Multiple sequence alignment - TraesCS2B01G534500

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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 TraesCS2B01G534500 chr2B 100.000 2589 0 0 1 2589 730647907 730645319 0.000000e+00 4782
1 TraesCS2B01G534500 chr2D 91.447 2654 103 43 1 2589 600435749 600433155 0.000000e+00 3530
2 TraesCS2B01G534500 chr2A 89.385 1950 89 40 691 2589 734102692 734100810 0.000000e+00 2346
3 TraesCS2B01G534500 chr2A 89.855 345 18 4 165 497 734103166 734102827 6.620000e-116 427


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 TraesCS2B01G534500 chr2B 730645319 730647907 2588 True 4782.0 4782 100.000 1 2589 1 chr2B.!!$R1 2588
1 TraesCS2B01G534500 chr2D 600433155 600435749 2594 True 3530.0 3530 91.447 1 2589 1 chr2D.!!$R1 2588
2 TraesCS2B01G534500 chr2A 734100810 734103166 2356 True 1386.5 2346 89.620 165 2589 2 chr2A.!!$R1 2424

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
777 810 0.03831 AGGAAGTTGCAACCCTAGCC 59.962 55.0 25.62 18.21 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2465 0.036765 GTTGTATCACACTCCCGGCA 60.037 55.0 0.0 0.0 0.0 5.69 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
25 26 0.760189 TACCATACGGGGGTAGTGGC 60.760 60.000 0.00 0.00 42.91 5.01
26 27 2.814835 CCATACGGGGGTAGTGGCC 61.815 68.421 0.00 0.00 0.00 5.36
27 28 2.067605 CATACGGGGGTAGTGGCCA 61.068 63.158 0.00 0.00 0.00 5.36
28 29 1.764854 ATACGGGGGTAGTGGCCAG 60.765 63.158 5.11 0.00 0.00 4.85
29 30 2.540842 ATACGGGGGTAGTGGCCAGT 62.541 60.000 19.15 19.15 0.00 4.00
30 31 4.096003 CGGGGGTAGTGGCCAGTG 62.096 72.222 23.96 0.63 0.00 3.66
31 32 3.728373 GGGGGTAGTGGCCAGTGG 61.728 72.222 23.96 4.20 0.00 4.00
389 409 4.269363 GTGTATATTTGTGTGTACCCTCGC 59.731 45.833 0.00 0.00 0.00 5.03
432 452 2.564721 GCAACCCCACTGGCACTTC 61.565 63.158 0.00 0.00 37.83 3.01
480 500 4.397417 GGATTTCCATGTCACCTCTTTCAG 59.603 45.833 0.00 0.00 35.64 3.02
537 562 3.366781 GCTTCTCCAAGTTGCATTTCCTC 60.367 47.826 0.00 0.00 31.45 3.71
538 563 3.507162 TCTCCAAGTTGCATTTCCTCA 57.493 42.857 0.00 0.00 0.00 3.86
539 564 4.038271 TCTCCAAGTTGCATTTCCTCAT 57.962 40.909 0.00 0.00 0.00 2.90
540 565 3.760151 TCTCCAAGTTGCATTTCCTCATG 59.240 43.478 0.00 0.00 0.00 3.07
569 594 6.144080 GCATGGTACGTATCAGAGTTAATCAC 59.856 42.308 14.85 0.00 0.00 3.06
583 608 7.758076 CAGAGTTAATCACCACGTGTAGAATTA 59.242 37.037 15.65 9.74 34.79 1.40
592 618 8.071368 TCACCACGTGTAGAATTATTGTTTTTC 58.929 33.333 15.65 0.00 34.79 2.29
669 702 1.952990 CATGGTGCTGGTGTTGTACAA 59.047 47.619 3.59 3.59 0.00 2.41
722 755 2.217167 AGTCGTACGTGAAAGCGTTTTC 59.783 45.455 16.81 16.81 43.04 2.29
