Multiple sequence alignment - TraesCS7A01G310400

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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 TraesCS7A01G310400 chr7A 100.000 2303 0 0 1 2303 439030398 439032700 0.000000e+00 4253
1 TraesCS7A01G310400 chr7A 94.878 1347 57 2 657 1991 639884927 639883581 0.000000e+00 2095
2 TraesCS7A01G310400 chr7A 96.420 419 14 1 1 418 639885382 639884964 0.000000e+00 689
3 TraesCS7A01G310400 chr5D 94.423 1847 86 13 457 2298 462907649 462909483 0.000000e+00 2824
4 TraesCS7A01G310400 chr1D 94.216 1850 90 10 457 2299 235547790 235545951 0.000000e+00 2808
5 TraesCS7A01G310400 chr1B 93.427 1856 87 15 457 2299 253825676 253823843 0.000000e+00 2719
6 TraesCS7A01G310400 chr1B 94.667 225 11 1 457 681 578103388 578103611 4.710000e-92 348
7 TraesCS7A01G310400 chr3D 97.177 1488 37 3 455 1940 143483568 143482084 0.000000e+00 2510
8 TraesCS7A01G310400 chr3D 97.381 420 11 0 1 420 143484848 143484429 0.000000e+00 715
9 TraesCS7A01G310400 chr3D 89.333 225 17 3 200 417 43023653 43023429 2.250000e-70 276
10 TraesCS7A01G310400 chr2B 92.905 1635 93 15 675 2299 13184003 13185624 0.000000e+00 2355
11 TraesCS7A01G310400 chr2B 95.858 169 5 1 252 420 13183389 13183555 2.920000e-69 272
12 TraesCS7A01G310400 chr2B 89.362 94 10 0 4 97 362585817 362585724 4.020000e-23 119
13 TraesCS7A01G310400 chr7D 94.179 1443 60 11 864 2299 635929327 635927902 0.000000e+00 2178
14 TraesCS7A01G310400 chr7D 94.737 228 11 1 457 684 635929552 635929326 1.010000e-93 353
15 TraesCS7A01G310400 chr2A 93.837 1444 76 7 861 2299 441110111 441111546 0.000000e+00 2161
16 TraesCS7A01G310400 chr2A 94.667 225 10 2 457 681 441109890 441110112 4.710000e-92 348
17 TraesCS7A01G310400 chr5B 93.568 1446 75 9 861 2301 89745418 89746850 0.000000e+00 2139
18 TraesCS7A01G310400 chr4A 93.060 1441 81 9 864 2298 281593802 281592375 0.000000e+00 2089
19 TraesCS7A01G310400 chr7B 95.030 1006 40 6 1297 2299 634824607 634825605 0.000000e+00 1572
20 TraesCS7A01G310400 chr7B 97.426 272 6 1 455 725 634824337 634824608 1.610000e-126 462
21 TraesCS7A01G310400 chr7B 90.722 97 9 0 1 97 593100224 593100320 1.860000e-26 130
22 TraesCS7A01G310400 chr6D 96.474 794 25 3 456 1247 298140111 298139319 0.000000e+00 1308
23 TraesCS7A01G310400 chr6D 95.024 422 19 1 1 420 298141394 298140973 0.000000e+00 662
24 TraesCS7A01G310400 chr3B 92.760 221 16 0 200 420 66955596 66955376 1.030000e-83 320
25 TraesCS7A01G310400 chr3A 91.628 215 18 0 200 414 55047643 55047429 4.810000e-77 298


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 TraesCS7A01G310400 chr7A 439030398 439032700 2302 False 4253.0 4253 100.0000 1 2303 1 chr7A.!!$F1 2302
1 TraesCS7A01G310400 chr7A 639883581 639885382 1801 True 1392.0 2095 95.6490 1 1991 2 chr7A.!!$R1 1990
2 TraesCS7A01G310400 chr5D 462907649 462909483 1834 False 2824.0 2824 94.4230 457 2298 1 chr5D.!!$F1 1841
3 TraesCS7A01G310400 chr1D 235545951 235547790 1839 True 2808.0 2808 94.2160 457 2299 1 chr1D.!!$R1 1842
4 TraesCS7A01G310400 chr1B 253823843 253825676 1833 True 2719.0 2719 93.4270 457 2299 1 chr1B.!!$R1 1842
5 TraesCS7A01G310400 chr3D 143482084 143484848 2764 True 1612.5 2510 97.2790 1 1940 2 chr3D.!!$R2 1939
6 TraesCS7A01G310400 chr2B 13183389 13185624 2235 False 1313.5 2355 94.3815 252 2299 2 chr2B.!!$F1 2047
7 TraesCS7A01G310400 chr7D 635927902 635929552 1650 True 1265.5 2178 94.4580 457 2299 2 chr7D.!!$R1 1842
8 TraesCS7A01G310400 chr2A 441109890 441111546 1656 False 1254.5 2161 94.2520 457 2299 2 chr2A.!!$F1 1842
9 TraesCS7A01G310400 chr5B 89745418 89746850 1432 False 2139.0 2139 93.5680 861 2301 1 chr5B.!!$F1 1440
10 TraesCS7A01G310400 chr4A 281592375 281593802 1427 True 2089.0 2089 93.0600 864 2298 1 chr4A.!!$R1 1434
11 TraesCS7A01G310400 chr7B 634824337 634825605 1268 False 1017.0 1572 96.2280 455 2299 2 chr7B.!!$F2 1844
12 TraesCS7A01G310400 chr6D 298139319 298141394 2075 True 985.0 1308 95.7490 1 1247 2 chr6D.!!$R1 1246

