Multiple sequence alignment - TraesCS4A01G041900

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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 TraesCS4A01G041900 chr4A 100.000 2462 0 0 1 2462 35352989 35355450 0.000000e+00 4547.0
1 TraesCS4A01G041900 chr5B 94.970 1809 64 10 3 1790 530189003 530190805 0.000000e+00 2811.0
2 TraesCS4A01G041900 chr5B 91.086 359 19 4 2102 2458 530190801 530191148 7.970000e-130 473.0
3 TraesCS4A01G041900 chr7A 91.770 1859 85 17 625 2459 721518412 721516598 0.000000e+00 2523.0
4 TraesCS4A01G041900 chr2D 86.554 1651 129 39 195 1806 29765610 29764014 0.000000e+00 1733.0
5 TraesCS4A01G041900 chr2D 90.110 910 62 6 451 1344 250284082 250284979 0.000000e+00 1157.0
6 TraesCS4A01G041900 chr2D 85.340 764 84 10 61 807 38765419 38764667 0.000000e+00 765.0
7 TraesCS4A01G041900 chr2D 82.561 820 95 24 808 1619 38764602 38763823 0.000000e+00 678.0
8 TraesCS4A01G041900 chr2D 88.325 394 24 13 1804 2189 250285462 250285841 1.040000e-123 453.0
9 TraesCS4A01G041900 chr2D 86.750 400 34 11 1804 2198 29763924 29763539 6.290000e-116 427.0
10 TraesCS4A01G041900 chr2D 85.464 399 44 12 1420 1807 250284978 250285373 1.060000e-108 403.0
11 TraesCS4A01G041900 chr2D 83.019 106 9 7 1803 1899 485086072 485085967 1.210000e-13 87.9
12 TraesCS4A01G041900 chr3A 86.985 1383 110 26 451 1807 746073523 746072185 0.000000e+00 1493.0
13 TraesCS4A01G041900 chr3A 87.237 760 76 9 71 811 741902270 741901513 0.000000e+00 846.0
14 TraesCS4A01G041900 chr3A 86.269 772 79 9 65 811 741032359 741033128 0.000000e+00 813.0
15 TraesCS4A01G041900 chr3A 87.981 416 28 12 1804 2211 746072096 746071695 2.870000e-129 472.0
16 TraesCS4A01G041900 chr3A 82.540 252 33 7 2207 2454 741036028 741036272 6.900000e-51 211.0
17 TraesCS4A01G041900 chr3A 82.203 236 31 7 2219 2450 741898549 741898321 2.500000e-45 193.0
18 TraesCS4A01G041900 chr1B 91.168 985 64 11 2 971 117709852 117710828 0.000000e+00 1315.0
19 TraesCS4A01G041900 chr1B 85.392 753 66 20 1066 1806 117710829 117711549 0.000000e+00 741.0
20 TraesCS4A01G041900 chr1B 88.293 410 33 11 1803 2206 117711638 117712038 6.160000e-131 477.0
21 TraesCS4A01G041900 chr3B 93.423 745 45 3 22 765 771525699 771526440 0.000000e+00 1101.0
22 TraesCS4A01G041900 chr4D 88.061 846 73 12 946 1780 90747759 90746931 0.000000e+00 977.0
23 TraesCS4A01G041900 chr4D 86.917 665 61 11 1803 2462 90746833 90746190 0.000000e+00 723.0
24 TraesCS4A01G041900 chrUn 85.993 871 94 12 946 1807 57096405 57095554 0.000000e+00 907.0
25 TraesCS4A01G041900 chrUn 80.971 1009 139 29 802 1777 316884003 316884991 0.000000e+00 750.0
26 TraesCS4A01G041900 chrUn 82.280 886 126 20 808 1682 380535115 380534250 0.000000e+00 737.0
27 TraesCS4A01G041900 chrUn 84.662 665 74 14 1803 2462 57095464 57094823 2.670000e-179 638.0
28 TraesCS4A01G041900 chrUn 84.420 552 60 16 1919 2459 316885191 316885727 1.010000e-143 520.0
29 TraesCS4A01G041900 chrUn 84.420 552 60 14 1919 2459 377404959 377404423 1.010000e-143 520.0
30 TraesCS4A01G041900 chr1D 88.934 741 75 5 22 759 319353786 319354522 0.000000e+00 907.0
31 TraesCS4A01G041900 chr1D 88.725 745 79 4 24 764 368539016 368539759 0.000000e+00 905.0
32 TraesCS4A01G041900 chr1D 82.423 1007 117 37 802 1777 368539868 368540845 0.000000e+00 824.0
33 TraesCS4A01G041900 chr1D 86.639 711 77 8 61 764 397375072 397374373 0.000000e+00 771.0
34 TraesCS4A01G041900 chr1D 81.835 545 57 19 1919 2447 368541010 368541528 1.050000e-113 420.0
35 TraesCS4A01G041900 chr7D 86.747 664 60 10 1803 2462 529366043 529366682 0.000000e+00 713.0
36 TraesCS4A01G041900 chr7D 82.075 106 10 8 1803 1899 94090942 94090837 5.640000e-12 82.4
37 TraesCS4A01G041900 chr6B 84.711 641 79 13 965 1599 313793693 313794320 7.480000e-175 623.0
38 TraesCS4A01G041900 chr3D 82.075 106 10 8 1803 1899 30036218 30036113 5.640000e-12 82.4
39 TraesCS4A01G041900 chr2A 82.828 99 10 4 1803 1894 3257066 3257164 5.640000e-12 82.4


