Multiple sequence alignment - TraesCS4A01G343100

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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 TraesCS4A01G343100 chr4A 100.000 3579 0 0 1 3579 622511602 622508024 0.000000e+00 6610.0
1 TraesCS4A01G343100 chr4A 99.111 2925 19 3 661 3579 622559507 622556584 0.000000e+00 5251.0
2 TraesCS4A01G343100 chr4A 98.185 2920 35 4 661 3579 622441875 622438973 0.000000e+00 5083.0
3 TraesCS4A01G343100 chr4A 99.399 1996 12 0 1584 3579 622475823 622473828 0.000000e+00 3620.0
4 TraesCS4A01G343100 chr4A 98.682 607 7 1 1 606 622443119 622442513 0.000000e+00 1075.0
5 TraesCS4A01G343100 chr4A 98.517 607 8 1 1 606 622560272 622559666 0.000000e+00 1070.0
6 TraesCS4A01G343100 chr4A 98.188 607 10 1 1 606 622477172 622476566 0.000000e+00 1059.0
7 TraesCS4A01G343100 chr4A 94.325 652 33 3 2753 3402 622351940 622352589 0.000000e+00 996.0
8 TraesCS4A01G343100 chr4A 97.816 412 9 0 1646 2057 507829517 507829106 0.000000e+00 712.0
9 TraesCS4A01G343100 chr4A 99.211 380 3 0 227 606 622442413 622442034 0.000000e+00 686.0
10 TraesCS4A01G343100 chr4A 86.730 211 28 0 842 1052 614004695 614004905 5.970000e-58 235.0
11 TraesCS4A01G343100 chr4A 91.579 95 8 0 669 763 99903673 99903767 8.060000e-27 132.0
12 TraesCS4A01G343100 chr4A 100.000 50 0 0 609 658 622441948 622441899 3.800000e-15 93.5
13 TraesCS4A01G343100 chr4A 87.342 79 4 4 240 317 629022427 629022354 6.370000e-13 86.1
14 TraesCS4A01G343100 chr4A 87.342 79 4 4 240 317 629040725 629040652 6.370000e-13 86.1
15 TraesCS4A01G343100 chr3A 96.308 650 21 2 2754 3402 51282373 51281726 0.000000e+00 1064.0
16 TraesCS4A01G343100 chr3A 90.278 72 6 1 246 317 163174157 163174227 3.800000e-15 93.5
17 TraesCS4A01G343100 chr3A 100.000 29 0 0 392 420 698006362 698006390 2.000000e-03 54.7
18 TraesCS4A01G343100 chr5B 91.338 785 34 15 822 1592 689669703 689670467 0.000000e+00 1042.0
19 TraesCS4A01G343100 chr5B 93.665 663 36 5 2754 3415 526646842 526647499 0.000000e+00 987.0
20 TraesCS4A01G343100 chr5B 93.788 660 36 4 2754 3412 536043200 536042545 0.000000e+00 987.0
21 TraesCS4A01G343100 chr5B 94.614 557 29 1 820 1375 689646135 689646691 0.000000e+00 861.0
22 TraesCS4A01G343100 chr5B 85.400 637 57 7 1 602 689667901 689668536 2.350000e-176 628.0
23 TraesCS4A01G343100 chr5B 93.939 363 19 1 2387 2746 689670846 689671208 2.430000e-151 545.0
24 TraesCS4A01G343100 chr5B 88.085 235 28 0 820 1054 492131932 492132166 2.720000e-71 279.0
25 TraesCS4A01G343100 chr5B 81.107 307 51 5 2389 2693 492134075 492134376 4.620000e-59 239.0
26 TraesCS4A01G343100 chr5B 86.256 211 29 0 842 1052 696154666 696154876 2.780000e-56 230.0
27 TraesCS4A01G343100 chr5B 89.944 179 13 3 3403 3579 689671202 689671377 3.600000e-55 226.0
28 TraesCS4A01G343100 chr5B 83.036 224 32 6 845 1066 27461609 27461390 7.840000e-47 198.0
29 TraesCS4A01G343100 chr5B 88.034 117 14 0 1462 1578 689647097 689647213 4.820000e-29 139.0
30 TraesCS4A01G343100 chr5B 91.176 102 9 0 659 760 689668705 689668806 4.820000e-29 139.0
31 TraesCS4A01G343100 chr5B 91.209 91 7 1 673 763 562337346 562337435 4.850000e-24 122.0
32 TraesCS4A01G343100 chr5B 91.463 82 7 0 2136 2217 689670481 689670562 2.920000e-21 113.0
33 TraesCS4A01G343100 chr5B 93.617 47 3 0 2202 2248 689670574 689670620 1.780000e-08 71.3
34 TraesCS4A01G343100 chr7D 94.334 653 34 2 2751 3402 421832668 421832018 0.000000e+00 998.0
35 TraesCS4A01G343100 chr7D 87.850 107 11 2 675 779 185371650 185371756 1.350000e-24 124.0
36 TraesCS4A01G343100 chr7D 77.619 210 25 6 392 579 75292090 75292299 1.360000e-19 108.0
37 TraesCS4A01G343100 chr7D 75.877 228 40 10 104 317 176580857 176580631 6.320000e-18 102.0
38 TraesCS4A01G343100 chr3B 94.172 652 35 2 2753 3403 368957892 368958541 0.000000e+00 990.0
39 TraesCS4A01G343100 chr5D 91.007 556 40 6 820 1375 546566157 546566702 0.000000e+00 741.0