734 767 5.066634 TGAAAGCGTTTTCATGTGTAGGAAA 59.933 36.000 21.56 0.00 45.77 3.13
745 778 5.820423 TCATGTGTAGGAAATATTTCGGTGG 59.180 40.000 19.41 6.19 38.06 4.61
777 810 0.038310 AGGAAGTTGCAACCCTAGCC 59.962 55.000 25.62 18.21 0.00 3.93
815 851 1.001746 CTCAGTCCCATCATCCATCCG 59.998 57.143 0.00 0.00 0.00 4.18
862 898 2.352915 CGCACTTCGCCGCAAAAA 60.353 55.556 0.00 0.00 37.30 1.94
891 927 1.257750 TGACCATCCAGACCAGTCCG 61.258 60.000 0.00 0.00 0.00 4.79
892 928 1.961180 GACCATCCAGACCAGTCCGG 61.961 65.000 0.00 0.00 42.50 5.14
893 929 2.735772 CCATCCAGACCAGTCCGGG 61.736 68.421 0.00 0.53 40.22 5.73
988 1024 3.444388 ACCGAGTCCAACTAAGATCAGTC 59.556 47.826 0.00 0.00 0.00 3.51
1237 1279 3.397439 ACCGCATCCAGCTCAGCT 61.397 61.111 0.00 0.00 42.61 4.24
1424 1472 4.009675 TGGAAGTAATCATCCACACTTGC 58.990 43.478 0.00 0.00 40.74 4.01
1428 1476 2.307496 AATCATCCACACTTGCCCAA 57.693 45.000 0.00 0.00 0.00 4.12
1443 1495 0.248866 CCCAACGGTTTCACTTGTGC 60.249 55.000 0.00 0.00 0.00 4.57
1471 1523 2.288961 TCCTTACCGAATTCTCGTGC 57.711 50.000 3.52 0.00 43.87 5.34
1573 1626 1.382522 GAAGGATCAAGCAATGCGGA 58.617 50.000 0.00 1.97 0.00 5.54
1589 1642 1.881709 GGAGGCGCGGTTAACTAGC 60.882 63.158 8.83 10.57 0.00 3.42
1590 1643 1.141234 GAGGCGCGGTTAACTAGCT 59.859 57.895 8.83 0.00 0.00 3.32
1591 1644 0.383231 GAGGCGCGGTTAACTAGCTA 59.617 55.000 8.83 0.00 0.00 3.32
1592 1645 0.384669 AGGCGCGGTTAACTAGCTAG 59.615 55.000 19.44 19.44 0.00 3.42
1655 1708 0.179062 CATACCTCTGCAGCTCCACC 60.179 60.000 9.47 0.00 0.00 4.61
1740 1793 2.857254 GAGAACTCGACGTCTCCCT 58.143 57.895 14.70 3.41 0.00 4.20
1742 1795 2.354259 GAGAACTCGACGTCTCCCTAA 58.646 52.381 14.70 0.00 0.00 2.69
1744 1797 3.152341 AGAACTCGACGTCTCCCTAAAA 58.848 45.455 14.70 0.00 0.00 1.52
1745 1798 3.762823 AGAACTCGACGTCTCCCTAAAAT 59.237 43.478 14.70 0.00 0.00 1.82
1746 1799 3.779271 ACTCGACGTCTCCCTAAAATC 57.221 47.619 14.70 0.00 0.00 2.17
1748 1801 3.508793 ACTCGACGTCTCCCTAAAATCAA 59.491 43.478 14.70 0.00 0.00 2.57
1893 1952 2.126110 ATGCGTGTCGTGCGATGA 60.126 55.556 0.00 0.00 34.24 2.92
2265 2351 2.109387 CGACGTGTGGGTGGGAAA 59.891 61.111 0.00 0.00 0.00 3.13
2327 2422 3.009723 GCTGCTGCCTGTTCAATTACTA 58.990 45.455 3.85 0.00 0.00 1.82
2331 2426 2.351726 CTGCCTGTTCAATTACTACGGC 59.648 50.000 0.00 0.00 34.41 5.68
2332 2427 1.326548 GCCTGTTCAATTACTACGGCG 59.673 52.381 4.80 4.80 0.00 6.46
2333 2428 1.931172 CCTGTTCAATTACTACGGCGG 59.069 52.381 13.24 0.00 0.00 6.13
2334 2429 1.326548 CTGTTCAATTACTACGGCGGC 59.673 52.381 13.24 0.00 0.00 6.53
2335 2430 0.299597 GTTCAATTACTACGGCGGCG 59.700 55.000 31.06 31.06 0.00 6.46
2336 2431 0.173029 TTCAATTACTACGGCGGCGA 59.827 50.000 38.93 19.91 0.00 5.54
