41999604 9723 True 17917.00 17917 100.000000 1 9724 1 chr3A.!!$R1 9723
1 TraesCS3A01G069700 chr3A 9074312 9075254 942 False 1476.00 1476 95.026000 1279 2216 1 chr3A.!!$F1 937
2 TraesCS3A01G069700 chr3A 657275999 657276547 548 True 318.00 318 77.758000 5659 6203 1 chr3A.!!$R2 544
3 TraesCS3A01G069700 chr6B 530992222 530996633 4411 True 3728.00 5799 99.056000 1283 5415 2 chr6B.!!$R2 4132
4 TraesCS3A01G069700 chr6B 45546479 45547007 528 True 409.00 409 80.899000 5654 6179 1 chr6B.!!$R1 525
5 TraesCS3A01G069700 chr3B 743789395 743793810 4415 False 3724.50 5777 99.050000 1277 5415 2 chr3B.!!$F2 4138
6 TraesCS3A01G069700 chr3B 123119796 123120731 935 True 1670.00 1670 98.932000 1284 2216 1 chr3B.!!$R2 932
7 TraesCS3A01G069700 chr3B 51814206 51819113 4907 True 1253.40 2241 91.635200 54 8790 5 chr3B.!!$R4 8736
8 TraesCS3A01G069700 chr3B 52769763 52773324 3561 False 1014.14 3341 91.505800 1 8792 5 chr3B.!!$F1 8791
9 TraesCS3A01G069700 chr2A 39171155 39174341 3186 True 5265.00 5265 96.487000 2228 5415 1 chr2A.!!$R1 3187
10 TraesCS3A01G069700 chr2A 575065632 575068819 3187 False 5068.00 5068 95.358000 2228 5415 1 chr2A.!!$F1 3187
11 TraesCS3A01G069700 chr2A 737499874 737504281 4407 True 3396.50 5326 95.930500 1285 5413 2 chr2A.!!$R3 4128
12 TraesCS3A01G069700 chr5A 603598248 603601433 3185 True 5241.00 5241 96.359000 2228 5413 1 chr5A.!!$R4 3185
13 TraesCS3A01G069700 chr5A 380624809 380625747 938 True 1463.00 1463 94.899000 1283 2216 1 chr5A.!!$R3 933
14 TraesCS3A01G069700 chr1A 48968799 48971985 3186 False 5221.00 5221 96.236000 2228 5415 1 chr1A.!!$F1 3187
15 TraesCS3A01G069700 chr1A 569143030 569143967 937 True 1482.00 1482 95.314000 1286 2216 1 chr1A.!!$R5 930
16 TraesCS3A01G069700 chr1A 494852474 494853002 528 False 316.00 316 77.757000 5653 6180 1 chr1A.!!$F2 527
17 TraesCS3A01G069700 chr1A 391749258 391749780 522 True 270.00 270 76.703000 5655 6203 1 chr1A.!!$R2 548
18 TraesCS3A01G069700 chr1A 391838374 391838896 522 True 270.00 270 76.703000 5655 6203 1 chr1A.!!$R3 548
19 TraesCS3A01G069700 chr1A 252279360 252279890 530 True 215.00 215 74.737000 5659 6224 1 chr1A.!!$R1 565
20 TraesCS3A01G069700 chr6A 29324983 29328171 3188 True 5217.00 5217 96.206000 2228 5415 1 chr6A.!!$R1 3187
21 TraesCS3A01G069700 chr7A 689672304 689675490 3186 True 5127.00 5127 95.703000 2228 5415 1 chr7A.!!$R2 3187
22 TraesCS3A01G069700 chr7A 621350427 621351366 939 True 1467.00 1467 94.904000 1281 2216 1 chr7A.!!$R1 935
23 TraesCS3A01G069700 chr7A 488496066 488497015 949 False 1459.00 1459 94.532000 1274 2216 1 chr7A.!!$F1 942
24 TraesCS3A01G069700 chr3D 30234926 30240502 5576 True 1256.35 4359 92.597167 1 9724 6 chr3D.!!$R2 9723
25 TraesCS3A01G069700 chr7B 20047792 20048730 938 False 1642.00 1642 98.300000 1281 2216 1 chr7B.!!$F1 935
26 TraesCS3A01G069700 chr4A 385780296 385781534 1238 True 1533.00 1533 88.898000 7507 8773 1 chr4A.!!$R1 1266
27 TraesCS3A01G069700 chr4A 72971930 72972454 524 False 396.00 396 80.529000 5659 6180 1 chr4A.!!$F1 521
28 TraesCS3A01G069700 chr4B 207123442 207125365 1923 True 460.70 1000 89.466667 6737 8265 3 chr4B.!!$R2 1528
29 TraesCS3A01G069700 chr4D 164904386 164905028 642 True 830.00 830 90.000000 7868 8513 1 chr4D.!!$R2 645
30 TraesCS3A01G069700 chr4D 391100340 391100853 513 False 355.00 355 79.502000 5659 6171 1 chr4D.!!$F5 512
31 TraesCS3A01G069700 chr4D 505969615 505970122 507 True 226.00 226 75.601000 5659 6187 1 chr4D.!!$R4 528
32 TraesCS3A01G069700 chr5B 498084754 498085303 549 True 351.00 351 78.750000 5675 6219 1 chr5B.!!$R1 544
33 TraesCS3A01G069700 chrUn 95003689 95004191 502 True 302.00 302 77.905000 5654 6173 1 chrUn.!!$R2 519
34 TraesCS3A01G069700 chr1D 136963189 136963717 528 True 239.00 239 75.627000 5658 6203 1 chr1D.!!$R3 545
35 TraesCS3A01G069700 chr5D 414230351 414230852 501 False 207.00 207 74.953000 5655 6174 1 chr5D.!!$F2 519

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
634 644 0.613260 ATGTCAGCCTTGGCGAGTAA 59.387 50.000 5.95 0.0 0.00 2.24 F
