Multiple sequence alignment - TraesCS6D01G404900
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 | TraesCS6D01G404900 | chr6D | 100.000 | 8612 | 0 | 0 | 1 | 8612 | 472431085 | 472422474 | 0.000000e+00 | 15904.0 |
1 | TraesCS6D01G404900 | chr6D | 82.861 | 776 | 75 | 21 | 2401 | 3151 | 472500932 | 472500190 | 2.030000e-180 | 643.0 |
2 | TraesCS6D01G404900 | chr6D | 84.832 | 567 | 47 | 11 | 5319 | 5854 | 472498059 | 472497501 | 1.270000e-147 | 534.0 |
3 | TraesCS6D01G404900 | chr6D | 79.564 | 734 | 86 | 28 | 745 | 1441 | 472502549 | 472501843 | 4.710000e-127 | 466.0 |
4 | TraesCS6D01G404900 | chr6D | 83.368 | 487 | 54 | 9 | 3152 | 3615 | 472499955 | 472499473 | 7.990000e-115 | 425.0 |
5 | TraesCS6D01G404900 | chr6D | 90.596 | 319 | 28 | 2 | 6224 | 6540 | 472958228 | 472957910 | 1.030000e-113 | 422.0 |
6 | TraesCS6D01G404900 | chr6D | 77.897 | 561 | 89 | 19 | 5485 | 6040 | 472489198 | 472488668 | 5.020000e-82 | 316.0 |
7 | TraesCS6D01G404900 | chr6D | 87.143 | 280 | 30 | 5 | 7062 | 7336 | 339272360 | 339272638 | 6.490000e-81 | 313.0 |
8 | TraesCS6D01G404900 | chr6D | 85.764 | 288 | 39 | 2 | 278 | 565 | 472504649 | 472504364 | 3.910000e-78 | 303.0 |
9 | TraesCS6D01G404900 | chr6D | 90.957 | 188 | 14 | 1 | 7337 | 7524 | 472497264 | 472497080 | 5.160000e-62 | 250.0 |
10 | TraesCS6D01G404900 | chr6D | 80.333 | 300 | 47 | 8 | 6680 | 6970 | 124947678 | 124947382 | 5.240000e-52 | 217.0 |
11 | TraesCS6D01G404900 | chr6D | 79.580 | 333 | 42 | 13 | 7572 | 7890 | 472497086 | 472496766 | 1.880000e-51 | 215.0 |
12 | TraesCS6D01G404900 | chr6D | 88.966 | 145 | 16 | 0 | 6538 | 6682 | 180342631 | 180342775 | 6.870000e-41 | 180.0 |
13 | TraesCS6D01G404900 | chr6D | 79.913 | 229 | 31 | 6 | 8276 | 8504 | 472496228 | 472496015 | 4.160000e-33 | 154.0 |
14 | TraesCS6D01G404900 | chr6D | 95.556 | 90 | 4 | 0 | 4638 | 4727 | 472498412 | 472498323 | 2.510000e-30 | 145.0 |
15 | TraesCS6D01G404900 | chr6D | 87.156 | 109 | 13 | 1 | 6114 | 6222 | 436407794 | 436407901 | 1.170000e-23 | 122.0 |
16 | TraesCS6D01G404900 | chr6D | 81.379 | 145 | 16 | 7 | 3621 | 3765 | 472499492 | 472499359 | 3.290000e-19 | 108.0 |
17 | TraesCS6D01G404900 | chr6D | 100.000 | 28 | 0 | 0 | 326 | 353 | 445738296 | 445738269 | 1.600000e-02 | 52.8 |
18 | TraesCS6D01G404900 | chr1A | 95.806 | 5150 | 135 | 22 | 973 | 6048 | 2843882 | 2838740 | 0.000000e+00 | 8239.0 |
19 | TraesCS6D01G404900 | chr1A | 93.516 | 1789 | 79 | 10 | 6092 | 7852 | 2838741 | 2836962 | 0.000000e+00 | 2627.0 |
20 | TraesCS6D01G404900 | chr1A | 84.848 | 1353 | 144 | 18 | 3165 | 4490 | 2657577 | 2656259 | 0.000000e+00 | 1306.0 |
21 | TraesCS6D01G404900 | chr1A | 90.996 | 522 | 22 | 2 | 8116 | 8612 | 2836363 | 2835842 | 0.000000e+00 | 680.0 |
22 | TraesCS6D01G404900 | chr1A | 78.586 | 976 | 109 | 51 | 552 | 1441 | 2648329 | 2647368 | 3.510000e-153 | 553.0 |
