Multiple sequence alignment - TraesCS3B01G355200

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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 TraesCS3B01G355200 chr3B 100.000 7042 0 0 1 7042 565436766 565429725 0.000000e+00 13005.0
1 TraesCS3B01G355200 chr3B 100.000 1949 0 0 7395 9343 565429372 565427424 0.000000e+00 3600.0
2 TraesCS3B01G355200 chr3B 95.470 2053 49 21 1839 3878 565564587 565562566 0.000000e+00 3236.0
3 TraesCS3B01G355200 chr3B 86.279 2150 193 44 4325 6421 51255226 51253126 0.000000e+00 2242.0
4 TraesCS3B01G355200 chr3B 97.197 1106 29 2 7395 8500 565561935 565560832 0.000000e+00 1869.0
5 TraesCS3B01G355200 chr3B 90.190 1264 30 19 631 1844 565565933 565564714 0.000000e+00 1561.0
6 TraesCS3B01G355200 chr3B 98.392 622 9 1 6421 7042 565562571 565561951 0.000000e+00 1092.0
7 TraesCS3B01G355200 chr3B 88.550 655 33 8 3880 4497 284382242 284382891 0.000000e+00 756.0
8 TraesCS3B01G355200 chr3B 96.112 463 18 0 8654 9116 565541965 565541503 0.000000e+00 756.0
9 TraesCS3B01G355200 chr3B 82.869 753 64 28 4221 4943 181301458 181302175 4.790000e-172 616.0
10 TraesCS3B01G355200 chr3B 94.215 363 5 1 3879 4225 565430708 565430346 2.970000e-149 540.0
11 TraesCS3B01G355200 chr3B 88.372 301 35 0 8678 8978 565413859 565413559 6.900000e-96 363.0
12 TraesCS3B01G355200 chr3B 93.909 197 10 2 220 414 565573934 565573738 7.090000e-76 296.0
13 TraesCS3B01G355200 chr3B 93.814 194 7 4 450 642 565573646 565573457 4.270000e-73 287.0
14 TraesCS3B01G355200 chr3B 92.063 189 11 3 3923 4111 70593844 70594028 7.190000e-66 263.0
15 TraesCS3B01G355200 chr3B 88.421 190 21 1 8931 9120 565413558 565413370 2.620000e-55 228.0
16 TraesCS3B01G355200 chr3B 99.174 121 1 0 64 184 565637188 565637068 1.580000e-52 219.0
17 TraesCS3B01G355200 chr3B 97.561 41 1 0 1 41 565637761 565637721 4.680000e-08 71.3
18 TraesCS3B01G355200 chr3B 100.000 28 0 0 227 254 173008639 173008666 1.700000e-02 52.8
19 TraesCS3B01G355200 chr1B 90.653 2589 124 45 3879 6421 348800282 348802798 0.000000e+00 3332.0
20 TraesCS3B01G355200 chr1B 87.244 2634 192 60 3879 6412 39736224 39738813 0.000000e+00 2870.0
21 TraesCS3B01G355200 chr1B 89.772 1926 126 36 4511 6421 529504161 529506030 0.000000e+00 2399.0
22 TraesCS3B01G355200 chr1B 87.237 666 62 9 2309 2960 591230394 591231050 0.000000e+00 737.0
23 TraesCS3B01G355200 chr1B 91.061 537 32 5 3879 4399 529503632 529504168 0.000000e+00 712.0
24 TraesCS3B01G355200 chr1B 87.115 520 41 15 7599 8104 591232880 591233387 4.900000e-157 566.0
25 TraesCS3B01G355200 chr1B 82.946 516 48 15 1240 1743 591229139 591229626 6.700000e-116 429.0
26 TraesCS3B01G355200 chr1B 90.154 325 27 5 4227 4550 324356472 324356792 1.450000e-112 418.0
27 TraesCS3B01G355200 chr1B 85.714 364 25 10 3879 4216 39738451 39738813 8.920000e-95 359.0
28 TraesCS3B01G355200 chr1B 84.638 345 37 6 6473 6816 591231562 591231891 6.990000e-86 329.0
29 TraesCS3B01G355200 chr1B 86.719 256 25 4 1843 2091 591229850 591230103 9.240000e-70 276.0
30 TraesCS3B01G355200 chr1B 87.952 83 10 0 3791 3873 591231439 591231521 2.150000e-16 99.0
31 TraesCS3B01G355200 chr1B 95.238 42 0 2 8457 8498 279914416 279914455 2.180000e-06 65.8
32 TraesCS3B01G355200 chr1B 90.000 50 2 2 8457 8504 666907878 666907830 2.820000e-05 62.1
33 TraesCS3B01G355200 chr1B 100.000 31 0 0 1134 1164 642076637 642076607 3.640000e-04 58.4
34 TraesCS3B01G355200 chr1B 97.059 34 1 0 381 414 667012210 667012177 3.640000e-04 58.4
35 TraesCS3B01G355200 chr5B 89.254 2559 192 39 3923 6421 645537583 645535048 0.000000e+00 3125.0
36 TraesCS3B01G355200 chr5B 87.041 2639 218 65 3879 6421 328209225 328206615 0.000000e+00 2865.0
37 TraesCS3B01G355200 chr5B 90.017 1783 131 24 4671 6421 328205820 328204053 0.000000e+00 2263.0
38 TraesCS3B01G355200 chr5B 84.375 736 69 18 4227 4943 228760202 228759494 0.000000e+00 680.0
39 TraesCS3B01G355200 chr5B 88.663 344 27 3 4227 4558 130925653 130925310 8.730000e-110 409.0
40 TraesCS3B01G355200 chr5B 85.629 334 48 0 4236 4569 81538075 81537742 1.490000e-92 351.0
41 TraesCS3B01G355200 chr5B 94.872 39 2 0 376 414 406547162 406547124 2.820000e-05 62.1
42 TraesCS3B01G355200 chr5B 97.059 34 0 1 414 447 664418300 664418268 1.000000e-03 56.5
43 TraesCS3B01G355200 chr5B 100.000 28 0 0 420 447 8413290 8413263 1.700000e-02 52.8
44 TraesCS3B01G355200 chr6B 86.999 2569 188 49 3923 6421 599812593 599810101 0.000000e+00 2760.0
45 TraesCS3B01G355200 chr6B 84.527 1215 92 26 3878 5050 268298426 268297266 0.000000e+00 1114.0
46 TraesCS3B01G355200 chr6B 79.217 741 82 39 4227 4943 117705176 117704484 5.150000e-122 449.0
47 TraesCS3B01G355200 chr6B 86.857 350 39 5 4588 4931 308581840 308582188 1.470000e-102 385.0
48 TraesCS3B01G355200 chr6B 84.636 371 45 8 4573 4943 284658800 284659158 8.920000e-95 359.0
49 TraesCS3B01G355200 chr6B 81.604 212 36 3 1175 1386 127847364 127847156 1.250000e-38 172.0
50 TraesCS3B01G355200 chr6B 95.349 43 2 0 8460 8502 22263916 22263874 1.680000e-07 69.4
51 TraesCS3B01G355200 chr6B 95.349 43 1 1 8450 8491 708101415 708101457 6.050000e-07 67.6
52 TraesCS3B01G355200 chr4B 91.377 1844 94 32 4602 6421 89522605 89524407 0.000000e+00 2464.0
53 TraesCS3B01G355200 chr4B 91.495 1552 101 18 4806 6338 285614642 285616181 0.000000e+00 2106.0
54 TraesCS3B01G355200 chr4B 92.163 1225 92 3 5201 6422 389112008 389110785 0.000000e+00 1727.0
55 TraesCS3B01G355200 chr4B 84.870 1725 181 51 4625 6329 222572920 222571256 0.000000e+00 1666.0
