Multiple sequence alignment - TraesCS7A01G205600

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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 TraesCS7A01G205600 chr7A 100.000 2288 0 0 1 2288 167800043 167797756 0.000000e+00 4226
1 TraesCS7A01G205600 chr1D 94.500 1709 92 2 2 1710 369900548 369902254 0.000000e+00 2634
2 TraesCS7A01G205600 chr6D 93.699 1714 103 3 1 1710 446604641 446602929 0.000000e+00 2562
3 TraesCS7A01G205600 chr2D 91.482 1714 139 5 2 1710 646800105 646798394 0.000000e+00 2350
4 TraesCS7A01G205600 chr2D 91.307 1714 143 4 2 1710 646961480 646959768 0.000000e+00 2335
5 TraesCS7A01G205600 chr2D 91.185 1713 144 3 2 1710 646883879 646882170 0.000000e+00 2320
6 TraesCS7A01G205600 chr2D 91.053 1710 134 5 2 1708 647091185 647089492 0.000000e+00 2292
7 TraesCS7A01G205600 chr2D 90.309 1713 140 9 2 1710 646863597 646861907 0.000000e+00 2220
8 TraesCS7A01G205600 chr2D 94.545 220 12 0 1492 1711 629244134 629244353 7.830000e-90 340
9 TraesCS7A01G205600 chr2D 82.500 120 21 0 1594 1713 317857013 317857132 3.110000e-19 106
10 TraesCS7A01G205600 chr2A 90.379 1715 154 7 1 1710 171849912 171851620 0.000000e+00 2242
11 TraesCS7A01G205600 chr2A 91.034 580 51 1 1710 2288 382159491 382158912 0.000000e+00 782
12 TraesCS7A01G205600 chr1A 90.332 1717 143 9 1 1713 463969299 463970996 0.000000e+00 2230
13 TraesCS7A01G205600 chr1A 90.345 580 54 2 1710 2288 238315640 238316218 0.000000e+00 760
14 TraesCS7A01G205600 chr3A 91.034 580 51 1 1710 2288 341445398 341445977 0.000000e+00 782
15 TraesCS7A01G205600 chr6A 90.674 579 52 2 1710 2288 303787572 303786996 0.000000e+00 769
16 TraesCS7A01G205600 chr6A 90.534 581 52 3 1710 2288 342802723 342803302 0.000000e+00 765
17 TraesCS7A01G205600 chr6A 90.625 576 52 2 1710 2285 241940494 241941067 0.000000e+00 763
18 TraesCS7A01G205600 chr4A 90.517 580 54 1 1710 2288 229888945 229888366 0.000000e+00 765
19 TraesCS7A01G205600 chr4A 90.361 581 53 3 1710 2288 407713720 407714299 0.000000e+00 760
20 TraesCS7A01G205600 chr5A 90.517 580 52 2 1712 2288 238067328 238066749 0.000000e+00 763


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 TraesCS7A01G205600 chr7A 167797756 167800043 2287 True 4226 4226 100.000 1 2288 1 chr7A.!!$R1 2287
1 TraesCS7A01G205600 chr1D 369900548 369902254 1706 False 2634 2634 94.500 2 1710 1 chr1D.!!$F1 1708
2 TraesCS7A01G205600 chr6D 446602929 446604641 1712 True 2562 2562 93.699 1 1710 1 chr6D.!!$R1 1709
3 TraesCS7A01G205600 chr2D 646798394 646800105 1711 True 2350 2350 91.482 2 1710 1 chr2D.!!$R1 1708
4 TraesCS7A01G205600 chr2D 646959768 646961480 1712 True 2335 2335 91.307 2 1710 1 chr2D.!!$R4 1708
5 TraesCS7A01G205600 chr2D 646882170 646883879 1709 True 2320 2320 91.185 2 1710 1 chr2D.!!$R3 1708
6 TraesCS7A01G205600 chr2D 647089492 647091185 1693 True 2292 2292 91.053 2 1708 1 chr2D.!!$R5 1706
