Multiple sequence alignment - TraesCS7A01G402600

Loading Multiple Alignment...

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 TraesCS7A01G402600 chr7A 100.000 2357 0 0 1 2357 582112545 582110189 0.000000e+00 4353
1 TraesCS7A01G402600 chr7A 73.845 1342 332 18 4 1335 51423586 51422254 1.250000e-142 516
2 TraesCS7A01G402600 chr5A 95.545 1751 78 0 1 1751 455337662 455335912 0.000000e+00 2802
3 TraesCS7A01G402600 chr3A 90.346 1357 129 2 4 1359 712704142 712702787 0.000000e+00 1779
4 TraesCS7A01G402600 chr3A 91.212 330 28 1 1422 1750 712702774 712702445 4.620000e-122 448
5 TraesCS7A01G402600 chr3A 76.963 573 91 28 1199 1749 595281336 595281889 2.960000e-74 289
6 TraesCS7A01G402600 chr7D 84.088 1766 249 20 2 1754 577855704 577853958 0.000000e+00 1676
7 TraesCS7A01G402600 chr7D 92.611 609 38 5 1749 2357 511073258 511072657 0.000000e+00 869
8 TraesCS7A01G402600 chr7D 91.030 602 47 5 1153 1750 158992799 158993397 0.000000e+00 806
9 TraesCS7A01G402600 chr2A 82.909 1767 267 26 2 1751 650490741 650492489 0.000000e+00 1557
10 TraesCS7A01G402600 chr5B 79.887 1770 296 43 11 1753 17684772 17683036 0.000000e+00 1242
11 TraesCS7A01G402600 chr5B 86.441 177 17 6 1579 1751 63735754 63735581 1.110000e-43 187
12 TraesCS7A01G402600 chr7B 79.508 1342 266 4 1 1338 87119160 87120496 0.000000e+00 946
13 TraesCS7A01G402600 chr7B 92.092 607 41 5 1751 2357 539916975 539916376 0.000000e+00 848
14 TraesCS7A01G402600 chr7B 94.382 534 24 3 1749 2280 539920067 539919538 0.000000e+00 815
15 TraesCS7A01G402600 chr6B 78.074 1350 281 12 3 1344 450591052 450592394 0.000000e+00 839
16 TraesCS7A01G402600 chr1D 77.066 1343 287 21 2 1334 431769669 431771000 0.000000e+00 754
17 TraesCS7A01G402600 chr4B 76.760 1364 296 20 2 1355 623488470 623489822 0.000000e+00 743
18 TraesCS7A01G402600 chr6A 74.112 1352 321 26 1 1333 456593231 456594572 4.460000e-147 531
19 TraesCS7A01G402600 chr6D 82.955 264 34 8 1498 1753 84476419 84476159 6.550000e-56 228


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 TraesCS7A01G402600 chr7A 582110189 582112545 2356 True 4353.0 4353 100.000 1 2357 1 chr7A.!!$R2 2356
1 TraesCS7A01G402600 chr7A 51422254 51423586 1332 True 516.0 516 73.845 4 1335 1 chr7A.!!$R1 1331
2 TraesCS7A01G402600 chr5A 455335912 455337662 1750 True 2802.0 2802 95.545 1 1751 1 chr5A.!!$R1 1750
3 TraesCS7A01G402600 chr3A 712702445 712704142 1697 True 1113.5 1779 90.779 4 1750 2 chr3A.!!$R1 1746
4 TraesCS7A01G402600 chr3A 595281336 595281889 553 False 289.0 289 76.963 1199 1749 1 chr3A.!!$F1 550
5 TraesCS7A01G402600 chr7D 577853958 577855704 1746 True 1676.0 1676 84.088 2 1754 1 chr7D.!!$R2 1752
6 TraesCS7A01G402600 chr7D 511072657 511073258 601 True 869.0 869 92.611 1749 2357 1 chr7D.!!$R1 608
7 TraesCS7A01G402600 chr7D 158992799 158993397 598 False 806.0 806 91.030 1153 1750 1 chr7D.!!$F1 597