1565 1861 0.110678 TATCCCGAGCGACCATCTCT 59.889 55.000 0.00 0.0 0.00 3.10 F
1609 1905 2.444706 CTCCCTGGCCTCCATCGA 60.445 66.667 3.32 0.0 30.82 3.59 F
2819 3391 8.929260 TCATGCTCCATAAAGATGATTGTATT 57.071 30.769 0.00 0.0 34.73 1.89 F
4806 5378 3.000815 GGTTTCCGACAGAGCAACA 57.999 52.632 0.00 0.0 0.00 3.33 F
5861 6577 1.447838 GCCGAATTGCCGAGTCTGA 60.448 57.895 0.00 0.0 0.00 3.27 F
6340 7062 0.179076 TAGTGCATGGATCACTGGCG 60.179 55.000 12.98 0.0 43.85 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1905 2.671351 CGTTCATGGTCGCTACTCACTT 60.671 50.000 0.00 0.0 0.00 3.16 R
2819 3391 1.611977 CCATCCTTCAGTACGCCGATA 59.388 52.381 0.00 0.0 0.00 2.92 R
4195 4767 2.681778 CGTGGACTCAGGGGAGCT 60.682 66.667 0.00 0.0 45.42 4.09 R
5151 5723 1.180029 GCAGTCAAGCCCATGAATGT 58.820 50.000 11.99 0.0 44.80 2.71 R
6054 6775 0.742505 CGTGCCGTTATAGGGTCTCA 59.257 55.000 0.00 0.0 0.00 3.27 R
8130 9522 0.320421 TGCGTTCACTTCTGTAGGGC 60.320 55.000 0.00 0.0 0.00 5.19 R
8857 10261 0.113776 ACACTACTTCCTCCGTCCCA 59.886 55.000 0.00 0.0 0.00 4.37 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
180 184 5.907207 AGCTTACATATATCATAGGGCACG 58.093 41.667 0.00 0.00 0.00 5.34
238 242 8.073355 GATCGTGTTCGGTCATAGAATAAAAT 57.927 34.615 0.00 0.00 45.34 1.82
303 310 8.019656 AGACGAAATAGAGGGTTAATGTACAT 57.980 34.615 1.41 1.41 0.00 2.29
309 316 8.562949 AATAGAGGGTTAATGTACATAGGTGT 57.437 34.615 9.21 0.00 42.39 4.16
326 334 1.523934 GTGTCATGTTTTGCAAGCAGC 59.476 47.619 0.00 0.00 45.96 5.25
354 362 7.743104 CGAAGCTTTAGCAAGAATTAAGAGAA 58.257 34.615 0.00 0.00 45.16 2.87
378 386 5.912892 AGCTAAATGAGTCTTAGGAAGAGC 58.087 41.667 0.00 0.00 38.41 4.09
409 417 7.040409 GGGGCTAATTGAGGTTAATATGTCTTG 60.040 40.741 0.00 0.00 0.00 3.02
410 418 7.719633 GGGCTAATTGAGGTTAATATGTCTTGA 59.280 37.037 0.00 0.00 0.00 3.02
443 451 2.031420 CGCCATCTCAATGCATGTAAGG 60.031 50.000 0.00 0.00 0.00 2.69
508 516 2.370349 TCTCGATCAGGAAGTCAGACC 58.630 52.381 0.00 0.00 0.00 3.85
513 521 3.368843 CGATCAGGAAGTCAGACCACAAT 60.369 47.826 0.00 0.00 0.00 2.71
596 606 7.891220 CACGTGTCATAAACATCTAACTTAACG 59.109 37.037 7.58 0.00 40.80 3.18
634 644 0.613260 ATGTCAGCCTTGGCGAGTAA 59.387 50.000 5.95 0.00 0.00 2.24
781 793 8.721019 AAATTATTTGGATTGCTTACCACATG 57.279 30.769 0.00 0.00 35.81 3.21
782 794 6.849085 TTATTTGGATTGCTTACCACATGT 57.151 33.333 0.00 0.00 35.81 3.21
783 795 4.517952 TTTGGATTGCTTACCACATGTG 57.482 40.909 19.31 19.31 35.81 3.21
784 796 3.153369 TGGATTGCTTACCACATGTGT 57.847 42.857 23.79 14.29 0.00 3.72
785 797 3.081061 TGGATTGCTTACCACATGTGTC 58.919 45.455 23.79 11.95 0.00 3.67
786 798 3.081061 GGATTGCTTACCACATGTGTCA 58.919 45.455 23.79 8.71 0.00 3.58
787 799 3.119849 GGATTGCTTACCACATGTGTCAC 60.120 47.826 23.79 9.40 0.00 3.67
788 800 1.507562 TGCTTACCACATGTGTCACG 58.492 50.000 23.79 11.29 0.00 4.35
789 801 1.202592 TGCTTACCACATGTGTCACGT 60.203 47.619 23.79 16.29 0.00 4.49
790 802 1.194547 GCTTACCACATGTGTCACGTG 59.805 52.381 23.79 21.25 40.80 4.49
792 804 4.454948 CCACATGTGTCACGTGGT 57.545 55.556 25.31 11.12 44.27 4.16
793 805 3.597550 CCACATGTGTCACGTGGTA 57.402 52.632 25.31 1.73 44.27 3.25
794 806 1.428448 CCACATGTGTCACGTGGTAG 58.572 55.000 25.31 15.71 44.27 3.18
795 807 1.270094 CCACATGTGTCACGTGGTAGT 60.270 52.381 25.31 5.33 44.27 2.73
796 808 2.479837 CACATGTGTCACGTGGTAGTT 58.520 47.619 25.31 4.98 39.36 2.24
797 809 3.553302 CCACATGTGTCACGTGGTAGTTA 60.553 47.826 25.31 0.00 44.27 2.24
798 810 4.242475 CACATGTGTCACGTGGTAGTTAT 58.758 43.478 25.31 3.65 39.36 1.89
799 811 5.404096 CACATGTGTCACGTGGTAGTTATA 58.596 41.667 25.31 0.00 39.36 0.98
800 812 5.287752 CACATGTGTCACGTGGTAGTTATAC 59.712 44.000 25.31 4.17 39.36 1.47
801 813 4.082274 TGTGTCACGTGGTAGTTATACG 57.918 45.455 17.00 0.00 42.98 3.06
815 827 3.629398 AGTTATACGTGACTCTAACCCGG 59.371 47.826 0.00 0.00 0.00 5.73
828 840 3.701040 TCTAACCCGGTATGTGGTAGTTC 59.299 47.826 0.00 0.00 33.52 3.01
830 842 2.105766 ACCCGGTATGTGGTAGTTCTC 58.894 52.381 0.00 0.00 31.61 2.87
906 1165 5.446143 ACGTCCTACAAAATTGCAAATCA 57.554 34.783 1.71 0.00 0.00 2.57