56 TraesCS3B01G355200 chr4B 92.786 707 44 4 3895 4599 89521501 89522202 0.000000e+00 1016.0
57 TraesCS3B01G355200 chr4B 83.514 740 69 21 3879 4576 285613471 285614199 7.910000e-180 641.0
58 TraesCS3B01G355200 chr4B 92.750 400 13 1 3879 4262 389112782 389112383 1.760000e-156 564.0
59 TraesCS3B01G355200 chr4B 93.407 364 8 1 3878 4225 389111149 389110786 8.310000e-145 525.0
60 TraesCS3B01G355200 chr4B 80.199 702 84 28 4227 4897 24838998 24839675 8.490000e-130 475.0
61 TraesCS3B01G355200 chr4B 88.380 284 8 8 3879 4142 285615903 285616181 1.510000e-82 318.0
62 TraesCS3B01G355200 chr4B 83.886 211 31 3 1177 1386 534718854 534719062 2.060000e-46 198.0
63 TraesCS3B01G355200 chr4B 82.075 212 35 3 1175 1386 411178075 411177867 2.680000e-40 178.0
64 TraesCS3B01G355200 chr4B 100.000 34 0 0 381 414 156524722 156524689 7.830000e-06 63.9
65 TraesCS3B01G355200 chr1D 92.725 1677 89 17 4768 6426 493215506 493217167 0.000000e+00 2390.0
66 TraesCS3B01G355200 chr1D 88.530 898 46 16 3879 4738 493214337 493215215 0.000000e+00 1035.0
67 TraesCS3B01G355200 chr1D 88.298 658 68 5 2310 2960 436212419 436213074 0.000000e+00 780.0
68 TraesCS3B01G355200 chr1D 84.477 612 59 19 1244 1855 436211365 436211940 1.050000e-158 571.0
69 TraesCS3B01G355200 chr1D 85.609 542 45 20 7599 8134 436214889 436215403 1.070000e-148 538.0
70 TraesCS3B01G355200 chr1D 83.699 319 36 6 6473 6790 436213466 436213769 4.270000e-73 287.0
71 TraesCS3B01G355200 chr1D 86.920 237 22 6 1862 2091 436212086 436212320 3.350000e-64 257.0
72 TraesCS3B01G355200 chr1D 85.185 162 8 8 6884 7041 436213823 436213972 1.620000e-32 152.0
73 TraesCS3B01G355200 chr1D 83.537 164 19 8 452 612 462387629 462387787 7.560000e-31 147.0
74 TraesCS3B01G355200 chr1D 82.258 124 20 2 452 574 49611439 49611561 1.280000e-18 106.0
75 TraesCS3B01G355200 chr1D 80.469 128 19 6 453 576 460307436 460307311 9.990000e-15 93.5
76 TraesCS3B01G355200 chr1D 95.238 42 0 2 8457 8498 199427834 199427873 2.180000e-06 65.8
77 TraesCS3B01G355200 chr1D 95.000 40 2 0 8457 8496 80001432 80001393 7.830000e-06 63.9
78 TraesCS3B01G355200 chr1D 100.000 34 0 0 8457 8490 291087477 291087510 7.830000e-06 63.9
79 TraesCS3B01G355200 chr1D 100.000 33 0 0 8457 8489 139162864 139162832 2.820000e-05 62.1
80 TraesCS3B01G355200 chr1D 100.000 33 0 0 8457 8489 431958053 431958021 2.820000e-05 62.1
81 TraesCS3B01G355200 chr1D 97.222 36 0 1 8455 8489 65902471 65902506 1.010000e-04 60.2
82 TraesCS3B01G355200 chr1D 97.222 36 0 1 8457 8491 106843237 106843202 1.010000e-04 60.2
83 TraesCS3B01G355200 chr1D 94.737 38 2 0 8457 8494 112467891 112467928 1.010000e-04 60.2
84 TraesCS3B01G355200 chr1D 91.304 46 0 3 8444 8486 247514059 247514103 1.010000e-04 60.2
85 TraesCS3B01G355200 chr1D 91.111 45 2 2 8457 8500 409047108 409047151 1.010000e-04 60.2
86 TraesCS3B01G355200 chr1D 94.737 38 2 0 8457 8494 462491239 462491276 1.010000e-04 60.2
87 TraesCS3B01G355200 chr1D 100.000 30 0 0 8457 8486 457037085 457037056 1.000000e-03 56.5
88 TraesCS3B01G355200 chr1D 85.965 57 2 4 8433 8486 457037082 457037135 1.000000e-03 56.5
89 TraesCS3B01G355200 chr3A 91.479 1420 75 26 1839 3243 571399063 571397675 0.000000e+00 1910.0
90 TraesCS3B01G355200 chr3A 88.995 1463 56 42 451 1844 571400616 571399190 0.000000e+00 1712.0
91 TraesCS3B01G355200 chr3A 94.502 1055 42 6 7395 8439 571396076 571395028 0.000000e+00 1613.0
92 TraesCS3B01G355200 chr3A 90.665 707 44 10 8657 9343 571334828 571334124 0.000000e+00 920.0
93 TraesCS3B01G355200 chr3A 92.991 585 28 6 6421 7002 571397314 571396740 0.000000e+00 841.0
94 TraesCS3B01G355200 chr3A 87.288 472 49 7 8654 9117 571316370 571315902 6.420000e-146 529.0
95 TraesCS3B01G355200 chr3A 91.857 307 19 3 3578 3878 571397615 571397309 3.120000e-114 424.0
96 TraesCS3B01G355200 chr3A 94.444 234 9 4 185 414 571400944 571400711 3.210000e-94 357.0
97 TraesCS3B01G355200 chr3A 93.706 143 8 1 43 184 571401226 571401084 7.350000e-51 213.0
98 TraesCS3B01G355200 chr3A 83.886 211 31 3 1177 1386 671024118 671023910 2.060000e-46 198.0
99 TraesCS3B01G355200 chr3A 92.063 126 4 2 8521 8643 571395000 571394878 1.250000e-38 172.0
100 TraesCS3B01G355200 chr3A 95.122 41 2 0 1 41 571401782 571401742 2.180000e-06 65.8
101 TraesCS3B01G355200 chr3A 95.000 40 2 0 414 453 571400692 571400653 7.830000e-06 63.9
102 TraesCS3B01G355200 chr3A 100.000 28 0 0 3563 3590 571397654 571397627 1.700000e-02 52.8
103 TraesCS3B01G355200 chr5A 86.356 1759 167 49 4658 6403 8805601 8807299 0.000000e+00 1851.0
104 TraesCS3B01G355200 chr5A 100.000 32 0 0 1134 1165 493020828 493020859 1.010000e-04 60.2
105 TraesCS3B01G355200 chr5A 100.000 32 0 0 1134 1165 493020909 493020878 1.010000e-04 60.2
106 TraesCS3B01G355200 chr3D 94.815 1080 49 3 7395 8468 433190062 433188984 0.000000e+00 1677.0
107 TraesCS3B01G355200 chr3D 92.367 773 25 12 1083 1844 433193919 433193170 0.000000e+00 1070.0
108 TraesCS3B01G355200 chr3D 94.366 639 28 5 2604 3235 433192339 433191702 0.000000e+00 974.0
109 TraesCS3B01G355200 chr3D 93.600 625 27 6 6421 7042 433191379 433190765 0.000000e+00 920.0
110 TraesCS3B01G355200 chr3D 89.510 734 37 23 1841 2565 433193041 433192339 0.000000e+00 893.0
111 TraesCS3B01G355200 chr3D 82.808 762 91 19 4221 4943 135250678 135251438 0.000000e+00 645.0
112 TraesCS3B01G355200 chr3D 87.318 481 32 18 615 1086 433194540 433194080 2.990000e-144 523.0
113 TraesCS3B01G355200 chr3D 88.380 284 13 6 8654 8917 433163691 433163408 3.250000e-84 324.0