23 | TraesCS6D01G404900 | chr1A | 84.303 | 567 | 50 | 13 | 5319 | 5854 | 2643803 | 2643245 | 1.280000e-142 | 518.0 |
24 | TraesCS6D01G404900 | chr1A | 81.803 | 588 | 74 | 11 | 7334 | 7894 | 2653588 | 2653007 | 6.090000e-126 | 462.0 |
25 | TraesCS6D01G404900 | chr1A | 86.095 | 338 | 36 | 6 | 4985 | 5317 | 2655781 | 2655450 | 3.820000e-93 | 353.0 |
26 | TraesCS6D01G404900 | chr1A | 96.226 | 212 | 6 | 2 | 4815 | 5025 | 2826143 | 2825933 | 6.400000e-91 | 346.0 |
27 | TraesCS6D01G404900 | chr1A | 86.392 | 316 | 40 | 3 | 5735 | 6047 | 2653965 | 2653650 | 8.280000e-90 | 342.0 |
28 | TraesCS6D01G404900 | chr1A | 83.377 | 379 | 34 | 11 | 2775 | 3143 | 2646189 | 2645830 | 3.000000e-84 | 324.0 |
29 | TraesCS6D01G404900 | chr1A | 84.871 | 271 | 26 | 5 | 2389 | 2645 | 2646468 | 2646199 | 8.580000e-65 | 259.0 |
30 | TraesCS6D01G404900 | chr1A | 90.426 | 188 | 15 | 1 | 7337 | 7524 | 2643006 | 2642822 | 2.400000e-60 | 244.0 |
31 | TraesCS6D01G404900 | chr1A | 93.056 | 144 | 10 | 0 | 4626 | 4769 | 2655988 | 2655845 | 2.440000e-50 | 211.0 |
32 | TraesCS6D01G404900 | chr1A | 78.979 | 333 | 44 | 12 | 7572 | 7890 | 2642828 | 2642508 | 4.080000e-48 | 204.0 |
33 | TraesCS6D01G404900 | chr1A | 86.628 | 172 | 20 | 2 | 3454 | 3622 | 2645382 | 2645211 | 4.100000e-43 | 187.0 |
34 | TraesCS6D01G404900 | chr1A | 90.909 | 132 | 12 | 0 | 6551 | 6682 | 248034405 | 248034274 | 2.470000e-40 | 178.0 |
35 | TraesCS6D01G404900 | chr1A | 95.506 | 89 | 4 | 0 | 5082 | 5170 | 2825930 | 2825842 | 9.010000e-30 | 143.0 |
36 | TraesCS6D01G404900 | chr1A | 93.333 | 90 | 6 | 0 | 4638 | 4727 | 2644155 | 2644066 | 5.420000e-27 | 134.0 |
37 | TraesCS6D01G404900 | chr1A | 82.069 | 145 | 15 | 7 | 3621 | 3765 | 2645238 | 2645105 | 7.070000e-21 | 113.0 |
38 | TraesCS6D01G404900 | chr1A | 90.769 | 65 | 6 | 0 | 6968 | 7032 | 163834555 | 163834619 | 4.280000e-13 | 87.9 |
39 | TraesCS6D01G404900 | chr1A | 90.769 | 65 | 6 | 0 | 6968 | 7032 | 163956808 | 163956872 | 4.280000e-13 | 87.9 |
40 | TraesCS6D01G404900 | chr1A | 87.671 | 73 | 9 | 0 | 7891 | 7963 | 2695247 | 2695175 | 1.540000e-12 | 86.1 |
41 | TraesCS6D01G404900 | chr1A | 100.000 | 34 | 0 | 0 | 7866 | 7899 | 2836966 | 2836933 | 7.220000e-06 | 63.9 |
42 | TraesCS6D01G404900 | chr6A | 95.760 | 3255 | 91 | 11 | 200 | 3411 | 617551598 | 617554848 | 0.000000e+00 | 5203.0 |
43 | TraesCS6D01G404900 | chr6A | 95.988 | 2642 | 60 | 14 | 3450 | 6048 | 617555170 | 617557808 | 0.000000e+00 | 4250.0 |
44 | TraesCS6D01G404900 | chr6A | 93.040 | 1839 | 81 | 19 | 6092 | 7899 | 617557807 | 617559629 | 0.000000e+00 | 2643.0 |
45 | TraesCS6D01G404900 | chr6A | 87.259 | 777 | 79 | 10 | 3725 | 4490 | 617237648 | 617238415 | 0.000000e+00 | 869.0 |
46 | TraesCS6D01G404900 | chr6A | 84.785 | 769 | 96 | 6 | 3730 | 4490 | 617224235 | 617224990 | 0.000000e+00 | 752.0 |
