Multiple sequence alignment - TraesCS7B01G186100

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 TraesCS7B01G186100 chr7B 100.000 2423 0 0 1 2423 304999954 305002376 0.000000e+00 4475
1 TraesCS7B01G186100 chr4B 99.183 1469 12 0 1 1469 654022305 654020837 0.000000e+00 2647
2 TraesCS7B01G186100 chr4B 97.079 1472 39 2 1 1469 659610786 659612256 0.000000e+00 2477
3 TraesCS7B01G186100 chr4B 96.596 1469 46 2 1 1469 259079338 259077874 0.000000e+00 2433
4 TraesCS7B01G186100 chr5A 99.047 1469 14 0 1 1469 423144511 423145979 0.000000e+00 2636
5 TraesCS7B01G186100 chr2A 98.911 1469 16 0 1 1469 40336553 40335085 0.000000e+00 2625
6 TraesCS7B01G186100 chr2B 98.434 1469 20 1 1 1469 750327822 750329287 0.000000e+00 2582
7 TraesCS7B01G186100 chr2B 97.686 1469 33 1 1 1469 704736848 704738315 0.000000e+00 2523
8 TraesCS7B01G186100 chrUn 97.549 1469 36 0 1 1469 304964335 304965803 0.000000e+00 2514
9 TraesCS7B01G186100 chr3B 97.481 1469 37 0 1 1469 788712701 788714169 0.000000e+00 2508
10 TraesCS7B01G186100 chr7D 89.364 771 72 5 1489 2250 309499667 309498898 0.000000e+00 961
11 TraesCS7B01G186100 chr7D 91.209 182 13 3 2245 2423 309496205 309496024 6.690000e-61 244
12 TraesCS7B01G186100 chr7A 90.866 635 45 9 1800 2423 372195178 372194546 0.000000e+00 839


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 TraesCS7B01G186100 chr7B 304999954 305002376 2422 False 4475.0 4475 100.0000 1 2423 1 chr7B.!!$F1 2422
1 TraesCS7B01G186100 chr4B 654020837 654022305 1468 True 2647.0 2647 99.1830 1 1469 1 chr4B.!!$R2 1468
2 TraesCS7B01G186100 chr4B 659610786 659612256 1470 False 2477.0 2477 97.0790 1 1469 1 chr4B.!!$F1 1468
3 TraesCS7B01G186100 chr4B 259077874 259079338 1464 True 2433.0 2433 96.5960 1 1469 1 chr4B.!!$R1 1468
4 TraesCS7B01G186100 chr5A 423144511 423145979 1468 False 2636.0 2636 99.0470 1 1469 1 chr5A.!!$F1 1468
5 TraesCS7B01G186100 chr2A 40335085 40336553 1468 True 2625.0 2625 98.9110 1 1469 1 chr2A.!!$R1 1468
6 TraesCS7B01G186100 chr2B 750327822 750329287 1465 False 2582.0 2582 98.4340 1 1469 1 chr2B.!!$F2 1468
7 TraesCS7B01G186100 chr2B 704736848 704738315 1467 False 2523.0 2523 97.6860 1 1469 1 chr2B.!!$F1 1468
8 TraesCS7B01G186100 chrUn 304964335 304965803 1468 False 2514.0 2514 97.5490 1 1469 1 chrUn.!!$F1 1468
9 TraesCS7B01G186100 chr3B 788712701 788714169 1468 False 2508.0 2508 97.4810 1 1469 1 chr3B.!!$F1 1468
10 TraesCS7B01G186100 chr7D 309496024 309499667 3643 True 602.5 961 90.2865 1489 2423 2 chr7D.!!$R1 934
11 TraesCS7B01G186100 chr7A 372194546 372195178 632 True 839.0 839 90.8660 1800 2423 1 chr7A.!!$R1 623