114 TraesCS3B01G355200 chr3D 90.141 213 15 3 3672 3878 433191586 433191374 1.200000e-68 272.0
115 TraesCS3B01G355200 chr3D 96.203 158 6 0 8956 9113 433163432 433163275 9.310000e-65 259.0
116 TraesCS3B01G355200 chr3D 92.778 180 7 4 450 629 433297172 433296999 1.200000e-63 255.0
117 TraesCS3B01G355200 chr3D 88.542 192 9 4 187 377 433297917 433297738 4.390000e-53 220.0
118 TraesCS3B01G355200 chr3D 89.683 126 7 2 8534 8656 433172652 433172530 1.260000e-33 156.0
119 TraesCS3B01G355200 chr3D 87.273 110 12 2 465 573 126385597 126385489 3.540000e-24 124.0
120 TraesCS3B01G355200 chr3D 95.775 71 3 0 3578 3648 433191654 433191584 2.130000e-21 115.0
121 TraesCS3B01G355200 chr3D 81.818 132 17 5 475 605 552764938 552764813 4.610000e-18 104.0
122 TraesCS3B01G355200 chr3D 79.104 134 13 4 9223 9341 433163112 433162979 2.800000e-10 78.7
123 TraesCS3B01G355200 chr3D 85.938 64 6 2 8457 8517 32753947 32754010 2.180000e-06 65.8
124 TraesCS3B01G355200 chr3D 94.872 39 2 0 8457 8495 431631861 431631899 2.820000e-05 62.1
125 TraesCS3B01G355200 chr3D 97.222 36 0 1 1131 1165 429097505 429097540 1.010000e-04 60.2
126 TraesCS3B01G355200 chr3D 88.462 52 2 3 8457 8506 570848723 570848772 1.010000e-04 60.2
127 TraesCS3B01G355200 chr3D 89.583 48 3 1 8439 8486 611414279 611414234 1.010000e-04 60.2
128 TraesCS3B01G355200 chr3D 97.059 34 1 0 3563 3596 433191693 433191660 3.640000e-04 58.4
129 TraesCS3B01G355200 chr3D 97.059 34 1 0 414 447 484827201 484827168 3.640000e-04 58.4
130 TraesCS3B01G355200 chr7B 90.850 1224 105 6 5201 6421 23634812 23636031 0.000000e+00 1633.0
131 TraesCS3B01G355200 chr7B 87.246 1035 72 19 4221 5209 23414910 23415930 0.000000e+00 1125.0
132 TraesCS3B01G355200 chr7B 88.080 797 57 16 3879 4643 255043264 255042474 0.000000e+00 911.0
133 TraesCS3B01G355200 chr7B 92.308 364 11 2 3878 4225 23635669 23636031 1.400000e-137 501.0
134 TraesCS3B01G355200 chr7B 81.978 627 56 21 4221 4790 233374861 233375487 6.560000e-131 479.0
135 TraesCS3B01G355200 chr7B 84.118 340 37 7 4588 4927 248589881 248590203 7.040000e-81 313.0
136 TraesCS3B01G355200 chr7B 100.000 32 0 0 1134 1165 635101256 635101287 1.010000e-04 60.2
137 TraesCS3B01G355200 chr7B 100.000 31 0 0 381 411 733924308 733924338 3.640000e-04 58.4
138 TraesCS3B01G355200 chr1A 88.754 658 66 5 2310 2960 533463990 533464646 0.000000e+00 798.0
139 TraesCS3B01G355200 chr1A 85.714 567 58 10 1174 1739 533462879 533463423 2.260000e-160 577.0
140 TraesCS3B01G355200 chr1A 85.846 544 56 13 7598 8134 533466754 533467283 8.190000e-155 558.0
141 TraesCS3B01G355200 chr1A 84.667 300 32 9 3108 3398 533465023 533465317 4.270000e-73 287.0
142 TraesCS3B01G355200 chr1A 87.109 256 24 4 1843 2091 533463636 533463889 1.990000e-71 281.0
143 TraesCS3B01G355200 chr1A 86.056 251 34 1 6567 6816 533465510 533465760 1.550000e-67 268.0
144 TraesCS3B01G355200 chr1A 85.965 171 23 1 7410 7579 533465976 533466146 2.070000e-41 182.0
145 TraesCS3B01G355200 chr1A 81.481 162 20 6 453 612 437724170 437724017 3.540000e-24 124.0
146 TraesCS3B01G355200 chr1A 87.500 88 11 0 3791 3878 533465306 533465393 1.660000e-17 102.0
147 TraesCS3B01G355200 chr1A 90.000 50 2 3 8457 8505 313907519 313907566 2.820000e-05 62.1
148 TraesCS3B01G355200 chr1A 100.000 31 0 0 384 414 65821486 65821456 3.640000e-04 58.4
149 TraesCS3B01G355200 chr1A 100.000 28 0 0 388 415 560253275 560253302 1.700000e-02 52.8
150 TraesCS3B01G355200 chr7A 84.486 593 65 15 4019 4587 43061842 43061253 2.280000e-155 560.0
151 TraesCS3B01G355200 chr7A 80.982 163 23 5 453 612 156321197 156321040 1.270000e-23 122.0
152 TraesCS3B01G355200 chr2B 83.788 623 50 29 4221 4793 519143148 519143769 2.290000e-150 544.0
153 TraesCS3B01G355200 chr2B 80.499 441 52 20 4221 4632 575139208 575139643 3.280000e-79 307.0
154 TraesCS3B01G355200 chr2B 97.059 34 1 0 414 447 775167962 775167995 3.640000e-04 58.4
155 TraesCS3B01G355200 chr5D 89.809 314 28 3 3416 3725 72370670 72370357 5.260000e-107 399.0
156 TraesCS3B01G355200 chr5D 83.740 123 15 5 455 574 549767535 549767415 2.760000e-20 111.0
157 TraesCS3B01G355200 chr5D 95.238 42 0 2 8457 8497 114214616 114214656 2.180000e-06 65.8
158 TraesCS3B01G355200 chr5D 93.182 44 1 2 8457 8500 111788673 111788632 7.830000e-06 63.9
159 TraesCS3B01G355200 chr5D 100.000 32 0 0 1134 1165 439643713 439643682 1.010000e-04 60.2
160 TraesCS3B01G355200 chr4A 87.240 337 34 7 3416 3744 707826913 707826578 8.860000e-100 375.0
161 TraesCS3B01G355200 chr4A 82.822 163 21 5 453 612 607282142 607281984 1.270000e-28 139.0
162 TraesCS3B01G355200 chr4A 90.000 50 2 2 8457 8504 250959782 250959734 2.820000e-05 62.1
163 TraesCS3B01G355200 chr4A 96.875 32 1 0 1134 1165 620113473 620113504 5.000000e-03 54.7
164 TraesCS3B01G355200 chr2A 83.412 211 32 3 1177 1386 719359137 719359345 9.570000e-45 193.0
165 TraesCS3B01G355200 chr2A 97.222 36 1 0 381 416 779301997 779301962 2.820000e-05 62.1
166 TraesCS3B01G355200 chr4D 85.401 137 16 3 454 589 323597341 323597208 1.270000e-28 139.0
167 TraesCS3B01G355200 chr4D 82.822 163 21 7 453 613 505514121 505514278 1.270000e-28 139.0
168 TraesCS3B01G355200 chr4D 85.714 112 11 4 465 574 74349035 74348927 7.670000e-21 113.0
169 TraesCS3B01G355200 chr4D 82.301 113 8 10 466 574 497250465 497250569 4.650000e-13 87.9
170 TraesCS3B01G355200 chr4D 95.349 43 0 2 8457 8497 20122051 20122093 6.050000e-07 67.6
171 TraesCS3B01G355200 chr4D 100.000 34 0 0 1132 1165 303079344 303079311 7.830000e-06 63.9
