Multiple sequence alignment - TraesCS2D01G206700

Loading Multiple Alignment...

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 TraesCS2D01G206700 chr2D 100.000 2822 0 0 1 2822 159863030 159860209 0.000000e+00 5212.0
1 TraesCS2D01G206700 chr2D 93.458 642 12 5 2046 2685 36677201 36677814 0.000000e+00 926.0
2 TraesCS2D01G206700 chr2D 94.545 330 6 6 2046 2365 381304237 381303910 1.510000e-137 499.0
3 TraesCS2D01G206700 chr2D 95.455 220 8 1 2603 2822 421811271 421811054 1.610000e-92 350.0
4 TraesCS2D01G206700 chr2D 79.132 484 71 19 12 473 588487791 588487316 9.820000e-80 307.0
5 TraesCS2D01G206700 chr2B 96.555 987 25 4 1066 2048 216947490 216946509 0.000000e+00 1626.0
6 TraesCS2D01G206700 chr2B 83.370 451 31 26 858 1273 216952777 216952336 7.380000e-101 377.0
7 TraesCS2D01G206700 chr2B 93.333 255 17 0 472 726 216953518 216953264 7.380000e-101 377.0
8 TraesCS2D01G206700 chr2B 89.831 236 16 6 489 724 216951532 216951305 2.130000e-76 296.0
9 TraesCS2D01G206700 chr2B 89.720 214 22 0 173 386 216953837 216953624 9.960000e-70 274.0
10 TraesCS2D01G206700 chr2B 91.489 188 12 1 859 1042 216948106 216947919 3.610000e-64 255.0
11 TraesCS2D01G206700 chr2B 95.302 149 6 1 3 150 216953980 216953832 4.700000e-58 235.0
12 TraesCS2D01G206700 chr2B 88.732 71 8 0 398 468 751313014 751313084 1.390000e-13 87.9
13 TraesCS2D01G206700 chr2B 97.059 34 1 0 1033 1066 216947913 216947880 1.090000e-04 58.4
14 TraesCS2D01G206700 chr2A 96.104 1001 30 4 1057 2048 171085100 171084100 0.000000e+00 1624.0
15 TraesCS2D01G206700 chr2A 82.688 491 56 16 6 473 171086917 171086433 2.620000e-110 409.0
16 TraesCS2D01G206700 chr2A 91.498 247 19 2 482 726 171086338 171086092 3.480000e-89 339.0
17 TraesCS2D01G206700 chr2A 86.758 219 19 4 765 983 171085739 171085531 4.700000e-58 235.0
18 TraesCS2D01G206700 chr2A 82.231 242 37 5 12 251 746681505 746681742 1.330000e-48 204.0
19 TraesCS2D01G206700 chr3D 97.969 640 10 2 2046 2685 545055456 545056092 0.000000e+00 1107.0
20 TraesCS2D01G206700 chr3D 97.306 297 6 1 2046 2342 374977260 374976966 1.170000e-138 503.0
21 TraesCS2D01G206700 chr3D 85.093 161 22 2 7 166 132234196 132234355 2.250000e-36 163.0
22 TraesCS2D01G206700 chr4D 88.264 818 49 25 2046 2822 508665154 508665965 0.000000e+00 935.0
23 TraesCS2D01G206700 chr4D 83.193 476 68 9 3 467 509808702 509808228 2.600000e-115 425.0
24 TraesCS2D01G206700 chr4D 98.522 203 1 1 2620 2822 339059347 339059147 9.610000e-95 357.0