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
881 885 5.755409 TCTGACTTGGCTATTTCAGGTAA 57.245 39.13 8.13 0.0 36.84 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1725 0.331616 TCATCGTCTCAGGACCTCCA 59.668 55.0 0.0 0.0 39.15 3.86 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
324 325 5.851720 TCAACCAAAGATATTTTGCAGCAA 58.148 33.333 2.83 2.83 0.00 3.91
478 479 8.565416 GTGATTCAGATGAAGATGAAATGCATA 58.435 33.333 0.00 0.00 38.80 3.14
881 885 5.755409 TCTGACTTGGCTATTTCAGGTAA 57.245 39.130 8.13 0.00 36.84 2.85
1220 1225 3.008485 AGCGAGTTCTTTCAAATCTCCCT 59.992 43.478 0.00 0.00 0.00 4.20
1469 1474 1.000274 GCGCCTTCCTTGTGTTCAAAT 60.000 47.619 0.00 0.00 32.87 2.32
1470 1475 2.545742 GCGCCTTCCTTGTGTTCAAATT 60.546 45.455 0.00 0.00 32.87 1.82
1471 1476 3.716601 CGCCTTCCTTGTGTTCAAATTT 58.283 40.909 0.00 0.00 32.87 1.82
1472 1477 4.119136 CGCCTTCCTTGTGTTCAAATTTT 58.881 39.130 0.00 0.00 32.87 1.82
1473 1478 4.570369 CGCCTTCCTTGTGTTCAAATTTTT 59.430 37.500 0.00 0.00 32.87 1.94
1510 1515 7.615757 AGTTTGCAAGTAATAAAGAAGGGCTAT 59.384 33.333 0.00 0.00 0.00 2.97
1527 1532 7.530426 AGGGCTATTTAATTGCTCCAATTAG 57.470 36.000 7.57 3.32 43.92 1.73
1537 1542 2.423185 TGCTCCAATTAGTGCGAAATGG 59.577 45.455 0.00 0.00 0.00 3.16
1539 1544 3.242870 GCTCCAATTAGTGCGAAATGGAG 60.243 47.826 18.59 18.59 43.15 3.86
1555 1560 6.403636 CGAAATGGAGAATAGTGTTTTGGGAG 60.404 42.308 0.00 0.00 0.00 4.30
1583 1588 3.947196 TGCATCCAACTGAATCCACATAC 59.053 43.478 0.00 0.00 0.00 2.39
1588 1593 3.426159 CCAACTGAATCCACATACGTTGC 60.426 47.826 0.00 0.00 31.53 4.17
1593 1598 5.237127 ACTGAATCCACATACGTTGCATATG 59.763 40.000 0.00 0.00 36.32 1.78
1594 1599 4.514816 TGAATCCACATACGTTGCATATGG 59.485 41.667 4.56 0.00 34.83 2.74
1596 1601 4.674281 TCCACATACGTTGCATATGGTA 57.326 40.909 4.56 0.00 34.83 3.25
1652 1659 7.055667 ACACTTCTCGGATAATGTACATCAT 57.944 36.000 9.23 0.00 38.57 2.45
1653 1660 7.500992 ACACTTCTCGGATAATGTACATCATT 58.499 34.615 9.23 0.00 46.82 2.57
1681 1688 8.345565 CAAAGAATAGTGTAGTTGCAACTTCTT 58.654 33.333 35.20 28.94 40.37 2.52
1686 1693 5.126067 AGTGTAGTTGCAACTTCTTGTCAT 58.874 37.500 35.20 12.09 40.37 3.06
1689 1696 5.764686 TGTAGTTGCAACTTCTTGTCATGAT 59.235 36.000 35.20 10.63 40.37 2.45
1693 1700 5.366829 TGCAACTTCTTGTCATGATGAAG 57.633 39.130 22.87 22.87 40.97 3.02
1694 1701 5.065235 TGCAACTTCTTGTCATGATGAAGA 58.935 37.500 27.44 21.30 39.17 2.87
1704 1711 5.563592 TGTCATGATGAAGAGGATGTTGTT 58.436 37.500 0.00 0.00 0.00 2.83
1718 1725 2.665165 TGTTGTTCATGGCCACTTCTT 58.335 42.857 8.16 0.00 0.00 2.52
1719 1726 2.361757 TGTTGTTCATGGCCACTTCTTG 59.638 45.455 8.16 1.02 0.00 3.02
