Multiple sequence alignment - TraesCS2D01G318000

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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 TraesCS2D01G318000 chr2D 100.000 2147 0 0 1 2147 407452693 407454839 0.000000e+00 3965.0
1 TraesCS2D01G318000 chr2D 92.124 838 33 18 1 806 447798560 447797724 0.000000e+00 1151.0
2 TraesCS2D01G318000 chr2D 94.847 718 19 4 802 1518 622711560 622712260 0.000000e+00 1105.0
3 TraesCS2D01G318000 chr2D 95.131 534 24 2 1 533 303753931 303754463 0.000000e+00 841.0
4 TraesCS2D01G318000 chr2D 95.131 534 25 1 1 533 447816626 447816093 0.000000e+00 841.0
5 TraesCS2D01G318000 chr2D 97.388 268 7 0 535 802 407440177 407440444 6.980000e-125 457.0
6 TraesCS2D01G318000 chr2D 96.043 278 8 3 524 801 300646204 300646478 1.170000e-122 449.0
7 TraesCS2D01G318000 chr2D 95.053 283 13 1 524 806 447816070 447815789 5.440000e-121 444.0
8 TraesCS2D01G318000 chr3A 96.381 1271 46 0 877 2147 152000825 151999555 0.000000e+00 2093.0
9 TraesCS2D01G318000 chr3A 96.703 819 18 3 1336 2147 697840804 697841620 0.000000e+00 1354.0
10 TraesCS2D01G318000 chr3A 95.870 460 19 0 934 1393 570198475 570198016 0.000000e+00 745.0
11 TraesCS2D01G318000 chr3A 97.849 93 2 0 2055 2147 11774632 11774540 6.130000e-36 161.0
12 TraesCS2D01G318000 chr4A 94.803 1347 61 2 802 2147 407814874 407816212 0.000000e+00 2091.0
13 TraesCS2D01G318000 chr4A 94.664 581 29 1 933 1513 657666627 657666049 0.000000e+00 900.0
14 TraesCS2D01G318000 chr4A 94.624 93 5 0 2055 2147 324858124 324858216 6.180000e-31 145.0
15 TraesCS2D01G318000 chr4A 93.548 93 6 0 2055 2147 416574109 416574017 2.870000e-29 139.0
16 TraesCS2D01G318000 chr4D 98.553 760 9 1 1388 2147 328701246 328700489 0.000000e+00 1341.0
17 TraesCS2D01G318000 chr4D 95.781 640 16 4 535 1173 328704405 328703776 0.000000e+00 1022.0
18 TraesCS2D01G318000 chr4D 97.749 533 12 0 1 533 328704970 328704438 0.000000e+00 918.0
19 TraesCS2D01G318000 chr4D 88.406 69 3 1 1449 1517 46139496 46139433 6.350000e-11 78.7
20 TraesCS2D01G318000 chr1A 97.030 707 20 1 1441 2147 16474745 16474040 0.000000e+00 1188.0
21 TraesCS2D01G318000 chr1A 95.207 459 22 0 935 1393 564808215 564807757 0.000000e+00 726.0
22 TraesCS2D01G318000 chr1A 97.101 345 10 0 1720 2064 564807538 564807194 1.100000e-162 582.0
23 TraesCS2D01G318000 chr1A 91.703 229 17 1 1747 1973 413888367 413888595 1.240000e-82 316.0
24 TraesCS2D01G318000 chr1A 95.652 69 3 0 1449 1517 570974829 570974761 6.260000e-21 111.0
25 TraesCS2D01G318000 chr6A 93.987 765 45 1 1383 2147 360195012 360195775 0.000000e+00 1157.0
26 TraesCS2D01G318000 chr6A 94.611 334 17 1 1514 1846 58340068 58340401 1.140000e-142 516.0
