Multiple sequence alignment - TraesCS2A01G301200

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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 TraesCS2A01G301200 chr2A 100.000 2222 0 0 1 2222 516398388 516396167 0 4104
1 TraesCS2A01G301200 chr2A 94.416 1540 76 4 1 1539 767163594 767162064 0 2359
2 TraesCS2A01G301200 chr3A 94.809 1541 69 5 1 1538 11599024 11597492 0 2392
3 TraesCS2A01G301200 chr3A 94.744 1541 70 5 1 1538 11605912 11604380 0 2386
4 TraesCS2A01G301200 chr3A 94.545 1540 73 7 1 1539 684743949 684745478 0 2368
5 TraesCS2A01G301200 chr7A 94.614 1541 73 4 1 1539 71221117 71222649 0 2377
6 TraesCS2A01G301200 chr4B 94.481 1540 74 6 1 1539 604142993 604144522 0 2362
7 TraesCS2A01G301200 chr4B 94.221 1540 77 6 1 1539 85985505 85987033 0 2340
8 TraesCS2A01G301200 chr5A 94.286 1540 77 7 1 1539 601068910 601070439 0 2346
9 TraesCS2A01G301200 chr6A 94.221 1540 78 6 1 1539 531392480 531390951 0 2340
10 TraesCS2A01G301200 chr2D 88.395 698 58 11 1532 2222 382172079 382171398 0 819
11 TraesCS2A01G301200 chr2B 87.175 616 55 9 1542 2152 453020609 453020013 0 678


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 TraesCS2A01G301200 chr2A 516396167 516398388 2221 True 4104 4104 100.000 1 2222 1 chr2A.!!$R1 2221
1 TraesCS2A01G301200 chr2A 767162064 767163594 1530 True 2359 2359 94.416 1 1539 1 chr2A.!!$R2 1538
2 TraesCS2A01G301200 chr3A 11597492 11599024 1532 True 2392 2392 94.809 1 1538 1 chr3A.!!$R1 1537
3 TraesCS2A01G301200 chr3A 11604380 11605912 1532 True 2386 2386 94.744 1 1538 1 chr3A.!!$R2 1537
4 TraesCS2A01G301200 chr3A 684743949 684745478 1529 False 2368 2368 94.545 1 1539 1 chr3A.!!$F1 1538
5 TraesCS2A01G301200 chr7A 71221117 71222649 1532 False 2377 2377 94.614 1 1539 1 chr7A.!!$F1 1538
6 TraesCS2A01G301200 chr4B 604142993 604144522 1529 False 2362 2362 94.481 1 1539 1 chr4B.!!$F2 1538
7 TraesCS2A01G301200 chr4B 85985505 85987033 1528 False 2340 2340 94.221 1 1539 1 chr4B.!!$F1 1538
8 TraesCS2A01G301200 chr5A 601068910 601070439 1529 False 2346 2346 94.286 1 1539 1 chr5A.!!$F1 1538
9 TraesCS2A01G301200 chr6A 531390951 531392480 1529 True 2340 2340 94.221 1 1539 1 chr6A.!!$R1 1538
10 TraesCS2A01G301200 chr2D 382171398 382172079 681 True 819 819 88.395 1532 2222 1 chr2D.!!$R1 690
11 TraesCS2A01G301200 chr2B 453020013 453020609 596 True 678 678 87.175 1542 2152 1 chr2B.!!$R1 610

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
913 916 1.244019 ATTGCTTGAAGCCCCACGAC 61.244 55.0 15.43 0.0 41.51 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2203 3.554934 TGAACATGGCAGTTGAACTTCT 58.445 40.909 0.0 0.0 0.0 2.85 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 3.721035 TGACTGCAGATATGTTGGATCG 58.279 45.455 23.35 0.00 0.00 3.69