8 TraesCS7A01G402600 chr2A 650490741 650492489 1748 False 1557.0 1557 82.909 2 1751 1 chr2A.!!$F1 1749
9 TraesCS7A01G402600 chr5B 17683036 17684772 1736 True 1242.0 1242 79.887 11 1753 1 chr5B.!!$R1 1742
10 TraesCS7A01G402600 chr7B 87119160 87120496 1336 False 946.0 946 79.508 1 1338 1 chr7B.!!$F1 1337
11 TraesCS7A01G402600 chr7B 539916376 539920067 3691 True 831.5 848 93.237 1749 2357 2 chr7B.!!$R1 608
12 TraesCS7A01G402600 chr6B 450591052 450592394 1342 False 839.0 839 78.074 3 1344 1 chr6B.!!$F1 1341
13 TraesCS7A01G402600 chr1D 431769669 431771000 1331 False 754.0 754 77.066 2 1334 1 chr1D.!!$F1 1332
14 TraesCS7A01G402600 chr4B 623488470 623489822 1352 False 743.0 743 76.760 2 1355 1 chr4B.!!$F1 1353
15 TraesCS7A01G402600 chr6A 456593231 456594572 1341 False 531.0 531 74.112 1 1333 1 chr6A.!!$F1 1332

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
660 670 0.182775 ACAAGTCTCAACCCCACACC 59.817 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 5267 0.824109 TGAGTGGACACATCGATCCC 59.176 55.0 5.14 0.0 33.69 3.85 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
52 53 2.407090 CTCAAGTGCTGTGAATCGTGA 58.593 47.619 0.00 0.00 0.00 4.35
191 196 5.457140 TGGATAAACATCACAAGCGTTTTC 58.543 37.500 0.00 0.00 34.78 2.29
219 224 0.804364 GAACATGATGGACGCAAGCA 59.196 50.000 0.00 0.00 45.62 3.91
290 295 2.359249 GGCCTGGGGGTGAAAGATTTAT 60.359 50.000 0.00 0.00 34.45 1.40
342 347 1.067071 GTGGTGGAAGTTAGAGACCCG 60.067 57.143 0.00 0.00 0.00 5.28
413 418 1.692411 GGTGGCATCCATTAAGACCC 58.308 55.000 0.00 0.00 35.28 4.46
642 652 5.365619 TGTGGAGGTGAACTTCTTTAGAAC 58.634 41.667 0.00 0.00 0.00 3.01
660 670 0.182775 ACAAGTCTCAACCCCACACC 59.817 55.000 0.00 0.00 0.00 4.16
683 695 0.324943 CGAACAATGGAGGGAGGTGT 59.675 55.000 0.00 0.00 0.00 4.16
1057 1075 2.303175 GTTGCCCTAACAACTTGTGGA 58.697 47.619 0.00 0.00 45.20 4.02
1067 1085 7.013846 CCCTAACAACTTGTGGAAATACTTTGA 59.986 37.037 0.00 0.00 0.00 2.69
1109 1127 4.324563 CCCTGATGGTGAGAGGTTTTACAT 60.325 45.833 0.00 0.00 0.00 2.29
1116 1134 4.583073 GGTGAGAGGTTTTACATGTTTGGT 59.417 41.667 2.30 0.00 0.00 3.67
1121 1139 4.542697 AGGTTTTACATGTTTGGTCTGGT 58.457 39.130 2.30 0.00 0.00 4.00
1148 1166 1.220749 GCTGGGCGATGTGGAACTA 59.779 57.895 0.00 0.00 38.04 2.24
1408 1431 1.606737 GCAGTGCTTCTTCTTCTCCGT 60.607 52.381 8.18 0.00 0.00 4.69
1409 1432 2.760374 CAGTGCTTCTTCTTCTCCGTT 58.240 47.619 0.00 0.00 0.00 4.44
1412 1435 2.872858 GTGCTTCTTCTTCTCCGTTTGT 59.127 45.455 0.00 0.00 0.00 2.83
1429 1452 2.949177 TGTGCTTCTTTTGGCTCCTA 57.051 45.000 0.00 0.00 0.00 2.94
1541 1566 1.771255 GGTGGCCTATCTGAATCAGGT 59.229 52.381 10.71 5.74 31.51 4.00
1693 1733 6.476378 TCTAGGTTTCCTGGATCTTTCAAAG 58.524 40.000 0.00 0.00 36.21 2.77