1741 1748 1.134068 AGGTCCTGAGACGATGATCGA 60.134 52.381 22.88 0.00 43.74 3.59
1763 1771 1.062880 TCGTTTTTGTGCCGTCAACTC 59.937 47.619 0.00 0.00 0.00 3.01
1780 1788 0.809241 CTCGAATGAGCTGGACCTGC 60.809 60.000 15.18 15.18 34.96 4.85
1781 1789 1.817099 CGAATGAGCTGGACCTGCC 60.817 63.158 18.87 11.37 37.10 4.85
1785 1793 4.704833 GAGCTGGACCTGCCGCAA 62.705 66.667 18.87 0.00 40.66 4.85
1791 1799 3.050275 GACCTGCCGCAAGTGGAC 61.050 66.667 0.00 0.00 0.00 4.02
1838 1846 3.070018 CTGAAGATGAAGTTTGTCGGCT 58.930 45.455 0.00 0.00 0.00 5.52
1840 1848 1.813513 AGATGAAGTTTGTCGGCTGG 58.186 50.000 0.00 0.00 0.00 4.85
1875 1883 3.891366 CAGGGGAGTTTTTCAGATGTTGT 59.109 43.478 0.00 0.00 0.00 3.32
1965 1973 0.610232 GGAGCTCAACATGGCAAGGT 60.610 55.000 17.19 0.00 0.00 3.50
1968 1976 0.675633 GCTCAACATGGCAAGGTTGT 59.324 50.000 25.10 9.86 45.88 3.32
1992 2000 5.262588 TCTGCTTCCAAAGAAAGAAAACC 57.737 39.130 0.00 0.00 0.00 3.27
2025 2033 2.562738 GGGCACTTCAAACCAATAAGCT 59.437 45.455 0.00 0.00 0.00 3.74
2094 2104 5.926542 CCTTTCTGACAAGATGAACGAGTTA 59.073 40.000 0.00 0.00 30.72 2.24
2100 2110 6.925211 TGACAAGATGAACGAGTTAATCTCT 58.075 36.000 14.40 5.17 39.32 3.10
2105 2115 2.666508 TGAACGAGTTAATCTCTTGCGC 59.333 45.455 0.00 0.00 40.75 6.09
2107 2117 3.777465 ACGAGTTAATCTCTTGCGCTA 57.223 42.857 9.73 0.00 40.75 4.26
2108 2118 4.308899 ACGAGTTAATCTCTTGCGCTAT 57.691 40.909 9.73 0.00 40.75 2.97
2125 2139 3.986572 CGCTATGAGTGCTTTCTATCCAG 59.013 47.826 0.00 0.00 0.00 3.86
2203 2217 2.962421 AGAGGAAGCCACTACTGCTATC 59.038 50.000 0.00 0.00 38.34 2.08
2255 4968 2.037251 GTGTCTTGGGAGTACTTGCTCA 59.963 50.000 0.00 0.00 37.24 4.26
2273 4986 1.031571 CAAGCTGCTTCGGGCCATAA 61.032 55.000 12.82 0.00 40.92 1.90
2277 4990 1.017387 CTGCTTCGGGCCATAAGTTC 58.983 55.000 4.39 0.00 40.92 3.01
2331 5045 1.037493 TATGCACCGTATCTTCCGCT 58.963 50.000 0.00 0.00 0.00 5.52
2347 5061 2.037251 TCCGCTATCAGCCTTAATGGTC 59.963 50.000 0.00 0.00 38.18 4.02
2356 5070 2.025037 AGCCTTAATGGTCTTGATGGCA 60.025 45.455 0.00 0.00 41.33 4.92
2359 5073 3.624777 CTTAATGGTCTTGATGGCACCT 58.375 45.455 0.00 0.00 0.00 4.00
2360 5074 2.610438 AATGGTCTTGATGGCACCTT 57.390 45.000 0.00 0.00 0.00 3.50
2361 5075 1.843368 ATGGTCTTGATGGCACCTTG 58.157 50.000 0.00 0.00 0.00 3.61
2402 5118 3.161450 GCGAGGGGCCCACTATCA 61.161 66.667 27.72 0.00 34.80 2.15
2408 5124 0.107165 GGGGCCCACTATCACAGTTC 60.107 60.000 26.86 0.00 34.26 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.018751 CACTATGTTGGACAATAAGGTGATCG 60.019 42.308 9.84 0.00 0.00 3.69
324 325 3.508793 CCATGAATTTGTGCTTCCAGACT 59.491 43.478 0.00 0.00 0.00 3.24
