Multiple sequence alignment - TraesCS2A01G290700

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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 TraesCS2A01G290700 chr2A 100.000 2336 0 0 1 2336 500979785 500977450 0.000000e+00 4314.0
1 TraesCS2A01G290700 chr2A 91.097 629 51 3 4 632 758016068 758015445 0.000000e+00 846.0
2 TraesCS2A01G290700 chr5A 95.377 2336 104 2 4 2336 448124159 448121825 0.000000e+00 3712.0
3 TraesCS2A01G290700 chr5A 94.130 1380 77 2 4 1380 448137874 448136496 0.000000e+00 2097.0
4 TraesCS2A01G290700 chr5A 96.150 961 37 0 1376 2336 448130775 448129815 0.000000e+00 1570.0
5 TraesCS2A01G290700 chr5A 91.434 537 35 11 1804 2334 265534261 265533730 0.000000e+00 726.0
6 TraesCS2A01G290700 chr5A 91.457 398 32 2 773 1169 293910049 293910445 1.580000e-151 545.0
7 TraesCS2A01G290700 chr5A 90.704 398 36 1 773 1169 293903030 293903427 1.590000e-146 529.0
8 TraesCS2A01G290700 chr5A 87.342 158 16 4 1425 1580 263227890 263227735 6.630000e-41 178.0
9 TraesCS2A01G290700 chr5A 86.207 145 16 4 1438 1580 263236024 263235882 1.120000e-33 154.0
10 TraesCS2A01G290700 chr7A 90.241 1496 115 12 4 1475 163313289 163311801 0.000000e+00 1925.0
11 TraesCS2A01G290700 chr7A 81.621 1197 155 48 4 1169 259583187 259582025 0.000000e+00 931.0
12 TraesCS2A01G290700 chr7A 86.093 604 59 18 1706 2298 445559743 445560332 5.480000e-176 627.0
13 TraesCS2A01G290700 chr7A 92.742 124 7 2 1459 1580 94840291 94840414 6.630000e-41 178.0
14 TraesCS2A01G290700 chr7A 88.966 145 12 4 1438 1580 404436094 404435952 2.390000e-40 176.0
15 TraesCS2A01G290700 chr7A 88.000 150 14 4 1433 1580 404428204 404428057 8.580000e-40 174.0
16 TraesCS2A01G290700 chr1A 83.104 1598 207 40 4 1562 222722323 222720750 0.000000e+00 1397.0
17 TraesCS2A01G290700 chr1A 86.593 813 70 22 660 1449 206952113 206952909 0.000000e+00 861.0
18 TraesCS2A01G290700 chr1A 89.810 579 48 7 4 580 301214035 301213466 0.000000e+00 732.0
19 TraesCS2A01G290700 chr1A 89.519 582 50 10 4 583 301222043 301221471 0.000000e+00 726.0
20 TraesCS2A01G290700 chr1A 83.871 124 15 5 1356 1475 545991150 545991028 1.900000e-21 113.0
21 TraesCS2A01G290700 chr1A 92.308 52 4 0 1589 1640 268890458 268890509 8.950000e-10 75.0
22 TraesCS2A01G290700 chr4A 94.058 791 41 5 1549 2336 201316610 201315823 0.000000e+00 1195.0
23 TraesCS2A01G290700 chr4A 93.932 791 42 5 1549 2336 201269586 201268799 0.000000e+00 1190.0
24 TraesCS2A01G290700 chr4A 93.829 794 41 7 1547 2336 201323436 201322647 0.000000e+00 1188.0
25 TraesCS2A01G290700 chr4A 93.451 794 36 8 1547 2336 201277511 201276730 0.000000e+00 1164.0
26 TraesCS2A01G290700 chr4A 86.101 813 75 22 660 1449 306487663 306486866 0.000000e+00 841.0
27 TraesCS2A01G290700 chr4A 89.474 627 60 5 547 1169 427041795 427042419 0.000000e+00 787.0
28 TraesCS2A01G290700 chr4A 90.232 604 58 1 567 1169 427075056 427075659 0.000000e+00 787.0
29 TraesCS2A01G290700 chr4A 79.407 607 93 24 1 591 126664168 126664758 1.300000e-107 399.0
30 TraesCS2A01G290700 chr4A 79.407 607 93 23 1 591 126970893 126971483 1.300000e-107 399.0
31 TraesCS2A01G290700 chr4A 79.035 601 85 32 4 585 278302221 278301643 7.880000e-100 374.0
