Multiple sequence alignment - TraesCS4A01G150700

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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 TraesCS4A01G150700 chr4A 100.000 3861 0 0 1 3861 297763800 297767660 0.000000e+00 7131.0
1 TraesCS4A01G150700 chr4A 89.910 2220 191 10 4 2198 297775359 297777570 0.000000e+00 2828.0
2 TraesCS4A01G150700 chr4A 87.766 940 84 20 1612 2530 221242695 221241766 0.000000e+00 1070.0
3 TraesCS4A01G150700 chr4A 86.357 645 69 8 623 1261 422962716 422963347 0.000000e+00 686.0
4 TraesCS4A01G150700 chr4A 85.607 535 60 14 168 692 25155274 25154747 2.620000e-151 545.0
5 TraesCS4A01G150700 chr4A 85.902 305 27 11 1 292 200242471 200242170 1.040000e-80 311.0
6 TraesCS4A01G150700 chr4A 85.246 305 33 8 1 294 200250364 200250061 1.740000e-78 303.0
7 TraesCS4A01G150700 chr7A 88.603 2255 198 34 1 2200 311983085 311985335 0.000000e+00 2686.0
8 TraesCS4A01G150700 chr7A 89.828 1740 157 11 478 2200 311959149 311960885 0.000000e+00 2215.0
9 TraesCS4A01G150700 chr7A 82.397 1477 196 52 1673 3108 391123889 391125342 0.000000e+00 1229.0
10 TraesCS4A01G150700 chr7A 88.842 941 91 13 2186 3115 342316387 342315450 0.000000e+00 1144.0
11 TraesCS4A01G150700 chr7A 87.889 933 85 16 1577 2495 577326693 577325775 0.000000e+00 1072.0
12 TraesCS4A01G150700 chr7A 85.938 640 84 3 623 1256 399556794 399556155 0.000000e+00 678.0
13 TraesCS4A01G150700 chr7A 87.726 497 48 7 1 485 311958624 311959119 5.600000e-158 568.0
14 TraesCS4A01G150700 chr7A 84.151 265 34 7 166 424 450455881 450455619 2.300000e-62 250.0
15 TraesCS4A01G150700 chr7A 90.909 121 8 3 2 120 191458260 191458379 3.990000e-35 159.0
16 TraesCS4A01G150700 chr7A 82.609 184 24 6 1 179 335909038 335909218 5.160000e-34 156.0
17 TraesCS4A01G150700 chr3A 89.867 1806 158 18 623 2413 105365276 105363481 0.000000e+00 2298.0
18 TraesCS4A01G150700 chr3A 89.648 937 89 8 2177 3107 362470141 362471075 0.000000e+00 1186.0
19 TraesCS4A01G150700 chr3A 92.095 759 50 9 3107 3861 466568053 466568805 0.000000e+00 1061.0
20 TraesCS4A01G150700 chr3A 87.430 899 104 6 623 1513 104914284 104915181 0.000000e+00 1026.0
21 TraesCS4A01G150700 chr3A 87.319 899 104 7 623 1513 104874454 104875350 0.000000e+00 1020.0
22 TraesCS4A01G150700 chr3A 90.671 611 54 3 1 610 104873864 104874472 0.000000e+00 809.0
23 TraesCS4A01G150700 chr3A 85.907 667 90 2 523 1185 376304529 376305195 0.000000e+00 708.0
24 TraesCS4A01G150700 chr3A 91.322 484 40 2 3 485 104913659 104914141 0.000000e+00 660.0
25 TraesCS4A01G150700 chr3A 91.170 487 39 4 1 485 104952458 104952942 0.000000e+00 658.0
26 TraesCS4A01G150700 chr3A 85.443 632 55 16 1 609 105365876 105365259 1.180000e-174 623.0
27 TraesCS4A01G150700 chr3A 88.382 241 23 5 1218 1455 448087461 448087223 6.310000e-73 285.0
28 TraesCS4A01G150700 chr3A 87.500 88 8 3 1165 1252 667908279 667908195 8.830000e-17 99.0
29 TraesCS4A01G150700 chr3A 85.714 56 8 0 1564 1619 363421377 363421322 4.170000e-05 60.2
30 TraesCS4A01G150700 chr2A 84.254 1575 180 46 1578 3107 511426384 511424833 0.000000e+00 1472.0
31 TraesCS4A01G150700 chr2A 83.333 1470 193 38 1673 3107 350277620 350276168 0.000000e+00 1310.0
32 TraesCS4A01G150700 chr2A 82.937 1389 167 55 1765 3107 368859476 368860840 0.000000e+00 1188.0
33 TraesCS4A01G150700 chr2A 82.347 946 126 24 167 1084 199949458 199950390 0.000000e+00 784.0
34 TraesCS4A01G150700 chr2A 91.765 85 7 0 1165 1249 300947355 300947439 6.780000e-23 119.0
35 TraesCS4A01G150700 chr2A 88.506 87 7 3 1533 1619 659581115 659581032 6.820000e-18 102.0
