Multiple sequence alignment - TraesCS5B01G452600

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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 TraesCS5B01G452600 chr5B 100.000 5315 0 0 384 5698 625452847 625447533 0.000000e+00 9816.0
1 TraesCS5B01G452600 chr5B 97.047 5350 95 18 384 5695 632805326 632810650 0.000000e+00 8946.0
2 TraesCS5B01G452600 chr5B 98.542 2813 19 1 2908 5698 629078445 629075633 0.000000e+00 4948.0
3 TraesCS5B01G452600 chr5B 99.130 2528 14 5 384 2906 629081081 629078557 0.000000e+00 4540.0
4 TraesCS5B01G452600 chr5B 95.488 2194 69 9 993 3170 604719190 604717011 0.000000e+00 3476.0
5 TraesCS5B01G452600 chr5B 92.486 1251 31 8 3326 4543 604717014 604715794 0.000000e+00 1731.0
6 TraesCS5B01G452600 chr5B 90.000 750 49 12 4603 5328 604715791 604715044 0.000000e+00 946.0
7 TraesCS5B01G452600 chr5B 100.000 309 0 0 1 309 625453230 625452922 6.400000e-159 571.0
8 TraesCS5B01G452600 chr5B 98.065 310 5 1 1 309 629081379 629081070 6.500000e-149 538.0
9 TraesCS5B01G452600 chr5B 96.463 311 7 4 1 309 632805029 632805337 1.420000e-140 510.0
10 TraesCS5B01G452600 chr5B 95.724 304 13 0 5395 5698 604715046 604714743 1.840000e-134 490.0
11 TraesCS5B01G452600 chr5B 90.265 226 7 8 863 1088 604355275 604355485 1.210000e-71 281.0
12 TraesCS5B01G452600 chr5B 78.616 318 62 3 1150 1461 622977742 622977425 7.480000e-49 206.0
13 TraesCS5B01G452600 chr5B 99.010 101 1 0 863 963 604719768 604719668 1.260000e-41 182.0
14 TraesCS5B01G452600 chr5B 87.671 146 6 8 4480 4615 632809601 632809458 5.910000e-35 159.0
15 TraesCS5B01G452600 chr5B 75.758 330 69 10 2201 2523 626803335 626803010 7.640000e-34 156.0
16 TraesCS5B01G452600 chr5B 86.111 144 18 2 2711 2853 394253475 394253617 2.750000e-33 154.0
17 TraesCS5B01G452600 chr5B 86.111 144 18 2 2711 2853 394256133 394256275 2.750000e-33 154.0
18 TraesCS5B01G452600 chr5B 91.304 115 4 6 4498 4610 625448616 625448726 9.890000e-33 152.0
19 TraesCS5B01G452600 chr5B 90.435 115 5 6 4498 4610 629076716 629076826 4.600000e-31 147.0
20 TraesCS5B01G452600 chr5B 78.151 238 33 14 2448 2680 627470593 627470370 3.580000e-27 134.0
21 TraesCS5B01G452600 chr5B 73.045 486 86 27 2201 2646 629281355 629281835 4.630000e-26 130.0
22 TraesCS5B01G452600 chr5B 73.045 486 86 27 2201 2646 629363649 629364129 4.630000e-26 130.0
23 TraesCS5B01G452600 chr5B 77.731 238 34 14 2448 2680 623866298 623866075 1.670000e-25 128.0
24 TraesCS5B01G452600 chr5B 92.958 71 1 1 4544 4610 604715762 604715832 3.630000e-17 100.0
25 TraesCS5B01G452600 chr5B 83.810 105 10 3 4173 4274 633281230 633281330 6.080000e-15 93.5
26 TraesCS5B01G452600 chr5B 80.508 118 22 1 5183 5300 648841032 648841148 7.860000e-14 89.8
