Multiple sequence alignment - TraesCS3A01G030900

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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 TraesCS3A01G030900 chr3A 100.000 4742 0 0 1 4742 16857103 16861844 0.000000e+00 8757.0
1 TraesCS3A01G030900 chr3A 98.761 4682 29 3 62 4742 16808504 16813157 0.000000e+00 8298.0
2 TraesCS3A01G030900 chr3A 79.728 809 116 11 3005 3795 16872511 16873289 4.170000e-150 542.0
3 TraesCS3A01G030900 chr3A 94.762 210 9 2 3835 4044 76343839 76343632 4.580000e-85 326.0
4 TraesCS3A01G030900 chr3A 92.035 226 14 3 3821 4043 378490859 378490635 9.910000e-82 315.0
5 TraesCS3A01G030900 chr3A 86.131 137 15 3 2765 2900 16871622 16871755 1.380000e-30 145.0
6 TraesCS3A01G030900 chr3A 98.551 69 0 1 1 69 16808380 16808447 2.320000e-23 121.0
7 TraesCS3A01G030900 chr3A 92.537 67 4 1 4 70 481087829 481087764 1.400000e-15 95.3
8 TraesCS3A01G030900 chr6A 100.000 1803 0 0 2317 4119 76434163 76435965 0.000000e+00 3330.0
9 TraesCS3A01G030900 chr6A 94.762 210 7 2 3835 4044 471195167 471195372 1.650000e-84 324.0
10 TraesCS3A01G030900 chr3B 89.009 1110 74 24 1869 2943 14370385 14369289 0.000000e+00 1330.0
11 TraesCS3A01G030900 chr3B 90.273 915 67 6 2941 3835 14368758 14367846 0.000000e+00 1177.0
12 TraesCS3A01G030900 chr3B 86.202 674 91 2 1924 2596 26770119 26770791 0.000000e+00 728.0
13 TraesCS3A01G030900 chr3B 85.816 705 77 13 4047 4742 14367855 14367165 0.000000e+00 726.0
14 TraesCS3A01G030900 chr3B 93.370 362 21 3 838 1197 14370733 14370373 2.510000e-147 532.0
15 TraesCS3A01G030900 chr3B 93.798 258 13 1 62 316 285093 285350 7.440000e-103 385.0
16 TraesCS3A01G030900 chr3B 78.505 535 115 0 3183 3717 26778625 26779159 7.550000e-93 351.0
17 TraesCS3A01G030900 chr3B 95.789 95 4 0 650 744 421670595 421670501 2.290000e-33 154.0
18 TraesCS3A01G030900 chr1A 96.618 680 21 2 1191 1868 534652304 534651625 0.000000e+00 1127.0
19 TraesCS3A01G030900 chr1A 93.948 694 30 3 1191 1872 534651237 534650544 0.000000e+00 1038.0
20 TraesCS3A01G030900 chr1A 93.458 214 12 2 3835 4048 352839718 352839929 2.750000e-82 316.0
21 TraesCS3A01G030900 chr5D 87.517 729 86 3 1869 2596 413283998 413284722 0.000000e+00 837.0
22 TraesCS3A01G030900 chr5D 86.220 254 25 7 317 565 341596526 341596774 2.810000e-67 267.0
23 TraesCS3A01G030900 chr5D 85.338 266 26 9 313 574 100056887 100057143 3.640000e-66 263.0
24 TraesCS3A01G030900 chr5D 97.802 91 2 0 654 744 225253180 225253270 1.770000e-34 158.0
25 TraesCS3A01G030900 chr5D 96.739 92 3 0 653 744 301581312 301581403 2.290000e-33 154.0
26 TraesCS3A01G030900 chr5D 79.741 232 32 11 1651 1870 555355001 555355229 2.290000e-33 154.0
27 TraesCS3A01G030900 chr5B 87.243 729 88 3 1869 2596 498080623 498081347 0.000000e+00 826.0
28 TraesCS3A01G030900 chrUn 86.557 729 96 2 1869 2596 36612554 36613281 0.000000e+00 802.0