36 TraesCS4A01G150700 chr2A 87.356 87 8 3 1533 1619 627631141 627631224 3.180000e-16 97.1
37 TraesCS4A01G150700 chr2A 86.207 87 9 3 1533 1619 627622646 627622729 1.480000e-14 91.6
38 TraesCS4A01G150700 chr1A 88.490 1086 108 13 2029 3107 122395298 122394223 0.000000e+00 1297.0
39 TraesCS4A01G150700 chr1A 85.774 1188 132 25 2701 3861 153326751 153325574 0.000000e+00 1223.0
40 TraesCS4A01G150700 chr1A 86.596 1037 119 17 2085 3107 127121591 127122621 0.000000e+00 1127.0
41 TraesCS4A01G150700 chr1A 91.214 774 54 13 3097 3860 278374404 278375173 0.000000e+00 1040.0
42 TraesCS4A01G150700 chr1A 91.470 762 56 7 3107 3861 348179815 348179056 0.000000e+00 1038.0
43 TraesCS4A01G150700 chr1A 84.000 850 110 22 183 1022 432406625 432405792 0.000000e+00 793.0
44 TraesCS4A01G150700 chr1A 83.759 862 104 24 168 1020 341916803 341917637 0.000000e+00 784.0
45 TraesCS4A01G150700 chr1A 82.827 856 109 29 168 1014 341924799 341925625 0.000000e+00 732.0
46 TraesCS4A01G150700 chr1A 86.598 582 69 8 523 1099 423609138 423608561 5.440000e-178 634.0
47 TraesCS4A01G150700 chr1A 92.800 250 18 0 513 762 175075391 175075640 2.840000e-96 363.0
48 TraesCS4A01G150700 chr1A 87.755 294 33 2 472 762 175061054 175061347 1.330000e-89 340.0
49 TraesCS4A01G150700 chr1A 85.855 304 36 7 168 469 129084373 129084671 2.240000e-82 316.0
50 TraesCS4A01G150700 chr1A 82.637 311 50 4 168 476 271132734 271133042 4.920000e-69 272.0
51 TraesCS4A01G150700 chr1A 78.700 446 66 17 168 609 357480739 357480319 1.770000e-68 270.0
52 TraesCS4A01G150700 chr1A 77.455 448 58 27 168 601 35655303 35654885 1.080000e-55 228.0
53 TraesCS4A01G150700 chr1A 76.509 464 81 17 168 609 399400452 399400909 1.080000e-55 228.0
54 TraesCS4A01G150700 chr1A 80.323 310 46 14 167 468 180001873 180001571 1.810000e-53 220.0
55 TraesCS4A01G150700 chr1A 76.275 451 68 19 1 415 351712062 351712509 1.820000e-48 204.0
56 TraesCS4A01G150700 chr1A 83.246 191 26 6 4 189 216197849 216197660 1.840000e-38 171.0
57 TraesCS4A01G150700 chr1A 73.414 662 88 55 1 608 79841228 79840601 2.390000e-37 167.0
58 TraesCS4A01G150700 chr1A 74.257 505 78 29 4 468 216182144 216181652 8.580000e-37 165.0
59 TraesCS4A01G150700 chr1A 83.333 174 23 6 1 170 227420350 227420521 5.160000e-34 156.0
60 TraesCS4A01G150700 chr1A 81.771 192 25 9 4 188 227451699 227451887 6.680000e-33 152.0
61 TraesCS4A01G150700 chr1A 89.431 123 7 6 2 120 42678973 42678853 2.400000e-32 150.0
62 TraesCS4A01G150700 chr1A 88.800 125 9 4 1 120 14660825 14660949 8.640000e-32 148.0
63 TraesCS4A01G150700 chr1A 89.744 117 8 4 1 114 42703668 42703553 3.110000e-31 147.0
64 TraesCS4A01G150700 chr1A 88.710 124 8 6 1 120 477363009 477362888 3.110000e-31 147.0
65 TraesCS4A01G150700 chr1A 83.125 160 26 1 864 1022 190169514 190169355 1.120000e-30 145.0
66 TraesCS4A01G150700 chr1A 89.167 120 8 5 4 120 280998600 280998483 1.120000e-30 145.0
67 TraesCS4A01G150700 chr5A 90.350 943 75 11 2181 3115 310297514 310298448 0.000000e+00 1223.0
68 TraesCS4A01G150700 chr5A 92.105 760 52 7 3107 3861 116718637 116717881 0.000000e+00 1064.0
69 TraesCS4A01G150700 chr5A 92.136 763 44 10 3107 3861 294282865 294282111 0.000000e+00 1062.0
70 TraesCS4A01G150700 chr5A 91.853 761 54 6 3107 3861 45892693 45891935 0.000000e+00 1055.0
71 TraesCS4A01G150700 chr5A 84.686 1084 129 25 1646 2710 263235427 263234362 0.000000e+00 1048.0
72 TraesCS4A01G150700 chr5A 91.732 762 52 10 3107 3861 301834736 301835493 0.000000e+00 1048.0