47 | TraesCS6D01G404900 | chr6A | 90.684 | 526 | 20 | 5 | 8116 | 8612 | 617560142 | 617560667 | 0.000000e+00 | 673.0 |
48 | TraesCS6D01G404900 | chr6A | 86.312 | 621 | 69 | 10 | 5440 | 6045 | 617351752 | 617352371 | 0.000000e+00 | 662.0 |
49 | TraesCS6D01G404900 | chr6A | 84.264 | 591 | 54 | 7 | 2389 | 2966 | 617349429 | 617349993 | 2.740000e-149 | 540.0 |
50 | TraesCS6D01G404900 | chr6A | 83.717 | 565 | 54 | 15 | 5319 | 5854 | 617322413 | 617322968 | 4.640000e-137 | 499.0 |
51 | TraesCS6D01G404900 | chr6A | 85.232 | 474 | 60 | 2 | 3250 | 3723 | 617237217 | 617237680 | 6.050000e-131 | 479.0 |
52 | TraesCS6D01G404900 | chr6A | 86.861 | 411 | 51 | 2 | 245 | 655 | 617234082 | 617234489 | 2.830000e-124 | 457.0 |
53 | TraesCS6D01G404900 | chr6A | 79.340 | 697 | 95 | 28 | 745 | 1406 | 617317983 | 617318665 | 2.210000e-120 | 444.0 |
54 | TraesCS6D01G404900 | chr6A | 86.600 | 403 | 53 | 1 | 4089 | 4490 | 617350450 | 617350852 | 2.210000e-120 | 444.0 |
55 | TraesCS6D01G404900 | chr6A | 83.468 | 496 | 53 | 16 | 7334 | 7802 | 617352435 | 617352928 | 1.330000e-117 | 435.0 |
56 | TraesCS6D01G404900 | chr6A | 85.383 | 431 | 42 | 14 | 2726 | 3143 | 617319875 | 617320297 | 2.220000e-115 | 427.0 |
57 | TraesCS6D01G404900 | chr6A | 79.154 | 662 | 70 | 36 | 712 | 1318 | 617217210 | 617217858 | 6.270000e-106 | 396.0 |
58 | TraesCS6D01G404900 | chr6A | 80.612 | 490 | 79 | 11 | 2674 | 3149 | 617236346 | 617236833 | 1.770000e-96 | 364.0 |
59 | TraesCS6D01G404900 | chr6A | 98.507 | 201 | 3 | 0 | 1 | 201 | 617551358 | 617551558 | 1.060000e-93 | 355.0 |
60 | TraesCS6D01G404900 | chr6A | 92.653 | 245 | 18 | 0 | 5486 | 5730 | 617239443 | 617239687 | 3.820000e-93 | 353.0 |
61 | TraesCS6D01G404900 | chr6A | 91.600 | 250 | 7 | 6 | 654 | 889 | 617317728 | 617317977 | 4.980000e-87 | 333.0 |
62 | TraesCS6D01G404900 | chr6A | 84.337 | 332 | 52 | 0 | 200 | 531 | 617232598 | 617232929 | 8.340000e-85 | 326.0 |
63 | TraesCS6D01G404900 | chr6A | 86.411 | 287 | 25 | 5 | 2389 | 2662 | 617319567 | 617319852 | 1.400000e-77 | 302.0 |
64 | TraesCS6D01G404900 | chr6A | 83.596 | 317 | 32 | 10 | 1121 | 1425 | 617234884 | 617235192 | 6.580000e-71 | 279.0 |
65 | TraesCS6D01G404900 | chr6A | 90.909 | 209 | 18 | 1 | 4984 | 5192 | 617351327 | 617351534 | 6.580000e-71 | 279.0 |
66 | TraesCS6D01G404900 | chr6A | 89.401 | 217 | 16 | 4 | 5828 | 6041 | 617239747 | 617239959 | 5.130000e-67 | 267.0 |
67 | TraesCS6D01G404900 | chr6A | 80.243 | 329 | 44 | 15 | 998 | 1316 | 617246646 | 617246963 | 2.420000e-55 | 228.0 |
68 | TraesCS6D01G404900 | chr6A | 85.845 | 219 | 22 | 5 | 5101 | 5317 | 617239011 | 617239222 | 3.130000e-54 | 224.0 |
69 | TraesCS6D01G404900 | chr6A | 87.845 | 181 | 15 | 3 | 2407 | 2580 | 617236127 | 617236307 | 1.130000e-48 | 206.0 |