25 TraesCS2D01G206700 chr4D 95.909 220 7 1 2603 2822 472678010 472677793 3.460000e-94 355.0
26 TraesCS2D01G206700 chr4D 95.111 225 6 3 2603 2822 282074600 282074824 1.610000e-92 350.0
27 TraesCS2D01G206700 chr4D 85.507 69 10 0 404 472 502077097 502077029 3.900000e-09 73.1
28 TraesCS2D01G206700 chr4D 100.000 35 0 0 436 470 487091456 487091490 6.530000e-07 65.8
29 TraesCS2D01G206700 chr5D 90.632 459 17 9 2046 2489 395736442 395736889 1.130000e-163 586.0
30 TraesCS2D01G206700 chr5D 94.242 330 8 5 2045 2365 463019167 463019494 7.020000e-136 494.0
31 TraesCS2D01G206700 chr5D 90.062 322 20 10 2512 2822 395737380 395737700 9.410000e-110 407.0
32 TraesCS2D01G206700 chr5D 95.918 245 3 2 2584 2822 490432018 490432261 9.480000e-105 390.0
33 TraesCS2D01G206700 chr5D 98.068 207 2 2 2616 2822 95871046 95871250 2.670000e-95 359.0
34 TraesCS2D01G206700 chr5D 81.304 230 38 5 7 235 291357138 291356913 6.210000e-42 182.0
35 TraesCS2D01G206700 chr5D 85.897 78 9 2 398 474 37634559 37634635 6.480000e-12 82.4
36 TraesCS2D01G206700 chr7D 95.751 353 9 5 2046 2396 606079158 606079506 5.280000e-157 564.0
37 TraesCS2D01G206700 chr7D 93.617 329 10 5 2046 2365 32624803 32625129 5.470000e-132 481.0
38 TraesCS2D01G206700 chr7D 98.522 203 3 0 2620 2822 84266307 84266105 2.670000e-95 359.0
39 TraesCS2D01G206700 chr7D 83.206 262 10 7 2428 2685 628696893 628697124 2.850000e-50 209.0
40 TraesCS2D01G206700 chr7D 74.268 478 78 24 12 468 47116101 47116554 2.910000e-35 159.0
41 TraesCS2D01G206700 chr7D 89.041 73 8 0 399 471 387916872 387916800 1.080000e-14 91.6
42 TraesCS2D01G206700 chr1D 98.636 220 1 1 2603 2822 44620697 44620480 3.410000e-104 388.0
43 TraesCS2D01G206700 chr1D 96.818 220 5 1 2603 2822 103258773 103258556 1.600000e-97 366.0
44 TraesCS2D01G206700 chr1D 100.000 40 0 0 435 474 41499695 41499656 1.080000e-09 75.0
45 TraesCS2D01G206700 chr6D 92.364 275 10 2 2411 2685 105059271 105059534 5.700000e-102 381.0
46 TraesCS2D01G206700 chr6D 72.864 398 74 23 95 468 449840964 449840577 3.840000e-19 106.0
47 TraesCS2D01G206700 chr6D 100.000 28 0 0 440 467 16712280 16712307 5.000000e-03 52.8
48 TraesCS2D01G206700 chr6D 94.286 35 1 1 435 469 316488308 316488341 5.000000e-03 52.8
49 TraesCS2D01G206700 chr3B 79.339 484 72 21 8 469 700779103 700778626 5.870000e-82 315.0
50 TraesCS2D01G206700 chr3B 80.571 175 29 5 222 395 700985969 700986139 2.280000e-26 130.0
51 TraesCS2D01G206700 chr6A 79.538 303 45 5 179 472 413729686 413729392 1.710000e-47 200.0