73 TraesCS4A01G150700 chr5A 91.436 759 58 6 3107 3861 116799521 116798766 0.000000e+00 1035.0
74 TraesCS4A01G150700 chr5A 84.791 526 62 15 168 682 202973582 202973064 2.660000e-141 512.0
75 TraesCS4A01G150700 chr5A 79.310 522 73 25 1 497 459707775 459707264 2.220000e-87 333.0
76 TraesCS4A01G150700 chr2D 89.456 901 75 14 1648 2534 443504725 443505619 0.000000e+00 1120.0
77 TraesCS4A01G150700 chr2D 87.311 993 97 20 1607 2584 424190259 424191237 0.000000e+00 1109.0
78 TraesCS4A01G150700 chr2D 74.236 458 67 32 168 608 424196654 424197077 1.120000e-30 145.0
79 TraesCS4A01G150700 chr2D 98.507 67 1 0 651 717 353056423 353056489 6.780000e-23 119.0
80 TraesCS4A01G150700 chr2D 94.118 68 4 0 501 568 553790886 553790953 1.900000e-18 104.0
81 TraesCS4A01G150700 chr4D 89.234 901 76 15 1648 2534 429683024 429682131 0.000000e+00 1107.0
82 TraesCS4A01G150700 chr4D 80.534 262 36 13 168 421 187067124 187066870 1.830000e-43 187.0
83 TraesCS4A01G150700 chr4D 90.805 87 8 0 651 737 145377682 145377768 2.440000e-22 117.0
84 TraesCS4A01G150700 chr4D 83.333 120 13 6 3 117 57992935 57993052 1.900000e-18 104.0
85 TraesCS4A01G150700 chr4D 92.857 70 5 0 648 717 89652903 89652972 6.820000e-18 102.0
86 TraesCS4A01G150700 chr4D 92.647 68 5 0 501 568 321721135 321721202 8.830000e-17 99.0
87 TraesCS4A01G150700 chr6A 82.944 856 112 26 168 1014 416472769 416473599 0.000000e+00 741.0
88 TraesCS4A01G150700 chr6A 82.990 194 27 6 1 190 253251847 253252038 1.840000e-38 171.0
89 TraesCS4A01G150700 chr6A 83.770 191 18 5 1 179 263797924 263797735 6.630000e-38 169.0
90 TraesCS4A01G150700 chr6A 84.211 171 24 3 2 170 233513161 233513330 3.090000e-36 163.0
91 TraesCS4A01G150700 chr6A 82.162 185 25 8 1 179 365132048 365132230 6.680000e-33 152.0
92 TraesCS4A01G150700 chr6D 78.514 498 70 22 1 468 103953284 103952794 3.770000e-75 292.0
93 TraesCS4A01G150700 chr6D 78.384 495 67 23 4 468 165143935 165144419 6.310000e-73 285.0
94 TraesCS4A01G150700 chr6D 77.778 495 70 25 4 468 165124468 165124952 6.360000e-68 268.0
95 TraesCS4A01G150700 chr6D 80.317 315 40 15 167 468 239763849 239764154 6.490000e-53 219.0
96 TraesCS4A01G150700 chr6D 79.936 314 43 13 167 468 239703619 239703924 3.020000e-51 213.0
97 TraesCS4A01G150700 chr6D 79.433 282 43 13 167 440 265190750 265190476 6.590000e-43 185.0
98 TraesCS4A01G150700 chr6D 78.723 282 45 13 167 440 265198593 265198319 1.430000e-39 174.0
99 TraesCS4A01G150700 chr6D 79.803 203 22 13 1 185 184598570 184598369 3.130000e-26 130.0
100 TraesCS4A01G150700 chr6D 83.594 128 11 7 1 120 177783100 177783225 1.130000e-20 111.0
101 TraesCS4A01G150700 chr6D 95.522 67 3 0 651 717 74397711 74397777 1.470000e-19 108.0
102 TraesCS4A01G150700 chr6D 94.030 67 4 0 651 717 73989771 73989837 6.820000e-18 102.0
103 TraesCS4A01G150700 chr6D 94.030 67 4 0 651 717 197638861 197638795 6.820000e-18 102.0
104 TraesCS4A01G150700 chr1D 79.954 439 47 25 1 410 66971145 66970719 6.310000e-73 285.0
105 TraesCS4A01G150700 chr1D 79.195 447 55 26 1 421 368955896 368956330 3.800000e-70 276.0
106 TraesCS4A01G150700 chr1D 80.952 273 37 13 167 431 489741003 489741268 6.540000e-48 202.0
107 TraesCS4A01G150700 chr1D 80.220 273 39 13 167 431 223196977 223197242 1.420000e-44 191.0
108 TraesCS4A01G150700 chr1D 80.682 264 34 15 167 421 223189282 223189537 5.090000e-44 189.0
109 TraesCS4A01G150700 chr1D 74.732 467 51 34 4 415 53696886 53697340 3.110000e-31 147.0
110 TraesCS4A01G150700 chr1D 78.351 194 23 13 1 178 186717885 186717695 1.470000e-19 108.0