2378 2479 4.101448 GGCTGCCGGGAGTGTGAT 62.101 66.667 24.99 0.00 0.00 3.06
2386 2487 1.067425 CCGGGAGTGTGATACAACGAA 60.067 52.381 0.00 0.00 0.00 3.85
2387 2488 2.610976 CCGGGAGTGTGATACAACGAAA 60.611 50.000 0.00 0.00 0.00 3.46
2426 2527 3.185188 CACAGTTGATTGGAGACTTGACG 59.815 47.826 0.00 0.00 0.00 4.35
2427 2528 3.069586 ACAGTTGATTGGAGACTTGACGA 59.930 43.478 0.00 0.00 0.00 4.20
2428 2529 3.430218 CAGTTGATTGGAGACTTGACGAC 59.570 47.826 0.00 0.00 0.00 4.34
2442 2543 4.889856 CGACGGCCATGGATCGCA 62.890 66.667 18.40 0.00 0.00 5.10
2466 2574 2.103537 CAGCATGACTGTCATCCACA 57.896 50.000 19.89 0.00 41.86 4.17
2467 2575 1.736126 CAGCATGACTGTCATCCACAC 59.264 52.381 19.89 7.96 41.86 3.82
2468 2576 1.627329 AGCATGACTGTCATCCACACT 59.373 47.619 19.89 9.88 34.28 3.55
2469 2577 2.005451 GCATGACTGTCATCCACACTC 58.995 52.381 19.89 1.33 34.28 3.51
2470 2578 2.625737 CATGACTGTCATCCACACTCC 58.374 52.381 19.89 0.00 34.28 3.85
2471 2579 1.715785 TGACTGTCATCCACACTCCA 58.284 50.000 6.36 0.00 0.00 3.86
2472 2580 1.344438 TGACTGTCATCCACACTCCAC 59.656 52.381 6.36 0.00 0.00 4.02
2564 2689 3.499737 GTGCGTGCCCTTGGATCG 61.500 66.667 0.00 0.00 0.00 3.69
2568 2693 2.511600 GTGCCCTTGGATCGACGG 60.512 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.032528 ACCGTGTCATGCCACTGG 59.967 61.111 13.63 13.63 36.08 4.00
26 27 2.327343 CCACCGTGTCATGCCACTG 61.327 63.158 5.22 0.66 33.07 3.66
27 28 2.032528 CCACCGTGTCATGCCACT 59.967 61.111 5.22 0.00 33.07 4.00
28 29 3.055719 CCCACCGTGTCATGCCAC 61.056 66.667 0.00 0.00 0.00 5.01
209 210 0.539986 GCGAGGGTTGAATAGTGGGA 59.460 55.000 0.00 0.00 0.00 4.37
262 267 0.036765 TAGATGGTCGTGTGTTGGCC 60.037 55.000 0.00 0.00 0.00 5.36
264 269 1.665679 GCATAGATGGTCGTGTGTTGG 59.334 52.381 0.00 0.00 0.00 3.77
265 270 1.665679 GGCATAGATGGTCGTGTGTTG 59.334 52.381 0.00 0.00 0.00 3.33
266 271 1.406887 GGGCATAGATGGTCGTGTGTT 60.407 52.381 0.00 0.00 0.00 3.32
267 272 0.178068 GGGCATAGATGGTCGTGTGT 59.822 55.000 0.00 0.00 0.00 3.72
389 409 2.808543 CAAGGTGAGAAAAGGAGAACGG 59.191 50.000 0.00 0.00 0.00 4.44
480 500 0.104120 GGGCAAACAGTGAAACCCAC 59.896 55.000 0.00 0.00 46.03 4.61
538 563 3.069289 CTGATACGTACCATGCATGCAT 58.931 45.455 27.46 27.46 37.08 3.96
539 564 2.102252 TCTGATACGTACCATGCATGCA 59.898 45.455 25.04 25.04 0.00 3.96
540 565 2.733552 CTCTGATACGTACCATGCATGC 59.266 50.000 21.69 11.82 0.00 4.06
569 594 8.286800 TCTGAAAAACAATAATTCTACACGTGG 58.713 33.333 21.57 2.57 0.00 4.94
583 608 4.050553 CGCCACACATTCTGAAAAACAAT 58.949 39.130 0.00 0.00 0.00 2.71
592 618 2.587956 CATTTCACGCCACACATTCTG 58.412 47.619 0.00 0.00 0.00 3.02