27 TraesCS2D01G318000 chr6A 94.982 279 14 0 1786 2064 41138591 41138313 2.530000e-119 438.0
28 TraesCS2D01G318000 chr6A 93.548 279 18 0 1786 2064 41190876 41190598 1.190000e-112 416.0
29 TraesCS2D01G318000 chr6A 97.059 34 1 0 1720 1753 41138617 41138584 8.280000e-05 58.4
30 TraesCS2D01G318000 chrUn 92.428 832 25 13 1 801 230383847 230383023 0.000000e+00 1153.0
31 TraesCS2D01G318000 chrUn 92.428 832 25 13 1 801 380710050 380709226 0.000000e+00 1153.0
32 TraesCS2D01G318000 chrUn 92.308 832 26 13 1 801 380683545 380682721 0.000000e+00 1147.0
33 TraesCS2D01G318000 chr7D 91.957 833 35 9 1 802 519074339 519075170 0.000000e+00 1138.0
34 TraesCS2D01G318000 chr7D 96.422 531 19 0 3 533 250991797 250991267 0.000000e+00 876.0
35 TraesCS2D01G318000 chr7D 94.221 571 20 3 805 1374 475101114 475100556 0.000000e+00 859.0
36 TraesCS2D01G318000 chr7D 95.455 88 4 0 1430 1517 475097455 475097368 7.990000e-30 141.0
37 TraesCS2D01G318000 chr7B 95.332 707 32 1 1441 2147 346799476 346800181 0.000000e+00 1122.0
38 TraesCS2D01G318000 chr7B 96.248 533 18 1 1513 2043 47936054 47935522 0.000000e+00 872.0
39 TraesCS2D01G318000 chr7B 96.774 93 3 0 2055 2147 62055738 62055830 2.850000e-34 156.0
40 TraesCS2D01G318000 chr3D 87.112 838 61 24 1 801 295905952 295905125 0.000000e+00 905.0
41 TraesCS2D01G318000 chr3D 89.796 539 49 5 1 537 578778806 578778272 0.000000e+00 686.0
42 TraesCS2D01G318000 chr3D 89.662 532 53 2 1 530 336043199 336043730 0.000000e+00 676.0
43 TraesCS2D01G318000 chr2B 96.209 554 18 3 1513 2064 795317409 795316857 0.000000e+00 904.0
44 TraesCS2D01G318000 chr2B 97.849 93 2 0 2055 2147 795316574 795316482 6.130000e-36 161.0
45 TraesCS2D01G318000 chr2A 95.668 554 21 3 1513 2064 762079974 762080526 0.000000e+00 887.0
46 TraesCS2D01G318000 chr2A 95.879 461 19 0 933 1393 121688158 121688618 0.000000e+00 747.0
47 TraesCS2D01G318000 chr2A 95.445 461 21 0 933 1393 736664475 736664935 0.000000e+00 736.0
48 TraesCS2D01G318000 chr2A 97.849 93 2 0 2055 2147 762080809 762080901 6.130000e-36 161.0
49 TraesCS2D01G318000 chr6B 95.118 553 25 2 1513 2064 310605584 310605033 0.000000e+00 870.0
50 TraesCS2D01G318000 chr5D 86.124 836 75 26 1 799 562547735 562548566 0.000000e+00 863.0
51 TraesCS2D01G318000 chr5D 96.328 463 15 1 1513 1973 290838081 290838543 0.000000e+00 760.0
52 TraesCS2D01G318000 chr5D 96.763 278 7 2 524 801 499899292 499899567 1.500000e-126 462.0
53 TraesCS2D01G318000 chr5D 100.000 63 0 0 1981 2043 290839442 290839504 1.350000e-22 117.0
54 TraesCS2D01G318000 chr1D 94.600 537 29 0 1 537 78575689 78575153 0.000000e+00 832.0
55 TraesCS2D01G318000 chr1D 97.026 269 8 0 535 803 64809399 64809667 9.030000e-124 453.0