306 308 4.202253 TGGAACGCAGTAGAGATTGCATAT 60.202 41.667 0.00 0.00 45.00 1.78
349 351 9.224058 GAGATATTCTCTAACAACAGTTACGAC 57.776 37.037 0.00 0.00 40.30 4.34
470 472 4.220693 ACTGGACTGCTGTGCAATTATA 57.779 40.909 18.02 0.00 43.72 0.98
485 487 6.353582 GTGCAATTATATTAAAGTGACGCGTC 59.646 38.462 31.66 31.66 0.00 5.19
587 589 6.379988 CCCACCTTAATTGTAGGTAAAGCAAT 59.620 38.462 12.24 0.00 44.12 3.56
588 590 7.558444 CCCACCTTAATTGTAGGTAAAGCAATA 59.442 37.037 12.24 0.00 44.12 1.90
650 652 4.168675 AGGCAATTCTAATCAAGGGGATGA 59.831 41.667 0.00 0.00 36.02 2.92
656 658 9.305555 CAATTCTAATCAAGGGGATGATGTTAT 57.694 33.333 0.00 0.00 39.90 1.89
913 916 1.244019 ATTGCTTGAAGCCCCACGAC 61.244 55.000 15.43 0.00 41.51 4.34
1009 1012 1.446966 TCAACGCGAATGCCGATGA 60.447 52.632 15.93 0.83 41.76 2.92
1016 1019 1.370900 GAATGCCGATGATTGCCGC 60.371 57.895 0.00 0.00 0.00 6.53
1044 1047 1.553690 CCCTGGACGTGGATGGAGTT 61.554 60.000 0.00 0.00 0.00 3.01
1083 1086 2.361610 CGCCTGGCCTCCAAACAT 60.362 61.111 14.12 0.00 30.80 2.71
1211 1214 3.912528 AGCTTCCTAATAGGATGGATGCA 59.087 43.478 19.76 0.00 45.34 3.96
1326 1331 6.046593 TGCACCGTGATTATTAGTTTCCTAG 58.953 40.000 1.65 0.00 0.00 3.02
1335 1340 8.758829 TGATTATTAGTTTCCTAGTTGCTCAGA 58.241 33.333 0.00 0.00 0.00 3.27
1362 1367 6.789268 TGGAGTTTCATATTTTCCTCCAAGA 58.211 36.000 3.81 0.00 43.97 3.02
1422 1427 7.683463 GCACACAGAAAATGGTTTAGGTTAAGT 60.683 37.037 0.00 0.00 0.00 2.24
1459 1464 3.706600 TTTTAGTGGGCCTAATCGTGT 57.293 42.857 4.53 0.00 35.59 4.49
1486 1491 4.634443 GGTATTGGATCTGTGTACGCTTTT 59.366 41.667 8.10 0.00 0.00 2.27
1490 1495 5.079689 TGGATCTGTGTACGCTTTTATGA 57.920 39.130 8.10 0.00 0.00 2.15
1516 1521 7.338449 AGGTGTGCTTAAAGAAGTTCTTGTTTA 59.662 33.333 18.70 5.25 36.71 2.01
1600 1609 8.889717 TCGATATTTTCTCGAAATTAAGGCTTT 58.110 29.630 4.45 0.00 41.79 3.51
1605 1614 7.447374 TTTCTCGAAATTAAGGCTTTCATGA 57.553 32.000 4.45 0.00 33.20 3.07
1633 1642 0.876342 CTCCGAAATGCCCTACTCGC 60.876 60.000 0.00 0.00 0.00 5.03
1642 1651 1.079127 CCCTACTCGCACAAGTGGG 60.079 63.158 10.63 10.63 45.03 4.61
1658 1667 2.305635 AGTGGGCATGACACTGTATTCA 59.694 45.455 18.93 0.00 46.67 2.57
1675 1684 7.280205 ACTGTATTCATACGTTTTGAGAATCCC 59.720 37.037 0.00 0.00 36.06 3.85
1702 1711 4.919774 TCAAAGTGGCCCTAGACATTAA 57.080 40.909 0.00 0.00 0.00 1.40
1769 1778 7.832187 TGTCCCTATAGAAACGAAAAATGGATT 59.168 33.333 0.00 0.00 0.00 3.01
1796 1807 6.872020 TCTTTAGTCTAACAAAGAACCATCCG 59.128 38.462 0.00 0.00 37.72 4.18