172 TraesCS3B01G355200 chr4D 97.059 34 1 0 414 447 496870040 496870007 3.640000e-04 58.4
173 TraesCS3B01G355200 chr4D 100.000 29 0 0 419 447 368706794 368706822 5.000000e-03 54.7
174 TraesCS3B01G355200 chr4D 100.000 28 0 0 420 447 477900525 477900552 1.700000e-02 52.8
175 TraesCS3B01G355200 chrUn 84.459 148 14 7 453 595 294376634 294376777 4.550000e-28 137.0
176 TraesCS3B01G355200 chrUn 82.857 140 17 5 453 589 61736508 61736643 1.650000e-22 119.0
177 TraesCS3B01G355200 chrUn 82.022 89 13 3 502 589 419376211 419376297 1.300000e-08 73.1
178 TraesCS3B01G355200 chrUn 100.000 35 0 0 8457 8491 84435409 84435375 2.180000e-06 65.8
179 TraesCS3B01G355200 chrUn 100.000 33 0 0 8457 8489 22763116 22763084 2.820000e-05 62.1
180 TraesCS3B01G355200 chrUn 97.059 34 1 0 8457 8490 65136721 65136688 3.640000e-04 58.4
181 TraesCS3B01G355200 chrUn 97.059 34 1 0 8457 8490 65138924 65138957 3.640000e-04 58.4
182 TraesCS3B01G355200 chrUn 94.595 37 2 0 8457 8493 137782264 137782228 3.640000e-04 58.4
183 TraesCS3B01G355200 chrUn 100.000 31 0 0 8457 8487 266536237 266536267 3.640000e-04 58.4
184 TraesCS3B01G355200 chrUn 100.000 31 0 0 8459 8489 273925301 273925271 3.640000e-04 58.4
185 TraesCS3B01G355200 chrUn 100.000 31 0 0 8457 8487 405825467 405825497 3.640000e-04 58.4
186 TraesCS3B01G355200 chrUn 100.000 31 0 0 8457 8487 473080423 473080453 3.640000e-04 58.4
187 TraesCS3B01G355200 chrUn 97.059 34 0 1 8457 8489 19086502 19086535 1.000000e-03 56.5
188 TraesCS3B01G355200 chrUn 96.970 33 1 0 8460 8492 37862195 37862163 1.000000e-03 56.5
189 TraesCS3B01G355200 chr7D 81.437 167 21 9 451 613 70836125 70836285 2.740000e-25 128.0
190 TraesCS3B01G355200 chr7D 89.796 49 3 2 8453 8499 13036184 13036136 2.820000e-05 62.1
191 TraesCS3B01G355200 chr2D 79.630 162 25 5 453 612 102856039 102856194 9.920000e-20 110.0
192 TraesCS3B01G355200 chr2D 88.235 51 4 2 8457 8507 53145782 53145830 1.010000e-04 60.2
193 TraesCS3B01G355200 chr2D 97.143 35 1 0 8457 8491 81327317 81327351 1.010000e-04 60.2
194 TraesCS3B01G355200 chr2D 97.059 34 1 0 414 447 543432925 543432892 3.640000e-04 58.4
195 TraesCS3B01G355200 chr6D 88.525 61 7 0 502 562 407212555 407212615 3.620000e-09 75.0
196 TraesCS3B01G355200 chr6D 97.297 37 1 0 8457 8493 78520546 78520582 7.830000e-06 63.9
197 TraesCS3B01G355200 chr6D 100.000 34 0 0 8457 8490 288470145 288470112 7.830000e-06 63.9
198 TraesCS3B01G355200 chr6D 91.489 47 3 1 8457 8502 387886019 387885973 7.830000e-06 63.9
199 TraesCS3B01G355200 chr6D 92.857 42 3 0 8457 8498 60049560 60049519 2.820000e-05 62.1
200 TraesCS3B01G355200 chr6D 94.737 38 2 0 1128 1165 52814549 52814586 1.010000e-04 60.2
201 TraesCS3B01G355200 chr6A 96.970 33 1 0 1133 1165 593820700 593820732 1.000000e-03 56.5


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 TraesCS3B01G355200 chr3B 565427424 565436766 9342 True 8302.500000 13005 100.000000 1 9343 2 chr3B.!!$R5 9342
1 TraesCS3B01G355200 chr3B 51253126 51255226 2100 True 2242.000000 2242 86.279000 4325 6421 1 chr3B.!!$R1 2096
2 TraesCS3B01G355200 chr3B 565560832 565565933 5101 True 1939.500000 3236 95.312250 631 8500 4 chr3B.!!$R6 7869
3 TraesCS3B01G355200 chr3B 284382242 284382891 649 False 756.000000 756 88.550000 3880 4497 1 chr3B.!!$F4 617
4 TraesCS3B01G355200 chr3B 181301458 181302175 717 False 616.000000 616 82.869000 4221 4943 1 chr3B.!!$F3 722
5 TraesCS3B01G355200 chr1B 348800282 348802798 2516 False 3332.000000 3332 90.653000 3879 6421 1 chr1B.!!$F3 2542
6 TraesCS3B01G355200 chr1B 39736224 39738813 2589 False 1614.500000 2870 86.479000 3879 6412 2 chr1B.!!$F4 2533
7 TraesCS3B01G355200 chr1B 529503632 529506030 2398 False 1555.500000 2399 90.416500 3879 6421 2 chr1B.!!$F5 2542
8 TraesCS3B01G355200 chr1B 591229139 591233387 4248 False 406.000000 737 86.101167 1240 8104 6 chr1B.!!$F6 6864
9 TraesCS3B01G355200 chr5B 645535048 645537583 2535 True 3125.000000 3125 89.254000 3923 6421 1 chr5B.!!$R6 2498
10 TraesCS3B01G355200 chr5B 328204053 328209225 5172 True 2564.000000 2865 88.529000 3879 6421 2 chr5B.!!$R8 2542
11 TraesCS3B01G355200 chr5B 228759494 228760202 708 True 680.000000 680 84.375000 4227 4943 1 chr5B.!!$R4 716
12 TraesCS3B01G355200 chr6B 599810101 599812593 2492 True 2760.000000 2760 86.999000 3923 6421 1 chr6B.!!$R5 2498
13 TraesCS3B01G355200 chr6B 268297266 268298426 1160 True 1114.000000 1114 84.527000 3878 5050 1 chr6B.!!$R4 1172
14 TraesCS3B01G355200 chr6B 117704484 117705176 692 True 449.000000 449 79.217000 4227 4943 1 chr6B.!!$R2 716
15 TraesCS3B01G355200 chr4B 89521501 89524407 2906 False 1740.000000 2464 92.081500 3895 6421 2 chr4B.!!$F3 2526
16 TraesCS3B01G355200 chr4B 222571256 222572920 1664 True 1666.000000 1666 84.870000 4625 6329 1 chr4B.!!$R2 1704
17 TraesCS3B01G355200 chr4B 285613471 285616181 2710 False 1021.666667 2106 87.796333 3879 6338 3 chr4B.!!$F4 2459
18 TraesCS3B01G355200 chr4B 389110785 389112782 1997 True 938.666667 1727 92.773333 3878 6422 3 chr4B.!!$R4 2544
19 TraesCS3B01G355200 chr4B 24838998 24839675 677 False 475.000000 475 80.199000 4227 4897 1 chr4B.!!$F1 670
20 TraesCS3B01G355200 chr1D 493214337 493217167 2830 False 1712.500000 2390 90.627500 3879 6426 2 chr1D.!!$F12 2547
21 TraesCS3B01G355200 chr1D 436211365 436215403 4038 False 430.833333 780 85.698000 1244 8134 6 chr1D.!!$F11 6890
22 TraesCS3B01G355200 chr3A 571334124 571334828 704 True 920.000000 920 90.665000 8657 9343 1 chr3A.!!$R2 686