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 TraesCS4A01G041900 chr4A 35352989 35355450 2461 False 4547.000000 4547 100.000000 1 2462 1 chr4A.!!$F1 2461
1 TraesCS4A01G041900 chr5B 530189003 530191148 2145 False 1642.000000 2811 93.028000 3 2458 2 chr5B.!!$F1 2455
2 TraesCS4A01G041900 chr7A 721516598 721518412 1814 True 2523.000000 2523 91.770000 625 2459 1 chr7A.!!$R1 1834
3 TraesCS4A01G041900 chr2D 29763539 29765610 2071 True 1080.000000 1733 86.652000 195 2198 2 chr2D.!!$R2 2003
4 TraesCS4A01G041900 chr2D 38763823 38765419 1596 True 721.500000 765 83.950500 61 1619 2 chr2D.!!$R3 1558
5 TraesCS4A01G041900 chr2D 250284082 250285841 1759 False 671.000000 1157 87.966333 451 2189 3 chr2D.!!$F1 1738
6 TraesCS4A01G041900 chr3A 746071695 746073523 1828 True 982.500000 1493 87.483000 451 2211 2 chr3A.!!$R2 1760
7 TraesCS4A01G041900 chr3A 741898321 741902270 3949 True 519.500000 846 84.720000 71 2450 2 chr3A.!!$R1 2379
8 TraesCS4A01G041900 chr3A 741032359 741036272 3913 False 512.000000 813 84.404500 65 2454 2 chr3A.!!$F1 2389
9 TraesCS4A01G041900 chr1B 117709852 117712038 2186 False 844.333333 1315 88.284333 2 2206 3 chr1B.!!$F1 2204
10 TraesCS4A01G041900 chr3B 771525699 771526440 741 False 1101.000000 1101 93.423000 22 765 1 chr3B.!!$F1 743
11 TraesCS4A01G041900 chr4D 90746190 90747759 1569 True 850.000000 977 87.489000 946 2462 2 chr4D.!!$R1 1516
12 TraesCS4A01G041900 chrUn 57094823 57096405 1582 True 772.500000 907 85.327500 946 2462 2 chrUn.!!$R3 1516
13 TraesCS4A01G041900 chrUn 380534250 380535115 865 True 737.000000 737 82.280000 808 1682 1 chrUn.!!$R2 874
14 TraesCS4A01G041900 chrUn 316884003 316885727 1724 False 635.000000 750 82.695500 802 2459 2 chrUn.!!$F1 1657
15 TraesCS4A01G041900 chrUn 377404423 377404959 536 True 520.000000 520 84.420000 1919 2459 1 chrUn.!!$R1 540
16 TraesCS4A01G041900 chr1D 319353786 319354522 736 False 907.000000 907 88.934000 22 759 1 chr1D.!!$F1 737
17 TraesCS4A01G041900 chr1D 397374373 397375072 699 True 771.000000 771 86.639000 61 764 1 chr1D.!!$R1 703
18 TraesCS4A01G041900 chr1D 368539016 368541528 2512 False 716.333333 905 84.327667 24 2447 3 chr1D.!!$F2 2423
19 TraesCS4A01G041900 chr7D 529366043 529366682 639 False 713.000000 713 86.747000 1803 2462 1 chr7D.!!$F1 659
20 TraesCS4A01G041900 chr6B 313793693 313794320 627 False 623.000000 623 84.711000 965 1599 1 chr6B.!!$F1 634