70 | TraesCS6D01G404900 | chr6A | 85.572 | 201 | 17 | 7 | 3 | 201 | 617233784 | 617233974 | 5.270000e-47 | 200.0 |
71 | TraesCS6D01G404900 | chr6A | 80.357 | 280 | 29 | 12 | 1143 | 1416 | 617348294 | 617348553 | 1.140000e-43 | 189.0 |
72 | TraesCS6D01G404900 | chr6A | 83.673 | 147 | 23 | 1 | 247 | 393 | 617253227 | 617253372 | 4.190000e-28 | 137.0 |
73 | TraesCS6D01G404900 | chr6A | 91.892 | 74 | 6 | 0 | 4984 | 5057 | 617238935 | 617239008 | 4.250000e-18 | 104.0 |
74 | TraesCS6D01G404900 | chr6A | 83.962 | 106 | 15 | 2 | 1632 | 1736 | 617218153 | 617218257 | 5.500000e-17 | 100.0 |
75 | TraesCS6D01G404900 | chr6B | 93.917 | 3436 | 86 | 35 | 2316 | 5676 | 717141701 | 717138314 | 0.000000e+00 | 5073.0 |
76 | TraesCS6D01G404900 | chr6B | 94.695 | 1263 | 44 | 10 | 187 | 1435 | 717143944 | 717142691 | 0.000000e+00 | 1940.0 |
77 | TraesCS6D01G404900 | chr6B | 95.159 | 785 | 31 | 5 | 7121 | 7899 | 717137891 | 717137108 | 0.000000e+00 | 1232.0 |
78 | TraesCS6D01G404900 | chr6B | 87.751 | 996 | 96 | 9 | 3502 | 4490 | 717401647 | 717400671 | 0.000000e+00 | 1140.0 |
79 | TraesCS6D01G404900 | chr6B | 91.701 | 723 | 56 | 3 | 7891 | 8611 | 717115981 | 717115261 | 0.000000e+00 | 1000.0 |
80 | TraesCS6D01G404900 | chr6B | 94.836 | 639 | 28 | 4 | 1693 | 2331 | 717142379 | 717141746 | 0.000000e+00 | 992.0 |
81 | TraesCS6D01G404900 | chr6B | 80.797 | 953 | 141 | 31 | 1750 | 2678 | 717403433 | 717402499 | 0.000000e+00 | 708.0 |
82 | TraesCS6D01G404900 | chr6B | 86.078 | 668 | 68 | 8 | 3831 | 4492 | 717417789 | 717417141 | 0.000000e+00 | 695.0 |
83 | TraesCS6D01G404900 | chr6B | 85.714 | 616 | 68 | 11 | 5440 | 6047 | 717399634 | 717399031 | 4.390000e-177 | 632.0 |
84 | TraesCS6D01G404900 | chr6B | 79.896 | 766 | 104 | 30 | 712 | 1441 | 717420719 | 717419968 | 4.610000e-142 | 516.0 |
85 | TraesCS6D01G404900 | chr6B | 88.942 | 416 | 30 | 5 | 6668 | 7068 | 717138317 | 717137903 | 4.640000e-137 | 499.0 |
86 | TraesCS6D01G404900 | chr6B | 87.119 | 427 | 41 | 6 | 2726 | 3143 | 717418764 | 717418343 | 1.010000e-128 | 472.0 |
87 | TraesCS6D01G404900 | chr6B | 85.622 | 466 | 46 | 12 | 5319 | 5772 | 717416249 | 717415793 | 3.640000e-128 | 470.0 |
88 | TraesCS6D01G404900 | chr6B | 86.647 | 337 | 35 | 6 | 4985 | 5317 | 717400180 | 717399850 | 1.770000e-96 | 364.0 |
89 | TraesCS6D01G404900 | chr6B | 97.487 | 199 | 5 | 0 | 3 | 201 | 717144170 | 717143972 | 2.980000e-89 | 340.0 |
90 | TraesCS6D01G404900 | chr6B | 87.097 | 279 | 22 | 5 | 2389 | 2654 | 717419070 | 717418793 | 3.910000e-78 | 303.0 |
91 | TraesCS6D01G404900 | chr6B | 93.960 | 149 | 9 | 0 | 4621 | 4769 | 717416836 | 717416688 | 8.700000e-55 | 226.0 |
92 | TraesCS6D01G404900 | chr6B | 81.979 | 283 | 30 | 13 | 1146 | 1423 | 717403955 | 717403689 | 4.050000e-53 | 220.0 |
93 | TraesCS6D01G404900 | chr6B | 88.757 | 169 | 15 | 4 | 4794 | 4960 | 704099409 | 704099243 | 4.080000e-48 | 204.0 |
