Multiple sequence alignment - TraesCS2D01G501300

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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 TraesCS2D01G501300 chr2D 100.000 2213 0 0 1 2213 595528586 595526374 0.000000e+00 4087.0
1 TraesCS2D01G501300 chr6D 98.609 1582 12 5 638 2213 455457080 455455503 0.000000e+00 2791.0
2 TraesCS2D01G501300 chr6D 94.237 642 10 6 7 634 455458046 455457418 0.000000e+00 955.0
3 TraesCS2D01G501300 chr6D 75.089 281 41 23 364 633 94933798 94934060 1.080000e-18 104.0
4 TraesCS2D01G501300 chr6D 96.078 51 2 0 630 680 455457128 455457078 1.410000e-12 84.2
5 TraesCS2D01G501300 chr2A 95.235 1595 55 5 638 2213 47355738 47357330 0.000000e+00 2505.0
6 TraesCS2D01G501300 chr2A 93.034 646 26 6 6 634 47354759 47355402 0.000000e+00 926.0
7 TraesCS2D01G501300 chr2A 86.574 648 78 9 831 1471 779329375 779328730 0.000000e+00 706.0
8 TraesCS2D01G501300 chr2A 85.420 631 74 8 1469 2084 779327444 779326817 6.660000e-180 640.0
9 TraesCS2D01G501300 chr2A 86.460 517 62 6 1469 1982 126655204 126655715 5.340000e-156 560.0
10 TraesCS2D01G501300 chr6B 85.419 823 74 18 658 1471 14021564 14020779 0.000000e+00 813.0
11 TraesCS2D01G501300 chr6B 86.128 483 54 10 1644 2115 14018941 14018461 1.960000e-140 508.0
12 TraesCS2D01G501300 chr6B 89.674 368 20 2 1863 2213 658560125 658560491 9.320000e-124 453.0
13 TraesCS2D01G501300 chr6B 86.605 433 28 7 7 417 658558967 658559391 3.350000e-123 451.0
14 TraesCS2D01G501300 chr6B 86.496 274 33 2 364 633 709011029 709010756 4.620000e-77 298.0
15 TraesCS2D01G501300 chr6B 90.323 62 6 0 2152 2213 84103786 84103847 5.060000e-12 82.4
16 TraesCS2D01G501300 chr6B 88.406 69 4 2 370 434 14021638 14021570 1.820000e-11 80.5
17 TraesCS2D01G501300 chr7D 85.236 806 84 24 679 1471 20431616 20432399 0.000000e+00 797.0
18 TraesCS2D01G501300 chr7D 89.286 84 9 0 2130 2213 20433859 20433942 3.010000e-19 106.0
19 TraesCS2D01G501300 chr4B 89.617 626 36 12 7 611 63845780 63845163 0.000000e+00 769.0
20 TraesCS2D01G501300 chr4B 91.917 433 27 6 638 1064 63816284 63815854 1.130000e-167 599.0
21 TraesCS2D01G501300 chr4B 88.798 366 21 4 1866 2213 63805540 63805177 4.370000e-117 431.0
22 TraesCS2D01G501300 chr3A 86.111 648 78 10 831 1471 735228553 735227911 0.000000e+00 688.0
23 TraesCS2D01G501300 chr3A 84.628 631 79 8 1469 2084 735226626 735225999 1.450000e-171 612.0
24 TraesCS2D01G501300 chr3A 73.163 667 114 35 7 633 508522323 508522964 1.750000e-41 180.0
25 TraesCS2D01G501300 chr3A 89.286 84 9 0 2130 2213 508523957 508524040 3.010000e-19 106.0
26 TraesCS2D01G501300 chr7B 84.421 674 86 16 812 1471 265362219 265362887 0.000000e+00 645.0
27 TraesCS2D01G501300 chr7B 83.234 167 21 6 5 169 15369810 15369971 1.770000e-31 147.0
28 TraesCS2D01G501300 chr7B 82.716 162 23 5 7 166 526717908 526718066 2.960000e-29 139.0