111 TraesCS4A01G150700 chr1D 86.667 60 7 1 62 120 166767443 166767502 8.950000e-07 65.8
112 TraesCS4A01G150700 chr1D 92.500 40 3 0 731 770 116568265 116568304 1.500000e-04 58.4
113 TraesCS4A01G150700 chr1D 92.500 40 3 0 731 770 116695484 116695445 1.500000e-04 58.4
114 TraesCS4A01G150700 chr7D 78.889 450 53 25 1 420 511362180 511362617 2.290000e-67 267.0
115 TraesCS4A01G150700 chr7D 78.889 450 53 26 1 421 571049605 571049169 2.290000e-67 267.0
116 TraesCS4A01G150700 chr7D 78.876 445 54 28 4 421 302511419 302511850 8.220000e-67 265.0
117 TraesCS4A01G150700 chr7D 77.215 474 54 31 7 440 321092371 321092830 1.080000e-55 228.0
118 TraesCS4A01G150700 chr7D 79.697 330 46 15 168 491 141958653 141958339 6.490000e-53 219.0
119 TraesCS4A01G150700 chr7D 80.586 273 38 13 167 431 617990333 617990598 3.040000e-46 196.0
120 TraesCS4A01G150700 chr7D 79.592 196 22 12 1 179 277576820 277577014 1.460000e-24 124.0
121 TraesCS4A01G150700 chr7D 86.207 116 9 7 7 117 146136703 146136816 6.780000e-23 119.0
122 TraesCS4A01G150700 chr7D 85.217 115 13 4 4 116 384679020 384678908 8.770000e-22 115.0
123 TraesCS4A01G150700 chr7D 89.041 73 8 0 502 574 433542997 433542925 1.480000e-14 91.6
124 TraesCS4A01G150700 chr6B 82.410 307 43 10 167 467 253452149 253451848 1.380000e-64 257.0
125 TraesCS4A01G150700 chr3D 77.024 457 69 25 168 608 74565461 74565897 3.000000e-56 230.0
126 TraesCS4A01G150700 chr3D 79.618 314 44 13 167 468 291858308 291858003 1.410000e-49 207.0
127 TraesCS4A01G150700 chr3D 75.664 452 82 22 167 608 341929765 341929332 2.350000e-47 200.0
128 TraesCS4A01G150700 chr3D 81.865 193 17 11 4 179 207185635 207185826 3.110000e-31 147.0
129 TraesCS4A01G150700 chr3D 86.290 124 7 10 4 120 71096589 71096709 4.050000e-25 126.0
130 TraesCS4A01G150700 chr3D 85.246 122 11 5 1 116 247919044 247918924 6.780000e-23 119.0
131 TraesCS4A01G150700 chr3D 97.015 67 2 0 651 717 49403846 49403912 3.150000e-21 113.0
132 TraesCS4A01G150700 chr3D 95.522 67 3 0 651 717 49396590 49396656 1.470000e-19 108.0
133 TraesCS4A01G150700 chr1B 80.727 275 47 5 945 1214 234096805 234097078 3.910000e-50 209.0
134 TraesCS4A01G150700 chr4B 76.410 390 35 29 1 338 393576135 393576519 1.440000e-34 158.0
135 TraesCS4A01G150700 chr4B 87.179 117 10 5 7 120 308898280 308898394 1.130000e-25 128.0
136 TraesCS4A01G150700 chr4B 85.366 123 9 9 4 120 299236474 299236593 6.780000e-23 119.0
137 TraesCS4A01G150700 chr4B 84.921 126 10 9 1 120 307545141 307545263 6.780000e-23 119.0
138 TraesCS4A01G150700 chr4B 94.444 72 4 0 537 608 233411447 233411376 1.130000e-20 111.0
139 TraesCS4A01G150700 chr4B 91.358 81 4 3 528 608 330045815 330045892 1.470000e-19 108.0
140 TraesCS4A01G150700 chr5D 80.203 197 19 13 1 179 30335563 30335757 3.130000e-26 130.0
141 TraesCS4A01G150700 chr5D 97.015 67 2 0 651 717 224009355 224009289 3.150000e-21 113.0


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 TraesCS4A01G150700 chr4A 297763800 297767660 3860 False 7131.0 7131 100.000 1 3861 1 chr4A.!!$F1 3860
1 TraesCS4A01G150700 chr4A 297775359 297777570 2211 False 2828.0 2828 89.910 4 2198 1 chr4A.!!$F2 2194
2 TraesCS4A01G150700 chr4A 221241766 221242695 929 True 1070.0 1070 87.766 1612 2530 1 chr4A.!!$R4 918
3 TraesCS4A01G150700 chr4A 422962716 422963347 631 False 686.0 686 86.357 623 1261 1 chr4A.!!$F3 638
4 TraesCS4A01G150700 chr4A 25154747 25155274 527 True 545.0 545 85.607 168 692 1 chr4A.!!$R1 524
5 TraesCS4A01G150700 chr7A 311983085 311985335 2250 False 2686.0 2686 88.603 1 2200 1 chr7A.!!$F2 2199