29 TraesCS3A01G030900 chrUn 86.557 729 96 2 1869 2596 301215041 301215768 0.000000e+00 802.0
30 TraesCS3A01G030900 chrUn 79.468 526 108 0 3192 3717 36595825 36595300 1.610000e-99 374.0
31 TraesCS3A01G030900 chr5A 86.575 730 91 5 1869 2596 525599776 525600500 0.000000e+00 798.0
32 TraesCS3A01G030900 chr5A 86.486 222 19 2 1656 1866 699803124 699803345 2.850000e-57 233.0
33 TraesCS3A01G030900 chr5A 86.486 222 19 2 1656 1866 699845888 699846109 2.850000e-57 233.0
34 TraesCS3A01G030900 chr5A 91.964 112 9 0 1247 1358 63879102 63878991 1.770000e-34 158.0
35 TraesCS3A01G030900 chr4B 85.675 733 94 8 1869 2594 642925026 642924298 0.000000e+00 761.0
36 TraesCS3A01G030900 chr4B 78.799 533 111 2 3182 3713 642923565 642923034 1.620000e-94 357.0
37 TraesCS3A01G030900 chr3D 81.413 807 107 17 3005 3795 10233783 10233004 1.870000e-173 619.0
38 TraesCS3A01G030900 chr3D 95.686 255 11 0 62 316 184141308 184141562 1.230000e-110 411.0
39 TraesCS3A01G030900 chr3D 89.024 246 19 4 317 558 336541163 336540922 9.980000e-77 298.0
40 TraesCS3A01G030900 chr3D 85.776 232 27 6 1283 1509 4936755 4936985 1.710000e-59 241.0
41 TraesCS3A01G030900 chr3D 84.066 182 19 5 2764 2944 10234659 10234487 2.940000e-37 167.0
42 TraesCS3A01G030900 chr3D 96.774 93 3 0 653 745 923117 923025 6.350000e-34 156.0
43 TraesCS3A01G030900 chr3D 80.275 218 30 9 1660 1866 97302671 97302456 8.220000e-33 152.0
44 TraesCS3A01G030900 chr7D 94.186 258 14 1 62 318 90838557 90838300 4.450000e-105 392.0
45 TraesCS3A01G030900 chr7D 85.075 268 27 11 1247 1509 634588222 634587963 1.310000e-65 261.0
46 TraesCS3A01G030900 chr7D 94.845 97 5 0 648 744 622185160 622185064 8.220000e-33 152.0
47 TraesCS3A01G030900 chr4A 94.163 257 13 1 62 316 552810884 552810628 1.600000e-104 390.0
48 TraesCS3A01G030900 chr4A 94.141 256 14 1 62 316 45107707 45107962 5.750000e-104 388.0
49 TraesCS3A01G030900 chr4A 92.830 265 17 2 56 318 613262495 613262759 2.680000e-102 383.0
50 TraesCS3A01G030900 chr4A 87.747 253 22 6 317 565 626320080 626319833 2.160000e-73 287.0
51 TraesCS3A01G030900 chr2B 93.822 259 13 2 62 317 23271793 23272051 2.070000e-103 387.0
52 TraesCS3A01G030900 chr2A 92.218 257 18 2 62 316 638304274 638304018 3.490000e-96 363.0
53 TraesCS3A01G030900 chr2A 94.737 209 10 1 3835 4043 35678295 35678502 1.650000e-84 324.0
54 TraesCS3A01G030900 chr2A 94.737 209 9 2 3835 4043 443920917 443921123 1.650000e-84 324.0
55 TraesCS3A01G030900 chr2A 94.286 210 11 1 3835 4044 519403790 519403998 2.130000e-83 320.0
56 TraesCS3A01G030900 chr6D 91.189 227 16 4 342 566 17303714 17303938 5.960000e-79 305.0
57 TraesCS3A01G030900 chr6D 88.182 220 12 10 1658 1866 15112307 15112523 2.830000e-62 250.0
58 TraesCS3A01G030900 chr6D 96.774 93 3 0 652 744 306876348 306876256 6.350000e-34 156.0