881 885 8.129211 GCCAAGAAGCGTCTTAATATATTTTGT 58.871 33.333 14.72 0.00 42.45 2.83
893 897 3.334583 TCTTATGCCAAGAAGCGTCTT 57.665 42.857 9.25 9.25 45.36 3.01
1478 1483 9.872757 CTTCTTTATTACTTGCAAACTAACGAA 57.127 29.630 0.00 5.06 0.00 3.85
1479 1484 8.500773 CCTTCTTTATTACTTGCAAACTAACGA 58.499 33.333 0.00 0.00 0.00 3.85
1480 1485 7.749126 CCCTTCTTTATTACTTGCAAACTAACG 59.251 37.037 0.00 0.00 0.00 3.18
1481 1486 7.541091 GCCCTTCTTTATTACTTGCAAACTAAC 59.459 37.037 0.00 0.00 0.00 2.34
1482 1487 7.450323 AGCCCTTCTTTATTACTTGCAAACTAA 59.550 33.333 0.00 0.00 0.00 2.24
1483 1488 6.946009 AGCCCTTCTTTATTACTTGCAAACTA 59.054 34.615 0.00 0.00 0.00 2.24
1484 1489 5.775195 AGCCCTTCTTTATTACTTGCAAACT 59.225 36.000 0.00 0.00 0.00 2.66
1485 1490 6.025749 AGCCCTTCTTTATTACTTGCAAAC 57.974 37.500 0.00 0.00 0.00 2.93
1486 1491 7.954666 ATAGCCCTTCTTTATTACTTGCAAA 57.045 32.000 0.00 0.00 0.00 3.68
1487 1492 7.954666 AATAGCCCTTCTTTATTACTTGCAA 57.045 32.000 0.00 0.00 0.00 4.08
1510 1515 5.888691 TCGCACTAATTGGAGCAATTAAA 57.111 34.783 11.43 0.00 43.01 1.52
1518 1523 4.542662 CTCCATTTCGCACTAATTGGAG 57.457 45.455 14.77 14.77 44.37 3.86
1527 1532 4.946784 AACACTATTCTCCATTTCGCAC 57.053 40.909 0.00 0.00 0.00 5.34
1537 1542 5.904362 ATTGCTCCCAAAACACTATTCTC 57.096 39.130 0.00 0.00 34.05 2.87
1539 1544 5.979517 GCATATTGCTCCCAAAACACTATTC 59.020 40.000 0.00 0.00 40.96 1.75
1555 1560 4.038282 TGGATTCAGTTGGATGCATATTGC 59.962 41.667 0.00 0.00 45.29 3.56
1567 1572 3.188254 TGCAACGTATGTGGATTCAGTTG 59.812 43.478 0.00 0.00 40.03 3.16
1569 1574 3.052455 TGCAACGTATGTGGATTCAGT 57.948 42.857 0.00 0.00 0.00 3.41
1624 1631 7.818997 TGTACATTATCCGAGAAGTGTATCT 57.181 36.000 0.00 0.00 0.00 1.98
1625 1632 8.297426 TGATGTACATTATCCGAGAAGTGTATC 58.703 37.037 10.30 0.00 0.00 2.24
1652 1659 8.671384 AGTTGCAACTACACTATTCTTTGTAA 57.329 30.769 30.25 0.00 37.52 2.41
1653 1660 8.671384 AAGTTGCAACTACACTATTCTTTGTA 57.329 30.769 31.31 0.00 38.57 2.41
1660 1667 6.765989 TGACAAGAAGTTGCAACTACACTATT 59.234 34.615 31.31 16.62 38.57 1.73
1663 1670 4.513442 TGACAAGAAGTTGCAACTACACT 58.487 39.130 31.31 24.87 38.57 3.55
1669 1676 5.112220 TCATCATGACAAGAAGTTGCAAC 57.888 39.130 22.17 22.17 37.14 4.17
1681 1688 5.169992 ACAACATCCTCTTCATCATGACA 57.830 39.130 0.00 0.00 0.00 3.58
1686 1693 4.945543 CCATGAACAACATCCTCTTCATCA 59.054 41.667 0.00 0.00 37.07 3.07
1689 1696 3.084039 GCCATGAACAACATCCTCTTCA 58.916 45.455 0.00 0.00 37.07 3.02
1693 1700 1.474077 GTGGCCATGAACAACATCCTC 59.526 52.381 9.72 0.00 37.07 3.71
1694 1701 1.076024 AGTGGCCATGAACAACATCCT 59.924 47.619 9.72 0.00 37.07 3.24