56 TraesCS2D01G318000 chr1D 95.714 280 11 1 523 802 334886936 334886658 1.170000e-122 449.0
57 TraesCS2D01G318000 chr5A 94.839 465 19 4 1513 1973 13166454 13166917 0.000000e+00 721.0
58 TraesCS2D01G318000 chr5A 94.130 460 24 2 1517 1973 699172785 699172326 0.000000e+00 697.0
59 TraesCS2D01G318000 chr5A 96.774 93 3 0 2055 2147 568230766 568230674 2.850000e-34 156.0
60 TraesCS2D01G318000 chr6D 90.977 532 46 2 1 530 113001314 113001845 0.000000e+00 715.0
61 TraesCS2D01G318000 chr6D 95.760 283 11 1 524 806 86306182 86306463 2.510000e-124 455.0
62 TraesCS2D01G318000 chr5B 93.548 93 5 1 2055 2147 670356178 670356087 1.030000e-28 137.0
63 TraesCS2D01G318000 chr5B 95.652 69 3 0 1449 1517 236414965 236415033 6.260000e-21 111.0


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 TraesCS2D01G318000 chr2D 407452693 407454839 2146 False 3965.000000 3965 100.0000 1 2147 1 chr2D.!!$F4 2146
1 TraesCS2D01G318000 chr2D 447797724 447798560 836 True 1151.000000 1151 92.1240 1 806 1 chr2D.!!$R1 805
2 TraesCS2D01G318000 chr2D 622711560 622712260 700 False 1105.000000 1105 94.8470 802 1518 1 chr2D.!!$F5 716
3 TraesCS2D01G318000 chr2D 303753931 303754463 532 False 841.000000 841 95.1310 1 533 1 chr2D.!!$F2 532
4 TraesCS2D01G318000 chr2D 447815789 447816626 837 True 642.500000 841 95.0920 1 806 2 chr2D.!!$R2 805
5 TraesCS2D01G318000 chr3A 151999555 152000825 1270 True 2093.000000 2093 96.3810 877 2147 1 chr3A.!!$R2 1270
6 TraesCS2D01G318000 chr3A 697840804 697841620 816 False 1354.000000 1354 96.7030 1336 2147 1 chr3A.!!$F1 811
7 TraesCS2D01G318000 chr4A 407814874 407816212 1338 False 2091.000000 2091 94.8030 802 2147 1 chr4A.!!$F2 1345
8 TraesCS2D01G318000 chr4A 657666049 657666627 578 True 900.000000 900 94.6640 933 1513 1 chr4A.!!$R2 580
9 TraesCS2D01G318000 chr4D 328700489 328704970 4481 True 1093.666667 1341 97.3610 1 2147 3 chr4D.!!$R2 2146
10 TraesCS2D01G318000 chr1A 16474040 16474745 705 True 1188.000000 1188 97.0300 1441 2147 1 chr1A.!!$R1 706
11 TraesCS2D01G318000 chr1A 564807194 564808215 1021 True 654.000000 726 96.1540 935 2064 2 chr1A.!!$R3 1129
12 TraesCS2D01G318000 chr6A 360195012 360195775 763 False 1157.000000 1157 93.9870 1383 2147 1 chr6A.!!$F2 764
13 TraesCS2D01G318000 chrUn 230383023 230383847 824 True 1153.000000 1153 92.4280 1 801 1 chrUn.!!$R1 800
14 TraesCS2D01G318000 chrUn 380709226 380710050 824 True 1153.000000 1153 92.4280 1 801 1 chrUn.!!$R3 800
15 TraesCS2D01G318000 chrUn 380682721 380683545 824 True 1147.000000 1147 92.3080 1 801 1 chrUn.!!$R2 800
16 TraesCS2D01G318000 chr7D 519074339 519075170 831 False 1138.000000 1138 91.9570 1 802 1 chr7D.!!$F1 801
17 TraesCS2D01G318000 chr7D 250991267 250991797 530 True 876.000000 876 96.4220 3 533 1 chr7D.!!$R1 530