94 | TraesCS6D01G404900 | chr6B | 90.728 | 151 | 12 | 1 | 4621 | 4769 | 717400394 | 717400244 | 5.270000e-47 | 200.0 |
95 | TraesCS6D01G404900 | chr6B | 81.356 | 236 | 42 | 2 | 5807 | 6040 | 717408005 | 717407770 | 3.170000e-44 | 191.0 |
96 | TraesCS6D01G404900 | chr6B | 80.816 | 245 | 38 | 7 | 2123 | 2364 | 717411183 | 717410945 | 5.310000e-42 | 183.0 |
97 | TraesCS6D01G404900 | chr6B | 90.909 | 132 | 12 | 0 | 4492 | 4623 | 717417079 | 717416948 | 2.470000e-40 | 178.0 |
98 | TraesCS6D01G404900 | chr6B | 90.769 | 130 | 12 | 0 | 7334 | 7463 | 717398969 | 717398840 | 3.200000e-39 | 174.0 |
99 | TraesCS6D01G404900 | chr6B | 91.667 | 120 | 4 | 1 | 1433 | 1546 | 717142588 | 717142469 | 2.490000e-35 | 161.0 |
100 | TraesCS6D01G404900 | chr6B | 86.207 | 145 | 19 | 1 | 3621 | 3765 | 717417963 | 717417820 | 1.160000e-33 | 156.0 |
101 | TraesCS6D01G404900 | chr6B | 75.375 | 333 | 68 | 6 | 8271 | 8603 | 717414328 | 717414010 | 1.940000e-31 | 148.0 |
102 | TraesCS6D01G404900 | chr6B | 88.785 | 107 | 12 | 0 | 6116 | 6222 | 448670912 | 448670806 | 1.950000e-26 | 132.0 |
103 | TraesCS6D01G404900 | chr6B | 92.593 | 54 | 4 | 0 | 3527 | 3580 | 717418028 | 717417975 | 2.580000e-10 | 78.7 |
104 | TraesCS6D01G404900 | chr5D | 94.771 | 306 | 15 | 1 | 7962 | 8267 | 221824578 | 221824274 | 7.820000e-130 | 475.0 |
105 | TraesCS6D01G404900 | chr5D | 89.967 | 299 | 19 | 3 | 7051 | 7338 | 210677899 | 210678197 | 8.160000e-100 | 375.0 |
106 | TraesCS6D01G404900 | chr5D | 82.609 | 299 | 39 | 8 | 6681 | 6969 | 210677899 | 210678194 | 1.440000e-62 | 252.0 |
107 | TraesCS6D01G404900 | chr5D | 79.817 | 327 | 46 | 12 | 6680 | 6990 | 354809097 | 354808775 | 4.050000e-53 | 220.0 |
108 | TraesCS6D01G404900 | chr4B | 90.252 | 318 | 27 | 4 | 6224 | 6538 | 171806343 | 171806027 | 6.220000e-111 | 412.0 |
109 | TraesCS6D01G404900 | chr3D | 90.031 | 321 | 28 | 4 | 6227 | 6543 | 79503272 | 79502952 | 6.220000e-111 | 412.0 |
110 | TraesCS6D01G404900 | chr3D | 90.291 | 309 | 30 | 0 | 7959 | 8267 | 420987233 | 420987541 | 1.040000e-108 | 405.0 |
111 | TraesCS6D01G404900 | chr3D | 88.449 | 303 | 24 | 4 | 7051 | 7342 | 175803379 | 175803077 | 1.060000e-93 | 355.0 |
112 | TraesCS6D01G404900 | chr3D | 86.598 | 291 | 33 | 4 | 7051 | 7336 | 524486669 | 524486380 | 5.020000e-82 | 316.0 |
113 | TraesCS6D01G404900 | chr3D | 90.173 | 173 | 6 | 5 | 4794 | 4956 | 580128344 | 580128515 | 1.880000e-51 | 215.0 |
114 | TraesCS6D01G404900 | chr3A | 90.820 | 305 | 28 | 0 | 7963 | 8267 | 644530532 | 644530228 | 8.050000e-110 | 409.0 |
115 | TraesCS6D01G404900 | chr3A | 89.655 | 145 | 15 | 0 | 6538 | 6682 | 698757007 | 698757151 | 1.480000e-42 | 185.0 |
116 | TraesCS6D01G404900 | chr3A | 84.492 | 187 | 28 | 1 | 16 | 201 | 492732646 | 492732832 | 5.310000e-42 | 183.0 |