27 TraesCS5B01G452600 chr5D 96.664 5366 93 21 384 5698 498930080 498924750 0.000000e+00 8839.0
28 TraesCS5B01G452600 chr5D 97.793 3263 41 4 2460 5698 501709513 501706258 0.000000e+00 5598.0
29 TraesCS5B01G452600 chr5D 98.275 2029 26 6 384 2407 501711536 501709512 0.000000e+00 3544.0
30 TraesCS5B01G452600 chr5D 81.373 816 133 11 1151 1949 501430235 501429422 0.000000e+00 647.0
31 TraesCS5B01G452600 chr5D 88.565 481 40 12 384 859 428703412 428703882 2.300000e-158 569.0
32 TraesCS5B01G452600 chr5D 96.743 307 8 2 5 309 498930488 498930182 1.420000e-140 510.0
33 TraesCS5B01G452600 chr5D 90.244 246 19 3 5455 5698 249522095 249521853 3.310000e-82 316.0
34 TraesCS5B01G452600 chr5D 88.755 249 23 4 5453 5698 294617126 294617372 3.340000e-77 300.0
35 TraesCS5B01G452600 chr5D 88.115 244 28 1 5456 5698 275164791 275164548 7.220000e-74 289.0
36 TraesCS5B01G452600 chr5D 95.758 165 7 0 3163 3327 478161355 478161191 3.380000e-67 267.0
37 TraesCS5B01G452600 chr5D 89.286 140 11 4 5317 5455 249522824 249522688 7.590000e-39 172.0
38 TraesCS5B01G452600 chr5D 87.586 145 8 6 4474 4610 501707304 501707446 5.910000e-35 159.0
39 TraesCS5B01G452600 chr5D 73.672 433 98 14 2104 2525 501439421 501438994 2.750000e-33 154.0
40 TraesCS5B01G452600 chr5D 77.824 239 51 2 1148 1385 296474740 296474977 4.600000e-31 147.0
41 TraesCS5B01G452600 chr5D 76.667 240 52 4 1148 1385 296450032 296450269 4.630000e-26 130.0
42 TraesCS5B01G452600 chr5D 82.000 150 19 5 4128 4274 501427950 501427806 2.790000e-23 121.0
43 TraesCS5B01G452600 chr5D 100.000 64 0 0 4569 4632 498925820 498925883 1.000000e-22 119.0
44 TraesCS5B01G452600 chr5D 92.188 64 2 3 4548 4610 498925861 498925922 2.830000e-13 87.9
45 TraesCS5B01G452600 chr5D 100.000 39 0 0 4505 4543 498925861 498925823 7.920000e-09 73.1
46 TraesCS5B01G452600 chr5D 93.023 43 3 0 4501 4543 240428037 240428079 4.770000e-06 63.9
47 TraesCS5B01G452600 chr5D 92.857 42 3 0 4484 4525 269336130 269336089 1.710000e-05 62.1
48 TraesCS5B01G452600 chr5D 90.909 44 4 0 4570 4613 60072222 60072265 6.170000e-05 60.2
49 TraesCS5B01G452600 chr5D 92.683 41 3 0 4569 4609 115640000 115640040 6.170000e-05 60.2
50 TraesCS5B01G452600 chr3B 81.149 870 140 14 1114 1962 462100099 462099233 0.000000e+00 676.0
51 TraesCS5B01G452600 chr3B 82.682 179 24 7 2999 3176 462097574 462097402 9.890000e-33 152.0
52 TraesCS5B01G452600 chr6D 90.208 480 32 12 384 859 422220655 422220187 3.770000e-171 612.0
53 TraesCS5B01G452600 chr6D 92.283 311 17 6 1 309 329073709 329074014 8.770000e-118 435.0
54 TraesCS5B01G452600 chr6D 92.739 303 17 4 1 303 63128728 63129025 3.150000e-117 433.0
55 TraesCS5B01G452600 chr6D 94.012 167 8 1 3167 3331 70040761 70040927 9.480000e-63 252.0