18 TraesCS2D01G318000 chr7D 475097368 475101114 3746 True 500.000000 859 94.8380 805 1517 2 chr7D.!!$R2 712
19 TraesCS2D01G318000 chr7B 346799476 346800181 705 False 1122.000000 1122 95.3320 1441 2147 1 chr7B.!!$F2 706
20 TraesCS2D01G318000 chr7B 47935522 47936054 532 True 872.000000 872 96.2480 1513 2043 1 chr7B.!!$R1 530
21 TraesCS2D01G318000 chr3D 295905125 295905952 827 True 905.000000 905 87.1120 1 801 1 chr3D.!!$R1 800
22 TraesCS2D01G318000 chr3D 578778272 578778806 534 True 686.000000 686 89.7960 1 537 1 chr3D.!!$R2 536
23 TraesCS2D01G318000 chr3D 336043199 336043730 531 False 676.000000 676 89.6620 1 530 1 chr3D.!!$F1 529
24 TraesCS2D01G318000 chr2B 795316482 795317409 927 True 532.500000 904 97.0290 1513 2147 2 chr2B.!!$R1 634
25 TraesCS2D01G318000 chr2A 762079974 762080901 927 False 524.000000 887 96.7585 1513 2147 2 chr2A.!!$F3 634
26 TraesCS2D01G318000 chr6B 310605033 310605584 551 True 870.000000 870 95.1180 1513 2064 1 chr6B.!!$R1 551
27 TraesCS2D01G318000 chr5D 562547735 562548566 831 False 863.000000 863 86.1240 1 799 1 chr5D.!!$F2 798
28 TraesCS2D01G318000 chr5D 290838081 290839504 1423 False 438.500000 760 98.1640 1513 2043 2 chr5D.!!$F3 530
29 TraesCS2D01G318000 chr1D 78575153 78575689 536 True 832.000000 832 94.6000 1 537 1 chr1D.!!$R1 536
30 TraesCS2D01G318000 chr6D 113001314 113001845 531 False 715.000000 715 90.9770 1 530 1 chr6D.!!$F2 529

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
53 54 0.337082 TCCGGGATCCTCTACAACCA 59.663 55.0 12.58 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 7340 0.17668 GGAAGCTCGAATCAGGCTGA 59.823 55.0 21.19 21.19 36.37 4.26 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
53 54 0.337082 TCCGGGATCCTCTACAACCA 59.663 55.000 12.58 0.00 0.00 3.67
89 90 7.628234 AGATTCCATGTCAAAGATAACACTCT 58.372 34.615 0.00 0.00 0.00 3.24
111 113 8.262227 ACTCTACGGATGACATTATAAAACCAA 58.738 33.333 0.00 0.00 0.00 3.67
150 152 3.493129 CGATCAAGGTGACTGAAACGAAA 59.507 43.478 0.00 0.00 42.68 3.46
202 205 2.305343 AGATGAAAGCAAGAGCCAGAGT 59.695 45.455 0.00 0.00 43.56 3.24
314 317 5.312708 CCTGACCTATACCTCCTACCTAAGA 59.687 48.000 0.00 0.00 0.00 2.10
346 349 1.902938 AAGCAAAGAGGTTCAGGAGC 58.097 50.000 0.00 0.00 30.75 4.70
680 718 2.439883 GGCTCCGAGACGTAGGGT 60.440 66.667 0.00 0.00 0.00 4.34
761 799 3.267031 AGCTAGGACCTTGCCTTTACATT 59.733 43.478 22.23 0.61 39.50 2.71
768 808 5.254115 GACCTTGCCTTTACATTCTTACCT 58.746 41.667 0.00 0.00 0.00 3.08
833 874 3.017442 GCAAGGTGAAGGGGAGATTTAC 58.983 50.000 0.00 0.00 0.00 2.01
834 875 3.308473 GCAAGGTGAAGGGGAGATTTACT 60.308 47.826 0.00 0.00 0.00 2.24