1826 1839 6.876155 TGTACTCTCTCTAGTTCACGTATCT 58.124 40.000 0.00 0.00 0.00 1.98
1827 1840 6.979817 TGTACTCTCTCTAGTTCACGTATCTC 59.020 42.308 0.00 0.00 0.00 2.75
1840 1853 3.680642 CGTATCTCGTACCCTCGAAAA 57.319 47.619 0.00 0.00 39.34 2.29
1841 1854 4.019919 CGTATCTCGTACCCTCGAAAAA 57.980 45.455 0.00 0.00 39.34 1.94
1845 1858 6.291479 CGTATCTCGTACCCTCGAAAAATTTC 60.291 42.308 0.00 0.00 39.34 2.17
1867 1881 4.391830 TCACTATCGCCAACATGAACTTTC 59.608 41.667 0.00 0.00 0.00 2.62
1941 1955 6.417191 TTTCTCTACCAACATTCATAACGC 57.583 37.500 0.00 0.00 0.00 4.84
1942 1956 5.079689 TCTCTACCAACATTCATAACGCA 57.920 39.130 0.00 0.00 0.00 5.24
1960 1974 9.454585 CATAACGCAAATCTCAATGTTCATATT 57.545 29.630 0.00 0.00 0.00 1.28
1987 2001 8.922931 AATGGTTCTTCCTTGCAAAATATTTT 57.077 26.923 7.64 7.64 37.07 1.82
1988 2002 8.922931 ATGGTTCTTCCTTGCAAAATATTTTT 57.077 26.923 10.77 0.00 37.07 1.94
2042 2056 7.763172 AATTGTTCTTAGCATCGACTTAGAG 57.237 36.000 0.00 0.00 0.00 2.43
2189 2203 7.009179 AGAGAGACATGTAATTGGAGTTTGA 57.991 36.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 98 7.664318 ACAGAGAAACCAAATACCTTTCGTTAT 59.336 33.333 0.00 0.00 27.52 1.89
99 101 5.374071 ACAGAGAAACCAAATACCTTTCGT 58.626 37.500 0.00 0.00 0.00 3.85
306 308 6.701145 ATATCTCTCGCTGTTCTGTAAAGA 57.299 37.500 0.00 0.00 0.00 2.52
348 350 1.549170 GGGTCACATGACTCCGTAAGT 59.451 52.381 11.63 0.00 44.20 2.24
349 351 1.548719 TGGGTCACATGACTCCGTAAG 59.451 52.381 9.40 0.00 44.78 2.34
470 472 6.535274 AAACTTTAGACGCGTCACTTTAAT 57.465 33.333 37.85 19.76 0.00 1.40
587 589 8.030106 TGATCAGTGTGTGTTTTACGTATGATA 58.970 33.333 0.00 0.00 0.00 2.15
588 590 6.871492 TGATCAGTGTGTGTTTTACGTATGAT 59.129 34.615 0.00 0.00 0.00 2.45
650 652 5.598830 ACTGGACCGTATCAAGAGATAACAT 59.401 40.000 0.00 0.00 38.41 2.71
656 658 5.988310 TTAAACTGGACCGTATCAAGAGA 57.012 39.130 0.00 0.00 31.90 3.10
851 853 6.708949 GGATTATCTTAGGTTGCCGATTGTTA 59.291 38.462 0.00 0.00 0.00 2.41
853 855 5.063880 GGATTATCTTAGGTTGCCGATTGT 58.936 41.667 0.00 0.00 0.00 2.71
979 982 3.479269 CGTTGACTTCCGCTCCGC 61.479 66.667 0.00 0.00 0.00 5.54
986 989 1.134694 GGCATTCGCGTTGACTTCC 59.865 57.895 5.77 0.00 39.92 3.46
999 1002 2.067091 CTGCGGCAATCATCGGCATT 62.067 55.000 3.44 0.00 38.71 3.56
1016 1019 2.513204 CGTCCAGGGCATGCTCTG 60.513 66.667 36.15 36.15 43.82 3.35
1083 1086 0.240145 CTATCGCCGCCATCGTCTTA 59.760 55.000 0.00 0.00 0.00 2.10
1106 1109 0.037232 GTCTTCCTCCGGGAACACAG 60.037 60.000 0.00 0.00 45.72 3.66
1259 1263 6.692849 ATCAGAGTGCATCCATCCTATTAA 57.307 37.500 0.00 0.00 0.00 1.40
1326 1331 1.527311 GAAACTCCACGTCTGAGCAAC 59.473 52.381 10.73 0.91 32.98 4.17