56 TraesCS5B01G452600 chr6D 94.012 167 8 1 3167 3331 320601456 320601290 9.480000e-63 252.0
57 TraesCS5B01G452600 chr6D 94.012 167 8 1 3167 3331 341737602 341737768 9.480000e-63 252.0
58 TraesCS5B01G452600 chr6D 93.491 169 9 1 3167 3333 305888403 305888235 3.410000e-62 250.0
59 TraesCS5B01G452600 chr6D 84.898 245 35 1 5456 5698 389575435 389575191 4.410000e-61 246.0
60 TraesCS5B01G452600 chr6D 83.936 249 35 4 5453 5698 463054660 463054414 3.430000e-57 233.0
61 TraesCS5B01G452600 chr6D 81.224 245 44 1 5456 5698 332790137 332789893 4.500000e-46 196.0
62 TraesCS5B01G452600 chr6D 97.674 43 1 0 4618 4660 368756615 368756573 2.200000e-09 75.0
63 TraesCS5B01G452600 chr6D 95.556 45 1 1 4617 4661 143406602 143406559 2.850000e-08 71.3
64 TraesCS5B01G452600 chr6D 93.182 44 3 0 4500 4543 85081778 85081821 1.330000e-06 65.8
65 TraesCS5B01G452600 chr6D 87.273 55 7 0 4606 4660 46709554 46709608 4.770000e-06 63.9
66 TraesCS5B01G452600 chr6D 93.023 43 2 1 4618 4660 33898152 33898193 1.710000e-05 62.1
67 TraesCS5B01G452600 chr6D 94.737 38 2 0 4503 4540 62245314 62245351 6.170000e-05 60.2
68 TraesCS5B01G452600 chr6D 91.304 46 0 3 4565 4609 396152431 396152473 6.170000e-05 60.2
69 TraesCS5B01G452600 chr6D 94.872 39 0 2 4506 4543 396152473 396152436 6.170000e-05 60.2
70 TraesCS5B01G452600 chr6D 90.909 44 2 2 4501 4543 367314769 367314811 2.220000e-04 58.4
71 TraesCS5B01G452600 chr6D 90.909 44 2 2 4501 4543 367341643 367341685 2.220000e-04 58.4
72 TraesCS5B01G452600 chr6D 100.000 28 0 0 4629 4656 129705857 129705884 1.000000e-02 52.8
73 TraesCS5B01G452600 chr6D 96.774 31 1 0 4587 4617 453367243 453367213 1.000000e-02 52.8
74 TraesCS5B01G452600 chr2B 84.530 627 81 10 1147 1757 667422781 667422155 1.760000e-169 606.0
75 TraesCS5B01G452600 chr2B 77.365 539 82 17 2014 2527 667421976 667421453 3.360000e-72 283.0
76 TraesCS5B01G452600 chr2B 81.957 327 55 3 5130 5455 179147133 179147456 2.020000e-69 274.0
77 TraesCS5B01G452600 chr2B 81.902 326 54 4 5131 5455 390611014 390610693 2.620000e-68 270.0
78 TraesCS5B01G452600 chr2B 81.651 327 56 4 5131 5455 669452794 669452470 9.410000e-68 268.0
79 TraesCS5B01G452600 chr3D 88.958 480 42 10 384 859 182343391 182343863 2.960000e-162 582.0
80 TraesCS5B01G452600 chr3D 88.272 486 41 12 384 865 90351523 90351050 8.290000e-158 568.0
81 TraesCS5B01G452600 chr3D 92.258 310 22 2 1 309 8467371 8467063 6.780000e-119 438.0
82 TraesCS5B01G452600 chr3D 93.529 170 9 2 3166 3334 475546301 475546133 9.480000e-63 252.0
83 TraesCS5B01G452600 chr3D 89.119 193 18 3 3167 3357 546474263 546474072 2.650000e-58 237.0
84 TraesCS5B01G452600 chr3D 98.077 52 0 1 4610 4660 119114446 119114497 7.860000e-14 89.8
85 TraesCS5B01G452600 chr3D 95.238 42 2 0 4574 4615 508185984 508185943 3.680000e-07 67.6