59 TraesCS3A01G030900 chr7A 87.815 238 23 4 333 566 509425608 509425843 1.680000e-69 274.0
60 TraesCS3A01G030900 chr1D 87.097 248 24 4 317 561 18776904 18776662 1.680000e-69 274.0
61 TraesCS3A01G030900 chr6B 85.882 255 26 5 317 567 715751823 715752071 3.640000e-66 263.0
62 TraesCS3A01G030900 chr2D 87.727 220 13 10 1658 1866 625907502 625907286 1.320000e-60 244.0
63 TraesCS3A01G030900 chr2D 87.727 220 13 10 1658 1866 625909670 625909454 1.320000e-60 244.0
64 TraesCS3A01G030900 chr2D 86.818 220 15 5 1658 1866 625908587 625908371 2.850000e-57 233.0
65 TraesCS3A01G030900 chr2D 95.876 97 3 1 652 747 263240594 263240498 6.350000e-34 156.0
66 TraesCS3A01G030900 chr2D 91.892 111 7 2 659 769 649821912 649821804 2.290000e-33 154.0
67 TraesCS3A01G030900 chr2D 95.238 42 0 1 1191 1232 167766817 167766856 1.100000e-06 65.8
68 TraesCS3A01G030900 chr4D 91.339 127 9 2 1232 1357 506043660 506043785 6.310000e-39 172.0
69 TraesCS3A01G030900 chr1B 89.764 127 11 1 1247 1373 19207090 19206966 1.370000e-35 161.0
70 TraesCS3A01G030900 chr1B 89.764 127 9 2 1248 1374 19209416 19209294 4.910000e-35 159.0


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 TraesCS3A01G030900 chr3A 16857103 16861844 4741 False 8757.000000 8757 100.0000 1 4742 1 chr3A.!!$F1 4741
1 TraesCS3A01G030900 chr3A 16808380 16813157 4777 False 4209.500000 8298 98.6560 1 4742 2 chr3A.!!$F2 4741
2 TraesCS3A01G030900 chr3A 16871622 16873289 1667 False 343.500000 542 82.9295 2765 3795 2 chr3A.!!$F3 1030
3 TraesCS3A01G030900 chr6A 76434163 76435965 1802 False 3330.000000 3330 100.0000 2317 4119 1 chr6A.!!$F1 1802
4 TraesCS3A01G030900 chr3B 14367165 14370733 3568 True 941.250000 1330 89.6170 838 4742 4 chr3B.!!$R2 3904
5 TraesCS3A01G030900 chr3B 26770119 26770791 672 False 728.000000 728 86.2020 1924 2596 1 chr3B.!!$F2 672
6 TraesCS3A01G030900 chr3B 26778625 26779159 534 False 351.000000 351 78.5050 3183 3717 1 chr3B.!!$F3 534
7 TraesCS3A01G030900 chr1A 534650544 534652304 1760 True 1082.500000 1127 95.2830 1191 1872 2 chr1A.!!$R1 681
8 TraesCS3A01G030900 chr5D 413283998 413284722 724 False 837.000000 837 87.5170 1869 2596 1 chr5D.!!$F5 727
9 TraesCS3A01G030900 chr5B 498080623 498081347 724 False 826.000000 826 87.2430 1869 2596 1 chr5B.!!$F1 727
10 TraesCS3A01G030900 chrUn 36612554 36613281 727 False 802.000000 802 86.5570 1869 2596 1 chrUn.!!$F1 727
11 TraesCS3A01G030900 chrUn 301215041 301215768 727 False 802.000000 802 86.5570 1869 2596 1 chrUn.!!$F2 727
12 TraesCS3A01G030900 chrUn 36595300 36595825 525 True 374.000000 374 79.4680 3192 3717 1 chrUn.!!$R1 525
13 TraesCS3A01G030900 chr5A 525599776 525600500 724 False 798.000000 798 86.5750 1869 2596 1 chr5A.!!$F1 727
14 TraesCS3A01G030900 chr4B 642923034 642925026 1992 True 559.000000 761 82.2370 1869 3713 2 chr4B.!!$R1 1844