117 | TraesCS6D01G404900 | chr3A | 91.089 | 101 | 9 | 0 | 6122 | 6222 | 28327028 | 28326928 | 4.190000e-28 | 137.0 |
118 | TraesCS6D01G404900 | chrUn | 90.554 | 307 | 29 | 0 | 7961 | 8267 | 103496586 | 103496892 | 2.890000e-109 | 407.0 |
119 | TraesCS6D01G404900 | chr5B | 90.228 | 307 | 29 | 1 | 7961 | 8267 | 11532671 | 11532976 | 4.840000e-107 | 399.0 |
120 | TraesCS6D01G404900 | chr5B | 89.231 | 65 | 5 | 2 | 6968 | 7031 | 12039997 | 12040060 | 7.170000e-11 | 80.5 |
121 | TraesCS6D01G404900 | chr4D | 90.228 | 307 | 24 | 6 | 7962 | 8267 | 497512349 | 497512650 | 6.270000e-106 | 396.0 |
122 | TraesCS6D01G404900 | chr4D | 80.972 | 247 | 31 | 10 | 6681 | 6917 | 70787949 | 70788189 | 1.910000e-41 | 182.0 |
123 | TraesCS6D01G404900 | chr4D | 79.151 | 259 | 28 | 14 | 6679 | 6919 | 108480713 | 108480963 | 1.160000e-33 | 156.0 |
124 | TraesCS6D01G404900 | chr4D | 85.075 | 134 | 17 | 1 | 7051 | 7181 | 128404671 | 128404804 | 5.420000e-27 | 134.0 |
125 | TraesCS6D01G404900 | chr1B | 87.736 | 318 | 22 | 7 | 6224 | 6538 | 329966624 | 329966927 | 1.060000e-93 | 355.0 |
126 | TraesCS6D01G404900 | chr1B | 81.356 | 295 | 38 | 12 | 6681 | 6963 | 609415322 | 609415611 | 3.130000e-54 | 224.0 |
127 | TraesCS6D01G404900 | chr4A | 86.458 | 288 | 35 | 3 | 7051 | 7337 | 661019093 | 661019377 | 6.490000e-81 | 313.0 |
128 | TraesCS6D01G404900 | chr4A | 92.424 | 132 | 10 | 0 | 6551 | 6682 | 740756896 | 740756765 | 1.140000e-43 | 189.0 |
129 | TraesCS6D01G404900 | chr4A | 93.103 | 58 | 4 | 0 | 6968 | 7025 | 106574557 | 106574500 | 1.540000e-12 | 86.1 |
130 | TraesCS6D01G404900 | chr4A | 90.000 | 60 | 6 | 0 | 6969 | 7028 | 743632977 | 743632918 | 2.580000e-10 | 78.7 |
131 | TraesCS6D01G404900 | chr7B | 83.904 | 292 | 39 | 8 | 7051 | 7337 | 688739185 | 688738897 | 1.100000e-68 | 272.0 |
132 | TraesCS6D01G404900 | chr7B | 83.895 | 267 | 29 | 5 | 7051 | 7306 | 453770709 | 453770446 | 8.640000e-60 | 243.0 |
133 | TraesCS6D01G404900 | chr7B | 81.169 | 308 | 31 | 11 | 6680 | 6969 | 728985749 | 728986047 | 1.130000e-53 | 222.0 |
134 | TraesCS6D01G404900 | chr7B | 88.276 | 145 | 16 | 1 | 12 | 156 | 613472001 | 613472144 | 1.150000e-38 | 172.0 |
135 | TraesCS6D01G404900 | chr2D | 81.789 | 313 | 38 | 8 | 6675 | 6969 | 154184981 | 154185292 | 2.400000e-60 | 244.0 |
136 | TraesCS6D01G404900 | chr2D | 80.000 | 300 | 47 | 8 | 6681 | 6970 | 282366111 | 282366407 | 8.760000e-50 | 209.0 |
137 | TraesCS6D01G404900 | chr2D | 92.414 | 145 | 11 | 0 | 6538 | 6682 | 375814383 | 375814527 | 3.150000e-49 | 207.0 |
138 | TraesCS6D01G404900 | chr2D | 83.735 | 166 | 23 | 4 | 14 | 177 | 471633157 | 471633320 | 4.160000e-33 | 154.0 |
139 | TraesCS6D01G404900 | chr1D | 80.667 | 300 | 44 | 7 | 6681 | 6970 | 111864727 | 111865022 | 4.050000e-53 | 220.0 |
140 | TraesCS6D01G404900 | chr1D | 89.630 | 135 | 13 | 1 | 6 | 139 | 317116577 | 317116443 | 4.130000e-38 | 171.0 |