86 TraesCS5B01G452600 chr3D 91.304 46 2 2 4569 4613 551242461 551242505 1.710000e-05 62.1
87 TraesCS5B01G452600 chr3D 92.683 41 3 0 4468 4508 403741646 403741686 6.170000e-05 60.2
88 TraesCS5B01G452600 chr3D 90.476 42 4 0 4467 4508 108210738 108210779 7.980000e-04 56.5
89 TraesCS5B01G452600 chr3D 100.000 29 0 0 4480 4508 442391542 442391514 3.000000e-03 54.7
90 TraesCS5B01G452600 chr2D 88.753 489 38 15 384 865 456961260 456961738 2.960000e-162 582.0
91 TraesCS5B01G452600 chr2D 88.353 249 25 3 5453 5698 322504830 322504583 4.320000e-76 296.0
92 TraesCS5B01G452600 chr2D 98.137 161 3 0 3168 3328 519335227 519335067 1.210000e-71 281.0
93 TraesCS5B01G452600 chr2D 95.181 166 7 1 3164 3328 399965146 399965311 1.570000e-65 261.0
94 TraesCS5B01G452600 chr2D 92.350 183 10 4 3165 3346 56541158 56540979 2.040000e-64 257.0
95 TraesCS5B01G452600 chr2D 88.136 59 5 2 4606 4663 14758928 14758985 1.020000e-07 69.4
96 TraesCS5B01G452600 chr2D 91.304 46 4 0 4500 4545 600429654 600429609 4.770000e-06 63.9
97 TraesCS5B01G452600 chr5A 88.727 479 42 11 385 859 423361981 423362451 4.950000e-160 575.0
98 TraesCS5B01G452600 chr5A 92.208 308 24 0 2 309 296306715 296306408 2.440000e-118 436.0
99 TraesCS5B01G452600 chr5A 75.489 869 169 28 1121 1956 599556959 599556102 8.960000e-103 385.0
100 TraesCS5B01G452600 chr5A 75.489 767 141 29 1196 1940 629372514 629373255 1.180000e-86 331.0
101 TraesCS5B01G452600 chr5A 74.548 609 115 26 2099 2681 629249618 629249024 4.440000e-56 230.0
102 TraesCS5B01G452600 chr5A 74.300 607 114 27 2099 2681 629373396 629373984 9.610000e-53 219.0
103 TraesCS5B01G452600 chr5A 71.966 824 162 35 1150 1942 625920795 625921580 1.630000e-40 178.0
104 TraesCS5B01G452600 chr5A 90.840 131 12 0 2723 2853 571787548 571787678 5.870000e-40 176.0
105 TraesCS5B01G452600 chr5A 79.079 239 48 2 1148 1385 626607144 626607381 4.570000e-36 163.0
106 TraesCS5B01G452600 chr5A 86.111 144 18 2 2711 2853 311019856 311019714 2.750000e-33 154.0
107 TraesCS5B01G452600 chr5A 78.846 208 44 0 1148 1355 627784826 627785033 2.140000e-29 141.0
108 TraesCS5B01G452600 chr5A 77.311 238 52 2 1148 1384 626447924 626448160 7.700000e-29 139.0
109 TraesCS5B01G452600 chr5A 82.051 156 19 7 2469 2616 599555671 599555517 2.160000e-24 124.0
110 TraesCS5B01G452600 chr5A 94.915 59 3 0 4606 4664 55159029 55158971 6.080000e-15 93.5
111 TraesCS5B01G452600 chr5A 92.982 57 1 3 4607 4661 700362865 700362920 4.730000e-11 80.5
112 TraesCS5B01G452600 chr2A 88.250 400 35 8 1148 1536 699529840 699529442 8.640000e-128 468.0
113 TraesCS5B01G452600 chr2A 77.572 593 93 13 1958 2526 699527576 699527000 7.120000e-84 322.0
114 TraesCS5B01G452600 chr2A 87.903 248 26 3 5453 5698 487998041 487998286 7.220000e-74 289.0