32 TraesCS2A01G290700 chr4A 85.088 114 14 1 1260 1373 524199372 524199482 1.900000e-21 113.0
33 TraesCS2A01G290700 chr6A 96.631 653 20 2 1686 2336 511353451 511354103 0.000000e+00 1083.0
34 TraesCS2A01G290700 chr6A 95.067 669 25 6 1673 2334 511361321 511361988 0.000000e+00 1046.0
35 TraesCS2A01G290700 chr6A 86.470 813 70 20 660 1449 592939098 592938303 0.000000e+00 856.0
36 TraesCS2A01G290700 chr6A 89.273 578 53 8 12 586 422633714 422633143 0.000000e+00 715.0
37 TraesCS2A01G290700 chr6A 87.793 598 63 3 488 1075 429933335 429933932 0.000000e+00 691.0
38 TraesCS2A01G290700 chr6A 86.271 641 74 6 447 1075 429938059 429938697 0.000000e+00 684.0
39 TraesCS2A01G290700 chr6A 87.479 599 65 3 487 1075 429928578 429929176 0.000000e+00 682.0
40 TraesCS2A01G290700 chr6A 90.850 153 12 2 1338 1488 121367279 121367127 1.090000e-48 204.0
41 TraesCS2A01G290700 chr6A 88.136 177 12 7 1410 1580 259131570 259131743 3.940000e-48 202.0
42 TraesCS2A01G290700 chr6A 89.542 153 14 2 1338 1488 319327323 319327171 2.370000e-45 193.0
43 TraesCS2A01G290700 chr6A 86.842 114 12 1 1260 1373 311831600 311831710 8.760000e-25 124.0
44 TraesCS2A01G290700 chr6A 87.037 108 11 2 1266 1373 311428887 311428783 4.080000e-23 119.0
45 TraesCS2A01G290700 chr6A 87.654 81 10 0 1293 1373 246646743 246646823 6.870000e-16 95.3
46 TraesCS2A01G290700 chr3A 84.122 592 70 20 1 585 193041193 193041767 3.390000e-153 551.0
47 TraesCS2A01G290700 chr3A 91.870 246 15 5 1338 1580 377723386 377723143 2.880000e-89 339.0
48 TraesCS2A01G290700 chr3A 90.441 136 11 2 1437 1570 355072323 355072188 6.630000e-41 178.0
49 TraesCS2A01G290700 chr3D 90.714 140 12 1 1337 1475 49330022 49330161 3.960000e-43 185.0
50 TraesCS2A01G290700 chr3D 90.000 140 13 1 1337 1475 49364485 49364624 1.840000e-41 180.0
51 TraesCS2A01G290700 chrUn 96.774 31 1 0 1344 1374 118658548 118658518 4.000000e-03 52.8


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 TraesCS2A01G290700 chr2A 500977450 500979785 2335 True 4314 4314 100.000 1 2336 1 chr2A.!!$R1 2335
1 TraesCS2A01G290700 chr2A 758015445 758016068 623 True 846 846 91.097 4 632 1 chr2A.!!$R2 628
2 TraesCS2A01G290700 chr5A 448121825 448124159 2334 True 3712 3712 95.377 4 2336 1 chr5A.!!$R4 2332
3 TraesCS2A01G290700 chr5A 448136496 448137874 1378 True 2097 2097 94.130 4 1380 1 chr5A.!!$R6 1376
4 TraesCS2A01G290700 chr5A 448129815 448130775 960 True 1570 1570 96.150 1376 2336 1 chr5A.!!$R5 960
5 TraesCS2A01G290700 chr5A 265533730 265534261 531 True 726 726 91.434 1804 2334 1 chr5A.!!$R3 530
6 TraesCS2A01G290700 chr7A 163311801 163313289 1488 True 1925 1925 90.241 4 1475 1 chr7A.!!$R1 1471
7 TraesCS2A01G290700 chr7A 259582025 259583187 1162 True 931 931 81.621 4 1169 1 chr7A.!!$R2 1165
8 TraesCS2A01G290700 chr7A 445559743 445560332 589 False 627 627 86.093 1706 2298 1 chr7A.!!$F2 592
9 TraesCS2A01G290700 chr1A 222720750 222722323 1573 True 1397 1397 83.104 4 1562 1 chr1A.!!$R1 1558
10 TraesCS2A01G290700 chr1A 206952113 206952909 796 False 861 861 86.593 660 1449 1 chr1A.!!$F1 789