23 TraesCS3B01G355200 chr3A 571394878 571401782 6904 True 674.954545 1910 93.650818 1 8643 11 chr3A.!!$R4 8642
24 TraesCS3B01G355200 chr5A 8805601 8807299 1698 False 1851.000000 1851 86.356000 4658 6403 1 chr5A.!!$F1 1745
25 TraesCS3B01G355200 chr3D 433188984 433194540 5556 True 722.488889 1677 92.772333 615 8468 9 chr3D.!!$R7 7853
26 TraesCS3B01G355200 chr3D 135250678 135251438 760 False 645.000000 645 82.808000 4221 4943 1 chr3D.!!$F2 722
27 TraesCS3B01G355200 chr3D 433296999 433297917 918 True 237.500000 255 90.660000 187 629 2 chr3D.!!$R8 442
28 TraesCS3B01G355200 chr3D 433162979 433163691 712 True 220.566667 324 87.895667 8654 9341 3 chr3D.!!$R6 687
29 TraesCS3B01G355200 chr7B 23414910 23415930 1020 False 1125.000000 1125 87.246000 4221 5209 1 chr7B.!!$F1 988
30 TraesCS3B01G355200 chr7B 23634812 23636031 1219 False 1067.000000 1633 91.579000 3878 6421 2 chr7B.!!$F6 2543
31 TraesCS3B01G355200 chr7B 255042474 255043264 790 True 911.000000 911 88.080000 3879 4643 1 chr7B.!!$R1 764
32 TraesCS3B01G355200 chr7B 233374861 233375487 626 False 479.000000 479 81.978000 4221 4790 1 chr7B.!!$F2 569
33 TraesCS3B01G355200 chr1A 533462879 533467283 4404 False 381.625000 798 86.451375 1174 8134 8 chr1A.!!$F3 6960
34 TraesCS3B01G355200 chr7A 43061253 43061842 589 True 560.000000 560 84.486000 4019 4587 1 chr7A.!!$R1 568
35 TraesCS3B01G355200 chr2B 519143148 519143769 621 False 544.000000 544 83.788000 4221 4793 1 chr2B.!!$F1 572

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
86 601 1.000385 CCTGCTGTTTTGCCGAAATCA 60.000 47.619 0.00 0.00 0.00 2.57 F
184 699 1.002430 AGATGCGTGGATGTTCTGTGT 59.998 47.619 0.00 0.00 0.00 3.72 F
185 700 1.394917 GATGCGTGGATGTTCTGTGTC 59.605 52.381 0.00 0.00 0.00 3.67 F
1607 3020 1.518572 CCGTGCTCGCGTTATCCTT 60.519 57.895 5.77 0.00 35.54 3.36 F
2378 4182 1.068541 GTGTTGATTTGAGGGTTCGGC 60.069 52.381 0.00 0.00 0.00 5.54 F
3768 5954 0.249911 GGCCACCAGCGTTAGGATAG 60.250 60.000 0.00 0.00 45.17 2.08 F
3786 5972 0.661187 AGTTTTGCTGCATTGCGACG 60.661 50.000 1.84 0.00 35.36 5.12 F
5560 9436 2.202492 CTGACCTCTTCGTCGGCG 60.202 66.667 1.15 1.15 35.40 6.46 F
6273 10152 0.756070 GAGACCTAACCCTAGCCGCT 60.756 60.000 0.00 0.00 0.00 5.52 F
6375 10264 2.896443 GACCAGCTCCCTCCTTCG 59.104 66.667 0.00 0.00 0.00 3.79 F
8153 13128 1.640428 CGCGAAAGGCAGTTCTGATA 58.360 50.000 0.00 0.00 43.84 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 2237 0.110509 CACAGCAGCGCTTACACAAG 60.111 55.000 7.50 0.00 36.40 3.16 R
1524 2936 1.459450 GCATTTCGCCCAAGTAGGAA 58.541 50.000 0.00 0.00 41.22 3.36 R
1852 3450 2.215196 TCCAAGTTGGTGTTCGCTAAC 58.785 47.619 21.35 4.81 39.03 2.34 R
3488 5620 1.457267 TGTGGTTGCATGGCTGGTT 60.457 52.632 0.00 0.00 0.00 3.67 R
3875 6063 0.618458 ACATGCCGGTCATAACACCT 59.382 50.000 1.90 0.00 33.77 4.00 R
5560 9436 0.250513 GGATATGATCCGGCAGACCC 59.749 60.000 0.00 0.00 40.13 4.46 R
5709 9588 4.379243 CCCTGCGCTGGAACGTCT 62.379 66.667 32.43 0.00 34.88 4.18 R
6928 10845 1.979155 TGACGACTCCCTCCTGCAG 60.979 63.158 6.78 6.78 0.00 4.41 R
8153 13128 2.278857 GCCGACGTCTGATCGCAT 60.279 61.111 14.70 0.00 38.27 4.73 R
8291 13270 3.057526 GCTTTCTTTCCCGTGTGCTAAAT 60.058 43.478 0.00 0.00 0.00 1.40 R
9305 14397 0.319040 CGATCGATGCAGTTCCCGAT 60.319 55.000 10.26 9.40 43.38 4.18 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
72 587 2.198906 TTTGATTTCCGCGCCTGCTG 62.199 55.000 0.00 0.00 39.65 4.41
86 601 1.000385 CCTGCTGTTTTGCCGAAATCA 60.000 47.619 0.00 0.00 0.00 2.57
93 608 3.571828 TGTTTTGCCGAAATCATCTGGAA 59.428 39.130 0.00 0.00 0.00 3.53
159 674 1.026718 GGTTCTTCGATGTGGGCTGG 61.027 60.000 0.00 0.00 0.00 4.85
181 696 4.024556 GGAAATAGATGCGTGGATGTTCTG 60.025 45.833 0.00 0.00 0.00 3.02
182 697 3.827008 ATAGATGCGTGGATGTTCTGT 57.173 42.857 0.00 0.00 0.00 3.41
183 698 1.730501 AGATGCGTGGATGTTCTGTG 58.269 50.000 0.00 0.00 0.00 3.66
184 699 1.002430 AGATGCGTGGATGTTCTGTGT 59.998 47.619 0.00 0.00 0.00 3.72
185 700 1.394917 GATGCGTGGATGTTCTGTGTC 59.605 52.381 0.00 0.00 0.00 3.67
193 708 5.408299 CGTGGATGTTCTGTGTCTGAAAATA 59.592 40.000 0.00 0.00 0.00 1.40
448 1560 3.729966 TGTGTTCGTTGTACTGCCATTA 58.270 40.909 0.00 0.00 0.00 1.90
1416 2827 9.166222 TCCAAATGGAGCCTTAGAATATTACTA 57.834 33.333 0.00 0.00 39.78 1.82
1475 2886 3.826729 TGAGTTGGACTTTCTCTCATCGA 59.173 43.478 0.00 0.00 31.51 3.59
1524 2936 7.391833 GGGTTGAGAATAAGAAACAGTGATCTT 59.608 37.037 16.33 16.33 39.19 2.40
1528 2940 8.378565 TGAGAATAAGAAACAGTGATCTTTCCT 58.621 33.333 16.99 12.66 37.16 3.36
1533 2945 7.736447 AAGAAACAGTGATCTTTCCTACTTG 57.264 36.000 0.00 0.00 32.05 3.16
1607 3020 1.518572 CCGTGCTCGCGTTATCCTT 60.519 57.895 5.77 0.00 35.54 3.36
1654 3094 5.865085 TGGCATGAATACCCTACTGTAATC 58.135 41.667 0.00 0.00 0.00 1.75
1739 3179 3.997021 CCGAGAGAAACAGTGTAAGCATT 59.003 43.478 0.00 0.00 0.00 3.56
1774 3224 5.108187 AGTGTAAGCATCTGTCCAATGAT 57.892 39.130 0.00 0.00 0.00 2.45
1852 3450 5.738208 GCCAATTCTTCCTCTGCCATATTTG 60.738 44.000 0.00 0.00 0.00 2.32
1917 3515 4.095036 GCACCTTTTCTTGCTACTATGGAC 59.905 45.833 0.00 0.00 35.74 4.02
1929 3527 4.580167 GCTACTATGGACAATGAAATGGCA 59.420 41.667 0.00 0.00 0.00 4.92
1955 3556 6.618287 TTATCTGGTTCCAATGCTTAATCG 57.382 37.500 0.00 0.00 0.00 3.34
1994 3599 4.479158 TCAGGTTGAAAAGGGTGCTAAAT 58.521 39.130 0.00 0.00 0.00 1.40
2094 3699 4.998033 CACCCAGAAGTAGGTTTCTTCTTC 59.002 45.833 5.60 5.12 46.09 2.87
2117 3722 9.562408 CTTCTAAAAGAAGGAAGTAGGTTTCTT 57.438 33.333 8.51 0.00 46.03 2.52