29 TraesCS2D01G501300 chr7B 94.444 54 3 0 2130 2183 15370776 15370829 1.410000e-12 84.2
30 TraesCS2D01G501300 chr7B 94.444 54 3 0 2130 2183 526729837 526729890 1.410000e-12 84.2
31 TraesCS2D01G501300 chr6A 80.824 850 127 24 640 1471 615377928 615377097 3.100000e-178 634.0
32 TraesCS2D01G501300 chr1D 85.977 599 76 6 880 1471 9255900 9255303 3.100000e-178 634.0
33 TraesCS2D01G501300 chr1D 87.402 254 30 1 1470 1723 9253525 9253274 7.730000e-75 291.0
34 TraesCS2D01G501300 chr3D 83.704 675 93 14 807 1471 309696796 309697463 2.410000e-174 621.0
35 TraesCS2D01G501300 chr3D 84.176 455 64 7 1470 1922 309719750 309720198 3.370000e-118 435.0
36 TraesCS2D01G501300 chr3D 76.871 294 42 15 352 633 309696077 309696356 2.290000e-30 143.0
37 TraesCS2D01G501300 chr3B 87.427 517 57 6 1469 1982 750876416 750875905 2.450000e-164 588.0
38 TraesCS2D01G501300 chr3B 84.259 540 62 9 1469 2003 17676165 17675644 2.540000e-139 505.0
39 TraesCS2D01G501300 chr3B 75.089 281 42 24 364 633 9361178 9360915 3.010000e-19 106.0
40 TraesCS2D01G501300 chr5B 83.735 166 22 5 6 169 624316 624154 3.810000e-33 152.0
41 TraesCS2D01G501300 chr5B 91.228 57 5 0 2130 2186 621159 621103 6.550000e-11 78.7
42 TraesCS2D01G501300 chr2B 76.923 286 45 14 7 274 453860929 453861211 2.290000e-30 143.0
43 TraesCS2D01G501300 chr2B 96.491 57 2 0 2131 2187 31056373 31056429 6.510000e-16 95.3


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 TraesCS2D01G501300 chr2D 595526374 595528586 2212 True 4087.000000 4087 100.0000 1 2213 1 chr2D.!!$R1 2212
1 TraesCS2D01G501300 chr6D 455455503 455458046 2543 True 1276.733333 2791 96.3080 7 2213 3 chr6D.!!$R1 2206
2 TraesCS2D01G501300 chr2A 47354759 47357330 2571 False 1715.500000 2505 94.1345 6 2213 2 chr2A.!!$F2 2207
3 TraesCS2D01G501300 chr2A 779326817 779329375 2558 True 673.000000 706 85.9970 831 2084 2 chr2A.!!$R1 1253
4 TraesCS2D01G501300 chr2A 126655204 126655715 511 False 560.000000 560 86.4600 1469 1982 1 chr2A.!!$F1 513
5 TraesCS2D01G501300 chr6B 14018461 14021638 3177 True 467.166667 813 86.6510 370 2115 3 chr6B.!!$R2 1745
6 TraesCS2D01G501300 chr6B 658558967 658560491 1524 False 452.000000 453 88.1395 7 2213 2 chr6B.!!$F2 2206
7 TraesCS2D01G501300 chr7D 20431616 20433942 2326 False 451.500000 797 87.2610 679 2213 2 chr7D.!!$F1 1534
8 TraesCS2D01G501300 chr4B 63845163 63845780 617 True 769.000000 769 89.6170 7 611 1 chr4B.!!$R3 604
9 TraesCS2D01G501300 chr3A 735225999 735228553 2554 True 650.000000 688 85.3695 831 2084 2 chr3A.!!$R1 1253
10 TraesCS2D01G501300 chr7B 265362219 265362887 668 False 645.000000 645 84.4210 812 1471 1 chr7B.!!$F1 659
11 TraesCS2D01G501300 chr6A 615377097 615377928 831 True 634.000000 634 80.8240 640 1471 1 chr6A.!!$R1 831
12 TraesCS2D01G501300 chr1D 9253274 9255900 2626 True 462.500000 634 86.6895 880 1723 2 chr1D.!!$R1 843
13 TraesCS2D01G501300 chr3D 309696077 309697463 1386 False 382.000000 621 80.2875 352 1471 2 chr3D.!!$F2 1119