7 TraesCS7A01G205600 chr2D 646861907 646863597 1690 True 2220 2220 90.309 2 1710 1 chr2D.!!$R2 1708
8 TraesCS7A01G205600 chr2A 171849912 171851620 1708 False 2242 2242 90.379 1 1710 1 chr2A.!!$F1 1709
9 TraesCS7A01G205600 chr2A 382158912 382159491 579 True 782 782 91.034 1710 2288 1 chr2A.!!$R1 578
10 TraesCS7A01G205600 chr1A 463969299 463970996 1697 False 2230 2230 90.332 1 1713 1 chr1A.!!$F2 1712
11 TraesCS7A01G205600 chr1A 238315640 238316218 578 False 760 760 90.345 1710 2288 1 chr1A.!!$F1 578
12 TraesCS7A01G205600 chr3A 341445398 341445977 579 False 782 782 91.034 1710 2288 1 chr3A.!!$F1 578
13 TraesCS7A01G205600 chr6A 303786996 303787572 576 True 769 769 90.674 1710 2288 1 chr6A.!!$R1 578
14 TraesCS7A01G205600 chr6A 342802723 342803302 579 False 765 765 90.534 1710 2288 1 chr6A.!!$F2 578
15 TraesCS7A01G205600 chr6A 241940494 241941067 573 False 763 763 90.625 1710 2285 1 chr6A.!!$F1 575
16 TraesCS7A01G205600 chr4A 229888366 229888945 579 True 765 765 90.517 1710 2288 1 chr4A.!!$R1 578
17 TraesCS7A01G205600 chr4A 407713720 407714299 579 False 760 760 90.361 1710 2288 1 chr4A.!!$F1 578
18 TraesCS7A01G205600 chr5A 238066749 238067328 579 True 763 763 90.517 1712 2288 1 chr5A.!!$R1 576

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
943 954 0.034059 CGGCCACTACCATCAGGATC 59.966 60.0 2.24 0.0 38.69 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2277 4.093408 CACCGAAATGTTCATCTCGTGATT 59.907 41.667 7.55 0.0 36.54 2.57 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
49 50 4.863548 TGGCCTTCATCATCTTCTTCATT 58.136 39.130 3.32 0.00 0.00 2.57
53 54 4.643334 CCTTCATCATCTTCTTCATTGCCA 59.357 41.667 0.00 0.00 0.00 4.92
60 61 2.173519 CTTCTTCATTGCCATGTGGGT 58.826 47.619 0.54 0.00 39.65 4.51
61 62 2.307496 TCTTCATTGCCATGTGGGTT 57.693 45.000 0.54 0.00 39.65 4.11
122 127 0.395311 CTGCCAGGTAGGACGGACTA 60.395 60.000 0.00 0.00 41.22 2.59
151 156 1.077930 CCTAGCTGGCATGTGCACT 60.078 57.895 19.41 0.15 44.36 4.40
254 259 2.399580 GGTCATTAGGAGCCCAGTAGT 58.600 52.381 0.00 0.00 38.08 2.73
346 351 2.202690 TCAACTACCATCGCGCCG 60.203 61.111 0.00 0.00 0.00 6.46
379 384 2.300152 AGGAATCAACGTCTTCAGCTCA 59.700 45.455 0.00 0.00 0.00 4.26
389 394 4.021894 ACGTCTTCAGCTCATCTTTAGTGT 60.022 41.667 0.00 0.00 0.00 3.55
415 420 2.689553 TGAGCACGGCATTAGATTCA 57.310 45.000 0.00 0.00 0.00 2.57
429 434 3.548745 AGATTCATTCTGCATGTCCGA 57.451 42.857 0.00 0.00 34.06 4.55
496 501 2.350895 CGGTCACCAGCCATCCAA 59.649 61.111 0.00 0.00 0.00 3.53
600 606 2.569404 GGAGGAAGGTTGACAGTGAGAT 59.431 50.000 0.00 0.00 0.00 2.75
749 757 1.446907 CCTGACTCCATGACTTGTGC 58.553 55.000 0.00 0.00 0.00 4.57
775 783 3.007973 GAGGACACGGAGGTGCTCC 62.008 68.421 12.43 0.00 46.73 4.70
942 953 0.691078 ACGGCCACTACCATCAGGAT 60.691 55.000 2.24 0.00 38.69 3.24