910 1169 7.120579 ACGTCCTACAAAATTGCAAATCATCTA 59.879 33.333 1.71 0.00 0.00 1.98
1023 1287 3.491652 GCGAAGGCTGTTCCTCGC 61.492 66.667 13.90 13.90 46.94 5.03
1026 1290 3.978571 GAAGGCTGTTCCTCGCCCC 62.979 68.421 0.00 0.00 46.94 5.80
1192 1474 3.277962 AAGCAGCCCTTCAATGGAG 57.722 52.632 0.00 0.00 0.00 3.86
1246 1528 3.304794 CGAGTCTTCTTCCTTCTCGTTGT 60.305 47.826 0.00 0.00 41.64 3.32
1385 1680 1.694150 CAAGGTTCCACAGTCTCCAGA 59.306 52.381 0.00 0.00 0.00 3.86
1426 1722 2.149578 GAAATGCAGCTCACACAGAGT 58.850 47.619 0.00 0.00 46.47 3.24
1565 1861 0.110678 TATCCCGAGCGACCATCTCT 59.889 55.000 0.00 0.00 0.00 3.10
1609 1905 2.444706 CTCCCTGGCCTCCATCGA 60.445 66.667 3.32 0.00 30.82 3.59
2819 3391 8.929260 TCATGCTCCATAAAGATGATTGTATT 57.071 30.769 0.00 0.00 34.73 1.89
4195 4767 8.239038 TGTGTTTTTGTTTCCTATATGGTTCA 57.761 30.769 0.00 0.00 37.07 3.18
4806 5378 3.000815 GGTTTCCGACAGAGCAACA 57.999 52.632 0.00 0.00 0.00 3.33
5119 5691 6.872020 GCTAGGTCCGCACATAGATTATTTAA 59.128 38.462 1.60 0.00 38.92 1.52
5120 5692 7.549488 GCTAGGTCCGCACATAGATTATTTAAT 59.451 37.037 1.60 0.00 38.92 1.40
5151 5723 4.849810 TCCCTAACTCCTCAATTTCCTCAA 59.150 41.667 0.00 0.00 0.00 3.02
5168 5740 3.087031 CTCAACATTCATGGGCTTGACT 58.913 45.455 0.00 0.00 0.00 3.41
5489 6069 8.810652 ATTGTGTTGTATAACCAAAATGTCAC 57.189 30.769 9.21 0.00 35.92 3.67
5496 6076 7.662897 TGTATAACCAAAATGTCACCTTTTCC 58.337 34.615 0.00 0.00 0.00 3.13
5576 6156 5.807011 ACAAGCGGAATTAGAAAAATGATGC 59.193 36.000 0.00 0.00 0.00 3.91
5756 6462 1.473278 GCAACTGTCGCTACTCCTAGT 59.527 52.381 0.00 0.00 0.00 2.57
5786 6494 2.351276 GGTGCAGATTGTCGGGGT 59.649 61.111 0.00 0.00 0.00 4.95
5795 6506 3.134081 CAGATTGTCGGGGTTACATACCT 59.866 47.826 0.00 0.00 46.86 3.08
5818 6532 1.541147 ACATCACATCAAAGCCCAACG 59.459 47.619 0.00 0.00 0.00 4.10
5861 6577 1.447838 GCCGAATTGCCGAGTCTGA 60.448 57.895 0.00 0.00 0.00 3.27
6069 6790 1.001597 GTCGCTGAGACCCTATAACGG 60.002 57.143 0.00 0.00 43.95 4.44
6099 6820 2.544685 GAGACTCCACATCGTTGATGG 58.455 52.381 11.17 4.86 43.60 3.51
6174 6895 3.940209 TGCACATCTCCAAAAATGACC 57.060 42.857 0.00 0.00 0.00 4.02
6203 6925 3.198635 CAGAGGATGGTACCACACAAGAT 59.801 47.826 19.09 0.00 0.00 2.40
6204 6926 4.405680 CAGAGGATGGTACCACACAAGATA 59.594 45.833 19.09 0.00 0.00 1.98
6298 7020 6.672266 TTCCCAAAGTAAAATTATGCCACA 57.328 33.333 0.00 0.00 0.00 4.17
6336 7058 5.804639 TGTAAAACTAGTGCATGGATCACT 58.195 37.500 9.09 9.09 45.71 3.41
6340 7062 0.179076 TAGTGCATGGATCACTGGCG 60.179 55.000 12.98 0.00 43.85 5.69
6348 7070 1.209261 TGGATCACTGGCGCTGAAATA 59.791 47.619 7.64 0.00 0.00 1.40
6351 7073 4.256920 GGATCACTGGCGCTGAAATATAT 58.743 43.478 7.64 0.00 0.00 0.86
6427 7326 1.625616 CTTGGACGTACTAACTGGCG 58.374 55.000 0.00 0.00 0.00 5.69
6428 7327 0.244450 TTGGACGTACTAACTGGCGG 59.756 55.000 0.00 0.00 0.00 6.13
6429 7328 1.517913 GGACGTACTAACTGGCGGC 60.518 63.158 0.00 0.00 0.00 6.53
6435 7334 0.454600 TACTAACTGGCGGCGAAGAG 59.545 55.000 12.98 4.72 0.00 2.85
6436 7335 1.248785 ACTAACTGGCGGCGAAGAGA 61.249 55.000 12.98 0.00 0.00 3.10
6438 7337 1.337071 CTAACTGGCGGCGAAGAGATA 59.663 52.381 12.98 0.53 0.00 1.98
6474 7374 4.688021 GATGCTTACAACTACTCCTCTGG 58.312 47.826 0.00 0.00 0.00 3.86
6525 7430 4.604697 CGTCAAAGTTCGTTAAGTTCGACC 60.605 45.833 0.00 0.00 31.07 4.79
6655 7561 4.058721 ACTTTGTGAAATTTGACCTGCC 57.941 40.909 5.29 0.00 0.00 4.85
6690 7597 7.333528 ACATGCAGAGTAAAAAGAAACAGAA 57.666 32.000 0.00 0.00 0.00 3.02
6764 7671 5.059833 CCATTTTATGAGTCCCTAGCTGAC 58.940 45.833 0.00 0.00 0.00 3.51
6823 7730 7.264221 TGGTGCATTAACATATTTGTGGATTC 58.736 34.615 0.00 0.00 35.83 2.52
6903 7819 2.073816 CAACAACCTCCATGTACGGAC 58.926 52.381 0.00 0.00 0.00 4.79
6995 7911 9.435802 GACTATACATAGTGTAACAGTTTCTCG 57.564 37.037 6.62 0.00 43.27 4.04
7117 8437 6.195600 ACTAAGACAAATAACCCCTGTCAA 57.804 37.500 4.43 0.00 41.58 3.18
7198 8520 5.301551 TGATGCTGACAAAACCATAGTTTGT 59.698 36.000 2.36 2.36 45.54 2.83
7238 8581 9.242477 GAGAACTTCAAGAAGAAAATGGAAAAG 57.758 33.333 16.16 0.00 40.79 2.27