6 TraesCS4A01G150700 chr7A 311958624 311960885 2261 False 1391.5 2215 88.777 1 2200 2 chr7A.!!$F5 2199
7 TraesCS4A01G150700 chr7A 391123889 391125342 1453 False 1229.0 1229 82.397 1673 3108 1 chr7A.!!$F4 1435
8 TraesCS4A01G150700 chr7A 342315450 342316387 937 True 1144.0 1144 88.842 2186 3115 1 chr7A.!!$R1 929
9 TraesCS4A01G150700 chr7A 577325775 577326693 918 True 1072.0 1072 87.889 1577 2495 1 chr7A.!!$R4 918
10 TraesCS4A01G150700 chr7A 399556155 399556794 639 True 678.0 678 85.938 623 1256 1 chr7A.!!$R2 633
11 TraesCS4A01G150700 chr3A 105363481 105365876 2395 True 1460.5 2298 87.655 1 2413 2 chr3A.!!$R4 2412
12 TraesCS4A01G150700 chr3A 362470141 362471075 934 False 1186.0 1186 89.648 2177 3107 1 chr3A.!!$F2 930
13 TraesCS4A01G150700 chr3A 466568053 466568805 752 False 1061.0 1061 92.095 3107 3861 1 chr3A.!!$F4 754
14 TraesCS4A01G150700 chr3A 104873864 104875350 1486 False 914.5 1020 88.995 1 1513 2 chr3A.!!$F5 1512
15 TraesCS4A01G150700 chr3A 104913659 104915181 1522 False 843.0 1026 89.376 3 1513 2 chr3A.!!$F6 1510
16 TraesCS4A01G150700 chr3A 376304529 376305195 666 False 708.0 708 85.907 523 1185 1 chr3A.!!$F3 662
17 TraesCS4A01G150700 chr2A 511424833 511426384 1551 True 1472.0 1472 84.254 1578 3107 1 chr2A.!!$R2 1529
18 TraesCS4A01G150700 chr2A 350276168 350277620 1452 True 1310.0 1310 83.333 1673 3107 1 chr2A.!!$R1 1434
19 TraesCS4A01G150700 chr2A 368859476 368860840 1364 False 1188.0 1188 82.937 1765 3107 1 chr2A.!!$F3 1342
20 TraesCS4A01G150700 chr2A 199949458 199950390 932 False 784.0 784 82.347 167 1084 1 chr2A.!!$F1 917
21 TraesCS4A01G150700 chr1A 122394223 122395298 1075 True 1297.0 1297 88.490 2029 3107 1 chr1A.!!$R5 1078
22 TraesCS4A01G150700 chr1A 153325574 153326751 1177 True 1223.0 1223 85.774 2701 3861 1 chr1A.!!$R6 1160
23 TraesCS4A01G150700 chr1A 127121591 127122621 1030 False 1127.0 1127 86.596 2085 3107 1 chr1A.!!$F2 1022
24 TraesCS4A01G150700 chr1A 278374404 278375173 769 False 1040.0 1040 91.214 3097 3860 1 chr1A.!!$F9 763
25 TraesCS4A01G150700 chr1A 348179056 348179815 759 True 1038.0 1038 91.470 3107 3861 1 chr1A.!!$R12 754
26 TraesCS4A01G150700 chr1A 432405792 432406625 833 True 793.0 793 84.000 183 1022 1 chr1A.!!$R15 839
27 TraesCS4A01G150700 chr1A 341916803 341917637 834 False 784.0 784 83.759 168 1020 1 chr1A.!!$F10 852
28 TraesCS4A01G150700 chr1A 341924799 341925625 826 False 732.0 732 82.827 168 1014 1 chr1A.!!$F11 846
29 TraesCS4A01G150700 chr1A 423608561 423609138 577 True 634.0 634 86.598 523 1099 1 chr1A.!!$R14 576
30 TraesCS4A01G150700 chr5A 310297514 310298448 934 False 1223.0 1223 90.350 2181 3115 1 chr5A.!!$F2 934
31 TraesCS4A01G150700 chr5A 116717881 116718637 756 True 1064.0 1064 92.105 3107 3861 1 chr5A.!!$R2 754
32 TraesCS4A01G150700 chr5A 294282111 294282865 754 True 1062.0 1062 92.136 3107 3861 1 chr5A.!!$R6 754
33 TraesCS4A01G150700 chr5A 45891935 45892693 758 True 1055.0 1055 91.853 3107 3861 1 chr5A.!!$R1 754
34 TraesCS4A01G150700 chr5A 263234362 263235427 1065 True 1048.0 1048 84.686 1646 2710 1 chr5A.!!$R5 1064
35 TraesCS4A01G150700 chr5A 301834736 301835493 757 False 1048.0 1048 91.732 3107 3861 1 chr5A.!!$F1 754
36 TraesCS4A01G150700 chr5A 116798766 116799521 755 True 1035.0 1035 91.436 3107 3861 1 chr5A.!!$R3 754
37 TraesCS4A01G150700 chr5A 202973064 202973582 518 True 512.0 512 84.791 168 682 1 chr5A.!!$R4 514
38 TraesCS4A01G150700 chr5A 459707264 459707775 511 True 333.0 333 79.310 1 497 1 chr5A.!!$R7 496