11 TraesCS2A01G290700 chr1A 301213466 301214035 569 True 732 732 89.810 4 580 1 chr1A.!!$R2 576
12 TraesCS2A01G290700 chr1A 301221471 301222043 572 True 726 726 89.519 4 583 1 chr1A.!!$R3 579
13 TraesCS2A01G290700 chr4A 201315823 201316610 787 True 1195 1195 94.058 1549 2336 1 chr4A.!!$R3 787
14 TraesCS2A01G290700 chr4A 201268799 201269586 787 True 1190 1190 93.932 1549 2336 1 chr4A.!!$R1 787
15 TraesCS2A01G290700 chr4A 201322647 201323436 789 True 1188 1188 93.829 1547 2336 1 chr4A.!!$R4 789
16 TraesCS2A01G290700 chr4A 201276730 201277511 781 True 1164 1164 93.451 1547 2336 1 chr4A.!!$R2 789
17 TraesCS2A01G290700 chr4A 306486866 306487663 797 True 841 841 86.101 660 1449 1 chr4A.!!$R6 789
18 TraesCS2A01G290700 chr4A 427041795 427042419 624 False 787 787 89.474 547 1169 1 chr4A.!!$F3 622
19 TraesCS2A01G290700 chr4A 427075056 427075659 603 False 787 787 90.232 567 1169 1 chr4A.!!$F4 602
20 TraesCS2A01G290700 chr4A 126664168 126664758 590 False 399 399 79.407 1 591 1 chr4A.!!$F1 590
21 TraesCS2A01G290700 chr4A 126970893 126971483 590 False 399 399 79.407 1 591 1 chr4A.!!$F2 590
22 TraesCS2A01G290700 chr4A 278301643 278302221 578 True 374 374 79.035 4 585 1 chr4A.!!$R5 581
23 TraesCS2A01G290700 chr6A 511353451 511354103 652 False 1083 1083 96.631 1686 2336 1 chr6A.!!$F7 650
24 TraesCS2A01G290700 chr6A 511361321 511361988 667 False 1046 1046 95.067 1673 2334 1 chr6A.!!$F8 661
25 TraesCS2A01G290700 chr6A 592938303 592939098 795 True 856 856 86.470 660 1449 1 chr6A.!!$R5 789
26 TraesCS2A01G290700 chr6A 422633143 422633714 571 True 715 715 89.273 12 586 1 chr6A.!!$R4 574
27 TraesCS2A01G290700 chr6A 429933335 429933932 597 False 691 691 87.793 488 1075 1 chr6A.!!$F5 587
28 TraesCS2A01G290700 chr6A 429938059 429938697 638 False 684 684 86.271 447 1075 1 chr6A.!!$F6 628
29 TraesCS2A01G290700 chr6A 429928578 429929176 598 False 682 682 87.479 487 1075 1 chr6A.!!$F4 588
30 TraesCS2A01G290700 chr3A 193041193 193041767 574 False 551 551 84.122 1 585 1 chr3A.!!$F1 584

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
406 434 0.031043 ATCGACGACGGTGTCAAACA 59.969 50.0 7.55 0.0 38.84 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 1714 0.682855 CCACTCTCGCTCTCTCCCTT 60.683 60.0 0.0 0.0 0.0 3.95 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
316 338 6.338937 GTTCCGGTACTTGATTGAGATACTT 58.661 40.000 0.00 0.00 0.00 2.24
337 359 1.896660 GCAAAGGGGAAGTGTGCGA 60.897 57.895 0.00 0.00 0.00 5.10
406 434 0.031043 ATCGACGACGGTGTCAAACA 59.969 50.000 7.55 0.00 38.84 2.83
456 487 3.374220 ACAACAACCAACATGCATCTG 57.626 42.857 0.00 0.00 0.00 2.90
477 516 4.119136 TGATACAACTCATGCATACGGTG 58.881 43.478 0.00 4.79 0.00 4.94
510 553 3.243002 CGTCTCAGGGTTATACCTTCGAC 60.243 52.174 0.00 0.00 39.34 4.20
723 782 2.439883 GTCGGTAGGGGAGCTCGT 60.440 66.667 7.83 0.00 0.00 4.18
767 826 0.393820 GGTCGTTGGGGTACTTGTCA 59.606 55.000 0.00 0.00 0.00 3.58
1122 1188 2.410466 GGCACGGGAAGAACAACAA 58.590 52.632 0.00 0.00 0.00 2.83
1218 1299 2.264120 GAGGAGCAGGGAAAGGAGGC 62.264 65.000 0.00 0.00 0.00 4.70
1299 1385 2.239654 CTGGAGAAATAGGAAGGCCACA 59.760 50.000 5.01 0.00 36.29 4.17