7332 8675 0.836400 TGTCTGGAACTGGGACCCTC 60.836 60.000 13.00 0.21 0.00 4.30
7420 8763 5.432885 TGTTTTACAAGCTTTAGCACTCC 57.567 39.130 0.00 0.00 45.16 3.85
7458 8801 5.851720 AGTCAATCATAGCAGAGTGTATGG 58.148 41.667 0.00 0.00 35.30 2.74
7554 8940 7.822161 TCTTTGGCAGCATTATACAATACAT 57.178 32.000 0.00 0.00 0.00 2.29
7670 9057 2.042686 TGGCATGACTGTCCAATAGC 57.957 50.000 0.00 2.35 0.00 2.97
7997 9388 5.613329 AGTAGGTATGTTTTGTCCGTTCAA 58.387 37.500 0.00 0.00 0.00 2.69
7999 9390 5.432885 AGGTATGTTTTGTCCGTTCAAAG 57.567 39.130 3.30 0.00 38.32 2.77
8130 9522 3.992427 TCTGCATTGCTAGCTTGATATCG 59.008 43.478 17.23 0.00 0.00 2.92
8316 9714 2.223805 CCCACTTGAAGTTTGTGAAGCC 60.224 50.000 0.00 0.00 33.95 4.35
8371 9769 5.925969 CGTGCAGGAAAAATCAAAGGTAAAT 59.074 36.000 0.00 0.00 0.00 1.40
8386 9784 4.998051 AGGTAAATGAACCAACTGACCAT 58.002 39.130 0.00 0.00 42.40 3.55
8400 9799 8.055181 ACCAACTGACCATCATCTTTATTATGT 58.945 33.333 0.00 0.00 0.00 2.29
8513 9913 5.578727 GCGCAAATATTTGAACACCCAAATA 59.421 36.000 28.33 10.33 46.61 1.40
8585 9989 6.263168 GGTTCCTAGTTCAATAATGATGGGTG 59.737 42.308 0.00 0.00 34.96 4.61
8803 10207 2.499566 AGGTACTCCCTCTGTCCCA 58.500 57.895 0.00 0.00 40.71 4.37
8804 10208 1.019650 AGGTACTCCCTCTGTCCCAT 58.980 55.000 0.00 0.00 40.71 4.00
8805 10209 2.224077 AGGTACTCCCTCTGTCCCATA 58.776 52.381 0.00 0.00 40.71 2.74
8806 10210 2.590611 AGGTACTCCCTCTGTCCCATAA 59.409 50.000 0.00 0.00 40.71 1.90
8807 10211 3.210074 AGGTACTCCCTCTGTCCCATAAT 59.790 47.826 0.00 0.00 40.71 1.28
8808 10212 4.422592 AGGTACTCCCTCTGTCCCATAATA 59.577 45.833 0.00 0.00 40.71 0.98
8809 10213 5.078006 AGGTACTCCCTCTGTCCCATAATAT 59.922 44.000 0.00 0.00 40.71 1.28
8810 10214 6.279682 AGGTACTCCCTCTGTCCCATAATATA 59.720 42.308 0.00 0.00 40.71 0.86
8811 10215 6.958192 GGTACTCCCTCTGTCCCATAATATAA 59.042 42.308 0.00 0.00 0.00 0.98
8812 10216 7.124448 GGTACTCCCTCTGTCCCATAATATAAG 59.876 44.444 0.00 0.00 0.00 1.73
8813 10217 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
8814 10218 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
8815 10219 6.875469 TCCCTCTGTCCCATAATATAAGAGT 58.125 40.000 0.00 0.00 0.00 3.24
8816 10220 6.726299 TCCCTCTGTCCCATAATATAAGAGTG 59.274 42.308 0.00 0.00 0.00 3.51
8817 10221 6.498651 CCCTCTGTCCCATAATATAAGAGTGT 59.501 42.308 0.00 0.00 0.00 3.55
8818 10222 7.016661 CCCTCTGTCCCATAATATAAGAGTGTT 59.983 40.741 0.00 0.00 0.00 3.32
8819 10223 8.432805 CCTCTGTCCCATAATATAAGAGTGTTT 58.567 37.037 0.00 0.00 0.00 2.83
8820 10224 9.838339 CTCTGTCCCATAATATAAGAGTGTTTT 57.162 33.333 0.00 0.00 0.00 2.43
8848 10252 8.776680 ACACTATTGTAATGTCAAAAACGTTC 57.223 30.769 0.00 0.00 38.14 3.95
8849 10253 8.617809 ACACTATTGTAATGTCAAAAACGTTCT 58.382 29.630 0.00 0.00 38.14 3.01
8850 10254 9.445786 CACTATTGTAATGTCAAAAACGTTCTT 57.554 29.630 0.00 0.00 38.14 2.52
8861 10265 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
8862 10266 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
8863 10267 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
8864 10268 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
8865 10269 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
8866 10270 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
8867 10271 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
8868 10272 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
8869 10273 6.294899 CGTTCTTATATTATGGGACGGAGGAA 60.295 42.308 0.00 0.00 0.00 3.36
8870 10274 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
8871 10275 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
8872 10276 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
8873 10277 7.614583 TCTTATATTATGGGACGGAGGAAGTAG 59.385 40.741 0.00 0.00 0.00 2.57
8874 10278 3.393426 TTATGGGACGGAGGAAGTAGT 57.607 47.619 0.00 0.00 0.00 2.73
8875 10279 1.486211 ATGGGACGGAGGAAGTAGTG 58.514 55.000 0.00 0.00 0.00 2.74
8886 10290 6.435277 ACGGAGGAAGTAGTGTTTATGTCTAA 59.565 38.462 0.00 0.00 0.00 2.10
8906 10310 9.330063 TGTCTAAAAAGAGTGATAATAGCATGG 57.670 33.333 0.00 0.00 0.00 3.66