52 TraesCS2D01G206700 chr6A 95.000 40 2 0 435 474 506112029 506112068 2.350000e-06 63.9
53 TraesCS2D01G206700 chr4B 73.684 266 65 5 8 272 601602824 601602563 6.430000e-17 99.0
54 TraesCS2D01G206700 chr4A 89.855 69 7 0 400 468 729195977 729196045 3.870000e-14 89.8
55 TraesCS2D01G206700 chr4A 80.412 97 12 3 376 471 498680313 498680223 1.810000e-07 67.6
56 TraesCS2D01G206700 chr6B 71.816 369 83 18 117 468 682421726 682422090 5.010000e-13 86.1
57 TraesCS2D01G206700 chr3A 83.117 77 13 0 398 474 512578896 512578820 1.400000e-08 71.3
58 TraesCS2D01G206700 chr5A 97.436 39 1 0 436 474 487804903 487804865 1.810000e-07 67.6


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 TraesCS2D01G206700 chr2D 159860209 159863030 2821 True 5212.00 5212 100.000000 1 2822 1 chr2D.!!$R1 2821
1 TraesCS2D01G206700 chr2D 36677201 36677814 613 False 926.00 926 93.458000 2046 2685 1 chr2D.!!$F1 639
2 TraesCS2D01G206700 chr2B 216946509 216953980 7471 True 437.30 1626 92.082375 3 2048 8 chr2B.!!$R1 2045
3 TraesCS2D01G206700 chr2A 171084100 171086917 2817 True 651.75 1624 89.262000 6 2048 4 chr2A.!!$R1 2042
4 TraesCS2D01G206700 chr3D 545055456 545056092 636 False 1107.00 1107 97.969000 2046 2685 1 chr3D.!!$F2 639
5 TraesCS2D01G206700 chr4D 508665154 508665965 811 False 935.00 935 88.264000 2046 2822 1 chr4D.!!$F3 776
6 TraesCS2D01G206700 chr5D 395736442 395737700 1258 False 496.50 586 90.347000 2046 2822 2 chr5D.!!$F5 776

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
920 6119 0.588233 CTGCACAAATCGCGATGCTC 60.588 55.0 26.97 14.44 38.9 4.26 F
1067 6572 0.318441 TCCAACGTCTCTGCTTCCTG 59.682 55.0 0.00 0.00 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 7723 2.224606 TGGAAGCTGCTTCTTCACTTG 58.775 47.619 33.75 0.0 43.14 3.16 R
1919 7835 4.274705 AGTTGCACAATGTCACATCGTTTA 59.725 37.500 0.00 0.0 0.00 2.01 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
163 190 3.115892 GCGGTCGGATGCGTCAAA 61.116 61.111 6.49 0.00 0.00 2.69
164 191 2.461110 GCGGTCGGATGCGTCAAAT 61.461 57.895 6.49 0.00 0.00 2.32
165 192 1.636340 CGGTCGGATGCGTCAAATC 59.364 57.895 6.49 0.00 0.00 2.17
166 193 0.806102 CGGTCGGATGCGTCAAATCT 60.806 55.000 6.49 0.00 0.00 2.40
167 194 1.535226 CGGTCGGATGCGTCAAATCTA 60.535 52.381 6.49 0.00 0.00 1.98
168 195 2.128035 GGTCGGATGCGTCAAATCTAG 58.872 52.381 6.49 0.00 0.00 2.43
169 196 2.481449 GGTCGGATGCGTCAAATCTAGT 60.481 50.000 6.49 0.00 0.00 2.57
170 197 2.535984 GTCGGATGCGTCAAATCTAGTG 59.464 50.000 6.49 0.00 0.00 2.74