115 TraesCS5B01G452600 chr2A 94.675 169 7 2 3167 3334 460904164 460903997 1.570000e-65 261.0
116 TraesCS5B01G452600 chr2A 95.349 43 2 0 4501 4543 582639958 582640000 1.020000e-07 69.4
117 TraesCS5B01G452600 chr7D 92.581 310 20 2 1 309 50711223 50711530 5.240000e-120 442.0
118 TraesCS5B01G452600 chr7D 87.550 249 27 3 5453 5698 212214185 212214432 9.340000e-73 285.0
119 TraesCS5B01G452600 chr7D 95.758 165 7 0 3172 3336 174342341 174342177 3.380000e-67 267.0
120 TraesCS5B01G452600 chr7D 95.349 43 2 0 4501 4543 131620133 131620175 1.020000e-07 69.4
121 TraesCS5B01G452600 chr7D 93.023 43 3 0 4570 4612 332365500 332365542 4.770000e-06 63.9
122 TraesCS5B01G452600 chr7D 95.000 40 2 0 4469 4508 632327892 632327931 4.770000e-06 63.9
123 TraesCS5B01G452600 chr1D 92.258 310 21 3 1 309 61976812 61976505 2.440000e-118 436.0
124 TraesCS5B01G452600 chr1D 88.710 248 24 3 5453 5697 479896712 479896958 3.340000e-77 300.0
125 TraesCS5B01G452600 chr1D 96.894 161 5 0 3167 3327 458883508 458883668 2.620000e-68 270.0
126 TraesCS5B01G452600 chr1D 95.679 162 6 1 3167 3327 37883904 37884065 5.660000e-65 259.0
127 TraesCS5B01G452600 chr1D 82.716 243 40 2 5458 5698 395504210 395504452 1.240000e-51 215.0
128 TraesCS5B01G452600 chr1D 86.735 98 6 6 4479 4570 84570963 84570867 1.010000e-17 102.0
129 TraesCS5B01G452600 chr1D 93.103 58 3 1 4606 4662 399819766 399819823 3.660000e-12 84.2
130 TraesCS5B01G452600 chr1D 100.000 33 0 0 4503 4535 260038017 260038049 1.710000e-05 62.1
131 TraesCS5B01G452600 chr1D 94.872 39 2 0 4501 4539 464733222 464733184 1.710000e-05 62.1
132 TraesCS5B01G452600 chr1D 94.737 38 1 1 4580 4617 260038049 260038013 2.220000e-04 58.4
133 TraesCS5B01G452600 chr1D 100.000 28 0 0 4584 4611 204481588 204481561 1.000000e-02 52.8
134 TraesCS5B01G452600 chr1A 89.113 248 25 1 5453 5698 576378470 576378717 1.990000e-79 307.0
135 TraesCS5B01G452600 chr1A 85.714 63 7 2 4606 4667 233008960 233009021 1.330000e-06 65.8
136 TraesCS5B01G452600 chr1A 93.182 44 3 0 5318 5361 366245982 366245939 1.330000e-06 65.8
137 TraesCS5B01G452600 chr1A 92.683 41 3 0 4503 4543 564767752 564767712 6.170000e-05 60.2
138 TraesCS5B01G452600 chr6A 88.306 248 27 1 5453 5698 80520497 80520744 4.320000e-76 296.0
139 TraesCS5B01G452600 chr6A 84.615 247 34 2 5453 5696 603811431 603811186 5.700000e-60 243.0
140 TraesCS5B01G452600 chr6A 84.082 245 36 2 5456 5698 223562794 223562551 3.430000e-57 233.0
141 TraesCS5B01G452600 chr6A 87.288 118 14 1 5245 5361 535823993 535823876 3.580000e-27 134.0
142 TraesCS5B01G452600 chr6A 82.906 117 20 0 5184 5300 381120330 381120446 7.810000e-19 106.0
143 TraesCS5B01G452600 chr6A 95.833 48 2 0 5317 5364 223563567 223563520 1.700000e-10 78.7