8907 10311 9.547753 GTCTAAAAAGAGTGATAATAGCATGGA 57.452 33.333 0.00 0.00 0.00 3.41
8942 10350 8.581057 ACATAAAGATCGAATCTGTACATCAC 57.419 34.615 0.00 0.00 40.13 3.06
8974 10382 5.845985 TTGAAATGTTTTGACGCAACAAA 57.154 30.435 1.92 1.92 37.67 2.83
9002 10410 0.599558 GTGTGGCTGTGTGCATTGAT 59.400 50.000 0.00 0.00 45.15 2.57
9011 10419 1.331756 GTGTGCATTGATCGATGGGAC 59.668 52.381 21.99 14.68 0.00 4.46
9013 10421 0.463620 TGCATTGATCGATGGGACGA 59.536 50.000 21.99 0.00 46.04 4.20
9017 10425 1.704641 TTGATCGATGGGACGAGGAT 58.295 50.000 0.54 0.00 45.22 3.24
9021 10429 2.134287 CGATGGGACGAGGATGGGT 61.134 63.158 0.00 0.00 35.09 4.51
9040 10448 2.490509 GGTACCCACCTGCATTTTGTAC 59.509 50.000 0.00 0.00 42.11 2.90
9058 10466 7.436430 TTTGTACAGTTCTAAACACACACAA 57.564 32.000 0.00 0.00 0.00 3.33
9066 10474 7.807907 CAGTTCTAAACACACACAAGAAAAACT 59.192 33.333 0.00 0.00 0.00 2.66
9095 10503 4.380843 TCTTGAAGCCACCCTGAAAATA 57.619 40.909 0.00 0.00 0.00 1.40
9102 10510 3.270960 AGCCACCCTGAAAATATACCCAA 59.729 43.478 0.00 0.00 0.00 4.12
9117 10525 0.035439 CCCAACCTGATTAGCACCGT 60.035 55.000 0.00 0.00 0.00 4.83
9151 10559 8.025445 GCCATTAGCAATTTAATATGACTGAGG 58.975 37.037 0.00 0.00 42.97 3.86
9176 10584 3.394606 ACTCCACCCGCATAGGAATATTT 59.605 43.478 0.00 0.00 45.00 1.40
9178 10586 3.392947 TCCACCCGCATAGGAATATTTCA 59.607 43.478 0.00 0.00 45.00 2.69
9183 10591 3.399330 CGCATAGGAATATTTCACCCGT 58.601 45.455 0.00 0.00 0.00 5.28
9202 10610 0.400213 TTGTGTCCCACTGATCCCAC 59.600 55.000 0.00 0.00 35.11 4.61
9223 10631 2.233271 CAATTGCGCTAATCCCTCCAT 58.767 47.619 9.73 0.00 0.00 3.41
9229 10637 3.072330 TGCGCTAATCCCTCCATATCAAA 59.928 43.478 9.73 0.00 0.00 2.69
9230 10638 4.072131 GCGCTAATCCCTCCATATCAAAA 58.928 43.478 0.00 0.00 0.00 2.44
9231 10639 4.154918 GCGCTAATCCCTCCATATCAAAAG 59.845 45.833 0.00 0.00 0.00 2.27
9252 10674 3.809013 CCTAACCCAGCGCCCCAT 61.809 66.667 2.29 0.00 0.00 4.00
9294 10716 3.425359 CCATTGATTCATCGCTAATCGCC 60.425 47.826 0.00 0.00 36.35 5.54
9416 10838 1.737008 GCCGTTGGTTCTCGAGGTC 60.737 63.158 13.56 5.92 0.00 3.85
9478 10900 1.667724 CACTAGCATAACCAGCAGCAC 59.332 52.381 0.00 0.00 0.00 4.40
9534 10956 4.760047 GCCACACGTCCGCCTGAT 62.760 66.667 0.00 0.00 0.00 2.90
9535 10957 2.047274 CCACACGTCCGCCTGATT 60.047 61.111 0.00 0.00 0.00 2.57
9563 10985 3.775654 CCTTTCTCGCCGCTCCCT 61.776 66.667 0.00 0.00 0.00 4.20
9581 11003 0.175760 CTGGGTTGGACGATGACGAT 59.824 55.000 0.00 0.00 42.66 3.73
9600 11022 2.886782 GCTATCGGCTTTGCTCGGC 61.887 63.158 0.00 0.00 38.06 5.54
9628 11050 3.157932 CTCCTCTTGAGAACATCGTCC 57.842 52.381 0.00 0.00 44.42 4.79
9676 11099 0.032952 GTGCTCGTGTAGGTGGTTGA 59.967 55.000 0.00 0.00 0.00 3.18
9707 11130 1.490910 TCTAGCATCTCCGTGAGAGGA 59.509 52.381 16.37 5.19 42.19 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 192 8.454894 TCTATTAACTCAATTTTACATGCGCAA 58.545 29.630 17.11 0.00 0.00 4.85
236 240 7.169158 TCTTGCCGATTCCTTGATTTTTATT 57.831 32.000 0.00 0.00 0.00 1.40
238 242 5.393027 GCTCTTGCCGATTCCTTGATTTTTA 60.393 40.000 0.00 0.00 0.00 1.52
303 310 2.954989 TGCTTGCAAAACATGACACCTA 59.045 40.909 0.00 0.00 0.00 3.08
326 334 3.754188 ATTCTTGCTAAAGCTTCGCTG 57.246 42.857 18.05 12.32 39.62 5.18
354 362 6.345298 GCTCTTCCTAAGACTCATTTAGCTT 58.655 40.000 0.00 0.00 33.12 3.74
378 386 1.345715 ACCTCAATTAGCCCCCTCGG 61.346 60.000 0.00 0.00 0.00 4.63
508 516 2.220653 AACCCACCCTCATCATTGTG 57.779 50.000 0.00 0.00 0.00 3.33
513 521 1.909302 GAGAGAAACCCACCCTCATCA 59.091 52.381 0.00 0.00 0.00 3.07
552 562 2.369394 GTGGGGCTCACTTATCCTTTG 58.631 52.381 11.06 0.00 42.86 2.77
596 606 5.048083 TGACATGGCATAAAAAGTTGACTCC 60.048 40.000 0.00 0.00 0.00 3.85
634 644 1.202417 CGGATTATGACAGTCGTGGCT 60.202 52.381 5.44 0.00 30.05 4.75
755 767 9.814899 CATGTGGTAAGCAATCCAAATAATTTA 57.185 29.630 0.00 0.00 35.38 1.40
756 768 8.320617 ACATGTGGTAAGCAATCCAAATAATTT 58.679 29.630 0.00 0.00 35.38 1.82
757 769 7.765360 CACATGTGGTAAGCAATCCAAATAATT 59.235 33.333 18.51 0.00 35.38 1.40