2118 3723 9.557061 TTCTAAAAGAAGGAAGTAGGTTTCTTC 57.443 33.333 0.00 0.00 38.54 2.87
2119 3724 6.862711 AAAAGAAGGAAGTAGGTTTCTTCG 57.137 37.500 1.06 0.00 41.26 3.79
2120 3725 5.548181 AAGAAGGAAGTAGGTTTCTTCGT 57.452 39.130 1.06 0.00 41.26 3.85
2121 3726 6.661304 AAGAAGGAAGTAGGTTTCTTCGTA 57.339 37.500 1.06 0.00 41.26 3.43
2122 3727 6.661304 AGAAGGAAGTAGGTTTCTTCGTAA 57.339 37.500 1.06 0.00 41.26 3.18
2123 3728 7.242322 AGAAGGAAGTAGGTTTCTTCGTAAT 57.758 36.000 1.06 0.00 41.26 1.89
2124 3729 7.321908 AGAAGGAAGTAGGTTTCTTCGTAATC 58.678 38.462 1.06 0.00 41.26 1.75
2125 3730 6.854091 AGGAAGTAGGTTTCTTCGTAATCT 57.146 37.500 0.00 0.00 41.26 2.40
2126 3731 7.951347 AGGAAGTAGGTTTCTTCGTAATCTA 57.049 36.000 0.00 0.00 41.26 1.98
2127 3732 8.536340 AGGAAGTAGGTTTCTTCGTAATCTAT 57.464 34.615 0.00 0.00 41.26 1.98
2159 3764 5.888982 TTTGTAGAAAGTCTTGAGAGGGT 57.111 39.130 0.00 0.00 0.00 4.34
2191 3994 7.798710 ATATACTGGATGCAGTAGTATGGTT 57.201 36.000 27.81 14.49 40.52 3.67
2220 4023 9.695526 TCTCATTTCAACAAATTTACATGGAAG 57.304 29.630 0.00 0.00 28.97 3.46
2248 4051 6.583806 CCACTTGTCAACTTAATGATGCTTTC 59.416 38.462 0.00 0.00 0.00 2.62
2250 4053 7.325338 CACTTGTCAACTTAATGATGCTTTCAG 59.675 37.037 0.00 0.00 37.89 3.02
2251 4054 6.882610 TGTCAACTTAATGATGCTTTCAGT 57.117 33.333 0.00 0.00 37.89 3.41
2252 4055 7.977789 TGTCAACTTAATGATGCTTTCAGTA 57.022 32.000 0.00 0.00 37.89 2.74
2317 4121 2.289274 TGTGGCTTGTGTGACGTAATTG 59.711 45.455 0.00 0.00 0.00 2.32
2378 4182 1.068541 GTGTTGATTTGAGGGTTCGGC 60.069 52.381 0.00 0.00 0.00 5.54
3104 4933 4.309933 ACATGCCTTTTTGCTTTAGCTTC 58.690 39.130 0.00 0.00 42.66 3.86
3599 5755 6.369065 CAGAAACTACTTACAATCAGGTCACC 59.631 42.308 0.00 0.00 0.00 4.02
3690 5872 1.208052 TCTACTGCATTGCTCACTCCC 59.792 52.381 10.49 0.00 0.00 4.30
3768 5954 0.249911 GGCCACCAGCGTTAGGATAG 60.250 60.000 0.00 0.00 45.17 2.08
3786 5972 0.661187 AGTTTTGCTGCATTGCGACG 60.661 50.000 1.84 0.00 35.36 5.12
3872 6060 5.221185 GGCATACTCTGGACGATGTACTTAA 60.221 44.000 0.00 0.00 0.00 1.85
3873 6061 6.448006 GCATACTCTGGACGATGTACTTAAT 58.552 40.000 0.00 0.00 0.00 1.40
3874 6062 6.924060 GCATACTCTGGACGATGTACTTAATT 59.076 38.462 0.00 0.00 0.00 1.40
3875 6063 8.080417 GCATACTCTGGACGATGTACTTAATTA 58.920 37.037 0.00 0.00 0.00 1.40
3876 6064 9.613957 CATACTCTGGACGATGTACTTAATTAG 57.386 37.037 0.00 0.00 0.00 1.73
4085 6295 2.444895 CCTAGCCGCCTCCTTCCT 60.445 66.667 0.00 0.00 0.00 3.36
4230 6466 5.605488 AGAACCCTAGTTTCTACCAGTTTGA 59.395 40.000 2.67 0.00 35.94 2.69
4369 6735 4.457496 CGCCACCGTCCAGATGCT 62.457 66.667 0.00 0.00 0.00 3.79
4884 8684 3.993234 GCATCGATCGCGCTGGTG 61.993 66.667 18.51 0.39 34.45 4.17
5215 9082 2.813908 GCACTTCGCCACCTACGG 60.814 66.667 0.00 0.00 32.94 4.02
5280 9153 3.332445 TTCCGGGGGCAATGTACGG 62.332 63.158 0.00 0.00 45.52 4.02
5392 9265 3.248043 CTCCATGGGAGCGTTTTCA 57.752 52.632 13.02 0.00 43.29 2.69
5489 9365 2.358737 GGTGCAGGACTTCACCGG 60.359 66.667 0.00 0.00 42.67 5.28
5560 9436 2.202492 CTGACCTCTTCGTCGGCG 60.202 66.667 1.15 1.15 35.40 6.46
5742 9621 2.432628 GGTCGTCCTGTTCAGGCG 60.433 66.667 20.69 20.69 0.00 5.52
5999 9878 2.996621 GTTGATCACCTCAAGGAGTTCG 59.003 50.000 2.30 0.00 44.44 3.95
6273 10152 0.756070 GAGACCTAACCCTAGCCGCT 60.756 60.000 0.00 0.00 0.00 5.52
6375 10264 2.896443 GACCAGCTCCCTCCTTCG 59.104 66.667 0.00 0.00 0.00 3.79
6459 10348 8.634475 TGACTGTAATCATCGTAATCTTGAAG 57.366 34.615 0.00 0.00 0.00 3.02
6499 10388 3.446442 AGATCTCAATGGTGGTTTGCT 57.554 42.857 0.00 0.00 0.00 3.91
7474 11843 3.891366 ACACCATTTCTCCCTTTTGTCTG 59.109 43.478 0.00 0.00 0.00 3.51
7609 12573 9.872721 GAGTTATTACTTCCCTACTATAATGGC 57.127 37.037 0.00 0.00 33.84 4.40
8153 13128 1.640428 CGCGAAAGGCAGTTCTGATA 58.360 50.000 0.00 0.00 43.84 2.15
8291 13270 5.779260 CCATCTCATCTTATTCCTCTCCTGA 59.221 44.000 0.00 0.00 0.00 3.86
8312 13291 4.215399 TGATTTAGCACACGGGAAAGAAAG 59.785 41.667 0.00 0.00 0.00 2.62
8332 13316 9.762933 AAGAAAGCAATCAATTTAAGCAGTTAA 57.237 25.926 0.00 0.00 0.00 2.01
8376 13360 0.401356 TGCTTGCATGAAGGAGACCA 59.599 50.000 3.33 0.00 31.56 4.02
8428 13412 5.053811 GCAGCTCCTCTACCTTAATCTTTC 58.946 45.833 0.00 0.00 0.00 2.62
8455 13440 3.252215 CGGTCTTGCCTAGTCTCATCTAG 59.748 52.174 0.00 0.00 37.66 2.43
8500 13485 6.435904 CGGAGGGAGTATTTCTCATCTTCTAT 59.564 42.308 0.00 0.00 44.40 1.98
8501 13486 7.039363 CGGAGGGAGTATTTCTCATCTTCTATT 60.039 40.741 0.00 0.00 44.40 1.73
8502 13487 8.655901 GGAGGGAGTATTTCTCATCTTCTATTT 58.344 37.037 0.00 0.00 44.40 1.40
8503 13488 9.705290 GAGGGAGTATTTCTCATCTTCTATTTC 57.295 37.037 0.00 0.00 44.40 2.17
8504 13489 9.218525 AGGGAGTATTTCTCATCTTCTATTTCA 57.781 33.333 0.00 0.00 44.40 2.69
8543 13528 5.985911 AGTACAAATTAGCGGTTCAGGTAT 58.014 37.500 0.00 0.00 0.00 2.73
8555 13543 4.262079 CGGTTCAGGTATGAGGAGGAATAC 60.262 50.000 0.00 0.00 36.61 1.89
8592 13580 1.000896 GGTATGGCTTGCCACACCT 60.001 57.895 28.87 11.94 34.70 4.00
8593 13581 1.315257 GGTATGGCTTGCCACACCTG 61.315 60.000 28.87 0.00 34.70 4.00
8594 13582 1.678635 TATGGCTTGCCACACCTGC 60.679 57.895 17.22 0.00 0.00 4.85
8605 13593 2.636830 CCACACCTGCAGGATTAGAAG 58.363 52.381 39.19 19.27 38.94 2.85
8647 13635 9.953697 ATCAAAGAATTACTCACTATAGTCGAC 57.046 33.333 7.70 7.70 0.00 4.20
8648 13636 8.404000 TCAAAGAATTACTCACTATAGTCGACC 58.596 37.037 13.01 0.00 0.00 4.79
8649 13637 6.880942 AGAATTACTCACTATAGTCGACCC 57.119 41.667 13.01 0.00 0.00 4.46
8650 13638 5.769162 AGAATTACTCACTATAGTCGACCCC 59.231 44.000 13.01 0.00 0.00 4.95