1335 1340 4.941873 GGAGGAAAATATGAAACTCCACGT 59.058 41.667 0.00 0.00 43.02 4.49
1360 1365 4.774726 ACATTGACTGACTGTACTCCATCT 59.225 41.667 0.00 0.00 0.00 2.90
1362 1367 6.605471 TTACATTGACTGACTGTACTCCAT 57.395 37.500 0.00 0.00 0.00 3.41
1371 1376 7.573843 GCACTTAGCAATTTACATTGACTGACT 60.574 37.037 5.78 0.00 42.35 3.41
1422 1427 9.667107 CCCACTAAAATCAATCTAACAGTTAGA 57.333 33.333 22.68 22.68 45.58 2.10
1428 1433 5.826643 AGGCCCACTAAAATCAATCTAACA 58.173 37.500 0.00 0.00 0.00 2.41
1459 1464 3.118920 CGTACACAGATCCAATACCACCA 60.119 47.826 0.00 0.00 0.00 4.17
1486 1491 6.769512 AGAACTTCTTTAAGCACACCTCATA 58.230 36.000 0.00 0.00 36.05 2.15
1490 1495 5.193679 ACAAGAACTTCTTTAAGCACACCT 58.806 37.500 0.92 0.00 33.78 4.00
1561 1567 8.831372 CGAGAAAATATCGAACTTTTCAGTTTG 58.169 33.333 25.28 13.04 43.79 2.93
1575 1581 9.159470 GAAAGCCTTAATTTCGAGAAAATATCG 57.841 33.333 2.17 0.00 36.54 2.92
1578 1584 9.787532 CATGAAAGCCTTAATTTCGAGAAAATA 57.212 29.630 2.17 0.00 39.10 1.40
1598 1607 2.386661 GGAGACCGAGCTTCATGAAA 57.613 50.000 9.88 0.00 0.00 2.69
1633 1642 0.594602 CAGTGTCATGCCCACTTGTG 59.405 55.000 13.29 3.05 41.10 3.33
1642 1651 5.718649 AACGTATGAATACAGTGTCATGC 57.281 39.130 0.00 0.01 36.00 4.06
1652 1661 7.065324 TGTGGGATTCTCAAAACGTATGAATAC 59.935 37.037 5.59 4.63 0.00 1.89
1658 1667 6.432783 TGATTTGTGGGATTCTCAAAACGTAT 59.567 34.615 0.00 0.00 40.68 3.06
1675 1684 3.191371 GTCTAGGGCCACTTTGATTTGTG 59.809 47.826 6.18 0.00 0.00 3.33
1735 1744 8.624367 TTCGTTTCTATAGGGACAATTTCAAA 57.376 30.769 0.00 0.00 0.00 2.69
1778 1789 5.988310 TCTACGGATGGTTCTTTGTTAGA 57.012 39.130 0.00 0.00 0.00 2.10
1780 1791 6.469410 ACAATCTACGGATGGTTCTTTGTTA 58.531 36.000 0.00 0.00 32.53 2.41
1796 1807 7.278424 ACGTGAACTAGAGAGAGTACAATCTAC 59.722 40.741 0.00 0.00 0.00 2.59
1826 1839 4.634199 AGTGAAATTTTTCGAGGGTACGA 58.366 39.130 0.00 0.00 40.01 3.43
1827 1840 6.507456 CGATAGTGAAATTTTTCGAGGGTACG 60.507 42.308 0.00 0.00 40.01 3.67
1840 1853 5.415701 AGTTCATGTTGGCGATAGTGAAATT 59.584 36.000 0.00 0.00 39.35 1.82
1841 1854 4.943705 AGTTCATGTTGGCGATAGTGAAAT 59.056 37.500 0.00 0.00 39.35 2.17
1845 1858 4.154015 TGAAAGTTCATGTTGGCGATAGTG 59.846 41.667 0.00 0.00 32.45 2.74
2021 2035 6.701145 ATCTCTAAGTCGATGCTAAGAACA 57.299 37.500 0.00 0.00 0.00 3.18
2031 2045 8.684386 TTCTATCTGTCAATCTCTAAGTCGAT 57.316 34.615 0.00 0.00 0.00 3.59
2042 2056 8.559536 TGTTGTCAGTTTTTCTATCTGTCAATC 58.440 33.333 0.00 0.00 38.57 2.67
2180 2194 3.627577 GCAGTTGAACTTCTCAAACTCCA 59.372 43.478 0.00 0.00 45.67 3.86
2189 2203 3.554934 TGAACATGGCAGTTGAACTTCT 58.445 40.909 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.