39 TraesCS4A01G150700 chr2D 443504725 443505619 894 False 1120.0 1120 89.456 1648 2534 1 chr2D.!!$F4 886
40 TraesCS4A01G150700 chr2D 424190259 424191237 978 False 1109.0 1109 87.311 1607 2584 1 chr2D.!!$F2 977
41 TraesCS4A01G150700 chr4D 429682131 429683024 893 True 1107.0 1107 89.234 1648 2534 1 chr4D.!!$R2 886
42 TraesCS4A01G150700 chr6A 416472769 416473599 830 False 741.0 741 82.944 168 1014 1 chr6A.!!$F4 846

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
160 195 0.033208 GAGGCATTTGTCCCCATGGA 60.033 55.0 15.22 0.0 38.75 3.41 F
1032 1176 0.621862 GGGATGAGGTGAGGAAGGGT 60.622 60.0 0.00 0.0 0.00 4.34 F
1550 1721 0.335019 GGGTTGGGCTATGGGAAACT 59.665 55.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 1721 0.899717 GCTGGCCCAAACCATCTTCA 60.900 55.0 0.00 0.00 39.54 3.02 R
2466 2718 0.242825 CTCGTTTCTACCGGAGTGCA 59.757 55.0 9.46 0.00 0.00 4.57 R
3364 3647 0.674895 CAGTAGTGGAGCCCAGTTGC 60.675 60.0 6.85 2.38 38.30 4.17 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
94 96 8.963725 ACATTCTTGATGTTGTTATCATGATGT 58.036 29.630 18.72 0.00 46.80 3.06
107 120 7.608761 TGTTATCATGATGTGGATGACATATGG 59.391 37.037 18.72 0.00 45.90 2.74
160 195 0.033208 GAGGCATTTGTCCCCATGGA 60.033 55.000 15.22 0.00 38.75 3.41
179 216 1.546029 GAGGAAAGAAATGGTGCCACC 59.454 52.381 7.01 7.01 39.22 4.61
390 435 1.560146 TGTATTTGGTCCATGGGCGTA 59.440 47.619 13.02 0.00 0.00 4.42
505 603 1.355563 CTAGCGATCTTGGCGACGA 59.644 57.895 0.00 0.00 35.00 4.20
822 965 2.559785 AGGCACTTGGCGAAATCAG 58.440 52.632 0.00 0.00 46.16 2.90
928 1072 1.705337 CGCTGCACCTATTCGGTTGG 61.705 60.000 0.00 0.00 46.37 3.77
933 1077 1.476488 GCACCTATTCGGTTGGCAAAT 59.524 47.619 0.00 0.00 46.37 2.32
944 1088 3.305950 CGGTTGGCAAATGGAAAGATGAA 60.306 43.478 0.00 0.00 0.00 2.57
1003 1147 3.838271 GAGGCGTGGCTCCGATGA 61.838 66.667 12.06 0.00 0.00 2.92
1032 1176 0.621862 GGGATGAGGTGAGGAAGGGT 60.622 60.000 0.00 0.00 0.00 4.34
1044 1201 1.375326 GAAGGGTGGCGAGGAACTT 59.625 57.895 0.00 0.00 41.55 2.66
1125 1282 1.675641 GGTTGAAGGCGAGGCACAT 60.676 57.895 0.00 0.00 0.00 3.21
1155 1312 3.842923 CGCGGCATCAGGGAGAGT 61.843 66.667 0.00 0.00 0.00 3.24
1162 1319 1.857965 CATCAGGGAGAGTGTGGAGA 58.142 55.000 0.00 0.00 0.00 3.71
1249 1415 2.753043 GGTGCTCCGACGGGACTA 60.753 66.667 15.25 0.00 37.43 2.59
1313 1479 2.045438 CAGTGGTGGGGCGCATTA 60.045 61.111 10.83 0.00 0.00 1.90
1385 1553 4.086547 GGGGGTTGGTACGACGGG 62.087 72.222 0.00 0.00 0.00 5.28
1387 1555 3.313524 GGGTTGGTACGACGGGGT 61.314 66.667 0.00 0.00 0.00 4.95
1398 1566 1.001376 GACGGGGTAGGAAGGAGGT 59.999 63.158 0.00 0.00 0.00 3.85
1524 1695 1.002533 AGCGGGCTAGGGTTAGGAA 59.997 57.895 0.00 0.00 0.00 3.36
1550 1721 0.335019 GGGTTGGGCTATGGGAAACT 59.665 55.000 0.00 0.00 0.00 2.66
1567 1738 0.482446 ACTGAAGATGGTTTGGGCCA 59.518 50.000 0.00 0.00 43.48 5.36
1575 1746 2.991540 GTTTGGGCCAGCCTGGTC 60.992 66.667 13.35 10.33 42.67 4.02
1739 1925 3.426615 TGCGGTGGTTCCAAGAAAATAT 58.573 40.909 0.00 0.00 35.57 1.28
1948 2145 6.641169 TTGCAAGTGTGTTATGGTGAATTA 57.359 33.333 0.00 0.00 0.00 1.40
2107 2328 4.770010 ATGGCATGATGACATGATGCAATA 59.230 37.500 31.93 21.27 46.11 1.90
2108 2329 5.422012 ATGGCATGATGACATGATGCAATAT 59.578 36.000 31.93 22.22 46.11 1.28
2109 2330 6.070824 ATGGCATGATGACATGATGCAATATT 60.071 34.615 31.93 11.49 46.11 1.28
2110 2331 7.123547 ATGGCATGATGACATGATGCAATATTA 59.876 33.333 31.93 16.04 46.11 0.98
2451 2703 7.611855 AGACATAAGAAAAGGGTTACAATGGAG 59.388 37.037 0.00 0.00 0.00 3.86