8651 13639 4.508551 TTACTCACTATAGTCGACCCCA 57.491 45.455 13.01 0.00 0.00 4.96
8652 13640 2.652590 ACTCACTATAGTCGACCCCAC 58.347 52.381 13.01 0.00 0.00 4.61
8788 13784 2.737252 GTCCGAAAAGATGACTCACACC 59.263 50.000 0.00 0.00 0.00 4.16
8795 13791 4.696479 AAGATGACTCACACCTTCAACT 57.304 40.909 0.00 0.00 0.00 3.16
8866 13875 1.592669 CATGGACGATCGCCTCACC 60.593 63.158 22.99 15.73 0.00 4.02
9047 14060 1.068753 CCTCTACTGAGCGCCATGG 59.931 63.158 7.63 7.63 38.93 3.66
9065 14078 4.815308 CCATGGATGATTGAGACAAGAGAC 59.185 45.833 5.56 0.00 0.00 3.36
9202 14247 1.226211 GCTGACGTGTCATGCATGC 60.226 57.895 22.25 11.82 39.13 4.06
9210 14255 0.603439 TGTCATGCATGCGACAGTGT 60.603 50.000 22.25 0.00 37.23 3.55
9282 14374 5.132897 TGTTCTTGTGCTGTTTCTTGTTT 57.867 34.783 0.00 0.00 0.00 2.83
9305 14397 4.330347 TGACTGTTTCGATGTGTTTTTCGA 59.670 37.500 0.00 0.00 42.19 3.71
9316 14408 1.533731 TGTTTTTCGATCGGGAACTGC 59.466 47.619 16.41 1.04 32.53 4.40
9331 14423 2.370281 ACTGCATCGATCGACTGTTT 57.630 45.000 22.06 0.09 0.00 2.83
9332 14424 1.995484 ACTGCATCGATCGACTGTTTG 59.005 47.619 22.06 15.41 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 2.028130 TCAAACGTGGAGCCAAACATT 58.972 42.857 0.00 0.00 0.00 2.71
41 42 2.035321 GGAAATCAAACGTGGAGCCAAA 59.965 45.455 0.00 0.00 0.00 3.28
72 587 3.848272 TCCAGATGATTTCGGCAAAAC 57.152 42.857 0.00 0.00 0.00 2.43
86 601 2.158623 TGCAAACACCTCTGTTCCAGAT 60.159 45.455 0.00 0.00 39.88 2.90
93 608 2.034124 AGCAATTGCAAACACCTCTGT 58.966 42.857 30.89 3.86 45.16 3.41
159 674 4.572389 ACAGAACATCCACGCATCTATTTC 59.428 41.667 0.00 0.00 0.00 2.17
264 921 9.965902 ACTTTTTCACAAGTATTATCTCCATCT 57.034 29.630 0.00 0.00 35.10 2.90
299 957 8.895737 TCGTATCTTTTTAAAAACAGTCAAGGT 58.104 29.630 9.31 0.00 0.00 3.50
379 1472 1.341531 ACTACAAGCACTGAAGCGAGT 59.658 47.619 0.00 0.00 40.15 4.18
1016 2237 0.110509 CACAGCAGCGCTTACACAAG 60.111 55.000 7.50 0.00 36.40 3.16
1416 2827 5.020132 GCCTCCTATATCCTCATGTGTAGT 58.980 45.833 0.00 0.00 0.00 2.73
1418 2829 4.202781 TGGCCTCCTATATCCTCATGTGTA 60.203 45.833 3.32 0.00 0.00 2.90
1419 2830 3.177228 GGCCTCCTATATCCTCATGTGT 58.823 50.000 0.00 0.00 0.00 3.72
1475 2886 5.136816 TGCATGAACAATTTGCAGTATGT 57.863 34.783 0.00 0.00 41.18 2.29
1524 2936 1.459450 GCATTTCGCCCAAGTAGGAA 58.541 50.000 0.00 0.00 41.22 3.36
1587 3000 2.228914 GGATAACGCGAGCACGGTC 61.229 63.158 15.93 0.31 40.15 4.79
1598 3011 6.498304 AGCATAAATGAAGCAAAGGATAACG 58.502 36.000 0.00 0.00 0.00 3.18
1643 3083 5.107837 CGAAATAAGCTGCGATTACAGTAGG 60.108 44.000 0.00 0.00 39.96 3.18
1654 3094 2.611974 AACAACCGAAATAAGCTGCG 57.388 45.000 0.00 0.00 0.00 5.18
1746 3187 3.512680 GACAGATGCTTACACTTAGCGT 58.487 45.455 0.00 0.00 41.54 5.07
1747 3188 2.860735 GGACAGATGCTTACACTTAGCG 59.139 50.000 0.00 0.00 41.54 4.26
1748 3189 3.861840 TGGACAGATGCTTACACTTAGC 58.138 45.455 0.00 0.00 39.10 3.09
1750 3191 6.048732 TCATTGGACAGATGCTTACACTTA 57.951 37.500 0.00 0.00 0.00 2.24
1751 3192 4.910195 TCATTGGACAGATGCTTACACTT 58.090 39.130 0.00 0.00 0.00 3.16
1752 3193 4.558226 TCATTGGACAGATGCTTACACT 57.442 40.909 0.00 0.00 0.00 3.55
1753 3194 7.502120 AATATCATTGGACAGATGCTTACAC 57.498 36.000 0.00 0.00 0.00 2.90
1852 3450 2.215196 TCCAAGTTGGTGTTCGCTAAC 58.785 47.619 21.35 4.81 39.03 2.34
1917 3515 7.816031 GGAACCAGATAATATGCCATTTCATTG 59.184 37.037 0.00 0.00 0.00 2.82
1929 3527 8.950210 CGATTAAGCATTGGAACCAGATAATAT 58.050 33.333 0.00 0.00 0.00 1.28
1954 3555 8.826710 TCAACCTGAACATAAAGAATATAAGCG 58.173 33.333 0.00 0.00 0.00 4.68
1994 3599 3.258123 GCAAGCCAAAATGGAAGGTCTAA 59.742 43.478 0.00 0.00 40.96 2.10
2092 3697 9.557061 GAAGAAACCTACTTCCTTCTTTTAGAA 57.443 33.333 0.00 0.00 38.05 2.10
2094 3699 7.656542 ACGAAGAAACCTACTTCCTTCTTTTAG 59.343 37.037 0.00 0.00 38.05 1.85
2096 3701 6.354938 ACGAAGAAACCTACTTCCTTCTTTT 58.645 36.000 0.00 0.00 38.05 2.27
2097 3702 5.926663 ACGAAGAAACCTACTTCCTTCTTT 58.073 37.500 0.00 0.00 38.05 2.52
2098 3703 5.548181 ACGAAGAAACCTACTTCCTTCTT 57.452 39.130 0.00 0.00 40.06 2.52
2099 3704 6.661304 TTACGAAGAAACCTACTTCCTTCT 57.339 37.500 0.00 0.00 40.11 2.85
2100 3705 7.321908 AGATTACGAAGAAACCTACTTCCTTC 58.678 38.462 0.00 0.00 40.11 3.46
2101 3706 7.242322 AGATTACGAAGAAACCTACTTCCTT 57.758 36.000 0.00 0.00 40.11 3.36
2102 3707 6.854091 AGATTACGAAGAAACCTACTTCCT 57.146 37.500 0.00 0.00 40.11 3.36
2103 3708 9.597170 AAATAGATTACGAAGAAACCTACTTCC 57.403 33.333 0.00 0.00 40.11 3.46
2147 3752 4.762289 ATATTGGTGACCCTCTCAAGAC 57.238 45.455 0.00 0.00 0.00 3.01
2191 3994 9.258826 CCATGTAAATTTGTTGAAATGAGAACA 57.741 29.630 0.00 0.00 31.83 3.18
2220 4023 5.858581 GCATCATTAAGTTGACAAGTGGAAC 59.141 40.000 0.00 0.00 0.00 3.62
2225 4028 7.013655 ACTGAAAGCATCATTAAGTTGACAAGT 59.986 33.333 0.00 0.00 37.44 3.16
2317 4121 1.372087 CCTTCCGAGTTCTGCATGCC 61.372 60.000 16.68 0.00 0.00 4.40
2378 4182 3.065371 CCAAGCTCATAAAAGTAAGGGCG 59.935 47.826 0.00 0.00 0.00 6.13
3104 4933 7.572759 TGAATCTTGTTAGAAGCAAAACTACG 58.427 34.615 0.00 0.00 33.20 3.51
3198 5301 6.603237 TCATTTCAAAGCGACCATATACTG 57.397 37.500 0.00 0.00 0.00 2.74
3455 5587 1.461127 GTCTTGTGTGACTCATTCGGC 59.539 52.381 0.00 0.00 34.39 5.54
3488 5620 1.457267 TGTGGTTGCATGGCTGGTT 60.457 52.632 0.00 0.00 0.00 3.67
3599 5755 7.919690 TCATGTTCTGTTCTAGTGTTTTTCTG 58.080 34.615 0.00 0.00 0.00 3.02
3690 5872 2.460918 CTACGTATTGAAGGTGCCTCG 58.539 52.381 0.00 0.00 0.00 4.63
3768 5954 1.608093 CCGTCGCAATGCAGCAAAAC 61.608 55.000 5.91 0.00 0.00 2.43