758 770 7.093377 ACACATGTGGTAAGCAATCCAAATAAT 60.093 33.333 28.64 0.00 35.38 1.28
759 771 6.210385 ACACATGTGGTAAGCAATCCAAATAA 59.790 34.615 28.64 0.00 35.38 1.40
760 772 5.714333 ACACATGTGGTAAGCAATCCAAATA 59.286 36.000 28.64 0.00 35.38 1.40
761 773 4.527816 ACACATGTGGTAAGCAATCCAAAT 59.472 37.500 28.64 0.00 35.38 2.32
762 774 3.894427 ACACATGTGGTAAGCAATCCAAA 59.106 39.130 28.64 0.00 35.38 3.28
763 775 3.495331 ACACATGTGGTAAGCAATCCAA 58.505 40.909 28.64 0.00 35.38 3.53
764 776 3.081061 GACACATGTGGTAAGCAATCCA 58.919 45.455 28.64 0.00 34.19 3.41
765 777 3.081061 TGACACATGTGGTAAGCAATCC 58.919 45.455 28.64 6.08 34.19 3.01
766 778 3.424829 CGTGACACATGTGGTAAGCAATC 60.425 47.826 28.64 14.99 34.19 2.67
767 779 2.483877 CGTGACACATGTGGTAAGCAAT 59.516 45.455 28.64 5.90 34.19 3.56
768 780 1.870402 CGTGACACATGTGGTAAGCAA 59.130 47.619 28.64 4.27 34.19 3.91
769 781 1.202592 ACGTGACACATGTGGTAAGCA 60.203 47.619 28.64 15.24 31.87 3.91
770 782 1.194547 CACGTGACACATGTGGTAAGC 59.805 52.381 28.64 13.03 44.71 3.09
777 789 2.902705 AACTACCACGTGACACATGT 57.097 45.000 19.30 7.66 33.47 3.21
778 790 4.497966 CGTATAACTACCACGTGACACATG 59.502 45.833 19.30 0.00 0.00 3.21
779 791 4.156556 ACGTATAACTACCACGTGACACAT 59.843 41.667 19.30 4.95 46.29 3.21
780 792 3.501828 ACGTATAACTACCACGTGACACA 59.498 43.478 19.30 0.00 46.29 3.72
781 793 4.083581 ACGTATAACTACCACGTGACAC 57.916 45.455 19.30 0.00 46.29 3.67
787 799 4.871993 AGAGTCACGTATAACTACCACG 57.128 45.455 0.00 0.00 41.32 4.94
788 800 6.458888 GGGTTAGAGTCACGTATAACTACCAC 60.459 46.154 13.22 5.30 0.00 4.16
789 801 5.590259 GGGTTAGAGTCACGTATAACTACCA 59.410 44.000 13.22 0.00 0.00 3.25
790 802 5.277538 CGGGTTAGAGTCACGTATAACTACC 60.278 48.000 0.00 0.00 0.00 3.18
791 803 5.277538 CCGGGTTAGAGTCACGTATAACTAC 60.278 48.000 0.00 0.00 0.00 2.73
792 804 4.816385 CCGGGTTAGAGTCACGTATAACTA 59.184 45.833 0.00 0.00 0.00 2.24
793 805 3.629398 CCGGGTTAGAGTCACGTATAACT 59.371 47.826 0.00 0.00 0.00 2.24
794 806 3.378427 ACCGGGTTAGAGTCACGTATAAC 59.622 47.826 6.32 0.00 0.00 1.89
795 807 3.620488 ACCGGGTTAGAGTCACGTATAA 58.380 45.455 6.32 0.00 0.00 0.98
796 808 3.281727 ACCGGGTTAGAGTCACGTATA 57.718 47.619 6.32 0.00 0.00 1.47
797 809 2.134789 ACCGGGTTAGAGTCACGTAT 57.865 50.000 6.32 0.00 0.00 3.06
798 810 2.779755 TACCGGGTTAGAGTCACGTA 57.220 50.000 4.31 0.00 0.00 3.57
799 811 1.747355 CATACCGGGTTAGAGTCACGT 59.253 52.381 4.31 0.00 0.00 4.49
800 812 1.747355 ACATACCGGGTTAGAGTCACG 59.253 52.381 4.31 0.00 0.00 4.35
801 813 2.159142 CCACATACCGGGTTAGAGTCAC 60.159 54.545 4.31 0.00 0.00 3.67
802 814 2.104967 CCACATACCGGGTTAGAGTCA 58.895 52.381 4.31 0.00 0.00 3.41
803 815 2.105766 ACCACATACCGGGTTAGAGTC 58.894 52.381 4.31 0.00 32.12 3.36
804 816 2.242882 ACCACATACCGGGTTAGAGT 57.757 50.000 4.31 0.00 32.12 3.24
805 817 3.294214 ACTACCACATACCGGGTTAGAG 58.706 50.000 4.31 0.00 38.60 2.43
806 818 3.386932 ACTACCACATACCGGGTTAGA 57.613 47.619 4.31 0.00 38.60 2.10
815 827 6.743575 AAATTGCAGAGAACTACCACATAC 57.256 37.500 0.00 0.00 0.00 2.39
828 840 2.094894 CGCCAGTGAGTAAATTGCAGAG 59.905 50.000 0.00 0.00 0.00 3.35
830 842 1.466360 GCGCCAGTGAGTAAATTGCAG 60.466 52.381 0.00 0.00 0.00 4.41
884 1143 5.446143 TGATTTGCAATTTTGTAGGACGT 57.554 34.783 0.00 0.00 0.00 4.34
1192 1474 3.446570 GTCACCTGCCATGGCTGC 61.447 66.667 35.53 18.83 42.51 5.25
1352 1647 2.093711 GGAACCTTGTTGGCACTTTTGT 60.094 45.455 0.00 0.00 40.22 2.83
1426 1722 4.022242 GTCTGTATATCTAGCCGCTTGGAA 60.022 45.833 0.00 0.00 33.02 3.53
1609 1905 2.671351 CGTTCATGGTCGCTACTCACTT 60.671 50.000 0.00 0.00 0.00 3.16
2819 3391 1.611977 CCATCCTTCAGTACGCCGATA 59.388 52.381 0.00 0.00 0.00 2.92
4195 4767 2.681778 CGTGGACTCAGGGGAGCT 60.682 66.667 0.00 0.00 45.42 4.09
4806 5378 6.049955 TCTCTGGAACATCGGTTAGATTTT 57.950 37.500 0.00 0.00 37.52 1.82
5120 5692 9.901172 GAAATTGAGGAGTTAGGGATAAAAGTA 57.099 33.333 0.00 0.00 0.00 2.24
5151 5723 1.180029 GCAGTCAAGCCCATGAATGT 58.820 50.000 11.99 0.00 44.80 2.71
5556 6136 4.597079 TCGCATCATTTTTCTAATTCCGC 58.403 39.130 0.00 0.00 0.00 5.54