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
996 1184 2.292845 GCAGGAGAATCAATTAGCAGCC 59.707 50.0 0.0 0.0 36.25 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 3762 1.135083 TCCTTTCGCATCGAGTCCTTC 60.135 52.381 0.0 0.0 37.14 3.46 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
583 603 7.701539 ACATGGTAAAAAGTGATGCTATCAA 57.298 32.000 0.00 0.00 41.69 2.57
667 696 8.854614 AGTGAAATAAACAGACAAGCTTCTAT 57.145 30.769 0.00 0.00 0.00 1.98
815 988 8.576442 CAATTTCTACTACCCAATTTGACACTT 58.424 33.333 0.00 0.00 0.00 3.16
896 1076 5.129634 TGTGCCAGTTTGAGACTATTTGAA 58.870 37.500 0.00 0.00 36.65 2.69
996 1184 2.292845 GCAGGAGAATCAATTAGCAGCC 59.707 50.000 0.00 0.00 36.25 4.85
1013 1201 0.107831 GCCGGCATGTACCCTCAATA 59.892 55.000 24.80 0.00 0.00 1.90
1124 1319 2.548920 GGATGGATTCCTCGTGGATGAC 60.549 54.545 7.11 1.34 42.81 3.06
1142 1338 0.900182 ACAGCAGATGACGAGGACCA 60.900 55.000 0.00 0.00 0.00 4.02
1149 1345 1.194781 ATGACGAGGACCAGTGGCTT 61.195 55.000 9.78 0.00 0.00 4.35
1238 1439 2.683465 GGAGGAAGGGATGGCTGCA 61.683 63.158 0.50 0.00 0.00 4.41
1449 1684 4.460683 GGCGTGGTATGCGGTGGA 62.461 66.667 0.00 0.00 0.00 4.02
1452 1687 1.373590 GCGTGGTATGCGGTGGATTT 61.374 55.000 0.00 0.00 0.00 2.17
1453 1688 1.942677 CGTGGTATGCGGTGGATTTA 58.057 50.000 0.00 0.00 0.00 1.40
1506 2947 7.831955 AGGAGAGAGAGGAGATAAAAGGATAA 58.168 38.462 0.00 0.00 0.00 1.75
1542 2984 2.597505 CGCAGCCGTTCGATTTAATCAG 60.598 50.000 5.76 0.00 0.00 2.90
1545 2987 4.766007 CAGCCGTTCGATTTAATCAGATG 58.234 43.478 5.76 0.00 0.00 2.90
1950 3586 9.774671 ACATTGTTTGTAATGGCAAGATGCACA 62.775 37.037 4.57 0.77 40.42 4.57
2013 3650 1.327303 TGTGGCCATCACCTTGAAAC 58.673 50.000 9.72 0.00 45.48 2.78
2040 3681 8.676401 TGAATGTTCATACATGATACCTTGTTG 58.324 33.333 0.00 0.00 44.14 3.33
2114 3762 2.223971 CCCCCGCAACTAGTACACATAG 60.224 54.545 0.00 0.00 0.00 2.23
2246 4148 6.408869 TGTGCTATGTGAGAGATTCATCAAA 58.591 36.000 0.00 0.00 38.29 2.69
2459 4374 2.577300 CATGTCAAACGACAAGGACG 57.423 50.000 0.00 0.00 46.16 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.492011 GCCACTCTGAAATTTTTGCACTG 59.508 43.478 0.00 0.00 0.00 3.66
490 508 5.251932 TCACCTTTTACCAAGTATCCATCCA 59.748 40.000 0.00 0.00 0.00 3.41
561 581 6.663093 TGGTTGATAGCATCACTTTTTACCAT 59.337 34.615 11.09 0.00 37.62 3.55
996 1184 2.288825 ACGATATTGAGGGTACATGCCG 60.289 50.000 0.00 0.00 0.00 5.69
1013 1201 4.427394 GCAAGATGCGAGGACGAT 57.573 55.556 0.00 0.00 42.66 3.73
1124 1319 0.179116 CTGGTCCTCGTCATCTGCTG 60.179 60.000 0.00 0.00 0.00 4.41
1142 1338 3.771160 CCCGCGGTAGAAGCCACT 61.771 66.667 26.12 0.00 0.00 4.00
1238 1439 4.541648 ATCTAGCCGGGGCCGTCT 62.542 66.667 2.18 0.00 43.17 4.18
1351 1559 2.125269 GTAGGTCGCCCACGCAAT 60.125 61.111 0.00 0.00 39.84 3.56
1449 1684 1.305201 CGCACGCCTACCCATTAAAT 58.695 50.000 0.00 0.00 0.00 1.40
1452 1687 1.153529 CACGCACGCCTACCCATTA 60.154 57.895 0.00 0.00 0.00 1.90
1453 1688 2.435938 CACGCACGCCTACCCATT 60.436 61.111 0.00 0.00 0.00 3.16
1542 2984 1.262151 ACACGTTGTAACCGTTGCATC 59.738 47.619 2.68 2.01 36.17 3.91
1545 2987 0.651551 TCACACGTTGTAACCGTTGC 59.348 50.000 0.00 0.00 36.17 4.17
1733 3249 6.695429 TCACAAGTGCATAAAAATATTGGCA 58.305 32.000 0.00 0.00 0.00 4.92
2013 3650 8.442632 ACAAGGTATCATGTATGAACATTCAG 57.557 34.615 0.00 0.00 44.07 3.02
2096 3744 4.097437 TCCTTCTATGTGTACTAGTTGCGG 59.903 45.833 0.00 0.00 0.00 5.69
2114 3762 1.135083 TCCTTTCGCATCGAGTCCTTC 60.135 52.381 0.00 0.00 37.14 3.46
2319 4234 2.691409 TGTACAGTTAGGCATGGCTC 57.309 50.000 26.96 12.64 0.00 4.70


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

AutoCloner maintained by Alex Coulton.