204 231 2.356135 CCTCAAATCTACCGGTTGTGG 58.644 52.381 15.04 11.37 31.68 4.17
275 302 4.308458 AACCTACAGGCGTGCGCA 62.308 61.111 18.36 5.66 44.11 6.09
386 424 2.040544 CAAGCCCGAGCGGTGAATT 61.041 57.895 8.25 0.00 46.67 2.17
390 428 0.806241 GCCCGAGCGGTGAATTAAAA 59.194 50.000 8.25 0.00 0.00 1.52
391 429 1.200484 GCCCGAGCGGTGAATTAAAAA 59.800 47.619 8.25 0.00 0.00 1.94
392 430 2.159296 GCCCGAGCGGTGAATTAAAAAT 60.159 45.455 8.25 0.00 0.00 1.82
393 431 3.065648 GCCCGAGCGGTGAATTAAAAATA 59.934 43.478 8.25 0.00 0.00 1.40
400 446 4.788521 GCGGTGAATTAAAAATAGAGGCGG 60.789 45.833 0.00 0.00 0.00 6.13
412 458 1.807814 AGAGGCGGGTGAGGATAATT 58.192 50.000 0.00 0.00 0.00 1.40
413 459 2.127708 AGAGGCGGGTGAGGATAATTT 58.872 47.619 0.00 0.00 0.00 1.82
414 460 3.314693 AGAGGCGGGTGAGGATAATTTA 58.685 45.455 0.00 0.00 0.00 1.40
416 462 4.020128 AGAGGCGGGTGAGGATAATTTATC 60.020 45.833 7.73 7.73 34.42 1.75
423 471 5.491982 GGTGAGGATAATTTATCATCCGCT 58.508 41.667 21.87 9.29 43.33 5.52
427 475 7.168302 GTGAGGATAATTTATCATCCGCTATCG 59.832 40.741 21.87 0.00 43.33 2.92
432 480 7.115095 GATAATTTATCATCCGCTATCGGCTAC 59.885 40.741 10.84 0.00 43.68 3.58
450 498 3.161450 TGGGGATCGGCTAGGTGC 61.161 66.667 0.00 0.00 41.94 5.01
585 720 6.374613 ACGAGTCTAATGTCTACATTCTCACA 59.625 38.462 11.45 0.00 44.67 3.58
588 723 5.457148 GTCTAATGTCTACATTCTCACAGCG 59.543 44.000 11.45 0.00 44.67 5.18
594 729 4.447724 GTCTACATTCTCACAGCGACAAAA 59.552 41.667 0.00 0.00 0.00 2.44
730 1175 6.289064 CCTTGTTAAGGCGTAATAGAATCCT 58.711 40.000 0.00 0.00 42.78 3.24
746 1191 9.930693 AATAGAATCCTAGAATATTTCGGTGTC 57.069 33.333 0.00 0.00 34.02 3.67
773 1224 3.733337 ACTATGATTGATCGGACCTTGC 58.267 45.455 0.00 0.00 0.00 4.01
782 1233 2.559698 TCGGACCTTGCTTGATTTCA 57.440 45.000 0.00 0.00 0.00 2.69
785 1236 2.417933 CGGACCTTGCTTGATTTCAGAG 59.582 50.000 0.00 0.00 0.00 3.35
839 1316 6.228995 CGGGATAGGCTACTATATCGTGATA 58.771 44.000 0.00 0.00 39.97 2.15
840 1317 6.879993 CGGGATAGGCTACTATATCGTGATAT 59.120 42.308 0.00 7.47 39.97 1.63
841 1318 8.039538 CGGGATAGGCTACTATATCGTGATATA 58.960 40.741 0.00 8.80 39.97 0.86
842 1319 9.908747 GGGATAGGCTACTATATCGTGATATAT 57.091 37.037 9.41 0.00 39.97 0.86
920 6119 0.588233 CTGCACAAATCGCGATGCTC 60.588 55.000 26.97 14.44 38.90 4.26
972 6171 1.112113 TTAGCAAAACCGCCCAAACA 58.888 45.000 0.00 0.00 0.00 2.83
997 6226 1.202533 ACCAACTCTGTTCGACCACTG 60.203 52.381 0.00 0.00 0.00 3.66
1061 6566 0.596600 TGTTCGTCCAACGTCTCTGC 60.597 55.000 0.00 0.00 43.14 4.26