40 TraesCS4A01G343100 chr5D 86.864 236 31 0 820 1055 410278128 410278363 7.620000e-67 265.0
41 TraesCS4A01G343100 chr5D 80.516 349 49 15 2389 2726 410284862 410285202 2.130000e-62 250.0
42 TraesCS4A01G343100 chr5D 87.204 211 27 0 842 1052 554577214 554577004 1.280000e-59 241.0
43 TraesCS4A01G343100 chr5D 82.843 204 33 2 848 1050 36626902 36626700 7.890000e-42 182.0
44 TraesCS4A01G343100 chr5D 89.744 117 12 0 1462 1578 546567140 546567256 2.230000e-32 150.0
45 TraesCS4A01G343100 chr5D 88.571 70 6 1 246 315 88467815 88467748 2.290000e-12 84.2
46 TraesCS4A01G343100 chr5D 88.372 43 5 0 537 579 439494683 439494725 6.000000e-03 52.8
47 TraesCS4A01G343100 chr6A 98.544 412 6 0 1645 2056 566444719 566444308 0.000000e+00 728.0
48 TraesCS4A01G343100 chr6A 96.117 412 14 2 1646 2057 24937322 24936913 0.000000e+00 671.0
49 TraesCS4A01G343100 chr6A 93.478 92 5 1 673 763 579055183 579055274 6.230000e-28 135.0
50 TraesCS4A01G343100 chr7A 97.842 417 8 1 1641 2057 33338590 33338175 0.000000e+00 719.0
51 TraesCS4A01G343100 chrUn 96.845 412 12 1 1646 2057 71622442 71622032 0.000000e+00 688.0
52 TraesCS4A01G343100 chr1A 96.386 415 13 2 1646 2060 568463678 568464090 0.000000e+00 682.0
53 TraesCS4A01G343100 chr1A 90.385 52 3 2 235 285 84721923 84721973 2.310000e-07 67.6
54 TraesCS4A01G343100 chr1A 92.683 41 1 2 550 589 547278606 547278645 1.390000e-04 58.4
55 TraesCS4A01G343100 chr4D 82.791 215 37 0 842 1056 477089281 477089067 3.650000e-45 193.0
56 TraesCS4A01G343100 chr4D 92.135 89 7 0 675 763 367049180 367049092 3.750000e-25 126.0
57 TraesCS4A01G343100 chr2D 82.927 205 35 0 845 1049 470543073 470542869 6.100000e-43 185.0
58 TraesCS4A01G343100 chr2D 80.083 241 39 2 1129 1360 593227027 593227267 1.710000e-38 171.0
59 TraesCS4A01G343100 chr2D 84.559 136 15 5 674 804 6910994 6911128 2.900000e-26 130.0
60 TraesCS4A01G343100 chr2D 89.247 93 8 1 673 763 192067221 192067129 8.120000e-22 115.0
61 TraesCS4A01G343100 chr2D 80.795 151 21 8 663 806 501306135 501306284 1.050000e-20 111.0
62 TraesCS4A01G343100 chr2D 87.179 78 8 2 241 317 372276817 372276893 1.770000e-13 87.9
63 TraesCS4A01G343100 chr2D 88.060 67 8 0 241 307 9663503 9663437 2.960000e-11 80.5
64 TraesCS4A01G343100 chr2D 88.060 67 8 0 235 301 176106333 176106399 2.960000e-11 80.5
65 TraesCS4A01G343100 chr2D 94.737 38 0 1 392 429 21921799 21921834 1.390000e-04 58.4
66 TraesCS4A01G343100 chr2A 79.668 241 40 2 1129 1360 728024607 728024847 7.950000e-37 165.0
67 TraesCS4A01G343100 chr2A 87.500 64 7 1 541 603 690603 690666 4.960000e-09 73.1
68 TraesCS4A01G343100 chr2A 77.600 125 24 4 479 599 78765132 78765008 4.960000e-09 73.1
69 TraesCS4A01G343100 chr2B 79.167 240 41 2 1129 1359 719499412 719499651 1.330000e-34 158.0
70 TraesCS4A01G343100 chr7B 78.689 244 40 6 82 316 293158624 293158384 6.190000e-33 152.0
71 TraesCS4A01G343100 chr7B 75.120 209 26 8 392 579 21306775 21306978 1.380000e-09 75.0
72 TraesCS4A01G343100 chr5A 93.478 92 4 2 673 763 346350937 346350847 6.230000e-28 135.0
73 TraesCS4A01G343100 chr6D 76.834 259 45 8 72 317 3599797 3599541 8.060000e-27 132.0
74 TraesCS4A01G343100 chr6D 92.473 93 6 1 671 763 77826316 77826407 8.060000e-27 132.0
75 TraesCS4A01G343100 chr6D 93.258 89 5 1 675 763 55101557 55101470 2.900000e-26 130.0
76 TraesCS4A01G343100 chr6D 87.778 90 11 0 674 763 117361885 117361974 4.890000e-19 106.0
77 TraesCS4A01G343100 chr6D 81.720 93 8 5 673 763 437661582 437661667 6.410000e-08 69.4
78 TraesCS4A01G343100 chr1D 92.045 88 7 0 674 761 448378199 448378112 1.350000e-24 124.0
79 TraesCS4A01G343100 chr1D 90.526 95 8 1 670 763 492139605 492139511 1.350000e-24 124.0
80 TraesCS4A01G343100 chr1B 73.853 218 43 10 111 317 885771 885557 1.380000e-09 75.0
81 TraesCS4A01G343100 chr6B 76.087 138 30 3 60 195 149578207 149578343 6.410000e-08 69.4