1736 1776 4.478686 AGAGTAATGGAAAGGGGTAATGCT 59.521 41.667 0.00 0.00 0.00 3.79
1848 4978 7.917505 AGTTGTAGCTTTCAGAAATTCAACTTG 59.082 33.333 18.66 1.79 39.48 3.16
1855 4985 9.122613 GCTTTCAGAAATTCAACTTGATTACTC 57.877 33.333 0.00 0.00 0.00 2.59
1858 4988 8.018677 TCAGAAATTCAACTTGATTACTCGAC 57.981 34.615 0.00 0.00 0.00 4.20
1861 4991 6.727824 AATTCAACTTGATTACTCGACCAG 57.272 37.500 0.00 0.00 0.00 4.00
1870 5000 6.961360 TGATTACTCGACCAGTTAGATCAT 57.039 37.500 0.00 0.00 36.43 2.45
1883 5013 9.019656 ACCAGTTAGATCATATCTGATGACTAC 57.980 37.037 0.00 0.00 42.27 2.73
1888 5018 4.505313 TCATATCTGATGACTACGGTGC 57.495 45.455 0.00 0.00 0.00 5.01
1900 5030 1.812571 CTACGGTGCTTTGCCTCAAAT 59.187 47.619 0.00 0.00 32.70 2.32
1901 5031 1.904287 ACGGTGCTTTGCCTCAAATA 58.096 45.000 0.00 0.00 32.70 1.40
1902 5032 2.235016 ACGGTGCTTTGCCTCAAATAA 58.765 42.857 0.00 0.00 32.70 1.40
1903 5033 2.030274 ACGGTGCTTTGCCTCAAATAAC 60.030 45.455 0.00 0.00 32.70 1.89
1904 5034 2.228822 CGGTGCTTTGCCTCAAATAACT 59.771 45.455 0.00 0.00 32.70 2.24
1905 5035 3.578688 GGTGCTTTGCCTCAAATAACTG 58.421 45.455 0.00 0.00 32.70 3.16
1954 5084 1.922570 TCGCTTCAACTATTCCGCTC 58.077 50.000 0.00 0.00 0.00 5.03
1964 5094 1.000496 CTATTCCGCTCGGGTAGTTCC 60.000 57.143 8.59 0.00 37.00 3.62
2036 5166 6.283544 TCATGGCTTGCAATATTTTTCTCA 57.716 33.333 0.00 0.00 0.00 3.27
2055 5185 2.629137 TCATGCATGGCTCAACAAAAGT 59.371 40.909 25.97 0.00 0.00 2.66
2056 5186 3.069872 TCATGCATGGCTCAACAAAAGTT 59.930 39.130 25.97 0.00 0.00 2.66
2171 5301 4.400884 GTCCACTCACACTGATCATAGAGT 59.599 45.833 11.45 11.45 36.84 3.24
2178 5308 5.948758 TCACACTGATCATAGAGTCTGACTT 59.051 40.000 12.27 4.93 0.00 3.01
2209 5339 8.657387 TGAGATAGCTATTTGTCTTAGCCTAT 57.343 34.615 7.87 0.00 42.46 2.57
2212 5342 9.762381 AGATAGCTATTTGTCTTAGCCTATAGT 57.238 33.333 7.87 0.00 42.46 2.12
2267 5397 8.579850 TCATTTTAGTTGCTTAGGACATCAAT 57.420 30.769 0.00 0.00 0.00 2.57
2304 5434 1.445871 TCTCGCGTACTAGACTTGCA 58.554 50.000 5.77 0.00 0.00 4.08
2345 5475 4.697352 GTCATGTGCTAAACCAAGTGAGAT 59.303 41.667 0.00 0.00 0.00 2.75
2347 5477 2.813754 TGTGCTAAACCAAGTGAGATGC 59.186 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 196 2.681848 GTCCATCATGTTCTTGCCAGAG 59.318 50.000 0.00 0.00 0.00 3.35
219 224 5.030147 TGGACCATTTGACTAGGTGATACT 58.970 41.667 0.00 0.00 35.36 2.12
290 295 7.764443 GGTGAGCAGACTTATATTCTGTTTACA 59.236 37.037 17.40 9.69 40.42 2.41
342 347 1.305213 TCCTGCCAAAGCCCATTCC 60.305 57.895 0.00 0.00 38.69 3.01
599 609 3.461085 ACATTCTCCCTGAACATAGCCAT 59.539 43.478 0.00 0.00 37.52 4.40
606 616 1.630369 CCTCCACATTCTCCCTGAACA 59.370 52.381 0.00 0.00 37.52 3.18
642 652 0.474184 AGGTGTGGGGTTGAGACTTG 59.526 55.000 0.00 0.00 0.00 3.16
660 670 1.137872 CCTCCCTCCATTGTTCGAGAG 59.862 57.143 0.00 0.00 0.00 3.20
683 695 0.824109 CAGTCCCGCACCTTATCTCA 59.176 55.000 0.00 0.00 0.00 3.27