5576 6156 3.311486 AGAACAGAAGAAGAAGGCTCG 57.689 47.619 0.00 0.00 0.00 5.03
5646 6334 1.952296 GCATGCATCACCCTCCTTTAG 59.048 52.381 14.21 0.00 0.00 1.85
5756 6462 1.699083 TCTGCACCCTTCATCAACTGA 59.301 47.619 0.00 0.00 0.00 3.41
5786 6494 7.710907 GCTTTGATGTGATGTCTAGGTATGTAA 59.289 37.037 0.00 0.00 0.00 2.41
5795 6506 3.998913 TGGGCTTTGATGTGATGTCTA 57.001 42.857 0.00 0.00 0.00 2.59
5818 6532 0.822164 TGGCTACTCCGGCTTTAGAC 59.178 55.000 0.00 0.00 37.80 2.59
5861 6577 4.388499 GGCGGACCGGTGTGTCAT 62.388 66.667 14.63 0.00 36.97 3.06
6054 6775 0.742505 CGTGCCGTTATAGGGTCTCA 59.257 55.000 0.00 0.00 0.00 3.27
6099 6820 3.723348 GCGGCGTTTCCTGTGACC 61.723 66.667 9.37 0.00 0.00 4.02
6181 6902 2.567169 TCTTGTGTGGTACCATCCTCTG 59.433 50.000 19.72 7.57 0.00 3.35
6182 6903 2.902608 TCTTGTGTGGTACCATCCTCT 58.097 47.619 19.72 0.00 0.00 3.69
6183 6904 3.914426 ATCTTGTGTGGTACCATCCTC 57.086 47.619 19.72 5.50 0.00 3.71
6194 6916 2.668250 TGACGACGGTTATCTTGTGTG 58.332 47.619 0.00 0.00 0.00 3.82
6289 7011 3.620427 ACGGAAGTATGTGTGGCATAA 57.380 42.857 0.00 0.00 46.88 1.90
6427 7326 2.288961 TCCACGTTTATCTCTTCGCC 57.711 50.000 0.00 0.00 0.00 5.54
6428 7327 4.859629 ATTTCCACGTTTATCTCTTCGC 57.140 40.909 0.00 0.00 0.00 4.70
6429 7328 5.287752 TCGAATTTCCACGTTTATCTCTTCG 59.712 40.000 0.00 0.00 34.65 3.79
6435 7334 5.156804 AGCATCGAATTTCCACGTTTATC 57.843 39.130 0.00 0.00 0.00 1.75
6436 7335 5.560966 AAGCATCGAATTTCCACGTTTAT 57.439 34.783 0.00 0.00 0.00 1.40
6438 7337 3.915437 AAGCATCGAATTTCCACGTTT 57.085 38.095 0.00 0.00 0.00 3.60
6501 7401 4.027377 GTCGAACTTAACGAACTTTGACGT 60.027 41.667 0.00 0.00 44.57 4.34
6571 7476 5.645067 TGCAATTTGTGAAATTTGACCAACA 59.355 32.000 5.29 0.00 38.97 3.33
6572 7477 6.116680 TGCAATTTGTGAAATTTGACCAAC 57.883 33.333 5.29 0.00 38.97 3.77
6593 7499 7.652105 AGAAAAATGTCATTAGATGCATCATGC 59.348 33.333 27.81 17.69 45.29 4.06
6655 7561 2.738846 ACTCTGCATGTAAGCTTTGTCG 59.261 45.455 3.20 0.00 34.99 4.35
6796 7703 7.180322 TCCACAAATATGTTAATGCACCATT 57.820 32.000 0.00 0.00 37.82 3.16
6823 7730 1.623311 GGGTTGGTTTTGAGGATTGGG 59.377 52.381 0.00 0.00 0.00 4.12
6903 7819 4.808895 TCATATTCACCCAAATCGTTCTCG 59.191 41.667 0.00 0.00 38.55 4.04
6995 7911 1.071299 CCTTTTTGCAAGCCCCACC 59.929 57.895 0.00 0.00 0.00 4.61
7024 8323 9.610104 AATAAACCCCTGTCCTTTAAATTAACT 57.390 29.630 0.00 0.00 0.00 2.24
7332 8675 2.133281 TGAGGTGAGCATCCCATTTG 57.867 50.000 0.00 0.00 0.00 2.32
7420 8763 9.695526 CTATGATTGACTCCATAAAGAGAAGAG 57.304 37.037 0.00 0.00 37.33 2.85
7458 8801 6.344500 TGAAGATCTAAGAAAGGTGCTGATC 58.656 40.000 0.00 0.00 0.00 2.92
7554 8940 7.036863 AGGTAAGGGTCTTGAAAGGATAAATCA 60.037 37.037 0.00 0.00 0.00 2.57
7572 8958 3.713826 TTCAGGCTTGTAAGGTAAGGG 57.286 47.619 0.00 0.00 0.00 3.95
7670 9057 3.737850 AGTTTCTGCCTCTCAAACTGAG 58.262 45.455 0.00 0.00 45.59 3.35
7997 9388 2.838202 ACGACCACAATACTGGGATCTT 59.162 45.455 0.00 0.00 35.34 2.40
7999 9390 2.981859 ACGACCACAATACTGGGATC 57.018 50.000 0.00 0.00 35.34 3.36
8130 9522 0.320421 TGCGTTCACTTCTGTAGGGC 60.320 55.000 0.00 0.00 0.00 5.19
8316 9714 1.928868 ACAAGCCTTTTGGATCCCTG 58.071 50.000 9.90 0.00 44.07 4.45
8371 9769 4.371624 AAGATGATGGTCAGTTGGTTCA 57.628 40.909 0.00 0.00 0.00 3.18
8404 9803 8.184192 CGGATGATTTACAAAGTAAGATTTGCT 58.816 33.333 0.00 0.00 42.68 3.91
8546 9946 2.896039 AGGAACCTCTTACAGAGCAGT 58.104 47.619 0.00 0.00 40.98 4.40
8585 9989 2.517321 GCTCACTCAGCGAAATGAAC 57.483 50.000 0.00 0.00 38.76 3.18
8822 10226 9.866936 GAACGTTTTTGACATTACAATAGTGTA 57.133 29.630 0.46 0.00 39.30 2.90
8823 10227 8.617809 AGAACGTTTTTGACATTACAATAGTGT 58.382 29.630 0.46 0.00 42.09 3.55
8824 10228 9.445786 AAGAACGTTTTTGACATTACAATAGTG 57.554 29.630 0.46 0.00 0.00 2.74
8835 10239 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
8836 10240 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
8837 10241 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
8838 10242 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
8839 10243 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