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 TraesCS4A01G343100 chr4A 622508024 622511602 3578 True 6610.000 6610 100.000000 1 3579 1 chr4A.!!$R2 3578
1 TraesCS4A01G343100 chr4A 622556584 622560272 3688 True 3160.500 5251 98.814000 1 3579 2 chr4A.!!$R7 3578
2 TraesCS4A01G343100 chr4A 622473828 622477172 3344 True 2339.500 3620 98.793500 1 3579 2 chr4A.!!$R6 3578
3 TraesCS4A01G343100 chr4A 622438973 622443119 4146 True 1734.375 5083 99.019500 1 3579 4 chr4A.!!$R5 3578
4 TraesCS4A01G343100 chr4A 622351940 622352589 649 False 996.000 996 94.325000 2753 3402 1 chr4A.!!$F3 649
5 TraesCS4A01G343100 chr3A 51281726 51282373 647 True 1064.000 1064 96.308000 2754 3402 1 chr3A.!!$R1 648
6 TraesCS4A01G343100 chr5B 526646842 526647499 657 False 987.000 987 93.665000 2754 3415 1 chr5B.!!$F1 661
7 TraesCS4A01G343100 chr5B 536042545 536043200 655 True 987.000 987 93.788000 2754 3412 1 chr5B.!!$R2 658
8 TraesCS4A01G343100 chr5B 689646135 689647213 1078 False 500.000 861 91.324000 820 1578 2 chr5B.!!$F5 758
9 TraesCS4A01G343100 chr5B 689667901 689671377 3476 False 394.900 1042 90.982429 1 3579 7 chr5B.!!$F6 3578
10 TraesCS4A01G343100 chr5B 492131932 492134376 2444 False 259.000 279 84.596000 820 2693 2 chr5B.!!$F4 1873
11 TraesCS4A01G343100 chr7D 421832018 421832668 650 True 998.000 998 94.334000 2751 3402 1 chr7D.!!$R2 651
12 TraesCS4A01G343100 chr3B 368957892 368958541 649 False 990.000 990 94.172000 2753 3403 1 chr3B.!!$F1 650
13 TraesCS4A01G343100 chr5D 546566157 546567256 1099 False 445.500 741 90.375500 820 1578 2 chr5D.!!$F4 758

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
128 129 5.250982 TCAGTGTTCAAGTCCGAGACTATA 58.749 41.667 6.93 0.0 42.59 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 5866 2.966915 ACTCCCAACACACCTACTACA 58.033 47.619 0.0 0.0 0.0 2.74 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
128 129 5.250982 TCAGTGTTCAAGTCCGAGACTATA 58.749 41.667 6.93 0.0 42.59 1.31
602 1113 6.206438 TGCACTCATATGACATCTAGAGACTC 59.794 42.308 14.88 0.0 0.00 3.36
606 1117 5.942826 TCATATGACATCTAGAGACTCGCAT 59.057 40.000 0.00 0.0 0.00 4.73
1264 3932 4.803426 CTCGCGCGCCCTCTTCTT 62.803 66.667 27.95 0.0 0.00 2.52
2305 5539 2.297698 TTGTACGAGGAGGGACAAGA 57.702 50.000 0.00 0.0 0.00 3.02
2767 6005 1.127951 CGTGTGTAGGGATGAAAACGC 59.872 52.381 0.00 0.0 0.00 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.944386 AAAAATGCGAGCACGAGTGT 59.056 45.000 8.01 0.0 42.66 3.55
602 1113 5.949735 AGGTGTTTCTTAATGGTTTATGCG 58.050 37.500 0.00 0.0 0.00 4.73
606 1117 8.754991 TTGAGAAGGTGTTTCTTAATGGTTTA 57.245 30.769 0.00 0.0 46.12 2.01
810 1446 1.669795 CCTTTGCTGCCGGTCAAATTC 60.670 52.381 15.41 0.0 32.51 2.17
2632 5866 2.966915 ACTCCCAACACACCTACTACA 58.033 47.619 0.00 0.0 0.00 2.74
2767 6005 2.356553 TTCCGTCCGTTTCCGCTG 60.357 61.111 0.00 0.0 0.00 5.18


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

AutoCloner maintained by Alex Coulton.