669 702 2.347490 CTGGCTGCCTTGTACCGT 59.653 61.111 21.03 0.00 0.00 4.83
722 755 5.820423 TCCACCGAAATATTTCCTACACATG 59.180 40.000 20.01 9.25 33.68 3.21
734 767 9.243105 CCTCCATTTAATAATCCACCGAAATAT 57.757 33.333 0.00 0.00 0.00 1.28
745 778 7.706607 GGTTGCAACTTCCTCCATTTAATAATC 59.293 37.037 27.64 1.70 0.00 1.75
862 898 3.632145 GTCTGGATGGTCAGTTGTGTTTT 59.368 43.478 0.00 0.00 36.25 2.43
863 899 3.214328 GTCTGGATGGTCAGTTGTGTTT 58.786 45.455 0.00 0.00 36.25 2.83
891 927 1.571773 TTTAGGAAGGAGGCCAGCCC 61.572 60.000 5.01 2.58 36.58 5.19
892 928 0.394488 GTTTAGGAAGGAGGCCAGCC 60.394 60.000 5.01 5.93 0.00 4.85
893 929 0.394488 GGTTTAGGAAGGAGGCCAGC 60.394 60.000 5.01 0.00 0.00 4.85
894 930 0.256177 GGGTTTAGGAAGGAGGCCAG 59.744 60.000 5.01 0.00 0.00 4.85
895 931 1.212250 GGGGTTTAGGAAGGAGGCCA 61.212 60.000 5.01 0.00 0.00 5.36
896 932 1.212250 TGGGGTTTAGGAAGGAGGCC 61.212 60.000 0.00 0.00 0.00 5.19
897 933 0.034380 GTGGGGTTTAGGAAGGAGGC 60.034 60.000 0.00 0.00 0.00 4.70
898 934 1.004394 GTGTGGGGTTTAGGAAGGAGG 59.996 57.143 0.00 0.00 0.00 4.30
899 935 1.338769 CGTGTGGGGTTTAGGAAGGAG 60.339 57.143 0.00 0.00 0.00 3.69
900 936 0.688487 CGTGTGGGGTTTAGGAAGGA 59.312 55.000 0.00 0.00 0.00 3.36
901 937 0.958876 GCGTGTGGGGTTTAGGAAGG 60.959 60.000 0.00 0.00 0.00 3.46
902 938 0.250553 TGCGTGTGGGGTTTAGGAAG 60.251 55.000 0.00 0.00 0.00 3.46
903 939 0.183014 TTGCGTGTGGGGTTTAGGAA 59.817 50.000 0.00 0.00 0.00 3.36
904 940 0.535553 GTTGCGTGTGGGGTTTAGGA 60.536 55.000 0.00 0.00 0.00 2.94
905 941 1.520600 GGTTGCGTGTGGGGTTTAGG 61.521 60.000 0.00 0.00 0.00 2.69
1188 1230 4.065281 CCGTCCAGGACCACCGTC 62.065 72.222 14.46 0.00 45.00 4.79
1411 1456 0.888736 CGTTGGGCAAGTGTGGATGA 60.889 55.000 0.00 0.00 0.00 2.92
1412 1457 1.580942 CGTTGGGCAAGTGTGGATG 59.419 57.895 0.00 0.00 0.00 3.51
1414 1459 2.203280 CCGTTGGGCAAGTGTGGA 60.203 61.111 0.00 0.00 0.00 4.02
1415 1460 1.671901 AAACCGTTGGGCAAGTGTGG 61.672 55.000 0.00 0.00 36.48 4.17
1424 1472 0.248866 GCACAAGTGAAACCGTTGGG 60.249 55.000 4.04 0.00 37.80 4.12
1428 1476 4.647825 TGGCACAAGTGAAACCGT 57.352 50.000 4.04 0.00 37.80 4.83
1443 1495 6.511767 CGAGAATTCGGTAAGGAAATCAATGG 60.512 42.308 0.00 0.00 43.05 3.16
1471 1523 1.142097 AACGGGCAAAAACCAACGG 59.858 52.632 0.00 0.00 0.00 4.44
1516 1569 1.277557 GGGATGATCCGGATCCTCTTG 59.722 57.143 34.49 0.00 39.61 3.02
1540 1593 1.174712 TCCTTCGGGTCGTCGACTTT 61.175 55.000 23.69 0.00 39.01 2.66
1573 1626 0.384669 CTAGCTAGTTAACCGCGCCT 59.615 55.000 12.92 0.00 0.00 5.52
1612 1665 5.106277 GGCTTAATTACACCTGTGGTTCTTC 60.106 44.000 1.91 0.00 31.02 2.87
1613 1666 4.765339 GGCTTAATTACACCTGTGGTTCTT 59.235 41.667 1.91 0.00 31.02 2.52