141 | TraesCS6D01G404900 | chr1D | 89.630 | 135 | 13 | 1 | 6 | 139 | 317121903 | 317121769 | 4.130000e-38 | 171.0 |
142 | TraesCS6D01G404900 | chr1D | 86.429 | 140 | 17 | 2 | 7334 | 7472 | 449121842 | 449121704 | 1.500000e-32 | 152.0 |
143 | TraesCS6D01G404900 | chr1D | 88.596 | 114 | 13 | 0 | 6109 | 6222 | 486311130 | 486311017 | 1.170000e-28 | 139.0 |
144 | TraesCS6D01G404900 | chr1D | 88.889 | 63 | 7 | 0 | 6968 | 7030 | 378750193 | 378750255 | 2.580000e-10 | 78.7 |
145 | TraesCS6D01G404900 | chr7D | 80.471 | 297 | 30 | 13 | 6679 | 6958 | 465688897 | 465688612 | 1.470000e-47 | 202.0 |
146 | TraesCS6D01G404900 | chr7D | 87.356 | 174 | 11 | 8 | 4794 | 4957 | 5318784 | 5318956 | 1.140000e-43 | 189.0 |
147 | TraesCS6D01G404900 | chr7D | 87.879 | 165 | 14 | 5 | 4794 | 4956 | 571809482 | 571809642 | 1.140000e-43 | 189.0 |
148 | TraesCS6D01G404900 | chr7D | 79.167 | 144 | 20 | 4 | 4794 | 4927 | 397201618 | 397201761 | 3.310000e-14 | 91.6 |
149 | TraesCS6D01G404900 | chr3B | 80.142 | 282 | 43 | 8 | 6704 | 6975 | 273904037 | 273903759 | 1.900000e-46 | 198.0 |
150 | TraesCS6D01G404900 | chr5A | 87.952 | 166 | 17 | 3 | 4794 | 4957 | 573814832 | 573814668 | 8.820000e-45 | 193.0 |
151 | TraesCS6D01G404900 | chr5A | 89.109 | 101 | 10 | 1 | 6123 | 6222 | 353596603 | 353596703 | 3.260000e-24 | 124.0 |
152 | TraesCS6D01G404900 | chr2B | 90.345 | 145 | 14 | 0 | 6538 | 6682 | 50023777 | 50023921 | 3.170000e-44 | 191.0 |
153 | TraesCS6D01G404900 | chr2B | 94.595 | 37 | 1 | 1 | 4794 | 4829 | 743735706 | 743735742 | 1.000000e-03 | 56.5 |
154 | TraesCS6D01G404900 | chr7A | 89.655 | 145 | 15 | 0 | 6538 | 6682 | 208520775 | 208520631 | 1.480000e-42 | 185.0 |
155 | TraesCS6D01G404900 | chr2A | 84.181 | 177 | 18 | 4 | 14 | 190 | 711665875 | 711666041 | 6.920000e-36 | 163.0 |
156 | TraesCS6D01G404900 | chr2A | 87.850 | 107 | 13 | 0 | 6116 | 6222 | 565266600 | 565266706 | 9.080000e-25 | 126.0 |
157 | TraesCS6D01G404900 | chr2A | 85.714 | 112 | 16 | 0 | 6110 | 6221 | 540047669 | 540047780 | 1.520000e-22 | 119.0 |
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 | TraesCS6D01G404900 | chr6D | 472422474 | 472431085 | 8611 | True | 15904.000000 | 15904 | 100.000000 | 1 | 8612 | 1 | chr6D.!!$R3 | 8611 |
1 | TraesCS6D01G404900 | chr6D | 472496015 | 472504649 | 8634 | True | 324.300000 | 643 | 84.377400 | 278 | 8504 | 10 | chr6D.!!$R6 | 8226 |
2 | TraesCS6D01G404900 | chr6D | 472488668 | 472489198 | 530 | True | 316.000000 | 316 | 77.897000 | 5485 | 6040 | 1 | chr6D.!!$R4 | 555 |
3 | TraesCS6D01G404900 | chr1A | 2835842 | 2843882 | 8040 | True | 2902.475000 | 8239 | 95.079500 | 973 | 8612 | 4 | chr1A.!!$R6 | 7639 |
4 | TraesCS6D01G404900 | chr1A | 2653007 | 2657577 | 4570 | True | 534.800000 | 1306 | 86.438800 | 3165 | 7894 | 5 | chr1A.!!$R4 | 4729 |