1718 1725 0.331616 TCATCGTCTCAGGACCTCCA 59.668 55.000 0.00 0.00 39.15 3.86
1719 1726 1.611491 GATCATCGTCTCAGGACCTCC 59.389 57.143 0.00 0.00 39.15 4.30
1741 1748 1.088306 TTGACGGCACAAAAACGAGT 58.912 45.000 0.00 0.00 0.00 4.18
1763 1771 1.817099 GGCAGGTCCAGCTCATTCG 60.817 63.158 6.19 0.00 34.01 3.34
1781 1789 0.670546 AGATTCACCGTCCACTTGCG 60.671 55.000 0.00 0.00 0.00 4.85
1785 1793 0.898320 CCAGAGATTCACCGTCCACT 59.102 55.000 0.00 0.00 0.00 4.00
1791 1799 0.460987 GCAGGTCCAGAGATTCACCG 60.461 60.000 0.00 0.00 33.78 4.94
1796 1804 0.915364 GAAGGGCAGGTCCAGAGATT 59.085 55.000 0.00 0.00 36.21 2.40
1838 1846 1.455849 CCTGTGAAGGGCTTGACCA 59.544 57.895 0.00 0.00 42.05 4.02
1840 1848 4.404691 CCCTGTGAAGGGCTTGAC 57.595 61.111 0.00 0.00 42.99 3.18
1858 1866 4.620982 CCCCAACAACATCTGAAAAACTC 58.379 43.478 0.00 0.00 0.00 3.01
1875 1883 2.361104 GCCTTGATCGTGCCCCAA 60.361 61.111 0.00 0.00 0.00 4.12
1965 1973 5.913137 TCTTTCTTTGGAAGCAGAAACAA 57.087 34.783 0.00 0.00 34.71 2.83
1968 1976 6.106003 GGTTTTCTTTCTTTGGAAGCAGAAA 58.894 36.000 9.17 9.17 36.92 2.52
1992 2000 0.748005 AAGTGCCCGATTTCATCCGG 60.748 55.000 0.00 0.00 44.94 5.14
2094 2104 2.158986 AGCACTCATAGCGCAAGAGATT 60.159 45.455 24.28 10.48 43.02 2.40
2100 2110 2.099141 AGAAAGCACTCATAGCGCAA 57.901 45.000 11.47 0.00 37.01 4.85
2105 2115 5.782047 CTCCTGGATAGAAAGCACTCATAG 58.218 45.833 0.00 0.00 0.00 2.23
2107 2117 3.181456 GCTCCTGGATAGAAAGCACTCAT 60.181 47.826 0.00 0.00 34.55 2.90
2108 2118 2.169352 GCTCCTGGATAGAAAGCACTCA 59.831 50.000 0.00 0.00 34.55 3.41
2125 2139 3.825328 AGGTAATTGTCATGGATGCTCC 58.175 45.455 0.00 0.00 36.96 4.70
2144 2158 4.092529 CAGACGACATTTCAGACATGAAGG 59.907 45.833 0.00 0.00 45.89 3.46
2203 2217 1.269726 GCACGGGCAATATCCATTTGG 60.270 52.381 3.77 0.00 40.72 3.28
2255 4968 0.749454 CTTATGGCCCGAAGCAGCTT 60.749 55.000 7.60 7.60 46.50 3.74
2273 4986 1.071471 CCCAACGCTGACTGGAACT 59.929 57.895 0.00 0.00 34.35 3.01
2277 4990 0.535102 AGTTTCCCAACGCTGACTGG 60.535 55.000 0.00 0.00 38.03 4.00
2331 5045 5.624159 CCATCAAGACCATTAAGGCTGATA 58.376 41.667 0.00 0.00 43.14 2.15
2347 5061 1.468565 CGCAATCAAGGTGCCATCAAG 60.469 52.381 0.00 0.00 38.86 3.02
2356 5070 3.055719 CCGGTGCGCAATCAAGGT 61.056 61.111 14.00 0.00 0.00 3.50
2359 5073 2.745884 CCTCCGGTGCGCAATCAA 60.746 61.111 14.00 0.00 0.00 2.57
2360 5074 4.776322 CCCTCCGGTGCGCAATCA 62.776 66.667 14.00 0.00 0.00 2.57
2387 5101 0.983378 ACTGTGATAGTGGGCCCCTC 60.983 60.000 22.27 13.04 38.49 4.30
2388 5102 0.550147 AACTGTGATAGTGGGCCCCT 60.550 55.000 22.27 18.54 40.26 4.79


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

AutoCloner maintained by Alex Coulton.