144 TraesCS5B01G452600 chr6A 88.462 52 5 1 4492 4543 200181394 200181344 1.710000e-05 62.1
145 TraesCS5B01G452600 chr6A 94.286 35 2 0 4474 4508 575239763 575239797 3.000000e-03 54.7
146 TraesCS5B01G452600 chr6A 100.000 28 0 0 4481 4508 596589302 596589329 1.000000e-02 52.8
147 TraesCS5B01G452600 chr3A 83.386 319 46 4 5129 5441 746561016 746561333 7.220000e-74 289.0
148 TraesCS5B01G452600 chr3A 90.400 125 12 0 2720 2844 177109083 177108959 1.270000e-36 165.0
149 TraesCS5B01G452600 chr3A 81.356 177 27 6 5188 5361 172628501 172628328 7.700000e-29 139.0
150 TraesCS5B01G452600 chrUn 94.048 168 9 1 3164 3331 31210738 31210904 2.640000e-63 254.0
151 TraesCS5B01G452600 chrUn 94.444 162 8 1 3167 3327 30323135 30323296 1.230000e-61 248.0
152 TraesCS5B01G452600 chrUn 93.939 165 9 1 3167 3330 375482380 375482216 1.230000e-61 248.0
153 TraesCS5B01G452600 chrUn 93.413 167 9 1 3167 3331 103856201 103856035 4.410000e-61 246.0
154 TraesCS5B01G452600 chrUn 93.413 167 9 1 3167 3331 308664895 308664729 4.410000e-61 246.0
155 TraesCS5B01G452600 chrUn 93.827 162 9 1 3167 3327 30331602 30331763 5.700000e-60 243.0
156 TraesCS5B01G452600 chrUn 82.857 245 39 2 5456 5698 137833459 137833702 3.460000e-52 217.0
157 TraesCS5B01G452600 chrUn 87.425 167 19 1 5534 5698 47426652 47426486 2.100000e-44 191.0
158 TraesCS5B01G452600 chrUn 87.425 167 19 1 5534 5698 47435041 47434875 2.100000e-44 191.0
159 TraesCS5B01G452600 chrUn 94.444 54 3 0 4606 4659 100236654 100236601 3.660000e-12 84.2
160 TraesCS5B01G452600 chrUn 89.831 59 3 3 4608 4664 314370622 314370565 7.920000e-09 73.1
161 TraesCS5B01G452600 chrUn 90.385 52 3 2 4606 4656 341053794 341053844 3.680000e-07 67.6
162 TraesCS5B01G452600 chrUn 97.143 35 1 0 4474 4508 21636679 21636713 6.170000e-05 60.2
163 TraesCS5B01G452600 chrUn 94.595 37 2 0 4472 4508 41911642 41911606 2.220000e-04 58.4
164 TraesCS5B01G452600 chrUn 100.000 29 0 0 4633 4661 65440881 65440853 3.000000e-03 54.7
165 TraesCS5B01G452600 chr4D 94.012 167 8 1 3167 3331 38630531 38630697 9.480000e-63 252.0
166 TraesCS5B01G452600 chr4D 93.529 170 9 1 3167 3334 49869568 49869399 9.480000e-63 252.0
167 TraesCS5B01G452600 chr4D 86.010 193 24 2 5509 5698 1813069 1812877 2.690000e-48 204.0
168 TraesCS5B01G452600 chr4D 86.567 67 7 2 4602 4666 362116451 362116517 7.920000e-09 73.1
169 TraesCS5B01G452600 chr4D 95.556 45 0 2 4615 4658 335044923 335044966 2.850000e-08 71.3
170 TraesCS5B01G452600 chr4D 97.500 40 1 0 4622 4661 26253986 26253947 1.020000e-07 69.4
171 TraesCS5B01G452600 chr4D 89.091 55 6 0 4606 4660 251523012 251523066 1.020000e-07 69.4
172 TraesCS5B01G452600 chr4D 97.143 35 1 0 4474 4508 170210458 170210424 6.170000e-05 60.2