943 954 0.034059 CGGCCACTACCATCAGGATC 59.966 60.000 2.24 0.00 38.69 3.36
947 958 2.369860 GCCACTACCATCAGGATCATGA 59.630 50.000 13.16 13.16 38.69 3.07
1040 1053 2.507102 CTTCGTCGCGGTGCTGAT 60.507 61.111 6.13 0.00 0.00 2.90
1059 1072 3.072915 TGATGGAGTTCAAGCTCAGGAAA 59.927 43.478 0.00 0.00 37.24 3.13
1067 1080 1.676006 CAAGCTCAGGAAAAACACCGT 59.324 47.619 0.00 0.00 0.00 4.83
1192 1205 1.269778 TGACGTTCAAGCTCCTCACTG 60.270 52.381 0.00 0.00 0.00 3.66
1224 1237 3.381590 TCAAGGTCATCATCTTCGACGAT 59.618 43.478 0.00 0.00 0.00 3.73
1239 1252 2.292267 GACGATGATGGCATTGAGGTT 58.708 47.619 0.00 0.00 38.02 3.50
1291 1304 2.301738 GCCACCAAGGAGTAGGGCT 61.302 63.158 0.00 0.00 41.22 5.19
1292 1305 1.853250 GCCACCAAGGAGTAGGGCTT 61.853 60.000 0.00 0.00 41.22 4.35
1357 1370 4.393680 TGTCTATGGTTTATGCGTTGAACC 59.606 41.667 14.00 14.00 42.44 3.62
1476 1489 3.306472 AACCTCACCAACTAGCCAAAA 57.694 42.857 0.00 0.00 0.00 2.44
1483 1496 5.390387 TCACCAACTAGCCAAAAAGGTTAT 58.610 37.500 0.00 0.00 40.61 1.89
1564 1577 1.391157 GCAACCAAACACCAGGCAGA 61.391 55.000 0.00 0.00 0.00 4.26
1608 1637 1.297364 GGCATGCAGGCAACCAAAT 59.703 52.632 26.25 0.00 43.51 2.32
1691 1720 2.918230 AATGCGGGTACTGTAGCGCC 62.918 60.000 21.60 12.27 36.83 6.53
1705 1734 3.679738 CGCCCGGCAACCAAACAT 61.680 61.111 10.77 0.00 0.00 2.71
1923 1955 3.488489 GCAACAAGTTAACATACCAGCG 58.512 45.455 8.61 0.00 0.00 5.18
2033 2065 5.529430 TCACCATAGGGCACATAAAAATACG 59.471 40.000 0.00 0.00 37.90 3.06
2046 2078 8.670135 CACATAAAAATACGAGGATTACACCAA 58.330 33.333 0.00 0.00 0.00 3.67
2083 2115 8.162878 CATGAAGATGCTCCTAAAACATGTAT 57.837 34.615 0.00 0.00 0.00 2.29
2110 2142 4.823442 TGATGCTCAAAAGATGAACACACT 59.177 37.500 0.00 0.00 36.98 3.55
2129 2161 7.298122 ACACACTAAATGCTATGAAAAAGACG 58.702 34.615 0.00 0.00 0.00 4.18
2232 2265 3.388345 AACATGCATGCAAATGACACA 57.612 38.095 26.68 0.00 0.00 3.72
2244 2277 4.154737 GCAAATGACACAAGCATGTAGAGA 59.845 41.667 0.00 0.00 37.82 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.028850 CCCACATGGCAATGAAGAAGAT 58.971 45.455 8.45 0.00 37.24 2.40
53 54 2.671619 CGAACCGCCAACCCACAT 60.672 61.111 0.00 0.00 0.00 3.21
60 61 1.079405 GATGAGGACGAACCGCCAA 60.079 57.895 0.00 0.00 44.74 4.52
61 62 2.577059 GATGAGGACGAACCGCCA 59.423 61.111 0.00 0.00 44.74 5.69
67 68 1.374343 CCGAGGACGATGAGGACGAA 61.374 60.000 0.00 0.00 42.66 3.85
151 156 0.415429 AGGAGGAGGAAGAAGAGGCA 59.585 55.000 0.00 0.00 0.00 4.75
254 259 4.150897 AGAAGTGGTGCAAGTACAAGAA 57.849 40.909 0.00 0.00 0.00 2.52
306 311 2.455557 TCATTCGTTGGGCCATGAATT 58.544 42.857 24.13 12.23 0.00 2.17
319 324 4.112634 CGATGGTAGTTGACATCATTCGT 58.887 43.478 0.00 0.00 42.72 3.85
346 351 0.036388 TGATTCCTGACCCAGCGAAC 60.036 55.000 0.00 0.00 0.00 3.95
379 384 5.181748 GTGCTCATGAAGGACACTAAAGAT 58.818 41.667 0.00 0.00 45.15 2.40