1066 6571 0.318762 GTCCAACGTCTCTGCTTCCT 59.681 55.000 0.00 0.00 0.00 3.36
1067 6572 0.318441 TCCAACGTCTCTGCTTCCTG 59.682 55.000 0.00 0.00 0.00 3.86
1635 7543 2.717809 GACGCTGCGGTTCTTCGTC 61.718 63.158 26.95 8.12 41.80 4.20
1810 7718 0.510359 CACAGTGAAGAAGCAGCGTC 59.490 55.000 0.00 0.00 0.00 5.19
1815 7723 0.937304 TGAAGAAGCAGCGTCACAAC 59.063 50.000 11.18 0.05 0.00 3.32
1888 7804 1.748244 GCCCATGCTGATTCTACTGCA 60.748 52.381 0.00 0.00 45.48 4.41
1889 7805 1.945394 CCCATGCTGATTCTACTGCAC 59.055 52.381 0.00 0.00 44.59 4.57
1890 7806 2.421107 CCCATGCTGATTCTACTGCACT 60.421 50.000 0.00 0.00 44.59 4.40
1891 7807 2.612672 CCATGCTGATTCTACTGCACTG 59.387 50.000 0.00 0.00 44.59 3.66
1892 7808 1.730501 TGCTGATTCTACTGCACTGC 58.269 50.000 0.00 0.00 39.16 4.40
1893 7809 1.002315 TGCTGATTCTACTGCACTGCA 59.998 47.619 3.11 3.11 39.16 4.41
1897 7813 3.999001 CTGATTCTACTGCACTGCAAGAA 59.001 43.478 16.82 16.82 38.95 2.52
2005 7921 5.411361 GGAACAGTATCACATTGTGCAACTA 59.589 40.000 17.86 1.60 38.04 2.24
2735 9172 0.799534 GGCTTCATGCGCATTCACAC 60.800 55.000 22.81 9.35 44.05 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.248866 CGGCAAAGAAACGCTTGGTT 60.249 50.000 0.00 0.00 41.76 3.67
1 2 1.358759 CGGCAAAGAAACGCTTGGT 59.641 52.632 0.00 0.00 36.80 3.67
146 173 2.361427 GATTTGACGCATCCGACCGC 62.361 60.000 0.00 0.00 38.29 5.68
147 174 0.806102 AGATTTGACGCATCCGACCG 60.806 55.000 0.00 0.00 38.29 4.79
148 175 2.128035 CTAGATTTGACGCATCCGACC 58.872 52.381 0.00 0.00 38.29 4.79
149 176 2.535984 CACTAGATTTGACGCATCCGAC 59.464 50.000 0.00 0.00 38.29 4.79
150 177 2.481276 CCACTAGATTTGACGCATCCGA 60.481 50.000 0.00 0.00 38.29 4.55
151 178 1.860950 CCACTAGATTTGACGCATCCG 59.139 52.381 0.00 0.00 41.14 4.18
152 179 1.599542 GCCACTAGATTTGACGCATCC 59.400 52.381 0.00 0.00 0.00 3.51
153 180 1.258982 CGCCACTAGATTTGACGCATC 59.741 52.381 0.00 0.00 0.00 3.91
154 181 1.134818 TCGCCACTAGATTTGACGCAT 60.135 47.619 0.00 0.00 0.00 4.73
155 182 0.245266 TCGCCACTAGATTTGACGCA 59.755 50.000 0.00 0.00 0.00 5.24
156 183 0.645868 GTCGCCACTAGATTTGACGC 59.354 55.000 0.00 0.00 0.00 5.19
157 184 0.914551 CGTCGCCACTAGATTTGACG 59.085 55.000 14.26 14.26 42.37 4.35
158 185 1.278238 CCGTCGCCACTAGATTTGAC 58.722 55.000 0.00 0.00 0.00 3.18
159 186 0.459585 GCCGTCGCCACTAGATTTGA 60.460 55.000 0.00 0.00 0.00 2.69
160 187 1.752501 CGCCGTCGCCACTAGATTTG 61.753 60.000 0.00 0.00 0.00 2.32
161 188 1.518572 CGCCGTCGCCACTAGATTT 60.519 57.895 0.00 0.00 0.00 2.17