8840 10244 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
8841 10245 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
8842 10246 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
8843 10247 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
8844 10248 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
8845 10249 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
8846 10250 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
8847 10251 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
8848 10252 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
8849 10253 7.177921 CACTACTTCCTCCGTCCCATAATATAA 59.822 40.741 0.00 0.00 0.00 0.98
8850 10254 6.662234 CACTACTTCCTCCGTCCCATAATATA 59.338 42.308 0.00 0.00 0.00 0.86
8851 10255 5.480772 CACTACTTCCTCCGTCCCATAATAT 59.519 44.000 0.00 0.00 0.00 1.28
8852 10256 4.831155 CACTACTTCCTCCGTCCCATAATA 59.169 45.833 0.00 0.00 0.00 0.98
8853 10257 3.641906 CACTACTTCCTCCGTCCCATAAT 59.358 47.826 0.00 0.00 0.00 1.28
8854 10258 3.028850 CACTACTTCCTCCGTCCCATAA 58.971 50.000 0.00 0.00 0.00 1.90
8855 10259 2.024655 ACACTACTTCCTCCGTCCCATA 60.025 50.000 0.00 0.00 0.00 2.74
8856 10260 1.273098 ACACTACTTCCTCCGTCCCAT 60.273 52.381 0.00 0.00 0.00 4.00
8857 10261 0.113776 ACACTACTTCCTCCGTCCCA 59.886 55.000 0.00 0.00 0.00 4.37
8858 10262 1.264295 AACACTACTTCCTCCGTCCC 58.736 55.000 0.00 0.00 0.00 4.46
8859 10263 4.081807 ACATAAACACTACTTCCTCCGTCC 60.082 45.833 0.00 0.00 0.00 4.79
8860 10264 5.069501 ACATAAACACTACTTCCTCCGTC 57.930 43.478 0.00 0.00 0.00 4.79
8861 10265 4.771054 AGACATAAACACTACTTCCTCCGT 59.229 41.667 0.00 0.00 0.00 4.69
8862 10266 5.326200 AGACATAAACACTACTTCCTCCG 57.674 43.478 0.00 0.00 0.00 4.63
8863 10267 9.498176 TTTTTAGACATAAACACTACTTCCTCC 57.502 33.333 0.00 0.00 30.58 4.30
8886 10290 8.579850 TGTTTCCATGCTATTATCACTCTTTT 57.420 30.769 0.00 0.00 0.00 2.27
8916 10320 9.035607 GTGATGTACAGATTCGATCTTTATGTT 57.964 33.333 0.33 0.00 37.58 2.71
8974 10382 1.229428 CACAGCCACACGAGTCATTT 58.771 50.000 0.00 0.00 0.00 2.32
9002 10410 1.832608 CCCATCCTCGTCCCATCGA 60.833 63.158 0.00 0.00 38.19 3.59
9021 10429 3.181438 ACTGTACAAAATGCAGGTGGGTA 60.181 43.478 0.00 0.00 44.84 3.69
9028 10436 7.165812 GTGTGTTTAGAACTGTACAAAATGCAG 59.834 37.037 0.00 0.00 45.94 4.41
9040 10448 7.807907 AGTTTTTCTTGTGTGTGTTTAGAACTG 59.192 33.333 0.00 0.00 0.00 3.16
9058 10466 8.695456 TGGCTTCAAGAAAGAAATAGTTTTTCT 58.305 29.630 3.03 3.03 41.53 2.52
9066 10474 4.766891 CAGGGTGGCTTCAAGAAAGAAATA 59.233 41.667 0.00 0.00 37.12 1.40
9078 10486 3.889538 GGGTATATTTTCAGGGTGGCTTC 59.110 47.826 0.00 0.00 0.00 3.86
9095 10503 2.158813 CGGTGCTAATCAGGTTGGGTAT 60.159 50.000 0.00 0.00 0.00 2.73
9102 10510 4.442706 CAATCTAACGGTGCTAATCAGGT 58.557 43.478 0.00 0.00 0.00 4.00
9151 10559 2.203070 CTATGCGGGTGGAGTGCC 60.203 66.667 0.00 0.00 0.00 5.01
9202 10610 0.954452 GGAGGGATTAGCGCAATTGG 59.046 55.000 11.47 0.00 0.00 3.16
9223 10631 4.595986 GCTGGGTTAGGGAACTTTTGATA 58.404 43.478 0.00 0.00 43.67 2.15
9229 10637 1.002502 GCGCTGGGTTAGGGAACTT 60.003 57.895 0.00 0.00 43.67 2.66
9231 10639 2.437895 GGCGCTGGGTTAGGGAAC 60.438 66.667 7.64 0.00 41.61 3.62
9331 10753 4.463186 CCTCCGATTACTCCGATAAAGGAT 59.537 45.833 0.00 0.00 39.96 3.24
9416 10838 4.327087 GTGTTGTTTTGGCTCTGTTCAAAG 59.673 41.667 0.00 0.00 34.83 2.77
9478 10900 4.728102 TACGAAGCGGCACCCACG 62.728 66.667 1.45 2.91 0.00 4.94
9505 10927 1.066858 ACGTGTGGCTCACCTCTATTG 60.067 52.381 13.55 1.21 43.51 1.90
9534 10956 1.136305 CGAGAAAGGTAGATCCGGCAA 59.864 52.381 0.00 0.00 41.99 4.52
9535 10957 0.744874 CGAGAAAGGTAGATCCGGCA 59.255 55.000 0.00 0.00 41.99 5.69
9563 10985 0.108377 CATCGTCATCGTCCAACCCA 60.108 55.000 0.00 0.00 38.33 4.51
9619 11041 4.035792 CGAGTCTATCTTCAGGACGATGTT 59.964 45.833 0.00 0.00 35.42 2.71
9624 11046 2.288458 GACCGAGTCTATCTTCAGGACG 59.712 54.545 0.00 0.00 35.42 4.79
9628 11050 3.563808 CCTCTGACCGAGTCTATCTTCAG 59.436 52.174 5.77 0.00 38.11 3.02


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

AutoCloner maintained by Alex Coulton.