173 TraesCS5B01G452600 chr4D 90.909 44 4 0 4500 4543 190533083 190533040 6.170000e-05 60.2
174 TraesCS5B01G452600 chr4D 91.304 46 0 3 4565 4609 495540311 495540353 6.170000e-05 60.2
175 TraesCS5B01G452600 chr4D 94.872 39 0 2 4506 4543 495540353 495540316 6.170000e-05 60.2
176 TraesCS5B01G452600 chr4D 92.500 40 2 1 4579 4618 109931835 109931797 7.980000e-04 56.5
177 TraesCS5B01G452600 chr4D 100.000 29 0 0 4587 4615 467755816 467755788 3.000000e-03 54.7
178 TraesCS5B01G452600 chr4D 100.000 29 0 0 4480 4508 472923963 472923935 3.000000e-03 54.7
179 TraesCS5B01G452600 chr7B 77.538 325 57 6 5131 5455 484431660 484431352 1.260000e-41 182.0
180 TraesCS5B01G452600 chr7B 86.111 144 18 2 2711 2853 645515319 645515177 2.750000e-33 154.0
181 TraesCS5B01G452600 chr4A 87.591 137 17 0 5314 5450 58538290 58538426 5.910000e-35 159.0
182 TraesCS5B01G452600 chr4A 93.333 45 3 0 4499 4543 687562991 687562947 3.680000e-07 67.6
183 TraesCS5B01G452600 chr4A 91.667 48 4 0 4570 4617 730998909 730998862 3.680000e-07 67.6
184 TraesCS5B01G452600 chr1B 97.561 41 1 0 4570 4610 304515073 304515113 2.850000e-08 71.3
185 TraesCS5B01G452600 chr1B 97.561 41 1 0 4503 4543 304515115 304515075 2.850000e-08 71.3
186 TraesCS5B01G452600 chr1B 97.561 41 1 0 4570 4610 653607031 653607071 2.850000e-08 71.3
187 TraesCS5B01G452600 chr1B 90.196 51 1 3 4485 4535 35096547 35096593 4.770000e-06 63.9
188 TraesCS5B01G452600 chr6B 97.500 40 1 0 4570 4609 277158980 277158941 1.020000e-07 69.4
189 TraesCS5B01G452600 chr4B 91.667 48 2 2 4570 4616 63847089 63847135 1.330000e-06 65.8
190 TraesCS5B01G452600 chr4B 97.143 35 1 0 4474 4508 399547295 399547261 6.170000e-05 60.2


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 TraesCS5B01G452600 chr5B 625447533 625453230 5697 True 5193.5 9816 100.0000 1 5698 2 chr5B.!!$R7 5697
1 TraesCS5B01G452600 chr5B 632805029 632810650 5621 False 4728.0 8946 96.7550 1 5695 2 chr5B.!!$F10 5694
2 TraesCS5B01G452600 chr5B 629075633 629081379 5746 True 3342.0 4948 98.5790 1 5698 3 chr5B.!!$R8 5697
3 TraesCS5B01G452600 chr5B 604714743 604719768 5025 True 1365.0 3476 94.5416 863 5698 5 chr5B.!!$R6 4835
4 TraesCS5B01G452600 chr5D 498924750 498930080 5330 True 8839.0 8839 96.6640 384 5698 1 chr5D.!!$R4 5314
5 TraesCS5B01G452600 chr5D 501706258 501711536 5278 True 4571.0 5598 98.0340 384 5698 2 chr5D.!!$R10 5314
6 TraesCS5B01G452600 chr5D 501427806 501430235 2429 True 384.0 647 81.6865 1151 4274 2 chr5D.!!$R9 3123
7 TraesCS5B01G452600 chr5D 249521853 249522824 971 True 244.0 316 89.7650 5317 5698 2 chr5D.!!$R8 381
8 TraesCS5B01G452600 chr3B 462097402 462100099 2697 True 414.0 676 81.9155 1114 3176 2 chr3B.!!$R1 2062