772 787 6.712547 GGGGTCTCTCCAAGTATTCATAAATG 59.287 42.308 0.00 0.00 38.11 2.32
1057 1075 9.691362 GTAACAATGACACCAATCAAAGTATTT 57.309 29.630 0.00 0.00 40.26 1.40
1067 1085 3.333680 AGGGAGGTAACAATGACACCAAT 59.666 43.478 9.82 0.00 41.41 3.16
1109 1127 2.039818 TAACGCAACCAGACCAAACA 57.960 45.000 0.00 0.00 0.00 2.83
1116 1134 0.676466 CCCAGCATAACGCAACCAGA 60.676 55.000 0.00 0.00 46.13 3.86
1121 1139 1.451207 ATCGCCCAGCATAACGCAA 60.451 52.632 0.00 0.00 46.13 4.85
1148 1166 8.717821 TGAATTCGAAGATTCTTTTGTTACGAT 58.282 29.630 3.35 0.00 35.04 3.73
1351 1369 3.947834 CACCTGAACTTCAACTTTCACCT 59.052 43.478 0.00 0.00 0.00 4.00
1408 1431 2.387757 AGGAGCCAAAAGAAGCACAAA 58.612 42.857 0.00 0.00 0.00 2.83
1409 1432 2.071778 AGGAGCCAAAAGAAGCACAA 57.928 45.000 0.00 0.00 0.00 3.33
1412 1435 3.371595 GGGTATAGGAGCCAAAAGAAGCA 60.372 47.826 0.00 0.00 45.84 3.91
1429 1452 4.250305 GCGCCATGACCGGGGTAT 62.250 66.667 6.32 0.00 40.99 2.73
1541 1566 6.825610 ACCAGAAAAATTCAGCCATTACAAA 58.174 32.000 0.00 0.00 0.00 2.83
1641 1677 3.131326 CGGGTTCAACGCATCACTA 57.869 52.632 5.33 0.00 0.00 2.74
1768 1808 6.180472 TCAACTGACAAGAAGGAAAACTCTT 58.820 36.000 0.00 0.00 0.00 2.85
1848 4978 8.952278 AGATATGATCTAACTGGTCGAGTAATC 58.048 37.037 0.00 0.00 38.00 1.75
1855 4985 7.026562 GTCATCAGATATGATCTAACTGGTCG 58.973 42.308 0.00 0.00 37.58 4.79
1858 4988 8.180920 CGTAGTCATCAGATATGATCTAACTGG 58.819 40.741 15.02 7.25 37.58 4.00
1861 4991 7.965655 CACCGTAGTCATCAGATATGATCTAAC 59.034 40.741 0.00 0.00 37.58 2.34
1870 5000 4.682787 CAAAGCACCGTAGTCATCAGATA 58.317 43.478 0.00 0.00 0.00 1.98
1883 5013 2.228822 AGTTATTTGAGGCAAAGCACCG 59.771 45.455 0.00 0.00 36.76 4.94
1888 5018 2.497273 CCCCCAGTTATTTGAGGCAAAG 59.503 50.000 0.00 0.00 36.76 2.77
1978 5108 1.881252 CGTTCCTATGGCCGTTCGG 60.881 63.158 0.77 4.53 0.00 4.30
1981 5111 1.219935 GGACGTTCCTATGGCCGTT 59.780 57.895 0.77 0.00 32.12 4.44
1982 5112 2.897972 GGACGTTCCTATGGCCGT 59.102 61.111 1.35 1.35 33.97 5.68
1994 5124 4.088056 TGAGCTAGCTAATCTAGGACGT 57.912 45.455 19.38 0.00 43.95 4.34
2036 5166 3.756933 AACTTTTGTTGAGCCATGCAT 57.243 38.095 0.00 0.00 41.77 3.96
2095 5225 3.887621 AGCTTGGTAATCGTCTTGCTA 57.112 42.857 0.00 0.00 0.00 3.49
2097 5227 3.426292 GGAAAGCTTGGTAATCGTCTTGC 60.426 47.826 0.00 0.00 0.00 4.01
2137 5267 0.824109 TGAGTGGACACATCGATCCC 59.176 55.000 5.14 0.00 33.69 3.85
2171 5301 2.692557 GCTATCTCAGCCTGAAGTCAGA 59.307 50.000 9.95 0.00 45.23 3.27
2183 5313 6.991938 AGGCTAAGACAAATAGCTATCTCAG 58.008 40.000 6.72 0.00 44.13 3.35
2267 5397 8.867112 ACGCGAGATCTAACAAGAAATATTAA 57.133 30.769 15.93 0.00 0.00 1.40
2304 5434 2.371841 TGACCTTGTACATCCTTGCACT 59.628 45.455 0.00 0.00 0.00 4.40
2314 5444 4.069304 GGTTTAGCACATGACCTTGTACA 58.931 43.478 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.