835 876 4.811063 GCAAGGTGAAGGGGAGATTTACTT 60.811 45.833 0.00 0.00 0.00 2.24
836 877 4.576330 AGGTGAAGGGGAGATTTACTTG 57.424 45.455 0.00 0.00 0.00 3.16
837 878 3.017442 GGTGAAGGGGAGATTTACTTGC 58.983 50.000 0.00 0.00 0.00 4.01
838 879 3.308473 GGTGAAGGGGAGATTTACTTGCT 60.308 47.826 0.00 0.00 0.00 3.91
839 880 4.336280 GTGAAGGGGAGATTTACTTGCTT 58.664 43.478 0.00 0.00 0.00 3.91
840 881 5.497474 GTGAAGGGGAGATTTACTTGCTTA 58.503 41.667 0.00 0.00 0.00 3.09
938 979 2.956987 CCTGCCTCCTTTGCAACG 59.043 61.111 0.00 0.00 38.46 4.10
1156 1197 1.001974 TCGTGGGGTGAATCTCACTTG 59.998 52.381 6.74 0.00 46.19 3.16
1767 7268 2.335712 CGCTCCTCCTTTTGCCCAC 61.336 63.158 0.00 0.00 0.00 4.61
1839 7340 3.471680 GTGCTCTGTTTCTTCTCAGGTT 58.528 45.455 0.00 0.00 33.13 3.50
2046 8447 2.221169 TCATCTGAACCACACTTGCAC 58.779 47.619 0.00 0.00 0.00 4.57
2060 8461 6.238731 CCACACTTGCACTTTTAAATCTCTGA 60.239 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.091545 ACATGGAATCTTTGGCGTGATT 58.908 40.909 0.00 0.00 35.83 2.57
89 90 7.171848 CCGATTGGTTTTATAATGTCATCCGTA 59.828 37.037 0.00 0.00 0.00 4.02
111 113 4.948847 TGATCGATTCAGAAATGACCGAT 58.051 39.130 0.00 11.88 37.88 4.18
314 317 4.080638 CCTCTTTGCTTCTAGGACAAGGAT 60.081 45.833 5.88 0.00 30.34 3.24
346 349 1.557832 TCGTTGGGTCCCCTCTATTTG 59.442 52.381 5.13 0.00 36.94 2.32
548 584 1.231068 CCCAGCCAGCCCACATTAT 59.769 57.895 0.00 0.00 0.00 1.28
680 718 2.565834 CCCTTCTCGGAGGAAGTAACAA 59.434 50.000 4.96 0.00 40.56 2.83
761 799 4.942944 TGACAGTAGAATGGGAGGTAAGA 58.057 43.478 0.00 0.00 0.00 2.10
768 808 5.827756 TCTAAGTCTGACAGTAGAATGGGA 58.172 41.667 10.88 0.00 0.00 4.37
833 874 1.063174 GCGGATGAGCAAGTAAGCAAG 59.937 52.381 0.00 0.00 36.85 4.01
834 875 1.086696 GCGGATGAGCAAGTAAGCAA 58.913 50.000 0.00 0.00 36.85 3.91
835 876 0.250234 AGCGGATGAGCAAGTAAGCA 59.750 50.000 0.00 0.00 40.15 3.91
836 877 0.933796 GAGCGGATGAGCAAGTAAGC 59.066 55.000 0.00 0.00 40.15 3.09
837 878 2.593346 AGAGCGGATGAGCAAGTAAG 57.407 50.000 0.00 0.00 40.15 2.34
838 879 3.002791 CAAAGAGCGGATGAGCAAGTAA 58.997 45.455 0.00 0.00 40.15 2.24
839 880 2.233676 TCAAAGAGCGGATGAGCAAGTA 59.766 45.455 0.00 0.00 40.15 2.24
840 881 1.002430 TCAAAGAGCGGATGAGCAAGT 59.998 47.619 0.00 0.00 40.15 3.16
1156 1197 3.072330 GGATTCAGAAGGGAGGATTCCTC 59.928 52.174 22.44 22.44 45.84 3.71
1767 7268 8.616076 CAGAGTACATTGCCTAGGAAAATAAAG 58.384 37.037 14.75 2.81 0.00 1.85
1839 7340 0.176680 GGAAGCTCGAATCAGGCTGA 59.823 55.000 21.19 21.19 36.37 4.26
2046 8447 8.077836 ACGTTGACTCTTCAGAGATTTAAAAG 57.922 34.615 10.93 3.11 44.74 2.27
2060 8461 1.664306 GGGGTCGACGTTGACTCTT 59.336 57.895 30.23 0.00 39.40 2.85


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

AutoCloner maintained by Alex Coulton.