14 TraesCS2D01G501300 chr3B 750875905 750876416 511 True 588.000000 588 87.4270 1469 1982 1 chr3B.!!$R3 513
15 TraesCS2D01G501300 chr3B 17675644 17676165 521 True 505.000000 505 84.2590 1469 2003 1 chr3B.!!$R2 534

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
634 678 0.037447 TGGCGGGATCAATGTTGTCA 59.963 50.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 5121 0.457681 GCGTGTTGGTGCAAGTGTTT 60.458 50.0 0.0 0.0 0.0 2.83 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
97 98 2.923020 GTGTGCATGGCTTTTTAATCGG 59.077 45.455 0.00 0.00 0.00 4.18
155 156 2.657237 GTGGGCTCGTGTGCTAGT 59.343 61.111 0.00 0.00 0.00 2.57
307 329 1.544724 AACCCCGGATGTGATGTTTG 58.455 50.000 0.73 0.00 0.00 2.93
344 372 1.682849 CCTTCCCGTGGAATGTGGA 59.317 57.895 5.92 0.00 41.23 4.02
508 547 1.469703 CTGCTCATTGATTTCACCGCA 59.530 47.619 0.00 0.00 0.00 5.69
634 678 0.037447 TGGCGGGATCAATGTTGTCA 59.963 50.000 0.00 0.00 0.00 3.58
635 679 1.340893 TGGCGGGATCAATGTTGTCAT 60.341 47.619 0.00 0.00 35.59 3.06
636 680 1.750778 GGCGGGATCAATGTTGTCATT 59.249 47.619 0.00 0.00 44.02 2.57
637 681 2.223572 GGCGGGATCAATGTTGTCATTC 60.224 50.000 0.00 0.00 41.66 2.67
654 1032 4.702131 GTCATTCCTTTGCTGTTAGACCAT 59.298 41.667 0.00 0.00 0.00 3.55
798 1188 7.065803 CCATAATTTTACAATCAGGTGTCGAGT 59.934 37.037 0.00 0.00 32.75 4.18
1324 1741 2.805886 ATCGAATAGCCGCTCGACGAT 61.806 52.381 16.94 16.94 46.01 3.73
1552 4533 4.099573 ACGGGTTTATCTGACAGATAGGTG 59.900 45.833 21.42 14.43 38.34 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.002900 CAAAACGCCACACTCGATTGT 60.003 47.619 2.04 2.04 0.00 2.71
1 2 1.662876 CCAAAACGCCACACTCGATTG 60.663 52.381 0.55 0.55 0.00 2.67
2 3 0.591170 CCAAAACGCCACACTCGATT 59.409 50.000 0.00 0.00 0.00 3.34
3 4 0.534203 ACCAAAACGCCACACTCGAT 60.534 50.000 0.00 0.00 0.00 3.59
4 5 1.153329 ACCAAAACGCCACACTCGA 60.153 52.632 0.00 0.00 0.00 4.04
97 98 5.943706 TCTGACAGCTATCGTATACCTTC 57.056 43.478 0.00 0.00 0.00 3.46
145 146 1.450533 CACGTACAACACTAGCACACG 59.549 52.381 0.00 0.00 0.00 4.49
155 156 2.340809 CGAGGCCCACGTACAACA 59.659 61.111 0.00 0.00 0.00 3.33
307 329 2.025887 AGGGGATGAATGAACTGACCAC 60.026 50.000 0.00 0.00 0.00 4.16
508 547 4.501743 GGGAGAAGAACTCAAGAACGAACT 60.502 45.833 0.00 0.00 46.54 3.01
634 678 6.313519 TCTATGGTCTAACAGCAAAGGAAT 57.686 37.500 0.00 0.00 35.67 3.01
635 679 5.755409 TCTATGGTCTAACAGCAAAGGAA 57.245 39.130 0.00 0.00 35.67 3.36
636 680 5.957771 ATCTATGGTCTAACAGCAAAGGA 57.042 39.130 0.00 0.00 35.67 3.36
637 681 5.882557 ACAATCTATGGTCTAACAGCAAAGG 59.117 40.000 0.00 0.00 35.67 3.11
654 1032 5.509163 GGCGATTACAGGAAGCTACAATCTA 60.509 44.000 0.00 0.00 0.00 1.98
1324 1741 3.490031 AACGCAGGGCATCCACACA 62.490 57.895 0.00 0.00 34.83 3.72
1858 5121 0.457681 GCGTGTTGGTGCAAGTGTTT 60.458 50.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.