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
881 1716 1.864711 TGTCTTGGTTTCGAAGAAGCG 59.135 47.619 0.0 0.0 45.9 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 3001 0.031721 GCACCCGCGCTACTACTAAT 59.968 55.0 5.56 0.0 0.0 1.73 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
21 22 4.083862 GACGCCGGGCTCCTTCTT 62.084 66.667 18.34 0.00 0.00 2.52
34 35 1.961277 CTTCTTCGCAACCACCGCT 60.961 57.895 0.00 0.00 0.00 5.52
221 224 7.151999 TGTTGTCCGCATATTTATTGTTTCT 57.848 32.000 0.00 0.00 0.00 2.52
249 252 6.793680 GCTTTAGTGTATTTTAAAAGACGCGT 59.206 34.615 25.26 13.85 43.26 6.01
259 262 5.793023 TTAAAAGACGCGTATGCAAAAAC 57.207 34.783 13.97 0.00 42.97 2.43
452 750 9.659135 TTGGATATTGGATATTTTTGTGATCCT 57.341 29.630 0.00 0.00 39.98 3.24
568 1399 4.612264 AGCTTGCTTTTCCATGTTCATT 57.388 36.364 0.00 0.00 0.00 2.57
655 1486 9.818796 GCTGTAGAAAAGAATGACTTTAAAGAG 57.181 33.333 21.92 3.95 46.55 2.85
669 1500 9.607988 TGACTTTAAAGAGAATGTACTTTGTGA 57.392 29.630 21.92 0.00 37.03 3.58
812 1646 5.165911 GAGTATCTTGGTGTATTCGACGA 57.834 43.478 0.00 0.00 0.00 4.20
881 1716 1.864711 TGTCTTGGTTTCGAAGAAGCG 59.135 47.619 0.00 0.00 45.90 4.68
888 1723 2.289820 GGTTTCGAAGAAGCGGAAAGTT 59.710 45.455 0.00 0.00 45.90 2.66
1182 2022 2.837591 TCATCTTGAATTCCCTGGACGA 59.162 45.455 2.27 0.00 0.00 4.20
1313 2153 5.774498 ATGAAGGGTTGACTGAACTTTTC 57.226 39.130 0.00 0.00 34.66 2.29
1319 2162 4.584743 GGGTTGACTGAACTTTTCAAGGAT 59.415 41.667 0.00 0.00 39.58 3.24
1394 2237 7.386025 CGATCTCTGCCAATATGAATTTGACTA 59.614 37.037 0.00 0.00 0.00 2.59
1602 2446 7.277760 TGCAGCACACTGTTAATAGTACTATTG 59.722 37.037 30.16 19.11 46.30 1.90
1672 2527 1.359475 GGCGTAGAGGTGATCGACC 59.641 63.158 6.29 6.29 46.58 4.79
1785 2640 1.445410 CAGGTGATTTCGACGCCGA 60.445 57.895 0.00 0.00 43.96 5.54
1840 2695 1.817209 GCGAGAGGGAGGATTCGTT 59.183 57.895 0.00 0.00 35.61 3.85
1845 2700 2.236395 GAGAGGGAGGATTCGTTTCCAA 59.764 50.000 8.69 0.00 38.32 3.53
1873 2728 4.017808 TCTGAACTCCTAGCCTTGTAGAC 58.982 47.826 0.00 0.00 0.00 2.59
1999 2870 2.757868 TCTGTGAGTTGGTTTGGTTTGG 59.242 45.455 0.00 0.00 0.00 3.28
2006 2877 3.387699 AGTTGGTTTGGTTTGGAATGGAG 59.612 43.478 0.00 0.00 0.00 3.86
2007 2878 3.039252 TGGTTTGGTTTGGAATGGAGT 57.961 42.857 0.00 0.00 0.00 3.85
2079 2952 7.281549 CCTAAATTGTTAATAGTAGCGTGGGTT 59.718 37.037 0.00 0.00 0.00 4.11
2128 3001 5.105756 GGTTAGTAGTAGCGTGGGTTTTAGA 60.106 44.000 0.00 0.00 0.00 2.10
2211 3087 3.824414 ACGCGCTACTGCTAAAAATTT 57.176 38.095 5.73 0.00 36.97 1.82
2265 3142 3.426159 CCACGCTACTGGTATGCAAAAAG 60.426 47.826 0.00 0.00 0.00 2.27
2270 3150 2.539302 ACTGGTATGCAAAAAGCCCAT 58.461 42.857 0.00 0.00 44.83 4.00
2301 3181 7.609056 TGGTAGTGTTTTTCCTAGTAGTGATC 58.391 38.462 0.00 0.00 0.00 2.92