9 TraesCS5B01G452600 chr2B 667421453 667422781 1328 True 444.5 606 80.9475 1147 2527 2 chr2B.!!$R3 1380
10 TraesCS5B01G452600 chr5A 629372514 629373984 1470 False 275.0 331 74.8945 1196 2681 2 chr5A.!!$F8 1485
11 TraesCS5B01G452600 chr5A 599555517 599556959 1442 True 254.5 385 78.7700 1121 2616 2 chr5A.!!$R5 1495
12 TraesCS5B01G452600 chr5A 629249024 629249618 594 True 230.0 230 74.5480 2099 2681 1 chr5A.!!$R4 582
13 TraesCS5B01G452600 chr2A 699527000 699529840 2840 True 395.0 468 82.9110 1148 2526 2 chr2A.!!$R2 1378

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
800 829 1.812214 GCGAATGACTAAGAGCGCGG 61.812 60.000 8.83 0.0 35.02 6.46 F
2056 4129 3.036084 CGTGTGTCCGTCAGCCAC 61.036 66.667 0.00 0.0 0.00 5.01 F
3439 5852 6.364945 TCACGAGACTGTTCACTATCTATG 57.635 41.667 0.00 0.0 0.00 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 4129 0.179156 GGACAAAGTGCATCATGCCG 60.179 55.000 7.30 0.0 44.23 5.69 R
3439 5852 3.064207 TGAATCAAGAACTACCACGTGC 58.936 45.455 10.91 0.0 0.00 5.34 R
5310 8050 0.463654 AGCTGGCTTTGTTGTCGTCA 60.464 50.000 0.00 0.0 0.00 4.35 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
800 829 1.812214 GCGAATGACTAAGAGCGCGG 61.812 60.000 8.83 0.0 35.02 6.46
2056 4129 3.036084 CGTGTGTCCGTCAGCCAC 61.036 66.667 0.00 0.0 0.00 5.01
3439 5852 6.364945 TCACGAGACTGTTCACTATCTATG 57.635 41.667 0.00 0.0 0.00 2.23
4470 7186 4.226846 GGATGATGGGATGAGGATGTGTAT 59.773 45.833 0.00 0.0 0.00 2.29
4929 7647 1.135721 GCAGATGGCACCAAAAGGATC 59.864 52.381 0.00 0.0 43.97 3.36
5119 7845 2.076622 CTAGCCGCCATAGTCACGCT 62.077 60.000 0.00 0.0 0.00 5.07
5310 8050 6.756542 GCCTTCACAATGAACAAGTTTTTAGT 59.243 34.615 0.00 0.0 32.21 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 406 1.214589 GCCGTGCCTCTCGTAAAGA 59.785 57.895 0.00 0.00 0.00 2.52
468 471 2.502213 TTTCTTTCGCGAGAGTCACA 57.498 45.000 24.05 4.18 43.69 3.58
574 579 1.004292 CTTTCGCGAAAGTCACGGTTT 60.004 47.619 40.16 0.00 42.02 3.27
743 772 1.073923 ACGCTCCCTCTGGATTTTGTT 59.926 47.619 0.00 0.00 40.80 2.83
800 829 1.675641 AACGATCAGGGCCACTTGC 60.676 57.895 6.18 0.00 40.16 4.01
2056 4129 0.179156 GGACAAAGTGCATCATGCCG 60.179 55.000 7.30 0.00 44.23 5.69
2566 4819 5.483811 ACACAACCATGTTGTATCGATACA 58.516 37.500 29.79 29.79 41.19 2.29
2906 5195 3.683822 CAGAAGTCCTTGTGCTGAGAATC 59.316 47.826 0.00 0.00 0.00 2.52
3070 5469 6.648879 TGACAGCAAATATATTAAAGGCCC 57.351 37.500 0.00 0.00 0.00 5.80
3439 5852 3.064207 TGAATCAAGAACTACCACGTGC 58.936 45.455 10.91 0.00 0.00 5.34
4470 7186 8.388656 AGACACTTATTTTGGGATAGAGGTAA 57.611 34.615 0.00 0.00 0.00 2.85
5119 7845 1.745115 GCATGAACCACAGCCGCTA 60.745 57.895 0.00 0.00 0.00 4.26
5310 8050 0.463654 AGCTGGCTTTGTTGTCGTCA 60.464 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.