162 189 2.104331 CGCCGTCGCCACTAGATT 59.896 61.111 0.00 0.00 0.00 2.40
163 190 3.900892 CCGCCGTCGCCACTAGAT 61.901 66.667 0.00 0.00 0.00 1.98
259 286 4.742201 CTGCGCACGCCTGTAGGT 62.742 66.667 5.66 0.00 41.09 3.08
294 332 2.985282 TACGTCGGTGCCGTCCTT 60.985 61.111 10.60 0.00 39.60 3.36
386 424 3.109151 TCCTCACCCGCCTCTATTTTTA 58.891 45.455 0.00 0.00 0.00 1.52
390 428 2.696526 TATCCTCACCCGCCTCTATT 57.303 50.000 0.00 0.00 0.00 1.73
391 429 2.696526 TTATCCTCACCCGCCTCTAT 57.303 50.000 0.00 0.00 0.00 1.98
392 430 2.696526 ATTATCCTCACCCGCCTCTA 57.303 50.000 0.00 0.00 0.00 2.43
393 431 1.807814 AATTATCCTCACCCGCCTCT 58.192 50.000 0.00 0.00 0.00 3.69
400 446 5.491982 AGCGGATGATAAATTATCCTCACC 58.508 41.667 16.33 10.62 39.92 4.02
423 471 0.611062 CCGATCCCCAGTAGCCGATA 60.611 60.000 0.00 0.00 0.00 2.92
427 475 1.533273 TAGCCGATCCCCAGTAGCC 60.533 63.158 0.00 0.00 0.00 3.93
432 480 3.142393 CACCTAGCCGATCCCCAG 58.858 66.667 0.00 0.00 0.00 4.45
491 625 3.636300 TCAAACTGTGGCTTTAGTTGCAT 59.364 39.130 0.00 0.00 37.23 3.96
585 720 6.238076 GGAAATTGTTTGTGAATTTTGTCGCT 60.238 34.615 0.00 0.00 34.00 4.93
588 723 7.313951 TGGGAAATTGTTTGTGAATTTTGTC 57.686 32.000 0.00 0.00 34.00 3.18
594 729 7.108847 TGTTCTTTGGGAAATTGTTTGTGAAT 58.891 30.769 0.00 0.00 35.51 2.57
660 795 2.121538 GCTTTCGGCCTGGGGATTC 61.122 63.158 0.00 0.00 34.27 2.52
726 862 5.786264 ACGACACCGAAATATTCTAGGAT 57.214 39.130 9.82 0.00 39.50 3.24
746 1191 6.853720 AGGTCCGATCAATCATAGTAATACG 58.146 40.000 0.00 0.00 0.00 3.06
972 6171 0.468226 TCGAACAGAGTTGGTTGCCT 59.532 50.000 0.00 0.00 0.00 4.75
1061 6566 2.046864 TCGGAGTCGGAGCAGGAAG 61.047 63.158 0.00 0.00 36.95 3.46
1066 6571 2.750637 GGAGTCGGAGTCGGAGCA 60.751 66.667 6.74 0.00 36.95 4.26
1067 6572 3.878519 CGGAGTCGGAGTCGGAGC 61.879 72.222 13.45 0.00 36.95 4.70
1548 7456 0.039798 CGACGAGGTCAAACCGAGAA 60.040 55.000 0.00 0.00 44.90 2.87
1635 7543 0.611896 GGAACACCACATCCCCCTTG 60.612 60.000 0.00 0.00 0.00 3.61
1810 7718 5.021611 GAAGCTGCTTCTTCACTTGTTGTG 61.022 45.833 29.91 0.00 41.48 3.33
1815 7723 2.224606 TGGAAGCTGCTTCTTCACTTG 58.775 47.619 33.75 0.00 43.14 3.16
1919 7835 4.274705 AGTTGCACAATGTCACATCGTTTA 59.725 37.500 0.00 0.00 0.00 2.01
2005 7921 6.313905 CAGCATACAACTAAATTCTCGTCCTT 59.686 38.462 0.00 0.00 0.00 3.36
2735 9172 4.498520 AGAGACGGATGCCACGCG 62.499 66.667 3.53 3.53 34.00 6.01


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

AutoCloner maintained by Alex Coulton.