2302 3182 6.750963 GGTAGTGTTTTTCCTAGTAGTGATCG 59.249 42.308 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.302511 TGGTTGCGAAGAAGGAGCC 60.303 57.895 0.00 0.00 33.67 4.70
221 224 8.445493 GCGTCTTTTAAAATACACTAAAGCCTA 58.555 33.333 14.57 0.00 0.00 3.93
245 248 3.157510 ACGTATTGTTTTTGCATACGCG 58.842 40.909 3.53 3.53 42.77 6.01
249 252 9.678941 TTGTGAAATACGTATTGTTTTTGCATA 57.321 25.926 21.00 0.00 32.77 3.14
428 726 9.918630 CAAGGATCACAAAAATATCCAATATCC 57.081 33.333 0.00 0.00 41.44 2.59
429 727 9.918630 CCAAGGATCACAAAAATATCCAATATC 57.081 33.333 0.00 0.00 41.44 1.63
432 730 6.673537 ACCCAAGGATCACAAAAATATCCAAT 59.326 34.615 0.00 0.00 41.44 3.16
433 731 6.022315 ACCCAAGGATCACAAAAATATCCAA 58.978 36.000 0.00 0.00 41.44 3.53
437 735 7.738437 AATCACCCAAGGATCACAAAAATAT 57.262 32.000 0.00 0.00 0.00 1.28
444 742 3.181435 TGTCAAATCACCCAAGGATCACA 60.181 43.478 0.00 0.00 0.00 3.58
445 743 3.191371 GTGTCAAATCACCCAAGGATCAC 59.809 47.826 0.00 0.00 32.81 3.06
450 748 0.240945 GCGTGTCAAATCACCCAAGG 59.759 55.000 0.00 0.00 35.18 3.61
452 750 1.511318 CGGCGTGTCAAATCACCCAA 61.511 55.000 0.00 0.00 35.18 4.12
503 1334 6.569179 AAGGTTCAAAATGTAATGCTACGT 57.431 33.333 0.00 0.00 0.00 3.57
504 1335 9.567848 AATTAAGGTTCAAAATGTAATGCTACG 57.432 29.630 0.00 0.00 0.00 3.51
669 1500 9.685276 TCAAAGTTCCATGACATATAGAACATT 57.315 29.630 19.40 14.11 39.39 2.71
1055 1895 2.118313 TGCCATGAGTGAATGTGGAG 57.882 50.000 0.00 0.00 33.53 3.86
1110 1950 5.977489 TTTTCTTCTCGTCCAGATGTCTA 57.023 39.130 0.00 0.00 0.00 2.59
1182 2022 8.318412 ACAACTTCACCAAATTTAACCTTTTCT 58.682 29.630 0.00 0.00 0.00 2.52
1283 2123 6.566079 TCAGTCAACCCTTCATATGAATCT 57.434 37.500 18.26 1.68 33.01 2.40
1313 2153 4.202503 ACTGAAGTATATGGGGCATCCTTG 60.203 45.833 0.00 0.00 36.20 3.61
1319 2162 2.126882 AGCACTGAAGTATATGGGGCA 58.873 47.619 0.00 0.00 0.00 5.36
1602 2446 3.480185 CGCAAATTGCATTAGTTCAACGC 60.480 43.478 18.65 0.00 45.36 4.84
1626 2470 4.577283 TCGGGAAAGTGAAAACTTGTTAGG 59.423 41.667 0.00 0.00 0.00 2.69
1755 2610 3.742433 AATCACCTGGACGATCATCTC 57.258 47.619 0.00 0.00 0.00 2.75
1785 2640 1.079127 CCTCCACATCGGCGACTTT 60.079 57.895 13.76 0.00 33.14 2.66
1840 2695 0.599204 GAGTTCAGACGCCGTTGGAA 60.599 55.000 0.00 0.00 0.00 3.53
1873 2728 3.360867 ACAGACCACCTCTCTAGATGTG 58.639 50.000 8.05 8.05 39.41 3.21
2065 2938 5.410355 TCACTTTTAACCCACGCTACTAT 57.590 39.130 0.00 0.00 0.00 2.12
2079 2952 7.559170 CCTAACTACTAGTAGCCCTCACTTTTA 59.441 40.741 26.54 14.18 36.66 1.52
2128 3001 0.031721 GCACCCGCGCTACTACTAAT 59.968 55.000 5.56 0.00 0.00 1.73
2174 3047 0.798159 CGTTTTTACCCCACGCTACC 59.202 55.000 0.00 0.00 0.00 3.18
2265 3142 0.541863 ACACTACCAGTAGCATGGGC 59.458 55.000 4.72 0.00 45.25 5.36
2270 3150 4.699925 AGGAAAAACACTACCAGTAGCA 57.300 40.909 4.72 0.00 36.66 3.49


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

AutoCloner maintained by Alex Coulton.