5 | TraesCS6D01G404900 | chr1A | 2642508 | 2648329 | 5821 | True | 281.777778 | 553 | 84.730222 | 552 | 7890 | 9 | chr1A.!!$R3 | 7338 |
6 | TraesCS6D01G404900 | chr6A | 617551358 | 617560667 | 9309 | False | 2624.800000 | 5203 | 94.795800 | 1 | 8612 | 5 | chr6A.!!$F8 | 8611 |
7 | TraesCS6D01G404900 | chr6A | 617224235 | 617224990 | 755 | False | 752.000000 | 752 | 84.785000 | 3730 | 4490 | 1 | chr6A.!!$F1 | 760 |
8 | TraesCS6D01G404900 | chr6A | 617348294 | 617352928 | 4634 | False | 424.833333 | 662 | 85.318333 | 1143 | 7802 | 6 | chr6A.!!$F7 | 6659 |
9 | TraesCS6D01G404900 | chr6A | 617317728 | 617322968 | 5240 | False | 401.000000 | 499 | 85.290200 | 654 | 5854 | 5 | chr6A.!!$F6 | 5200 |
10 | TraesCS6D01G404900 | chr6A | 617232598 | 617239959 | 7361 | False | 344.000000 | 869 | 86.758750 | 3 | 6041 | 12 | chr6A.!!$F5 | 6038 |
11 | TraesCS6D01G404900 | chr6A | 617217210 | 617218257 | 1047 | False | 248.000000 | 396 | 81.558000 | 712 | 1736 | 2 | chr6A.!!$F4 | 1024 |
12 | TraesCS6D01G404900 | chr6B | 717137108 | 717144170 | 7062 | True | 1462.428571 | 5073 | 93.814714 | 3 | 7899 | 7 | chr6B.!!$R4 | 7896 |
13 | TraesCS6D01G404900 | chr6B | 717115261 | 717115981 | 720 | True | 1000.000000 | 1000 | 91.701000 | 7891 | 8611 | 1 | chr6B.!!$R3 | 720 |
14 | TraesCS6D01G404900 | chr6B | 717398840 | 717420719 | 21879 | True | 371.300000 | 1140 | 85.863842 | 712 | 8603 | 19 | chr6B.!!$R5 | 7891 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
431 | 1685 | 0.318762 | GGATGGGACGTCTATCAGCC | 59.681 | 60.000 | 24.36 | 21.92 | 0.00 | 4.85 | F |
1133 | 4425 | 0.317603 | CTCACCGACGACTTCAACGT | 60.318 | 55.000 | 0.00 | 0.00 | 46.58 | 3.99 | F |
2041 | 5723 | 0.531974 | ATCAACACTTGTCGCCGTGT | 60.532 | 50.000 | 0.00 | 0.00 | 45.55 | 4.49 | F |
2799 | 6651 | 1.461127 | GTGTTTGCTACTTCAGGCTCG | 59.539 | 52.381 | 0.00 | 0.00 | 0.00 | 5.03 | F |
4365 | 9244 | 1.332178 | GTGAGACTGCGTTCTCTTCG | 58.668 | 55.000 | 13.83 | 0.00 | 42.36 | 3.79 | F |
5655 | 11391 | 2.353208 | CCTTCTGTCTACACTGTGGAGC | 60.353 | 54.545 | 15.35 | 10.75 | 0.00 | 4.70 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1649 | 5319 | 1.199097 | CCACGTGTGCTGTAATTTCCC | 59.801 | 52.381 | 15.65 | 0.00 | 0.00 | 3.97 | R |
2478 | 6314 | 0.605589 | CCGGGTCCTTTGTTCCAGTC | 60.606 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 | R |
3490 | 8290 | 1.202177 | GCTGCACATTGTATCAACCCG | 60.202 | 52.381 | 0.00 | 0.00 | 0.00 | 5.28 | R |
4607 | 9836 | 1.030488 | TGCGGAAACCCAAACGACAA | 61.030 | 50.000 | 0.00 | 0.00 | 0.00 | 3.18 | R |
6072 | 12861 | 1.358152 | ACTCCCTCCGTTCCAATCAA | 58.642 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 | R |
7654 | 30969 | 0.331278 | CACCATTTGGGGTAGCCTCA | 59.669 | 55.000 | 11.48 | 4.45 | 39.79 | 3.86 | R |
All possible primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.