1301 1387 2.239907 GGAGAAATAGGAAGGCCACAGT 59.760 50.000 5.01 0.00 36.29 3.55
1306 1392 3.689872 ATAGGAAGGCCACAGTAGAGA 57.310 47.619 5.01 0.00 36.29 3.10
1333 1419 4.039357 CCGACGACGAGGTGCAGT 62.039 66.667 9.28 0.00 42.66 4.40
1381 1467 2.284331 TGAGGCGGGGTAGAGCAA 60.284 61.111 0.00 0.00 34.54 3.91
1623 1714 2.347490 GGCGCAAGGGAAGAGACA 59.653 61.111 10.83 0.00 38.28 3.41
1701 1797 1.937924 AATGGTGGGCTTAGGAGGGC 61.938 60.000 0.00 0.00 0.00 5.19
1702 1798 3.015145 GGTGGGCTTAGGAGGGCA 61.015 66.667 0.00 0.00 0.00 5.36
1703 1799 2.386935 GGTGGGCTTAGGAGGGCAT 61.387 63.158 0.00 0.00 0.00 4.40
1704 1800 1.060163 GGTGGGCTTAGGAGGGCATA 61.060 60.000 0.00 0.00 0.00 3.14
1705 1801 1.068121 GTGGGCTTAGGAGGGCATAT 58.932 55.000 0.00 0.00 0.00 1.78
1706 1802 1.067295 TGGGCTTAGGAGGGCATATG 58.933 55.000 0.00 0.00 0.00 1.78
1709 1805 0.322906 GCTTAGGAGGGCATATGGGC 60.323 60.000 4.56 0.00 42.44 5.36
1831 1928 9.500785 CAGAAAAGAAGTTAGAGAGAGGAAAAT 57.499 33.333 0.00 0.00 0.00 1.82
2076 2176 2.484889 GTTTGAGGAGCAACTCGAAGT 58.515 47.619 9.78 0.00 40.57 3.01
2230 2339 4.576463 ACCGAAGATCCATGCAATTTACTC 59.424 41.667 0.00 0.00 0.00 2.59
2317 2436 2.290464 ACGAACCAAAACGAATCACCA 58.710 42.857 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.264067 AGTTTACTTTTGCTTCATCTCTTGCT 59.736 34.615 0.00 0.0 0.00 3.91
261 282 1.129064 CCGTGGCACCGTTATTGTTAC 59.871 52.381 12.86 0.0 0.00 2.50
290 311 2.901192 TCTCAATCAAGTACCGGAACCA 59.099 45.455 9.46 0.0 0.00 3.67
316 338 1.544724 GCACACTTCCCCTTTGCATA 58.455 50.000 0.00 0.0 33.24 3.14
337 359 1.337074 CCACCATCTTTTGCACGCATT 60.337 47.619 0.00 0.0 0.00 3.56
406 434 3.809279 CCGTAAACGTTAGTTGTTCCCTT 59.191 43.478 0.00 0.0 41.05 3.95
456 487 4.715520 CACCGTATGCATGAGTTGTATC 57.284 45.455 10.16 0.0 32.43 2.24
477 516 0.389166 CCTGAGACGACCACTCTTGC 60.389 60.000 0.00 0.0 35.66 4.01
510 553 1.511887 CGTTCCGAAAAGGCATGCG 60.512 57.895 12.44 0.0 40.77 4.73
632 691 7.085116 GTGGATCCGACAAGACTAAGTATATG 58.915 42.308 7.39 0.0 0.00 1.78
633 692 6.776116 TGTGGATCCGACAAGACTAAGTATAT 59.224 38.462 7.39 0.0 0.00 0.86
723 782 4.342665 TGTACCACTATCATCGCAATACCA 59.657 41.667 0.00 0.0 0.00 3.25
1122 1188 3.001406 GTAGCCACCCCGTCCTGT 61.001 66.667 0.00 0.0 0.00 4.00
1185 1266 3.461773 CCTCCTCGTGTGCCCGAT 61.462 66.667 0.00 0.0 36.08 4.18
1192 1273 2.681778 CCCTGCTCCTCCTCGTGT 60.682 66.667 0.00 0.0 0.00 4.49
1319 1405 2.567049 GCTACTGCACCTCGTCGT 59.433 61.111 0.00 0.0 39.41 4.34
1523 1614 1.076438 CCTTTCCTCCCTTCCACCTT 58.924 55.000 0.00 0.0 0.00 3.50
1586 1677 1.905512 CCGAAAATCCCGTCTCCCT 59.094 57.895 0.00 0.0 0.00 4.20
1623 1714 0.682855 CCACTCTCGCTCTCTCCCTT 60.683 60.000 0.00 0.0 0.00 3.95
1831 1928 2.312741 TCCGTCCCTAACCCTCTCTTTA 59.687 50.000 0.00 0.0 0.00 1.85
1883 1980 6.587206 TCTTGGATCATACACATTTTTGCA 57.413 33.333 0.00 0.0 0.00 4.08
2076 2176 7.931407 TGCAATGTAACTCTCAAGTCTTTTCTA 59.069 33.333 0.00 0.0 33.48 2.10
2186 2290 2.914278 TCCATTTAAACCGAGGGAAGGA 59.086 45.455 0.00 0.0 0.00 3.36
2230 2339 6.329496 TCAAAGCCAACTAAAAACTCACTTG 58.671 36.000 0.00 0.0 0.00 3.16


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

AutoCloner maintained by Alex Coulton.