389 394 0.035152 AATGCCGTGCTCATGAAGGA 60.035 50.000 0.00 0.00 0.00 3.36
429 434 0.108615 CTCGAACTTCGGCTCCATGT 60.109 55.000 11.21 0.00 40.88 3.21
491 496 0.253327 GCCTTCTTCCTCGGTTGGAT 59.747 55.000 0.00 0.00 35.83 3.41
496 501 1.990614 GAGGGCCTTCTTCCTCGGT 60.991 63.158 7.89 0.00 39.95 4.69
600 606 3.519370 ATTTACCCACCCCCTCTCTTA 57.481 47.619 0.00 0.00 0.00 2.10
708 716 1.985473 TTGCACAGAGTTCATGGCTT 58.015 45.000 0.00 0.00 0.00 4.35
749 757 2.278206 CCGTGTCCTCGATCTGCG 60.278 66.667 0.00 0.00 42.69 5.18
808 819 2.727392 CCTCGTCGGGCATTGGGTA 61.727 63.158 0.00 0.00 0.00 3.69
858 869 2.750350 CCACCCTCAGGCGTCTTT 59.250 61.111 0.00 0.00 36.11 2.52
906 917 1.154469 GTAGTTGCGGCGCTTGTTC 60.154 57.895 33.26 16.20 0.00 3.18
942 953 2.550855 GCAGAAGTGAGTTGGGTCATGA 60.551 50.000 0.00 0.00 0.00 3.07
943 954 1.808945 GCAGAAGTGAGTTGGGTCATG 59.191 52.381 0.00 0.00 0.00 3.07
947 958 1.477558 CCTTGCAGAAGTGAGTTGGGT 60.478 52.381 0.00 0.00 0.00 4.51
1037 1050 2.259917 TCCTGAGCTTGAACTCCATCA 58.740 47.619 0.00 0.00 35.72 3.07
1040 1053 3.576078 TTTTCCTGAGCTTGAACTCCA 57.424 42.857 0.00 0.00 35.72 3.86
1059 1072 1.071471 CCAGGAGCAGACGGTGTTT 59.929 57.895 0.00 0.00 0.00 2.83
1067 1080 0.471780 TGTCACCTTCCAGGAGCAGA 60.472 55.000 0.00 0.00 37.67 4.26
1224 1237 2.557924 GTTGACAACCTCAATGCCATCA 59.442 45.455 7.10 0.00 41.10 3.07
1239 1252 1.340502 TGCTTCCCACAGTTGTTGACA 60.341 47.619 0.00 0.00 0.00 3.58
1248 1261 1.284982 CTTCGTCGTGCTTCCCACAG 61.285 60.000 0.00 0.00 44.91 3.66
1357 1370 3.585862 AGCAGTACCACACTTCATAACG 58.414 45.455 0.00 0.00 34.26 3.18
1476 1489 1.610624 CGCCTGGTGTGTGATAACCTT 60.611 52.381 0.00 0.00 37.36 3.50
1483 1496 2.899838 GCAACGCCTGGTGTGTGA 60.900 61.111 14.59 0.00 37.86 3.58
1564 1577 1.303888 CTGCATGGGCTGAACCACT 60.304 57.895 0.00 0.00 44.72 4.00
1767 1797 6.491745 TGTCATTACCATGCTTTCCTTTTACA 59.508 34.615 0.00 0.00 0.00 2.41
1769 1799 7.531857 TTGTCATTACCATGCTTTCCTTTTA 57.468 32.000 0.00 0.00 0.00 1.52
1777 1807 4.588899 TGTAGCTTGTCATTACCATGCTT 58.411 39.130 0.00 0.00 41.71 3.91
1918 1950 4.693566 TCTTTTCCTGTTACATTACGCTGG 59.306 41.667 0.00 0.00 0.00 4.85
1921 1953 5.857822 AGTCTTTTCCTGTTACATTACGC 57.142 39.130 0.00 0.00 0.00 4.42
1923 1955 8.319143 TGCTAAGTCTTTTCCTGTTACATTAC 57.681 34.615 0.00 0.00 0.00 1.89
2033 2065 7.230510 TGCCATATTTACATTGGTGTAATCCTC 59.769 37.037 2.26 0.00 46.91 3.71
2110 2142 9.176181 GTTGTTTCGTCTTTTTCATAGCATTTA 57.824 29.630 0.00 0.00 0.00 1.40
2129 2161 8.106247 TGGGAACTATCATAACTTGTTGTTTC 57.894 34.615 0.00 0.00 39.89 2.78
2185 2218 8.172741 ACTGTCCATATTGATGCCCTAATATTT 58.827 33.333 0.00 0.00 29.45 1.40
2232 2265 4.991153 TCTCGTGATTCTCTACATGCTT 57.009 40.909 0.00 0.00 0.00 3.91
2244 2277 4.093408 CACCGAAATGTTCATCTCGTGATT 59.907 41.667 7.55 0.00 36.54 2.57


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

AutoCloner maintained by Alex Coulton.