15 TraesCS3A01G030900 chr3D 10233004 10234659 1655 True 393.000000 619 82.7395 2764 3795 2 chr3D.!!$R4 1031
16 TraesCS3A01G030900 chr2D 625907286 625909670 2384 True 240.333333 244 87.4240 1658 1866 3 chr2D.!!$R3 208

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
444 509 3.549471 CGCAAAACAAGTTTATGTGCACA 59.451 39.130 24.08 24.08 34.98 4.57 F
1185 1278 0.178068 TCTATTTCGAGGTGGCAGGC 59.822 55.000 0.00 0.00 0.00 4.85 F
1186 1279 1.153449 TATTTCGAGGTGGCAGGCG 60.153 57.895 0.00 0.00 0.00 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1530 0.682292 TGATGGACGTGTGCTAACCA 59.318 50.000 0.00 0.00 35.09 3.67 R
2074 2244 1.409064 TGATGACGATGCTGAGGTACC 59.591 52.381 2.73 2.73 0.00 3.34 R
4367 7199 8.997323 TCAAATATTTGGATTTGATTTTGCGTT 58.003 25.926 24.40 0.00 46.12 4.84 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
108 173 9.614792 AAACAAATTCCTGACAGTATATAGGAC 57.385 33.333 0.93 0.00 38.96 3.85
211 276 6.885922 ACCAGTCCTTAAGAATATGTGTACC 58.114 40.000 3.36 0.00 0.00 3.34
444 509 3.549471 CGCAAAACAAGTTTATGTGCACA 59.451 39.130 24.08 24.08 34.98 4.57
464 529 7.693951 GTGCACATAGAATGTCAAAATGTAGTC 59.306 37.037 13.17 0.00 42.70 2.59
608 673 7.362834 CCCCAAAATGAAAATGATTAAAAGGGC 60.363 37.037 0.00 0.00 0.00 5.19
642 707 8.094798 TCGAAGGCGATATTTTATTTGCTATT 57.905 30.769 0.00 0.00 42.51 1.73
683 748 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
1185 1278 0.178068 TCTATTTCGAGGTGGCAGGC 59.822 55.000 0.00 0.00 0.00 4.85
1186 1279 1.153449 TATTTCGAGGTGGCAGGCG 60.153 57.895 0.00 0.00 0.00 5.52
1187 1280 2.587322 TATTTCGAGGTGGCAGGCGG 62.587 60.000 0.00 0.00 0.00 6.13
1343 1437 1.202976 ACATTGTTTCTGCCTCAGCCT 60.203 47.619 0.00 0.00 38.69 4.58
1436 1530 2.616256 CCCATGCACACACACTCACTAT 60.616 50.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 360 1.528129 GAAAAGTGCCTGCAGCTACT 58.472 50.000 8.66 11.63 44.23 2.57
307 372 6.476380 ACATGGCATATAAAATGCGAAAAGTG 59.524 34.615 0.00 0.00 45.41 3.16
444 509 6.884832 TCCCGACTACATTTTGACATTCTAT 58.115 36.000 0.00 0.00 0.00 1.98
464 529 6.646240 ACAAAATTCTGACAAAATGATTCCCG 59.354 34.615 0.00 0.00 0.00 5.14
608 673 3.741029 TCGCCTTCGAGATGGAAAG 57.259 52.632 8.95 0.72 40.21 2.62
642 707 8.921205 GGAGGGAGTAGTAAATAATACTGTTCA 58.079 37.037 5.39 0.00 37.24 3.18
683 748 6.973229 ACTACAGTAGTGTCAAAAACGTTT 57.027 33.333 12.75 7.96 37.69 3.60
1189 1282 3.793144 GAGAAGCGGCGCCAACAG 61.793 66.667 30.40 11.41 0.00 3.16
1343 1437 2.859165 AGAATGAAAGAGGCCGTGAA 57.141 45.000 0.00 0.00 0.00 3.18
1436 1530 0.682292 TGATGGACGTGTGCTAACCA 59.318 50.000 0.00 0.00 35.09 3.67
2074 2244 1.409064 TGATGACGATGCTGAGGTACC 59.591 52.381 2.73 2.73 0.00 3.34
4367 7199 8.997323 TCAAATATTTGGATTTGATTTTGCGTT 58.003 25.926 24.40 0.00 46.12 4.84


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

AutoCloner maintained by Alex Coulton.