3786 5972 9.467258 GTTTATTTGGGAAAACTTAGTTACACC 57.533 33.333 0.00 1.71 33.71 4.16
3872 6060 3.118038 ACATGCCGGTCATAACACCTAAT 60.118 43.478 1.90 0.00 33.77 1.73
3873 6061 2.237643 ACATGCCGGTCATAACACCTAA 59.762 45.455 1.90 0.00 33.77 2.69
3874 6062 1.834896 ACATGCCGGTCATAACACCTA 59.165 47.619 1.90 0.00 33.77 3.08
3875 6063 0.618458 ACATGCCGGTCATAACACCT 59.382 50.000 1.90 0.00 33.77 4.00
3876 6064 1.459450 AACATGCCGGTCATAACACC 58.541 50.000 1.90 0.00 33.19 4.16
4085 6295 1.964608 CTGAGAGGGAGATGGCGCAA 61.965 60.000 10.83 0.00 0.00 4.85
4161 6397 1.613630 GGAAGGAGGGAGCTGGTCA 60.614 63.158 9.30 0.00 0.00 4.02
4230 6466 3.833732 TCGGAACTGAGCTACCTGATAT 58.166 45.455 0.00 0.00 0.00 1.63
4304 6561 1.898330 TAGAGATTGGCAGTGGCGCA 61.898 55.000 10.83 1.15 42.47 6.09
4408 6817 2.041922 CCCCGGTGATCTCCTCCA 60.042 66.667 11.86 0.00 0.00 3.86
4444 6853 1.682451 CCGGATTTCCTGGACGGCTA 61.682 60.000 10.09 0.00 37.93 3.93
4606 7813 4.514577 CTGGAGGCGCGTCGGAAT 62.515 66.667 22.46 0.00 0.00 3.01
4644 7857 4.969196 CCACGACAGCCACAGCGT 62.969 66.667 0.00 0.00 46.67 5.07
4880 8680 3.319198 GAGCGGAACTCCCCACCA 61.319 66.667 0.00 0.00 39.75 4.17
5392 9265 2.705821 CGAAGGAGGCAGAGCTCGT 61.706 63.158 8.37 0.00 0.00 4.18
5547 9423 4.493747 GACCCGCCGACGAAGAGG 62.494 72.222 0.00 0.00 43.93 3.69
5560 9436 0.250513 GGATATGATCCGGCAGACCC 59.749 60.000 0.00 0.00 40.13 4.46
5709 9588 4.379243 CCCTGCGCTGGAACGTCT 62.379 66.667 32.43 0.00 34.88 4.18
5870 9749 1.025812 CAGGTAGAAGAGTCGCGGAT 58.974 55.000 6.13 0.00 0.00 4.18
6273 10152 2.257409 GAGATGGCGCAGGGAAGGAA 62.257 60.000 10.83 0.00 0.00 3.36
6459 10348 7.740805 AGATCTATATCTGGGTCCTTGAAAAC 58.259 38.462 0.00 0.00 41.08 2.43
6499 10388 6.596106 TGTTCTAGTGCACACTAAAGTTGAAA 59.404 34.615 21.04 0.00 42.72 2.69
6525 10414 7.167468 GCCGGCTACTAAACATTCAATTATTTG 59.833 37.037 22.15 0.00 0.00 2.32
6687 10584 7.211573 TCTGAGAATAGTTACACCGTTTCAAA 58.788 34.615 0.00 0.00 0.00 2.69
6928 10845 1.979155 TGACGACTCCCTCCTGCAG 60.979 63.158 6.78 6.78 0.00 4.41
7450 11819 5.048713 CAGACAAAAGGGAGAAATGGTGTAC 60.049 44.000 0.00 0.00 0.00 2.90
7474 11843 7.070571 TCCATACAAATTAATGGGATTGGGAAC 59.929 37.037 12.18 0.00 42.51 3.62
7513 11882 7.633193 TTACCTTTCAAAGTTTTGTGCTAGA 57.367 32.000 0.00 0.00 39.18 2.43
7609 12573 6.093495 TCGGTGAGCAAAATAATTTAGTCTGG 59.907 38.462 0.00 0.00 0.00 3.86
8153 13128 2.278857 GCCGACGTCTGATCGCAT 60.279 61.111 14.70 0.00 38.27 4.73
8291 13270 3.057526 GCTTTCTTTCCCGTGTGCTAAAT 60.058 43.478 0.00 0.00 0.00 1.40
8332 13316 4.649692 ACAGAGATTCACAAGTCAGCATT 58.350 39.130 0.00 0.00 0.00 3.56
8376 13360 4.012374 CAACTGCATAACTGATGGGAACT 58.988 43.478 0.00 0.00 35.91 3.01
8428 13412 1.352156 GACTAGGCAAGACCGCAACG 61.352 60.000 0.00 0.00 46.52 4.10
8455 13440 4.157289 TCCGTCCCATAATATAAGAGCGTC 59.843 45.833 0.00 0.00 0.00 5.19
8511 13496 9.903682 GAACCGCTAATTTGTACTAGTATCATA 57.096 33.333 5.75 2.60 0.00 2.15
8512 13497 8.418662 TGAACCGCTAATTTGTACTAGTATCAT 58.581 33.333 5.75 0.00 0.00 2.45
8513 13498 7.774134 TGAACCGCTAATTTGTACTAGTATCA 58.226 34.615 5.75 3.68 0.00 2.15
8514 13499 7.381678 CCTGAACCGCTAATTTGTACTAGTATC 59.618 40.741 5.75 1.02 0.00 2.24
8515 13500 7.147776 ACCTGAACCGCTAATTTGTACTAGTAT 60.148 37.037 5.75 0.00 0.00 2.12
8516 13501 6.153340 ACCTGAACCGCTAATTTGTACTAGTA 59.847 38.462 0.00 0.00 0.00 1.82
8517 13502 5.046807 ACCTGAACCGCTAATTTGTACTAGT 60.047 40.000 0.00 0.00 0.00 2.57
8518 13503 5.416947 ACCTGAACCGCTAATTTGTACTAG 58.583 41.667 0.00 0.00 0.00 2.57
8519 13504 5.410355 ACCTGAACCGCTAATTTGTACTA 57.590 39.130 0.00 0.00 0.00 1.82
8543 13528 6.183360 CGTTTAGATCTGTGTATTCCTCCTCA 60.183 42.308 5.18 0.00 0.00 3.86
8555 13543 1.920574 CCGACAGCGTTTAGATCTGTG 59.079 52.381 5.18 0.00 40.74 3.66
8592 13580 4.040339 TCAGTTGTGACTTCTAATCCTGCA 59.960 41.667 0.00 0.00 32.54 4.41
8593 13581 4.569943 TCAGTTGTGACTTCTAATCCTGC 58.430 43.478 0.00 0.00 32.54 4.85
8643 13631 0.326927 GAATTGGAAGGTGGGGTCGA 59.673 55.000 0.00 0.00 0.00 4.20
8644 13632 0.328258 AGAATTGGAAGGTGGGGTCG 59.672 55.000 0.00 0.00 0.00 4.79
8645 13633 1.839424 CAGAATTGGAAGGTGGGGTC 58.161 55.000 0.00 0.00 0.00 4.46
8646 13634 0.251787 GCAGAATTGGAAGGTGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
8647 13635 0.972471 GGCAGAATTGGAAGGTGGGG 60.972 60.000 0.00 0.00 0.00 4.96
8648 13636 0.972471 GGGCAGAATTGGAAGGTGGG 60.972 60.000 0.00 0.00 0.00 4.61
8649 13637 0.972471 GGGGCAGAATTGGAAGGTGG 60.972 60.000 0.00 0.00 0.00 4.61
8650 13638 0.251742 TGGGGCAGAATTGGAAGGTG 60.252 55.000 0.00 0.00 0.00 4.00
8651 13639 0.486879 TTGGGGCAGAATTGGAAGGT 59.513 50.000 0.00 0.00 0.00 3.50
8652 13640 1.483415 CATTGGGGCAGAATTGGAAGG 59.517 52.381 0.00 0.00 0.00 3.46
8681 13669 1.062002 CACGCGTACAAGGCCAATTAG 59.938 52.381 13.44 0.00 0.00 1.73
8788 13784 7.370383 AGTACATTTTGTTGGCATAGTTGAAG 58.630 34.615 0.00 0.00 0.00 3.02
8897 13906 1.691195 GGGGGTAGGCTCAGCTTCTC 61.691 65.000 0.00 0.00 0.00 2.87
9047 14060 3.870419 GCAGGTCTCTTGTCTCAATCATC 59.130 47.826 0.00 0.00 0.00 2.92
9065 14078 1.273048 TGGCTTTGTAATGCAAGCAGG 59.727 47.619 8.01 0.00 38.47 4.85
9130 14175 2.067766 CCCAATGGTTTTGCATTGACG 58.932 47.619 0.00 0.00 40.22 4.35
9202 14247 3.036084 GCACCCGTCACACTGTCG 61.036 66.667 0.00 0.00 0.00 4.35
9282 14374 4.330347 TCGAAAAACACATCGAAACAGTCA 59.670 37.500 0.00 0.00 44.32 3.41
9305 14397 0.319040 CGATCGATGCAGTTCCCGAT 60.319 55.000 10.26 9.40 43.38 4.18


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

AutoCloner maintained by Alex Coulton.