2466 2718 5.503927 ACAATGGAGAAGAAGTACATGCAT 58.496 37.500 0.00 0.00 0.00 3.96
2512 2765 6.984474 TGTACAAGGAACGATAAGGATCAATC 59.016 38.462 0.00 0.00 31.78 2.67
2540 2794 2.235016 CACTCCGGTTGGAAATGGAAA 58.765 47.619 0.00 0.00 45.87 3.13
2620 2875 3.370953 GGAATGATAGCCACAACACTCCT 60.371 47.826 0.00 0.00 0.00 3.69
2621 2876 4.265073 GAATGATAGCCACAACACTCCTT 58.735 43.478 0.00 0.00 0.00 3.36
2634 2889 7.222611 CCACAACACTCCTTTTAAAACAAGATG 59.777 37.037 10.39 8.75 0.00 2.90
2983 3250 5.390387 AGAATAAGGTTGTTGTGGGCTTAA 58.610 37.500 0.00 0.00 0.00 1.85
3060 3335 5.370584 TGGATTGATATCACCAAGGAGATGT 59.629 40.000 11.63 2.72 32.09 3.06
3061 3337 5.704515 GGATTGATATCACCAAGGAGATGTG 59.295 44.000 4.48 0.00 32.09 3.21
3122 3398 5.353123 GTCATTTATGTAACACCCACGATGT 59.647 40.000 0.00 0.00 0.00 3.06
3221 3497 6.406370 TCTTTACACATCCCATGTACTGAAG 58.594 40.000 0.00 0.00 42.70 3.02
3292 3570 8.429493 ACATGAATATAGCATTACATCATCCG 57.571 34.615 0.00 0.00 0.00 4.18
3300 3579 5.620206 AGCATTACATCATCCGGATACAAA 58.380 37.500 18.63 7.90 33.95 2.83
3308 3587 3.517901 TCATCCGGATACAAACAAGGTCT 59.482 43.478 18.63 0.00 0.00 3.85
3364 3647 2.878429 CTAGATCCCCGATCGCCG 59.122 66.667 10.32 0.98 43.17 6.46
3388 3671 0.324368 TGGGCTCCACTACTGATCGT 60.324 55.000 0.00 0.00 0.00 3.73
3401 3685 6.748198 CACTACTGATCGTCTAGAAAGGAAAC 59.252 42.308 0.00 0.00 0.00 2.78
3403 3687 4.217983 ACTGATCGTCTAGAAAGGAAACGT 59.782 41.667 0.00 0.00 35.04 3.99
3405 3689 5.877031 TGATCGTCTAGAAAGGAAACGTAG 58.123 41.667 0.00 0.00 35.04 3.51
3406 3690 5.645067 TGATCGTCTAGAAAGGAAACGTAGA 59.355 40.000 0.00 0.00 35.04 2.59
3440 3724 1.107114 TCATCGAGCTCCTCCTTGAC 58.893 55.000 8.47 0.00 0.00 3.18
3534 3822 1.375908 GCAATCTCACACCCTCGCA 60.376 57.895 0.00 0.00 0.00 5.10
3584 3873 3.965347 GGTAAAGGTATGAGGTGGAGCTA 59.035 47.826 0.00 0.00 0.00 3.32
3587 3876 3.116096 AGGTATGAGGTGGAGCTACAA 57.884 47.619 0.00 0.00 0.00 2.41
3630 3921 3.933332 GGCTAACTTACGCAAATGAGAGT 59.067 43.478 0.00 0.00 0.00 3.24
3655 3947 0.884704 GAGAAGGCAAAGCACGGTCA 60.885 55.000 0.00 0.00 0.00 4.02
3714 4014 1.855513 TAACTCCAACACCGTGTTCG 58.144 50.000 14.11 8.29 38.77 3.95
3764 4064 2.663852 GGCTACACACGCGGTTGT 60.664 61.111 12.47 15.59 0.00 3.32
3776 4076 3.914966 CACGCGGTTGTTGCATTTTAATA 59.085 39.130 12.47 0.00 0.00 0.98
3841 4141 4.169696 CTGCCCATAACCGCGGGA 62.170 66.667 31.76 18.02 46.34 5.14
3844 4144 2.269562 CCCATAACCGCGGGAACA 59.730 61.111 31.76 11.59 46.34 3.18
3854 4154 1.635663 CGCGGGAACAGCTTTCGAAT 61.636 55.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 4.952957 TGCATATGAGGATTTTTCGGGAAA 59.047 37.500 6.97 0.00 0.00 3.13
21 23 6.671190 TGCTAATGCATATGAGGATTTTTCG 58.329 36.000 6.97 0.00 45.31 3.46
94 96 9.473007 TTTGATAAAACTTCCATATGTCATCCA 57.527 29.630 1.24 0.00 0.00 3.41
160 195 1.147817 AGGTGGCACCATTTCTTTCCT 59.852 47.619 36.28 10.69 41.95 3.36
179 216 2.596904 ACCGGAACCGATATGTTGAG 57.403 50.000 9.46 0.00 42.83 3.02
340 383 2.044123 ATGAGATGAACCCCGCTTTC 57.956 50.000 0.00 0.00 0.00 2.62
390 435 2.027385 GAAGGTATAACCGTCGGGACT 58.973 52.381 17.28 1.95 44.90 3.85
415 462 2.900167 GAACCGTCCCGTTTGCACC 61.900 63.158 0.00 0.00 0.00 5.01
505 603 5.410746 TGAGACTAAGAACGTGAACGACTAT 59.589 40.000 10.26 0.00 43.02 2.12
822 965 1.376037 CCGTTGCTTCCTCCCTGAC 60.376 63.158 0.00 0.00 0.00 3.51
890 1034 1.069227 CGCCACAAGTTTTGCCTCTAC 60.069 52.381 0.00 0.00 0.00 2.59
928 1072 3.428045 CGACCCTTCATCTTTCCATTTGC 60.428 47.826 0.00 0.00 0.00 3.68