1614 1667 4.202524 TGGCTTAATTACACCTGTGGTTCT 60.203 41.667 1.91 0.00 31.02 3.01
1655 1708 1.256361 TGAGCTGAGCTGAGAGTGGG 61.256 60.000 13.71 0.00 39.88 4.61
1722 1775 2.021355 TAGGGAGACGTCGAGTTCTC 57.979 55.000 10.46 12.86 0.00 2.87
1724 1777 3.565905 TTTTAGGGAGACGTCGAGTTC 57.434 47.619 10.46 1.61 0.00 3.01
1726 1779 3.087031 TGATTTTAGGGAGACGTCGAGT 58.913 45.455 10.46 0.00 0.00 4.18
1730 1783 5.107133 TCGATTTGATTTTAGGGAGACGTC 58.893 41.667 7.70 7.70 0.00 4.34
1731 1784 5.080969 TCGATTTGATTTTAGGGAGACGT 57.919 39.130 0.00 0.00 0.00 4.34
1732 1785 5.177696 GGATCGATTTGATTTTAGGGAGACG 59.822 44.000 0.00 0.00 37.47 4.18
1733 1786 6.055588 TGGATCGATTTGATTTTAGGGAGAC 58.944 40.000 0.00 0.00 37.47 3.36
1734 1787 6.247229 TGGATCGATTTGATTTTAGGGAGA 57.753 37.500 0.00 0.00 37.47 3.71
1735 1788 6.238759 GGTTGGATCGATTTGATTTTAGGGAG 60.239 42.308 0.00 0.00 37.47 4.30
1736 1789 5.592688 GGTTGGATCGATTTGATTTTAGGGA 59.407 40.000 0.00 0.00 37.47 4.20
1737 1790 5.594317 AGGTTGGATCGATTTGATTTTAGGG 59.406 40.000 0.00 0.00 37.47 3.53
1738 1791 6.699575 AGGTTGGATCGATTTGATTTTAGG 57.300 37.500 0.00 0.00 37.47 2.69
1870 1929 2.906185 CACGACACGCATCGATCG 59.094 61.111 9.36 9.36 45.13 3.69
1871 1930 2.615618 GCACGACACGCATCGATC 59.384 61.111 15.07 3.36 45.13 3.69
1872 1931 2.936829 ATCGCACGACACGCATCGAT 62.937 55.000 15.07 0.00 45.13 3.59
1873 1932 3.677099 ATCGCACGACACGCATCGA 62.677 57.895 15.07 0.00 45.13 3.59
2178 2260 0.109919 CACACGACATTCCGTCTCGA 60.110 55.000 0.00 0.00 42.98 4.04
2249 2335 1.599797 CCTTTCCCACCCACACGTC 60.600 63.158 0.00 0.00 0.00 4.34
2364 2465 0.036765 GTTGTATCACACTCCCGGCA 60.037 55.000 0.00 0.00 0.00 5.69
2378 2479 2.647381 GCGTCCGCGTTTCGTTGTA 61.647 57.895 4.92 0.00 40.81 2.41
2426 2527 2.051804 CTTTGCGATCCATGGCCGTC 62.052 60.000 21.65 15.97 0.00 4.79
2427 2528 2.045438 TTTGCGATCCATGGCCGT 60.045 55.556 21.65 0.00 0.00 5.68
2428 2529 2.717485 CTTTGCGATCCATGGCCG 59.283 61.111 18.22 18.22 0.00 6.13
2470 2578 1.546923 TCTGCCAATTTCCATGCTGTG 59.453 47.619 0.00 0.00 0.00 3.66
2471 2579 1.547372 GTCTGCCAATTTCCATGCTGT 59.453 47.619 0.00 0.00 0.00 4.40
2472 2580 1.134907 GGTCTGCCAATTTCCATGCTG 60.135 52.381 0.00 0.00 34.09 4.41
2487 2595 3.072476 CCAGGGTGGTCTGGTCTG 58.928 66.667 2.93 0.00 46.89 3.51
2507 2622 6.351456 CCCATTTTACCGGGAAACAATAATGT 60.351 38.462 12.64 0.00 46.34 2.71
2546 2661 3.499737 GATCCAAGGGCACGCACG 61.500 66.667 0.00 0.00 0.00 5.34
2564 2689 0.251916 TGATTCCCCACATGACCGTC 59.748 55.000 0.00 0.00 0.00 4.79
2568 2693 3.287867 AGACATGATTCCCCACATGAC 57.712 47.619 12.90 7.59 44.28 3.06


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

AutoCloner maintained by Alex Coulton.