933 1077 1.555075 CCTCGACCCTTCATCTTTCCA 59.445 52.381 0.00 0.00 0.00 3.53
944 1088 1.985116 GGTCTTCTGCCTCGACCCT 60.985 63.158 0.00 0.00 41.00 4.34
1003 1147 2.770048 CTCATCCCCGGCCCTTCT 60.770 66.667 0.00 0.00 0.00 2.85
1032 1176 2.954684 ATCGCCAAGTTCCTCGCCA 61.955 57.895 0.00 0.00 0.00 5.69
1044 1201 2.350895 CTGTTGTCCCCATCGCCA 59.649 61.111 0.00 0.00 0.00 5.69
1057 1214 0.963962 CACCAGCAGCAATTCCTGTT 59.036 50.000 0.00 0.00 35.28 3.16
1060 1217 1.980772 GCCACCAGCAGCAATTCCT 60.981 57.895 0.00 0.00 42.97 3.36
1086 1243 2.435938 GCTTTCGCGTCCCATGGA 60.436 61.111 15.22 0.00 0.00 3.41
1099 1256 1.966451 CGCCTTCAACCTCGGCTTT 60.966 57.895 0.00 0.00 41.61 3.51
1155 1312 2.033141 GGCAGCAGCTTCTCCACA 59.967 61.111 0.00 0.00 41.70 4.17
1224 1390 1.309499 CGTCGGAGCACCTCTTCTCT 61.309 60.000 0.00 0.00 0.00 3.10
1249 1415 2.434884 CGGCCATCGTCAGCAAGT 60.435 61.111 2.24 0.00 0.00 3.16
1385 1553 1.133104 CCCCTCTACCTCCTTCCTACC 60.133 61.905 0.00 0.00 0.00 3.18
1387 1555 2.315503 TCCCCTCTACCTCCTTCCTA 57.684 55.000 0.00 0.00 0.00 2.94
1398 1566 2.065470 CTCGTCCCCGATCCCCTCTA 62.065 65.000 0.00 0.00 43.27 2.43
1550 1721 0.899717 GCTGGCCCAAACCATCTTCA 60.900 55.000 0.00 0.00 39.54 3.02
1902 2097 7.930865 GCAAATTATCCCAATGCCTTTGTTATA 59.069 33.333 0.00 0.00 33.15 0.98
2112 2333 8.436046 TCATTTGTGCTTGCTCTTTTATTTTT 57.564 26.923 0.00 0.00 0.00 1.94
2466 2718 0.242825 CTCGTTTCTACCGGAGTGCA 59.757 55.000 9.46 0.00 0.00 4.57
2512 2765 1.495584 CCAACCGGAGTGTTGTCGTG 61.496 60.000 9.46 0.00 43.22 4.35
2559 2813 5.302568 TCTCATCCAAGTGCTTTCATTTTGT 59.697 36.000 0.00 0.00 0.00 2.83
2667 2923 5.988310 TCCTTCCATTTACAGTCGAAGTA 57.012 39.130 0.00 0.00 0.00 2.24
2734 2992 0.677288 ATTCAACCGGAGTGTCGTGA 59.323 50.000 9.46 0.00 0.00 4.35
2823 3083 7.070074 AGCTATCTTCTATTCTTTCTTCCGGAA 59.930 37.037 17.73 17.73 0.00 4.30
2956 3223 4.749598 GCCCACAACAACCTTATTCTTTTG 59.250 41.667 0.00 0.00 0.00 2.44
2968 3235 4.116961 GTTTTCCTTAAGCCCACAACAAC 58.883 43.478 0.00 0.00 0.00 3.32
3010 3283 2.163818 TGTTTCCGTAGTGGCAGAAG 57.836 50.000 0.00 0.00 37.80 2.85
3060 3335 4.577988 TCCTCCCGGTGAAATAATTTCA 57.422 40.909 0.00 0.00 46.68 2.69
3061 3337 7.576861 TTTATCCTCCCGGTGAAATAATTTC 57.423 36.000 0.00 0.00 40.08 2.17
3122 3398 1.961394 GACACGTGGGAGATATAGCCA 59.039 52.381 21.57 0.00 0.00 4.75
3185 3461 6.424032 GGATGTGTAAAGATTACCCCTCTTT 58.576 40.000 4.01 4.01 43.49 2.52
3221 3497 3.997681 GCCAACTCTGTACCTCTTTCTTC 59.002 47.826 0.00 0.00 0.00 2.87
3292 3570 4.863131 CGTAGTCAGACCTTGTTTGTATCC 59.137 45.833 0.00 0.00 0.00 2.59
3300 3579 1.617357 GGTTCCGTAGTCAGACCTTGT 59.383 52.381 0.00 0.00 0.00 3.16
3308 3587 7.716123 TCTTCTTTTATTTTGGTTCCGTAGTCA 59.284 33.333 0.00 0.00 0.00 3.41
3364 3647 0.674895 CAGTAGTGGAGCCCAGTTGC 60.675 60.000 6.85 2.38 38.30 4.17
3401 3685 8.358541 CGATGAAGATCGTGTTCGTTTCTACG 62.359 46.154 0.00 0.00 45.43 3.51
3403 3687 4.791676 CGATGAAGATCGTGTTCGTTTCTA 59.208 41.667 0.00 0.00 45.43 2.10
3405 3689 3.900913 CGATGAAGATCGTGTTCGTTTC 58.099 45.455 0.00 0.00 45.43 2.78
3406 3690 3.972706 CGATGAAGATCGTGTTCGTTT 57.027 42.857 0.00 0.00 45.43 3.60
3440 3724 2.738521 CAGGTGACGCAACCGAGG 60.739 66.667 1.72 0.00 45.53 4.63
3584 3873 5.528690 CACCATATATGCTAGTGCTTGTTGT 59.471 40.000 7.24 0.00 40.48 3.32
3587 3876 4.645535 CCACCATATATGCTAGTGCTTGT 58.354 43.478 7.24 0.00 40.48 3.16
3630 3921 2.498167 GTGCTTTGCCTTCTCTTCTCA 58.502 47.619 0.00 0.00 0.00 3.27
3776 4076 8.880750 GTTGTAGAGAACTTGACACTTAACTTT 58.119 33.333 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.